HIV Sequence Compendium 2013

HIV Sequence Compendium 2013Thomas Leitner Los Alamos National Laboratory
Cristian Apetrei University of Pittsburgh
Beatrice Hahn University of Pennsylvania
Ilene Mizrachi National Center for Biotechnology Information
James Mullins University of Washington
Andrew Rambaut University of Edinburgh
Steven Wolinsky Northwestern University
Project Officer Stuart Shapiro
Division of AIDS National Institute of Allergy and Infectious Diseases
Los Alamos HIV Sequence Database and Analysis Staff Werner Abfalterer, Mira Dimitrijevic, Shihai Feng, Will Fischer, Bob Funkhouser,
Peter Hraber, Jennifer Macke, James J. Szinger, Hyejin Yoon
This publication is funded by the Division of AIDS, National Institute of Allergy and Infectious Diseases, through interagency agreement IAA Y1-AI-8309-1 “HIV/SIV Database and Analysis Unit”
with the U.S. Department of Energy.
Published by Theoretical Biology and Biophysics
Group T-6, Mail Stop K710 Los Alamos National Laboratory
Los Alamos, New Mexico 87545 U.S.A.
HIV Sequence Compendium 2013
Published by Theoretical Biology and Biophysics Group T-6, Mail Stop K710 Los Alamos National Laboratory Los Alamos, New Mexico 87545 U.S.A.
LA-UR-13-26007 Approved for public release; distribution is unlimited.
Los Alamos National Laboratory, an affirmative action/equal opportunity employer, is operated by Los Alamos National Se- curity, LLC, for the National Nuclear Security Administration of the U.S. Department of Energy under contract DE-AC52- 06NA25396.
This report was prepared as an account of work sponsored by an agency of the U.S. Government. Neither Los Alamos National Security, LLC, the U.S. Government nor any agency thereof, nor any of their employees make any warranty, express or im- plied, or assume any legal liability or responsibility for the accu- racy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represent that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily con- stitute or imply its endorsement, recommendation, or favoring by Los Alamos National Security, LLC, the U.S. Government, or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of Los Alamos National Security, LLC, the U.S. Government, or any agency thereof.
Los Alamos National Laboratory strongly supports academic freedom and a researcher’s right to publish; as an institution, however, the Laboratory does not endorse the viewpoint of a publication or guarantee its technical correctness.
This report was prepared as an account of work sponsored by NIH/NIAID/DAIDS under contract number IAA Y1-AI-8309-1 “HIV/SIV Database and Analysis Unit”.
Contents
Contents iii
I Preface 1 I-1 Introduction . . . . . . . . . . . . . . . . 1 I-2 Acknowledgements . . . . . . . . . . . . 1 I-3 Citing the compendium or database . . . . 1 I-4 About the PDF . . . . . . . . . . . . . . 1 I-5 About the cover . . . . . . . . . . . . . . 2 I-6 Genome maps . . . . . . . . . . . . . . . 4 I-7 HIV/SIV proteins . . . . . . . . . . . . . 5 I-8 Landmarks of the genome . . . . . . . . . 6 I-9 Amino acid codes . . . . . . . . . . . . . 8 I-10 Nucleic acid codes . . . . . . . . . . . . 8
II HIV-1/SIVcpz Complete Genomes 9 II-1 Introduction . . . . . . . . . . . . . . . . 9 II-2 Annotated features . . . . . . . . . . . . 10 II-3 Sequences . . . . . . . . . . . . . . . . . 13 II-4 Alignments . . . . . . . . . . . . . . . . 18
III HIV-2/SIV Complete Genomes 155 III-1 Introduction . . . . . . . . . . . . . . . . 155 III-2 Annotated features . . . . . . . . . . . . 156 III-3 Sequences . . . . . . . . . . . . . . . . . 158 III-4 Alignments . . . . . . . . . . . . . . . . 161
IV PLV Complete Genomes 227 IV-1 Introduction . . . . . . . . . . . . . . . . 227 IV-2 Sequences . . . . . . . . . . . . . . . . . 228 IV-3 Alignments . . . . . . . . . . . . . . . . 231
V HIV-1/SIVcpz Proteins 311 V-1 Introduction . . . . . . . . . . . . . . . . 311 V-2 Annotated features . . . . . . . . . . . . 312 V-3 Sequences . . . . . . . . . . . . . . . . . 314 V-4 Alignments . . . . . . . . . . . . . . . . 320
VI HIV-2/SIV Proteins 373 VI-1 Introduction . . . . . . . . . . . . . . . . 373 VI-2 Annotated features . . . . . . . . . . . . 374 VI-3 Sequences . . . . . . . . . . . . . . . . . 375 VI-4 Alignments . . . . . . . . . . . . . . . . 378
VII PLV Proteins 405 VII-1 Introduction . . . . . . . . . . . . . . . . 405 VII-2 Sequences . . . . . . . . . . . . . . . . . 406 VII-3 Alignments . . . . . . . . . . . . . . . . 416
HIV Sequence Compendium 2013 iii
iv HIV Sequence Compendium 2013
Pr ef
ac e
I-1 Introduction
This compendium is an annual printed summary of the data con- tained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus.
This compendium contains sequences published before Janu- ary 1, 2013. Hence, though it is published in 2013 and called the 2013 Compendium, its contents correspond to the 2012 curated alignments on our website.
The number of sequences in the HIV database is still increas- ing. In total, at the end of 2012, there were 518,163 sequences in the HIV Sequence Database, an increase of 12% since the previous year.
The number of near complete genomes (>7000 nucleotides) increased to 5013 by end of 2012. However, as in previous years, the compendium alignments contain only a small frac- tion of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (groups N, O, and P and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html
Reprints are available from our website in the form of PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to [email protected].
I-2 Acknowledgements
The HIV Sequence Database and Analysis Project is funded by the Vaccine and Prevention Research Program of the AIDS Division of the National Institute of Allergy and Infectious Diseases (Stuart Shapiro, Project Officer) through interagency agreement IAA Y1-AI-8309-1 “HIV/SIV Database and Analy- sis Unit” with the U.S. Department of Energy.
I-3 Citing the compendium or database
The LANL HIV Sequence Database may be cited in the same manner as this compendium:
HIV Sequence Compendium 2013. Brian Foley, Thomas Leitner, Cristian Apetrei, Beatrice Hahn, Ilene Mizrachi, James Mullins, Andrew Rambaut, Steven Wolinsky, and Bette Korber editors. 2013. Publisher: Los Alamos Na- tional Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico. LA-UR-13-26007.
I-4 About the PDF
The complete HIV Sequence Compendium 2013 is available in Adobe Portable Document Format (PDF) from our website, http://www.hiv.lanl.gov/. The PDF version is hy- pertext enabled and features ‘clickable’ table-of-contents, in- dexes, references and links to external web sites.
This volume is typeset using LATEX.
HIV Sequence Compendium 2013 1
Preface About the cover
I-5 About the cover
Human Immunodeficiency Virus Illustration
On this year’s cover is a cutaway view of an HIV-1 virion purchased from Visual Science. It won the Illustration cat- egory of Visualization Challenge in 2010 (Nesbit and Nor- man, 2011), and has appeared on the covers of Nature Medicine (October 2010) and the IAVI Report (May-June 2011). For additional details about the highlighted features, references, and all inquiries about the use of this image, please visit http://visualscience.ru/en/ projects/hiv/illustrations/.
Virus-derived molecules (shades of orange)
Glycosylated envelope trimer The envelope protein is synthe- sized as a precursor protein, gp160, which is cleaved by the cellular enzyme furin into gp41 and gp120 subunits. Each trimer of the envelope “spike” complex is composed of 3 molecules each of gp41 and gp120. The gp41 transmembrane protein anchors the spike to the lipid membrane. Envelope trimers are central to viral fusion and cell entry. The envelope spike is glycosylated by the attachment of carbohydrate moieties, depicted in dark orange.
Matrix – Gag p17 The HIV-1 gag gene encodes the p55 polyprotein, which initiates formation of new virions. Dur- ing maturation, p55 is cleaved into 4 structural proteins: p17, p24, p6, and p7. A layer of matrix protein p17 (MA) lies just below the lipid bilayer. In addition to its structural role, p17 has various functions throughout the replicative cycle of the virus (reviewed by Fiorentini et al. (2006)).
Capsid – Gag p24 The Gag p24 (CA) protein forms a cone- shaped shell, the capsid, which encloses the viral genomic RNA. While most p24 molecules are involved in forming the mature capsid (solid line), some exist as free dimers (dashed line). For recent information about capsid structure, see Zhao et al. (2013).
Nucleocapsid – Gag p7 The nucleocapsid protein binds to RNA to protect it from degradation by nucleases. It is closely associated with p6 and CA.
Gag p6 This small protein binds avidly to Vpr and membranes, and is important for virion budding.
Integrase Integrase is encoded by the pol gene. It forms a ho- motetrameric enzyme complex that integrates viral DNA into the host cell’s genomic DNA.
Viral RNA The viral genome is encoded as a single strand of RNA, which is packed inside the capsid. Two unpaired strands are present per virion.
Reverse transcriptase After cell entry, this pol-encoded protein transcribes viral RNA to DNA. It is a heterodimer, composed of p66 (polymerase + RNase H) and p51 (polymerase only). After polymerase transcribes the genome to DNA, RNase H degrades the RNA part of RNA-DNA complexes, leaving a single strand of viral DNA to be integrated into the host genome.
Vpr Viral Protein R is a 96-amino acid protein that performs several crucial functions in the HIV-1 replicative cycle. In HIV-2, the function of Vpr is shared by another protein, Vpx.
Host-derived molecules (shades of gray)
Host proteins are incorporated into the virion during budding. A few of these host proteins that are that are directly relevant to HIV biology are illustrated in the figure.
CD55 This host protein helps protect HIV from the membrane- attack complex by attenuating the host’s complement system (Marschang et al., 1995).
HLA-DR1 Human leukocyte antigens (HLA) molecules are best known for their role in presenting extracellular antigens to helper T cells. DR1 is just one example of a human protein that may be present on HIV virions; the specific HLA molecules present will depend on the alleles carried by the host. In HIV infection, these HLA molecules are significant for their binding to CD4 receptors.
Lipid bilayer The viral membrane is derived from the host cell.
ICAM-1 The human Intercellular Adhesion Molecule-1 is a member of the immunoglobulin superfamily of adhesion proteins. Its presence on the virion increases infectivity.
Lys-tRNA and lysyl-tRNA synthetase The cellular protein lysyl-tRNA synthetase and the corresponding transfer RNA, Lys-tRNA, are found inside the capsid; these molecules initi- ate reverse transcription.
Cyclophilin This host protein binds to the viral capsid. Cy- clophilin is an isomerase involved in protein folding, and is required for HIV infectivity.
Actin Host cell actin is commonly captured during HIV budding.
References
S. Fiorentini, E. Marini, S. Caracciolo, and A. Caruso. Functions of the HIV-1 matrix protein p17. New Microbiol., 29(1):1–10, Jan 2006.
P. Marschang, J. Sodroski, R. Würzner, and M. P. Dierich. Decay- accelerating factor (CD55) protects human immunodeficiency virus type 1 from inactivation by human complement. Eur. J. Immunol., 25 (1):285–290, Jan 1995.
J. Nesbit and C. Norman. 2010 visualization challenge. Science, 331 (6019):847–856, 18 Feb 2011.
G. Zhao, J. R. Perilla, E. L. Yufenyuy, X. Meng, B. Chen, J. Ning, J. Ahn, A. M. Gronenborn, K. Schulten, C. Aiken, and P. Zhang. Ma- ture HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature, 497(7451):643–646, 30 May 2013.
2 HIV Sequence Compendium 2013
Preface
2292
5096
F R A M E
0 1000 2000 3000 4000 5000 6000 7000 8000 9000 9719
LTR 1
2249 2396
5754
F R A M E
0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 10359
LTR 1
2459
5293
F R A M E
0 1000 2000 3000 4000 5000 6000 7000 8000 9000 9597
tat
tat
rev
rev
env
p15
p7
p6
3
3
3
5
5
5
Landmarks of the HIV-1, HIV-2, and SIV genomes. Open reading frames are shown as rectangles. The gene start, indicated by the small number in the upper left corner of each rectangle normally records the position of the a in the atg start codon for that gene, while the number in the lower right records the last position of the stop codon. For pol, the start is taken to be the first t in the sequence ttttttag, which forms part of the stem loop that potentiates ribosomal slippage on the RNA and a resulting 1 frameshift and the translation of the Gag-Pol polyprotein. The tat and rev spliced exons are shown as shaded rectangles. In HXB2, *5772 marks the position of a frameshift in the vpr gene caused by an “extra” t relative to most other subtype B viruses; !6062 indicates a defective acg start codon in vpu; †8424 and †9168 mark premature stop codons in tat and nef. See Korber et al., Numbering Positions in HIV Relative to HXB2CG, in Human Retroviruses and AIDS, 1998, p. 102. Available from http://www.hiv.lanl.gov/content/sequence/HIV/REVIEWS/HXB2.html
4 H
IV Sequence
C om
pendium 2013
transport of viral core (myristylated protein) virion
CA p24 core capsid virion NC p7 nucleocapsid, binds RNA virion
p6 binds Vpr virion
Pol Protease (PR) p15 Gag/Pol cleavage and maturation virion Reverse Transcriptase (RT)
p66, p51 reverse transcription, RNAse H activity virion
RNase H p15 virion Integrase (IN) p31 DNA provirus integration virion
Env gp120/gp41 external viral glycoproteins bind to CD4 and secondary receptors
plasma membrane, virion envelope
Rev p19 RNA transport, stability and utilization factor (phosphoprotein)
primarily in nuleolus/nucleus shuttling between nucleolus and cytoplasm
Vif p23 promotes virion maturation and infectivity cytoplasm (cytosol, membranes), virion
Vpr p10-15 promotes nuclear localization of preintegration complex, inhibits cell division, arrests infected cells at G2/M
virion nucleus (nuclear membrane?)
Vpu p16 promotes extracellular release of viral particles; degrades CD4 in the ER; (phosphoprotein only in HIV-1 and SIVcpz)
integral membrane protein
Nef p27-p25 CD4 and class I downregulation (myristylated protein) plasma membrane, cytoplasm, (virion?)
Vpx p12-16 Vpr homolog present in HIV-2 and some SIVs, absent in HIV-1
virion (nucleus?)
Tev p28 tripartite tat-env-rev protein (also named Tnv) primarily in nucleolus/nucleus
Preface
HIV genomic structural elements
LTR Long terminal repeat, the DNA sequence flanking the genome of integrated proviruses. It contains important regulatory regions, especially those for transcription initiation and polyadenylation.
TAR Target sequence for viral transactivation, the binding site for Tat protein and for cellular proteins; consists of approximately the first 45 nucleotides of the viral mRNAs in HIV-1 (or the first 100 nucleotides in HIV-2 and SIV.) TAR RNA forms a hairpin stem-loop structure with a side bulge; the bulge is necessary for Tat binding and function.
RRE Rev responsive element, an RNA element encoded within the env region of HIV-1. It consists of approximately 200 nucleotides (positions 7327 to 7530 from the start of transcription in HIV-1, spanning the border of gp120 and gp41). The RRE is necessary for Rev function; it contains a high affinity site for Rev; in all, approximately seven binding sites for Rev exist within the RRE RNA. Other lentiviruses (HIV- 2, SIV, visna, CAEV) have similar RRE elements in similar locations within env, while HTLVs have an analogous RNA element (RXRE) serving the same purpose within their LTR; RRE is the binding site for Rev protein, while RXRE is the binding site for Rex protein. RRE (and RXRE) form complex secondary structures, necessary for specific protein binding.
PE Psi elements, a set of 4 stem-loop structures preceding and overlapping the Gag start codon which are the sites recog- nized by the cysteine histidine box, a conserved motif with the canonical sequence CysX2CysX4HisX4Cys, present in the Gag p7 NC protein. The Psi Elements are present in unspliced genomic transcripts but absent from spliced viral mRNAs.
SLIP A TTTTTT slippery site, followed by a stem-loop structure, is responsible for regulating the -1 ribosomal frameshift out of the Gag reading frame into the Pol reading frame.
CRS Cis-acting repressive sequences postulated to inhibit structural protein expression in the absence of Rev. One such site was mapped within the pol region of HIV-1. The exact function has not been defined; splice sites have been postulated to act as CRS sequences.
INS Inhibitory/Instability RNA sequences found within the structural genes of HIV-1 and of other complex retroviruses. Multiple INS elements exist within the genome and can act independently; one of the best characterized elements spans nucleotides 414 to 631 in the gag region of HIV-1. The INS elements have been defined by functional assays as elements that inhibit expression posttranscriptionally. Mutation of the RNA elements was shown to lead to INS inactivation and up regulation of gene expression.
Genes and gene products
GAG The genomic region encoding the capsid proteins (group specific antigens). The precursor is the p55 myristylated pro-
tein, which is processed to p17 (MAtrix), p24 (CApsid), p7 (NucleoCapsid), and p6 proteins, by the viral protease. Gag associates with the plasma membrane where the virus assembly takes place. The 55 kDa Gag precursor is called assem- blin to indicate its role in viral assembly.
POL The genomic region encoding the viral enzymes protease, reverse transcriptase, RNAse, and integrase. These enzymes are produced as a Gag-Pol precursor polyprotein, which is processed by the viral protease; the Gag-Pol precursor is produced by ribosome frameshifting near the 30end of gag.
ENV Viral glycoproteins produced as a precursor (gp160) which is processed to give a noncovalent complex of the external glycoprotein gp120 and the transmembrane glycoprotein gp41. The mature gp120-gp41 proteins are bound by non-covalent interactions and are associated as a trimer on the cell surface. A substantial amount of gp120 can be found released in the medium. gp120 contains the binding site for the CD4 receptor, and the seven transmembrane domain chemokine receptors that serve as co-receptors for HIV-1.
TAT Transactivator of HIV gene expression. One of two essential viral regulatory factors (Tat and Rev) for HIV gene expression. Two forms are known, Tat-1 exon (minor form) of 72 amino acids and Tat-2 exon (major form) of 86 amino acids. Low levels of both proteins are found in persistently infected cells. Tat has been localized primarily in the nucleolus/nucleus by immunofluorescence. It acts by binding to the TAR RNA element and activating transcription initiation and elongation from the LTR promoter, preventing the 50LTR AATAAA polyadenylation signal from causing premature termination of transcription and polyadenylation. It is the first eukaryotic transcription factor known to interact with RNA rather than DNA and may have similarities with prokaryotic anti-termination factors. Extracellular Tat can be found and can be taken up by cells in culture.
REV The second necessary regulatory factor for HIV expression. A 19 kDa phosphoprotein, localized primarily in the nucleolus/nucleus, Rev acts by binding to RRE and promot- ing the nuclear export, stabilization and utilization of the unspliced viral mRNAs containing RRE. Rev is considered the most functionally conserved regulatory protein of lentiviruses. Rev cycles rapidly between the nucleus and the cytoplasm.
VIF Viral infectivity factor, a basic protein of typically 23 kDa. Promotes the infectivity but not the production of viral particles. In the absence of Vif the produced viral particles are defective, while the cell-to-cell transmission of virus is not affected significantly. Found in almost all lentiviruses, Vif is a cytoplasmic protein, existing in both a soluble cytoso- lic form and a membrane-associated form. The latter form of Vif is a peripheral membrane protein that is tightly associated with the cytoplasmic side of cellular membranes. In 2003, it was discovered that Vif prevents the action of the cellular APOBEC-3G protein which deaminates DNA:RNA heteroduplexes in the cytoplasm.
VPR Vpr (viral protein R) is a 96-amino acid (14 kDa) protein, which is incorporated into the virion. It interacts with the p6
Landmarks of the genome Preface
Pr ef
ac e
Gag part of the Pr55 Gag precursor. Vpr detected in the cell is localized to the nucleus. Proposed functions for Vpr include the targeting the nuclear import of preintegration complexes, cell growth arrest, transactivation of cellular genes, and in- duction of cellular differentiation. In HIV-2, SIV-SMM, SIV- RCM, SIV-MND-2 and SIV-DRL the Vpx gene is apparently the result of a Vpr gene duplication event, possibly by recom- bination.
VPU Vpu (viral protein U) is unique to HIV-1, SIVcpz (the closest SIV relative of HIV-1), SIV-GSN, SIV-MUS, SIV- MON and SIV-DEN. There is no similar gene in HIV-2, SIV-SMM or other SIVs. Vpu is a 16 kDa (81-amino acid) type I integral membrane protein with at least two different biological functions: (a) degradation of CD4 in the endoplas- mic reticulum, and (b) enhancement of virion release from the plasma membrane of HIV-1-infected cells. Env and Vpu are expressed from a bicistronic mRNA. Vpu probably pos- sesses an N-terminal hydrophobic membrane anchor and a hydrophilic moiety. It is phosphorylated by casein kinase II at positions Ser52 and Ser56. Vpu is involved in Env maturation and is not found in the virion. Vpu has been found to increase susceptibility of HIV-1 infected cells to Fas killing.
NEF A multifunctional 27-kDa myristylated protein produced by an ORF located at the 30end of the primate lentiviruses. Other forms of Nef are known, including nonmyristylated variants. Nef is predominantly cytoplasmic and associated with the plasma membrane via the myristyl residue linked to the conserved second amino acid (Gly). Nef has also been identified in the nucleus and found associated with the cy- toskeleton in some experiments. One of the first HIV proteins to be produced in infected cells, it is the most immuno- genic of the accessory proteins. The nef genes of HIV and SIV are dispensable in vitro, but are essential for efficient viral spread and disease progression in vivo. Nef is necessary for the maintenance of high virus loads and for the develop- ment of AIDS in macaques, and viruses with defective Nef have been detected in some HIV-1 infected long term sur- vivors. Nef downregulates CD4, the primary viral receptor, and MHC class I molecules, and these functions map to different parts of the protein. Nef interacts with components of host cell signal transduction and clathrin-dependent protein sorting pathways. It increases viral infectivity. Nef contains PxxP motifs that bind to SH3 domains of a subset of Src ki- nases and are required for the enhanced growth of HIV but not for the downregulation of CD4.
VPX A virion protein of 12 kDa found in HIV-2, SIV-SMM, SIV-RCM, SIV-MND-2 and SIV-DRL and not in HIV-1 or other SIVs. This accessory gene is a homolog of HIV-1 vpr, and viruses with Vpx carry both vpr and vpx. Vpx function in relation to Vpr is not fully elucidated; both are incorporated into virions at levels comparable to Gag proteins through interactions with Gag p6. Vpx is necessary for efficient replica- tion of SIV-SMM in PBMCs. Progression to AIDS and death in SIV-infected animals can occur in the absence of Vpr or Vpx. Double mutant virus lacking both vpr and vpx was at-
tenuated, whereas the single mutants were not, suggesting a redundancy in the function of Vpr and Vpx related to virus pathogenicity.
Structural proteins/viral enzymes The products of gag, pol, and env genes, which are essential components of the retro- viral particle.
Regulatory proteins Tat and Rev proteins of HIV/SIV and Tax and Rex proteins of HTLVs. They modulate transcriptional and posttranscriptional steps of virus gene expression and are essential for virus propagation.
Accessory or auxiliary proteins Additional virion and non- virion-associated proteins produced by HIV/SIV retroviruses: Vif, Vpr, Vpu, Vpx, Nef. Although the accessory proteins are in general not necessary for viral propagation in tissue culture, they have been conserved in the different iso- lates; this conservation and experimental observations sug- gest that their role in vivo is very important. Their functional importance continues to be elucidated.
Complex retroviruses Retroviruses regulating their expression via viral factors and expressing additional proteins (regulatory and accessory) essential for their life cycle.
Preface
Preface Amino acid codes
I-9 Amino acid codes
A Alanine B Aspartic Acid or Asparagine C Cysteine D Aspartic Acid E Glutamic Acid F Phenylalanine G Glycine H Histidine I Isoleucine K Lysine L Leucine M Methionine N Asparagine P Proline Q Glutamine R Arginine S Serine T Threonine V Valine W Tryptophan X unknown or “other” amino acid Y Tyrosine Z Glutamic Acid or Glutamine . gap - identity * stop codon # incomplete codon
I-10 Nucleic acid codes
A Adenine C Cytosine G Guanine T Thymine U Uracil M A or C R A or G W A or T S C or G Y C or T K G or T V A or C or G H A or C or T D A or G or T B C or G or T N unknown . gap - identity
H IV
-1 G
en om
HIV-1/SIVcpz Complete Genomes
Contents II-1 Introduction . . . . . . . . . . . . 9 II-2 Annotated features . . . . . . . . . 10 II-3 Sequences . . . . . . . . . . . . . 13 II-4 Alignments . . . . . . . . . . . . . 18
II-1 Introduction
While the “web-alignment” this year has grown to 2229 full- length genomes, the compendium alignment herein has strict page limitations. The selection here was made such that subtypes A-G, CRF’s 01 and 02, and CPZ are represented with one sequence from most countries where the subtype has been sequenced. Priority was given to more recently sampled sequences to reflect the current pandemic diversity. For the rare subtypes H–K and groups N–P most available sequences are included, and for CRF’s 03 and up, one representative is included. Unique recombinant forms and unclassified sequences are not included. This resulted in 199 sequences of HIV-1/SIVcpz from all over the world.
The HXB2 sequence (accession K03455) is the master sequence in this alignment. This is also the genome coordi- nate standard used throughout the HIV Database. The alignment was generated by MAFFT v7.043 (E-INS-i with gap open penalty 2.0). The alignment was subsequently codon-aligned using GeneCutter, followed by a few manual edits to fix ob- vious misalignments. The alignment presented cannot be considered an “optimal alignment” to any single criterion; it is a compromise between optimal alignment, readability, and codon alignment. Most gaps have been introduced in multiples of 3 bases to maintain open reading frames when the alignment is translated.
Also part of this nucleotide alignment is a translation to protein sequence based on the HXB2 sequence; the HIV genome has many overlapping coding regions, and all are shown. For more complete annotation of functional domains, see the protein sequence alignments in Chapter V.
H IV
-1 G
enom es
II-2 Annotated features
Feature Location Page
5’ LTR U3 start 1 18 TCF-1 alpha 315-329 20 NF-κ-B-II 350-359 22 NF-κ-B-I 364-373 22 Sp1-III 375-386 22 Sp1-II 388-397 22 Sp1-I 398-408 22 TATA Box 427-431 22 TAR element start 453 24 5’ LTR U3 end 455 24 +1 mRNA start site 456 24 5’ LTR R repeat begin 456 24 TAR element end 513 24 Poly-A signal 527-532 24 5’ LTR R repeat end 551 24 5’ LTR U5 start 552 24 Extensive secondary structure 568-605 24 5’ LTR U5 end 633 26 Lys tRNA primer binding site 634-653 26 Packaging loops begin 681 26 Packaging loops end 789 28 Gag and Gag-Pol start 790 28 Gag p17 Matrix end 1185 34 Gag p24 Capsid start 1186 34 Gag p24 Capsid end 1881 42 Gag p2 start 1882 42 Gag p2 end 1920 44 Gag-Pol fusion TF protein start 1921 44 Gag p7 nucleocapsid start 1921 44 Gag p7 nucleocapsid end 2085 46 Gag-Pol -1 ribosomal slip site 2085 46 Pol start 2085 46 Gag p1 start 2086 46 Gag p1 end 2133 46 Gag p6 start 2134 46 Gag-Pol TF end 2252 50 Pol protease start 2253 50 Gag p6 end 2292 50 Gag end 2292 50 Pol Protease end 2549 52 Pol p66 and p51 RT start 2550 52 p51 end and p66 RT continue 3869 68 Pol p15 RNAse H start 3870 68 Pol p66 RT, Pol p15 Rnase H end 4229 72 Pol p31 Integrase start 4230 72 Vif start 5041 82 Pol, Gag-Pol, and p31 integrase end 5096 84 Vpr start 5559 90
Annotated features HIV-1/SIVcpz Complete Genomes
H IV
-1 G
en om
Vif end 5619 90 frameshift insert in HXB2 5772 92 Vpr premature end (HXB2 only) 5795 92 Tat exon 1 start 5831 94 Vpr end 5850 94 Rev exon 1 start 5970 94 Tat Rev exon 1 end 6045 96 intron start 6046 96 Vpu start (ACG in HXB2) 6062 96 Vpu transmembrane domain start 6062 96 Vpu transmembrane domain end 6143 98 Env start 6225 100 Vpu end 6310 100 Env signal peptide end 6314 100 Env gp120 start 6315 100 V1 loop start 6615 104 V1 loop end 6692 106 V2 loop start 6696 106 V2 loop end 6812 110 V3 loop start 7110 112 V3 loop end 7217 114 V4 loop start 7377 116 V4 loop end 7478 118 V5 start 7602 120 V5 end 7634 122 Rev Responsive Element (RRE) region 7710 122 Env gp120 end 7757 122 Env gp41 start 7758 122 RRE end 8061 126 Env gp41 transmembrane domain 8277-8336 130 Tat Rev intron end 8378 130 Tat Rev exon 2 start 8379 130 Tat premature stop in HXB2 8424 132 Tat end 8469 132 Rev end (TAA) in some lineages 8605 134 Rev end 8653 134 Env gp41, gp160 end 8795 136 Nef start 8797 136 3’ LTR U3 start 9086 142 Nef premature end in HXB2 9168 142 TCF-1 alpha binding 9400-9414 146 Nef end 9417 146 NF-κ-B-II 9435-9444 148 NF-κ-B-I 9449-9458 148 Sp1-III 9462-9471 148 Sp1-II 9473-9482 148 Sp1-I 9483-9493 148 TATA box 9512-9516 148 TAR element start 9538 148 3’ LTR U3 end 9540 148 3’ LTR repeat start 9541 148 TAR element end 9599 150 Poly-A signal 9612-9617 150
H IV
-1 G
enom es
3’ LTR R repeat end 9636 150 3’ LTR U5 start 9637 150 3’ LTR U5 end 9719 152
Sequences HIV-1/SIVcpz Complete Genomes
Name Accession Country Author Reference
B.FR.83.HXB2 K03455 France Wong-Staal, F. Nature 313(6000):277-284 (1985) A1.AU.03.PS1044_Day0 DQ676872 Australia Li, B. J Virol 81(1):193-201 (2007) A1.CH.03.HIV_CH_BID_V3538 JQ403028 Switzerland Henn, M.R. PLoS Pathog 8(3):E1002529
(2012) A1.ES.06.X2110 FJ670523 Spain Cuevas, M.T. ARHR 26(9); 1019-25 (2010) A1.IT.02.60000 EU861977 Italy Riva, C. ARHR 24(10); 1319-25 (2008) A1.KE.06.06KECst_001 FJ623487 Kenya Tovanabutra, S. ARHR 26(2); 123-31 (2010) A1.RU.11.11RU6950 JX500694 Russia Baryshev, P.B. Unpublished A1.RW.07.pR463F JX236677 Rwanda Baalwa, J. Virology 436(1):33-48 (2013) A1.SE.95.SE8538 AF069669 Sweden Carr, J.K. AIDS 13(14); 1819-26 (1999) A1.TZ.01.A341 AY253314 Tanzania Arroyo, M.A. ARHR 20(8):895-901 (2004) A1.UA.01.01UADN139 DQ823357 Ukraine Saad, M.D. ARHR 22(8):709-714 (2006) A1.UG.07.p191845 JX236671 Uganda Baalwa, J. Virology 436(1):33-48 (2013) A1.ZA.04.04ZASK162B1 DQ396400 S. Africa Rousseau, C.M. J Virol Methods 136(1-2):118-125
(2006) A2.CD.97.97CDKTB48 AF286238 D.R.C. Gao, F. ARHR 17(8):675-688 (2001) A2.CM.01.01CM_1445MV GU201516 Cameroon Carr, J.K. Retrovirology 2010 Apr 28;7:39 A2.CY.94.94CY017_41 AF286237 Cyprus Gao, F. ARHR 17(8):675-688 (2001) B.AR.04.04AR143170 DQ383750 Argentina Pando, M.A. Retrovirology 3 , 59 (2006) B.AU.04.PS1038_Day174 DQ676871 Australia Li, B. J Virol 81(1):193-201 (2007) B.BO.09.DEMB09BO001 JX140656 Bolivia Hora, B. Unpublished B.BR.06.06BR1119 JN692480 Brazil Sanabani, S.S. PLoS ONE 6(10):E25869 (2011) B.CA.07.502_1191_03 JF320424 Canada Rolland, M. Nat Med 17(3); 366-71 (2011) B.CH.04.HIV_CH_BID_V4408 JQ403042 Switzerland Henn, M.R. PLoS Pathog 8(3):E1002529
(2012) B.CN.10.DEMB10CN002 JX140658 China Hora, B. Unpublished B.CO.01.PCM001 AY561236 Colombia Sanchez, G.I. Am J Trop Med Hyg 74(4); 674-7
(2006) B.CU.99.Cu19 AY586542 Cuba Sierra, M. JAIDS 45(2):151-160 (2007) B.CY.09.CY266 JF683807 Cyprus Kousiappa, I. ARHR 27(11); 1183-99 (2011) B.DE.04.HIV_DE_BID_V4131 JQ403037 Germany Henn, M.R. PLoS Pathog 8(3):E1002529
(2012) B.DK.07.PMVL_011 FJ694790 Denmark Vinner, L. APMIS 119(8); 487-97 (2011) B.DO.05.05DO_160884 EU839597 Dominican
Republic Nadai, Y. PLoS ONE 4(3):E4814 (2009)
B.ES.09.P2149_3 GU362881 Spain Cuevas, M.T. ARHR 26(9); 1019-25 (2010) B.FR.08.DEMB08FR002 JX140654 France Hora, B. Unpublished B.GE.03.03GEMZ004 DQ207940 Georgia Zarandia, M. ARHR 22(5):470-476 (2006) B.HT.05.05HT_129389 EU839602 Haiti Nadai, Y. PLoS ONE 4(3):E4814 (2009) B.JM.05.05JM_KJ108 EU839605 Jamaica Nadai, Y. PLoS ONE 4(3):E4814 (2009) B.JP.05.DR6538 AB287363 Japan Sakamoto, Y. Unpublished B.KR.07.07KYY4 JQ341411 S. Korea Cho, Y.-K. ARHR 29(4); 738-43 (2013) B.NL.00.671_00T36 AY423387 Netherlands Geels, M.J. J Virol 77(23):12430-12440 (2003) B.PE.07.502_2649_wg8 JF320019 Peru Rolland, M. Nat Med 17(3); 366-71 (2011) B.PY.03.03PY_PSP0115 JN251906 Paraguay Eyzaguirre, L.M. Unpublished B.RU.11.11RU21n JX500708 Russia Baryshev, P.B. Unpublished B.TH.07.AA040a_WG11 JX447156 Thailand Rolland, M. Nature 490(7420); 417-20 (2012)
Nadai, Y. PLoS ONE 4(3):E4814 (2009)
B.TW.94.TWCYS_LM49 AF086817 Taiwan Huang, L.-M. Unpublished B.UA.01.01UAKV167 DQ823362 Ukraine Saad, M.D. ARHR 22(8):709-714 (2006) B.US.11.ES38 JN397362 United States Buckheit, R.W.3. Nat Commun 3, 716 (2012) B.UY.02.02UY_TSU1290 JN235958 Uruguay Eyzaguirre, L.M. Unpublished B.VE.10.DEMB10VE001 JX140659 Venezuela Hora, B. Unpublished B.YE.02.02YE507 AY795904 Yemen Saad, M.D. ARHR 21(7):644-648 (2005) C.AR.01.ARG4006 AY563170 Argentina Carrion, G. ARHR 20(9):1022-1025 (2004) C.BR.07.DEMC07BR003 JX140663 Brazil Hora, B. Unpublished C.BW.00.00BW07621 AF443088 Botswana Novitsky, V. J Virol 76(11):5435-5451 (2002) C.CN.98.YNRL9840 AY967806 China Qiu, Z. ARHR 21(12):1051-1056 (2005) C.CY.09.CY260 JF683803 Cyprus Kousiappa, I. ARHR 27(11); 1183-99 (2011) C.ES.07.X2118_2 EU884500 Spain Fernandez-Garcia,
A. ARHR 25(1); 93-102 (2009)
C.ET.02.02ET_288 AY713417 Ethiopia Brown, B.K. J Virol 79(10):6089-6101 (2005) C.GE.03.03GEMZ033 DQ207941 Georgia Zarandia, M. ARHR 22(5):470-476 (2006) C.IL.98.98IS002 AF286233 Israel Rodenburg, C.M. ARHR 17(2):161-168 (2001) C.IN.03.D24 EF469243 India Dash, P.K. Retrovirology 5(1):25 (2008) C.KE.00.KER2010 AF457054 Kenya Dowling, W.E. AIDS 16(13):1809-1820 (2002) C.MM.99.mIDU101_3 AB097871 Myanmar Takebe, Y. AIDS 17(14):2077-87 (2003) C.MW.93.93MW_965 AY713413 Malawi Brown, B.K. J Virol 79(10):6089-6101 (2005) C.SN.90.90SE_364 AY713416 Senegal Brown, B.K. J Virol 79(10):6089-6101 (2005) C.SO.89.89SM_145 AY713415 Somalia Brown, B.K. J Virol 79(10):6089-6101 (2005) C.TZ.02.CO178 AY734556 Tanzania Arroyo, M.A. AIDS 19(14):1517-1524 (2005) C.US.98.98US_MSC3018 AY444800 United States Tovanabutra, S. ARHR 21(5):424-429 (2005) C.UY.01.TRA3011 AY563169 Uruguay Carrion, G. ARHR 20(9):1022-1025 (2004) C.YE.02.02YE511 AY795906 Yemen Saad, M.D. ARHR 21(7):644-648 (2005) C.ZA.10.DEMC10ZA001 JX140669 S. Africa Hora, B. Unpublished C.ZM.02.02ZM108 AB254141 Zambia Tatsumi, M. Unpublished D.CD.83.ELI K03454 D.R.C. Alizon, M. Cell 46(1):63-74 (1986) D.CM.10.DEMD10CM009 JX140670 Cameroon Hora, B. Unpublished D.CY.06.CY163 FJ388945 Cyprus Kousiappa, I. ARHR 25(8); 727-40 (2009) D.KE.97.ML415_2 AY322189 Kenya Fang, G. J Infect Dis 190(4):697-701 (2004) D.KR.04.04KBH8 DQ054367 S. Korea Cho, Y.-K. ARHR 29(4); 738-43 (2013) D.SN.90.SE365 AB485648 Senegal Takekawa, N. Unpublished D.TD.99.MN011 AJ488926 Chad Vidal, N. JAIDS 33(2):239-246 (2003) D.TZ.01.A280 AY253311 Tanzania Arroyo, M.A. ARHR 20(8):895-901 (2004) D.UG.08.p191859 JX236672 Uganda Baalwa, J. Virology 436(1):33-48 (2013) D.YE.02.02YE516 AY795907 Yemen Saad, M.D. ARHR 21(7):644-648 (2005) D.ZA.90.R1 EF633445 S. Africa Jacobs, G.B. ARHR 23(12):1575-8 (2007) F1.AO.06.AO_06_ANG125 FJ900269 Angola Guimaraes, M.L. Retrovirology 6, 39 (2009) F1.AR.02.ARE933 DQ189088 Argentina Aulicino, P.C. ARHR 21(2):158-164 (2005) F1.BE.93.VI850 AF077336 Belgium Laukkanen, T. Virology 269(1):95-104 (2000) F1.BR.07.07BR844 FJ771010 Brazil Sanabani, S.S. Virol J 2009 Jun 16;6:78 F1.CY.08.CY222 JF683771 Cyprus Kousiappa, I. ARHR 27(11); 1183-99 (2011) F1.ES.11.DEMF110ES001 JX140671 Spain Hora, B. Unpublished F1.FI.93.FIN9363 AF075703 Finland Laukkanen, T. Virology 269(1):95-104 (2000) F1.FR.96.96FR_MP411 AJ249238 France Triques, K. ARHR 16(2):139-151 (2000) F1.RO.96.BCI_R07 AB485658 Romania Takekawa, N. Unpublished F1.RU.08.D88_845 GQ290462 Russia Fernandez-Garcia,
A. ARHR 25(11):1187-1191 (2009)
F2.CM.97.CM53657 AF377956 Cameroon Carr, J.K. Virology 286(1):168-181 (2001) G.BE.96.DRCBL AF084936 Belgium Oelrichs, R.B. ARHR 15(6):585-589 (1999) G.CM.10.DEMG10CM008 JX140676 Cameroon Hora, B. Unpublished G.CN.08.GX_2084_08 JN106043 China Li, L. Unpublished G.CU.99.Cu74 AY586547 Cuba Sierra, M. JAIDS 45(2):151-160 (2007) G.ES.09.X2634_2 GU362882 Spain Cuevas, M.T. ARHR 26(9); 1019-25 (2010) G.GH.03.03GH175G AB287004 Ghana Takekawa, N. Unpublished G.KE.93.HH8793_12_1 AF061641 Kenya Salminen, M. ARHR 8(9):1733-1742 (1992) G.NG.09.09NG_SC62 JN248593 Nigeria Charurat, M. J Infect Dis 2012 Feb 21 G.PT.x.PT3306 FR846409 Portugal Freitas, F.B. ARHR 2012 Sep 25 G.SE.93.SE6165_G6165 AF061642 Sweden Carr, J.K. Virology 247(1):22-31 (1998) H.BE.93.VI991 AF190127 Belgium Janssens, W. AIDS 14(11):1533-1543 (2000) H.BE.93.VI997 AF190128 Belgium Janssens, W. AIDS 14(11):1533-1543 (2000) H.CF.90.056 AF005496 C.A.R. Gao, F. J Virol 72(7):5680-5698 (1998) H.GB.00.00GBAC4001 FJ711703 United
Kingdom Holzmayer, V. ARHR 25(7):721-726 (2009)
J.CD.97.J_97DC_KTB147 EF614151 D.R.C. Abecasis, A.B. J Virol 81(16):8543-8551 (2007) J.CM.04.04CMU11421 GU237072 Cameroon Yamaguchi, J. ARHR 26(6); 693-7 (2010) J.SE.93.SE9280_7887 AF082394 Sweden Laukkanen, T. ARHR 15(3):293-297 (1999) J.SE.94.SE9173_7022 AF082395 Sweden Laukkanen, T. ARHR 15(3):293-297 (1999) K.CD.97.97ZR_EQTB11 AJ249235 D.R.C. Triques, K. ARHR 16(2):139-151 (2000) K.CM.96.96CM_MP535 AJ249239 Cameroon Triques, K. ARHR 16(2):139-151 (2000) 01_AE.AF.07.569M GQ477441 Afghanistan Sanders-Buell, E. ARHR 26(5):605-608 (2010) 01_AE.CN.09.1119 HQ215553 China Li, L. Infect Genet Evol 2011 May 27 01_AE.HK.04.HK001 DQ234790 Hong Kong Tsui, S.K.W. Unpublished 01_AE.JP.x.DR0492 AB253423 Japan Sakamoto, Y. Unpublished 01_AE.TH.04.BKM DQ314732 Thailand Thitithanyanont, A. Unpublished 01_AE.TH.09.AA111a_WG11 JX448059 Thailand Rolland, M. Nature 490(7420); 417-20 (2012) 01_AE.TH.90.CM240 U54771 Thailand Carr, J.K. J Virol 70(9):5935-5943 (1996) 01_AE.VN.98.98VNND15 FJ185235 Viet Nam Liao, H. Virology 391(1):51-56 (2009) 02_AG.CM.08.DE00208CM001 JX140646 Cameroon Hora, B. Unpublished 02_AG.ES.06.P1261 EU786671 Spain Fernandez-Garcia,
A. ARHR 25(1); 93-102 (2009)
02_AG.FR.91.DJ263 AF063223 France Carr, J.K. Virology 247(1):22-31 (1998) 02_AG.GH.03.03GH181AG AB286855 Ghana Sakamoto, Y. Unpublished 02_AG.LR.x.POC44951 AB485636 Liberia Takekawa, N. Unpublished 02_AG.NG.x.IBNG L39106 Nigeria Howard, T.M. ARHR 10(12):1755-1757 (1994) 02_AG.SN.98.98SE_MP1211 AJ251056 Senegal Toure-Kane, C. ARHR 16(6):603-609 (2000) 02_AG.US.06.502_2696_FL01 JF320297 United States Rolland, M. Nat Med 17(3); 366-71 (2011) 02_AG.UZ.02.02UZ0683 AY829214 Uzbekistan Carr, J.K. JAIDS 39(5):570-575 (2005) 03_AB.RU.97.KAL153_2 AF193276 Russia Liitsola, K. ARHR 16(11):1047-1053 (2000) 04_cpx.CY.94.94CY032_3 AF049337 Cyprus Gao, F. J Virol 72(12):10234-10241 (1998) 05_DF.BE.x.VI1310 AF193253 Belgium Laukkanen, T. Virology 269(1):95-104 (2000) 06_cpx.AU.96.BFP90 AF064699 Australia Oelrichs, R.B. ARHR 14(16):1495-1500 (1998) 07_BC.CN.98.98CN009 AF286230 China Rodenburg, C.M. ARHR 17(2):161-168 (2001) 08_BC.CN.06.nx2 HM067748 China Miao, W. Unpublished 09_cpx.GH.96.96GH2911 AY093605 Ghana McCutchan, F.E. ARHR 20(8):819-826 (2004) 10_CD.TZ.96.96TZ_BF061 AF289548 Tanzania Koulinska, I.N. ARHR 17(5):423-431 (2001) 11_cpx.CM.95.95CM_1816 AF492624 Cameroon Wilbe, K. ARHR 18(12):849-56 (2002) 12_BF.AR.99.ARMA159 AF385936 Argentina Carr, J.K. AIDS 15(15):F41-F47 (2001) 13_cpx.CM.96.96CM_1849 AF460972 Cameroon Wilbe, K. ARHR 18(12):849-56 (2002) 14_BG.ES.05.X1870 FJ670522 Spain Cuevas, M.T. ARHR 26(9); 1019-25 (2010) 15_01B.TH.99.99TH_MU2079 AF516184 Thailand Viputtijul, K. ARHR 18(16):1235-1237 (2002)
16_A2D.KR.97.97KR004 AF286239 S. Korea Gao, F. ARHR 17(8):675-688 (2001) 17_BF.AR.99.ARMA038 AY037281 Argentina Carr, J.K. AIDS 15(15):F41-F47 (2001) 18_cpx.CU.99.CU76 AY586540 Cuba Thomson, M.M. AIDS 19(11):1155-63 (2005) 19_cpx.CU.99.CU7 AY894994 Cuba Casado, G. JAIDS 40(5):532-537 (2005) 20_BG.CU.99.Cu103 AY586545 Cuba Sierra, M. JAIDS 45(2):151-160 (2007) 21_A2D.KE.99.KER2003 AF457051 Kenya Dowling, W.E. AIDS 16(13):1809-1820 (2002) 22_01A1.CM.01.01CM_0001BBY AY371159 Cameroon Kijak, G.H. ARHR 20(5):521-530 (2004) 23_BG.CU.03.CB118 AY900571 Cuba Sierra, M. JAIDS 45(2):151-160 (2007) 24_BG.ES.08.X2456_2 FJ670526 Spain Cuevas, M.T. ARHR 26(9); 1019-25 (2010) 25_cpx.CM.02.1918LE AY371169 Cameroon Kijak, G.H. ARHR 20(5):521-530 (2004) 26_AU.CD.02.02CD_MBTB047 FM877782 D.R.C. Vidal, N. ARHR 25(8):823-832 (2009) 27_cpx.FR.04.04CD_FR_KZS AM851091 France Vidal, N. ARHR 24(2):315-321 (2008) 28_BF.BR.99.BREPM12609 DQ085873 Brazil Sa Filho, D.J. ARHR 22(1):1-13 (2006) 29_BF.BR.01.BREPM16704 DQ085876 Brazil Sa Filho, D.J. ARHR 22(1):1-13 (2006) 31_BC.BR.04.04BR142 AY727527 Brazil Sanabani, S. ARHR 22(2):171-176 (2006) 32_06A1.EE.01.EE0369 AY535660 Estonia Adojaan, M. JAIDS 39(5):598-605 (2005) 33_01B.ID.07.JKT189_C AB547463 Indonesia SahBandar, I.N. ARHR 2010 Oct 19 34_01B.TH.99.OUR2478P EF165541 Thailand Tovanabutra, S. ARHR 23(6):829-833 (2007) 35_AD.AF.07.169H GQ477446 Afghanistan Sanders-Buell, E. ARHR 26(5):605-608 (2010) 36_cpx.CM.00.00CMNYU830 EF087994 Cameroon Powell, R.L. ARHR 23(8):1008-1019 (2007) 37_cpx.CM.00.00CMNYU926 EF116594 Cameroon Powell, R.L. ARHR 23(7):923-933 (2007) 38_BF1.UY.03.UY03_3389 FJ213783 Uruguay Ruchansky, D. ARHR 25(3); 351-6 (2009) 39_BF.BR.04.04BRRJ179 EU735535 Brazil Guimaraes, M.L. AIDS 22(3):433-435 (2008) 40_BF.BR.05.05BRRJ055 EU735537 Brazil Guimaraes, M.L. AIDS 22(3):433-435 (2008) 42_BF.LU.03.luBF_05_03 EU170155 Luxembourg Struck, D. Unpublished 43_02G.SA.03.J11223 EU697904 Saudi Arabia Badreddine, S. ARHR 23(5):667-674 (2007) 44_BF.CL.00.CH80 FJ358521 Chile Delgado, E. ARHR 26(7); 821-6 (2010) 45_cpx.FR.04.04FR_AUK EU448295 France Frange, P. Retrovirology 2008 Aug 1;5:69 46_BF.BR.07.07BR_FPS625 HM026456 Brazil Sanabani, S.S. Virol J 2010 Apr 16;7:74 47_BF.ES.08.P1942 GQ372987 Spain Fernandez-Garcia,
A. ARHR 26(7); 827-32 (2010)
48_01B.MY.07.07MYKT021 GQ175883 Malaysia Li, Y. JAIDS 54(2):129-136 (2010) 49_cpx.GM.03.N26677 HQ385479 Gambia de Silva, T.I. Retrovirology 7(1):82 (2010) 51_01B.SG.11.11SG_HM021 JN029801 Singapore Ng, O.T. ARHR 2011 Sep 23 52_01B.MY.03.03MYKL018_1 DQ366664 Malaysia Tee, K.K. JAIDS 43(5):523-529 (2006) 53_01B.MY.11.11FIR164 JX390610 Malaysia Chow, W.Z. J Virol 86(20):11398-11399 (2012) 54_01B.MY.09.09MYSB023 JX390976 Malaysia Ng, K.T. J Virol 86(20):11405-11406 (2012) 55_01B.CN.10.HNCS102056 JX574661 China Han, X. Genome Announc 1(1):E00050-12
(2013) O.BE.87.ANT70 L20587 Belgium Vanden
Haesevelde, M. J Virol 68(3):1586-1596 (1994)
O.CM.91.MVP5180 L20571 Cameroon Gurtler, L.G. J Virol 68(3):1581-1585 (1994) O.CM.98.98CMA104 AY169802 Cameroon Yamaguchi, J. ARHR 19(11):979-988 (2003) O.FR.92.VAU AF407418 France Vartanian, J.P. J Gen Virol 83(Pt 4):801-805
(2002) O.SN.99.99SE_MP1299 AJ302646 Senegal Toure-Kane, C. ARHR 17(12):1211-1216 (2001) O.US.10.LTNP JN571034 United States Buckheit, R.W. III Unpublished O.US.97.97US08692A AY169805 United States Yamaguchi, J. ARHR 19(11):979-988 (2003) N.CM.02.DJO0131 AY532635 Cameroon Bodelle, P. ARHR 20(8):902-908 (2004) N.CM.04.04CM_1015_04 DQ017382 Cameroon Yamaguchi, J. ARHR 22(1):83-92 (2006) N.CM.06.U14842 GQ324958 Cameroon Vallari, A. ARHR 26(1):109-115 (2010) N.CM.95.YBF30 AJ006022 Cameroon Simon, F. Nat Med 4(9):1032-1037 (1998) N.CM.97.YBF106 AJ271370 Cameroon Roques, P. AIDS 18(10):1371-1381 (2004)
N.FR.11.N1_FR_2011 JN572926 France Delaugerre, C. Lancet 378(9806); 1894 (2011) P.CM.06.U14788 HQ179987 Cameroon Vallari, A. J Virol 85(3); 1403-7 (2011) P.FR.09.RBF168 GU111555 France Plantier, J.-C. Nat Med 15(8); 871-2 (2009) CPZ.CD.06.BF1167 JQ866001 D.R.C. Li, Y. J Virol 86(19):10776-10791 (2012) CPZ.CM.05.SIVcpzMT145 DQ373066 Cameroon Keele, B.F. Science 313(5786):523-526 (2006) CPZ.GA.88.GAB1 X52154 Gabon Huet, T. Nature 345(6273):356-359 (1990) CPZ.TZ.06.SIVcpzTAN13 JQ768416 Tanzania Takehisa, J. Unpublished CPZ.US.85.US_Marilyn AF103818 United States Gao, F. Nature 397(6718):436-441 (1999)
18 H
IV Sequence
C om
pendium 2013
A lignm
ents H
IV-1/SIV cpz
C om
plete G
enom es
HIV-1 Genomes
20 H
IV Sequence
C om
pendium 2013
A lignm
ents H
IV-1/SIV cpz
C om
plete G
enom es
HIV-1 Genomes
22 H
IV Sequence
C om
pendium 2013
A lignm
ents H
IV-1/SIV cpz
C om
plete G
enom es
HIV-1 Genomes
H IV-1/SIV
cpz C
om plete
G enom
es A
lignm ents
5’ LTR U3 end 5’ LTR R repeat begin Poly-A signal 5’ LTR R repeat end 5’ LTR U5 start TAR element start TAR element end Extensive secondary structure
+1 mRNA start site
24 H
IV Sequence
C om
pendium 2013
A lignm
ents H
IV-1/SIV cpz
C om
plete G
enom es
HIV-1 Genomes
5’ LTR U3 end 5’ LTR R repeat begin Poly-A signal 5’ LTR R repeat end 5’ LTR U5 start TAR element start TAR element end Extensive secondary structure
+1 mRNA start site
H IV-1/SIV
cpz C
om plete
G enom
es A
lignm ents
5’ LTR U5 end Packaging loops begin Lys tRNA primer binding site
B.FR.83.HXB2 TTTAGTCAGTGTGG.AAAATCTCTAGCAGTGGCGCCCGAACAGGGACC.TGAAAGCGAAAG.....................GGAAACCAGAGG...AGCTCTCTCGAC.GCA...GGACTCGGCTTGCTG......AAGCGC..GCACGGCAAGAGGCGAGGGGC...G 736 A1.AU.03.PS1044_Day0 .......................................................................................................................................................................... 0 A1.CH.03.HIV_CH_BID_V3538 .......................................................................................................................................................................... 0 A1.ES.06.X2110 .......................................................................................................................................................................... 0 A1.IT.02.60000 -C---A-T----AA.------------------------------.........................ACTCGAAAGCGAAAGTT------A...--W---------.---...---------------......-G-T--..A---A------------A---...- 747 A1.KE.06.06KECst_001 .......................................................................................................................................................................... 0 A1.RU.11.11RU6950 -C---G-G----A..------------------------------.........................ACTTGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 277 A1.RW.07.pR463F -C---A-T-A--A..--------------------------------T.------T-----TTAATAGGGACTTGAAAGCGAAAGTT------A...--T---------.---...---------------......-GTGC...A---A------------A-CG...- 755 A1.SE.95.SE8538 .......................................................................................................................................................................... 0 A1.TZ.01.A341 .......................................................................................................................................................................... 0 A1.UA.01.01UADN139 .......................................................................................................................................................................... 0 A1.UG.07.p191845 -C---A-T--A-A..--------------------------------T.-T---AGCG--AGTAACAGGGACTCGAAAGCGGAAGTT------A...--A---------.---...---------------......-G-T--..A---A------------A-CG...- 778 A1.ZA.04.04ZASK162B1 -C---A-T-A--A..G-----------------------------.........................ACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 166 A2.CD.97.97CDKTB48 ......................................................................TTTTTCGAAGCGAAGT-----G-A...--T---------.---...A--------------......-G-T--..A----------------AA--...- 82 A2.CM.01.01CM_1445MV .......................................................................................................................................................................... 0 A2.CY.94.94CY017_41 ................................................T-----AGCG--AGTAACAGGGACTCGAAAGCGAAAGTT-------...--T---------.---...---------------......-G-T--..A--------------------...- 104 B.AR.04.04AR143170 .......................................................................................................................................................................... 0 B.AU.04.PS1038_Day174 .......................................................................................................................................................................... 0 B.BO.09.DEMB09BO001 ............................-------------------T.------------.....................TAG---------...--A---------.---...---------------......------..----A---------------A...- 102 B.BR.06.06BR1119 --------------.--------------------------------T.------------.....................TA--G-------...--A---------.---...---------------.......-----..----A---------------AC..- 146 B.CA.07.502_1191_03 --------------.---------------------------------.C-----------.....................TAG---------...--A---------.---...---------------......------..--G------------------...- 155 B.CH.04.HIV_CH_BID_V4408 .......................................................................................................................................................................... 0 B.CN.10.DEMB10CN002 ...........................---------------------.------------.....................TAG---------...------------.---...---------------......------..----A----------------...- 103 B.CO.01.PCM001 .......................................................................................................................................................................... 0 B.CU.99.Cu19 C-------------.------------------------------G...................................................------------.---...---------------......------..----A----------------...- 277 B.CY.09.CY266 .......................................................................................................................................................................... 0 B.DE.04.HIV_DE_BID_V4131 .......................................................................................................................................................................... 0 B.DK.07.PMVL_011 ...................................------------T.------T-----.....................A----------A...------------.---...---------------......------..---------------------...- 95 B.DO.05.05DO_160884 .......................................................................................................................................................................... 0 B.ES.09.P2149_3 --AGTCAGTGTG-A.--------------------------------T.------------.....................TA----------...--AA--------.---...---------------AAGC..........----A----------------...A 190 B.FR.08.DEMB08FR002 ........................................-------T.------T-----.....................TTG---------...------------.---...-------------C-......------..---------------------...- 90 B.GE.03.03GEMZ004 .......................................................................................................................................................................... 0 B.HT.05.05HT_129389 .......................................................................................................................................................................... 0 B.JM.05.05JM_KJ108 .......................................................................................................................................................................... 0 B.JP.05.DR6538 --------------.--------------------------------T.------T-----.....................TAG---------...------------.---...---------------.......-----..---------------------...- 737 B.KR.07.07KYY4 ------T-------.--------------------------------T.------------.....................TAGT---G----...------------.---...---------------......------..---------------------...- 400 B.NL.00.671_00T36 --------------.--------------------------------T.---...A-----.....................TA----------...--A---------.---...---------------AAGAAG------..--G------------------...- 261 B.PE.07.502_2649_wg8 --------------.--------------------------------T.------------.....................TAG---------...------------.---...---------------......-GCGC...-----------------A---...- 148 B.PY.03.03PY_PSP0115 .......................................................................................................................................................................... 0 B.RU.11.11RU21n --------------.--------------------------------T.------T-----.....................TA--C-AGAG-A......G----T---.---...---------------......---T--..---------------------...- 278 B.TH.07.AA040a_WG11 ...........................................----T.-----A------.....................T--G--------...------------.---...---------------......------..----A-----------.-A--...- 86 B.TT.01.01TT_CRC50069 .......................................................................................................................................................................... 0 B.TW.94.TWCYS_LM49 --------------.---------------------------------.-------A----.....................A-----------...--A---------.---...---------------......---T--..---------------------...- 735 B.UA.01.01UAKV167 .......................................................................................................................................................................... 0 B.US.11.ES38 CG-----------A.---------------------------------T-A----------.....................A-----------...------------.---...---------------.....A------..------------------A--...- 662 B.UY.02.02UY_TSU1290 .......................................................................................................................................................................... 0 B.VE.10.DEMB10VE001 ..........................................-----G.C-----------.....................TAG---------...------------.---...---------------......------..----A----------------...- 88 B.YE.02.02YE507 .......................................................................................................................................................................... 0 C.AR.01.ARG4006 .......................................................................................................................................................................... 0 C.BR.07.DEMC07BR003 ..................................-------------T.C-----------.....................TA-G-------A...--A---------.---...---------------......---T--..A----------------A-CG...- 96 C.BW.00.00BW07621 ...................----------------------------T.------T-----.....................TA-G--------...--A---------.---...---------------......---T--..A-T--------------A-CGGC.. 112 C.CN.98.YNRL9840 .......................................................................................................................................................................... 0 C.CY.09.CY260 .......................................................................................................................................................................... 0 C.ES.07.X2118_2 ---G--TGTGTG-..--------------------------------T.------------.....................TA-G--------...--A---------.---...---------------......---T--..A-T--------------A-CG...- 177 C.ET.02.02ET_288 .......................................................................................................................................................................... 0 C.GE.03.03GEMZ033 .......................................................................................................................................................................... 0 C.IL.98.98IS002 ..................................................----A------.....................T--G--------...--A---------.---...--------------A......---T--..A-TT-------------A-CGGC.. 82 C.IN.03.D24 ---G--AGTGTG-..--------------------------------G.C----A------.....................T--G-------A...--A---------.---...---------------......---T--..A-T--------------A--GGC.. 758 C.KE.00.KER2010 .......................................................................................................................................................................... 0 C.MM.99.mIDU101_3 ................--------------------------------.------------.....................TA-G--------...--A---------.---...---------------......---T--..A-T--------------A--GGC.. 115 C.MW.93.93MW_965 .......................................................................................................................................................................... 0 C.SN.90.90SE_364 .......................................................................................................................................................................... 0 C.SO.89.89SM_145 .......................................................................................................................................................................... 0 C.TZ.02.CO178 .......................................................................................................................................................................... 0 C.US.98.98US_MSC3018 .......................................................................................................................................................................... 0 C.UY.01.TRA3011 .......................................................................................................................................................................... 0 C.YE.02.02YE511 .......................................................................................................................................................................... 0 C.ZA.10.DEMC10ZA001 ................................---------------T.------------.....................TA-G--------...--A---------.---...---------------......---T--..A-T------------------...- 98 C.ZM.02.02ZM108 ---T-GT-------.--------------------------------G.C-----------.....................TAG---------...--AA--------.---...---------------......---T--..A-T--------------A-CG...- 736 D.CD.83.ELI ---------A----.---------------------------------.------------.....................TAG---------...------------.---...---------------......------..---------------------...A 282 D.CM.10.DEMD10CM009 ............................-------------------T.------------.....................TAG---------...------------.---...---------------......-GCGC...--------------------T...A 101 D.CY.06.CY163 .......................................................................................................................................................................... 0 D.KE.97.ML415_2 -G-----------..--------------------------------T.------------.....................TAG---------...------------.---...---------------......------..----A--------------CA...- 203 D.KR.04.04KBH8 G--T--------AA.---------C----------------------T.------------.....................TAG---------...-------C----.---...-----T---------......------..----A---------------T...A 693 D.SN.90.SE365 --------------.---------------------------------.C-----------.....................TAG---------...------------.---...---------------......------..---------------------...A 735 D.TD.99.MN011 .......................................................................................................................................................................... 0 D.TZ.01.A280 .......................................................................................................................................................................... 0 D.UG.08.p191859 -------C-G----.--------------------------------G.C-----------.....................TAG----G---A...--A---------.---...---------------......------..----A----------------...A 754 D.YE.02.02YE516 .......................................................................................................................................................................... 0 D.ZA.90.R1 .......................................................................TCGGCTGGAAC-AGTTAAGTGA-...GAG-------C..---...---------------......------..--G------------------...A 80 F1.AO.06.AO_06_ANG125 .......................................................................................................................................................................... 0 F1.AR.02.ARE933 ...........................................................................................................TT.---...---------------......---T--..A----------------A-CG...- 48 F1.BE.93.VI850 ...........................................----..-TG---------.....................TAG--------A...--A---------.--GG..---------------......---T--A.A----------------A-CG...- 88 F1.BR.07.07BR844 --------------.--------------------------------G.C----A------.....................TAG--------A...--A---------.---...---------------......---T--..A---A------------A-CG...- 502 F1.CY.08.CY222 .......................................................................................................................................................................... 0 F1.ES.11.DEMF110ES001 ..........................................--AC-..-----A------.....................TAG--------A...--A---------.---...---------------......---T--..A--------------------...- 87 F1.FI.93.FIN9363 ...................................................----------.....................TAG--------A...--A---------.---...---------------......---T--..A----------------A-CG...- 80 F1.FR.96.96FR_MP411 .......................................................................................................................................................................... 0 F1.RO.96.BCI_R07 --------------.--------------------------------T.------------.....................TAG--------A...--A---------.---...---------------......---T--..A----------------A-CG...- 779 F1.RU.08.D88_845 --------------.--------------------------------G.C-----------.....................TAG---------...--A---------.---...---------------......-G-T--..A---A------------A-CG...- 193 F2.CM.10.DEMF210CM007 ............................--------------------.------------.....................TAG---------...--A---------.---...---------------......-GTGC...A-G-A------------AA--...- 101 F2.CM.97.CM53657 .......................................................................................................................................................................... 0 G.BE.96.DRCBL -C---AT-----A..--------------------------------T.-----A------TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 722 G.CM.10.DEMG10CM008 .............................------------------T.------T-----TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...--------------A......---T--..A---A------------A-CG...- 122 G.CN.08.GX_2084_08 .......................................................................................................................................................................... 0 G.CU.99.Cu74 -C---A-G----A..--------------------------------T.------------TTAACAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 350 G.ES.09.X2634_2 -C----G-----A..--------------------------------T.------------TTAACAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......---GTGC.A-G-A------------A-CG...- 214 G.GH.03.03GH175G -C---A------A..---------------------------------.C-----T-----TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......---T--..A---A------------A-CG...- 779 G.KE.93.HH8793_12_1 ...........G-CTT-------------------------------T.------T-.---TTAACAGGGACTCGAAAGCGAAAGTT------A...--A---------.---...---------------......-G-T--..A-G-A------------A-CG...- 139 G.NG.09.09NG_SC62 .......................................................................................................................................................................... 0
26 H
IV Sequence
C om
pendium 2013
A lignm
ents H
IV-1/SIV cpz
C om
plete G
enom es
HIV-1 Genomes
5’ LTR U5 end Packaging loops begin Lys tRNA primer binding site
B.FR.83.HXB2 TTTAGTCAGTGTGG.AAAATCTCTAGCAGTGGCGCCCGAACAGGGACC.TGAAAGCGAAAG.....................GGAAACCAGAGG...AGCTCTCTCGAC.GCA...GGACTCGGCTTGCTG......AAGCGC..GCACGGCAAGAGGCGAGGGGC...G 736 G.PT.x.PT3306 -C--AA------A..--------------------------------T.--G---------TTAACAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......---GTGC.A----------------A-CG...- 688 G.SE.93.SE6165_G6165 ...........G-CTT-------------------------------T.------------TTAACAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 140 H.BE.93.VI991 ................-------------------------------T.------------.....................CA---------A...------------.---...---------------......---T--..A---A----------------GG.C 116 H.BE.93.VI997 ....................................................................................................---------.---...---------------......---T--..A--------------------GG.C 57 H.CF.90.056 ...............................................T.---T--T-----.....................TA---------A...--A---------.---...---------------......---T--..A---A------------A-CG...- 83 H.GB.00.00GBAC4001 -Y------------.--------------------------------T.------------.....................TA---------A...--T---------.---...---------------......-GTGC...A--------------------GG.C 249 J.CD.97.J_97DC_KTB147 .......................................................................................................................................................................... 0 J.CM.04.04CMU11421 --------------.---------------------------------T------T-----.....................TAGG-------A...--T---------.---...---------------......---T--..A---A------------A-CG...- 252 J.SE.93.SE9280_7887 ...................................................................................................T---------.---...---------------......---T--..A--------------------...- 56 J.SE.94.SE9173_7022 ...................................................................................................T---------.---...---------------......---T--..A---------------A----...- 56 K.CD.97.97ZR_EQTB11 .......................................................................................................................................................................... 0 K.CM.96.96CM_MP535 .......................................................................................................................................................................... 0 01_AE.AF.07.569M .......................................................................................................................................................................... 0 01_AE.CN.09.1119 .......................................................................................................................................................................... 0 01_AE.HK.04.HK001 ....................................-----------T.------------TTAATAGGGACTCGAAAGCGAAAGTT------A...--T--------GC---...---------------......-G-T--..A---A------------A-CG...- 116 01_AE.JP.x.DR0492 -C---A-T-A--A..--------------------------------T.------T-----TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 756 01_AE.TH.04.BKM -C---A-T-A--A..--------------------------------T.------------TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......CG-T--..A---A-----C------A-CG...- 700 01_AE.TH.09.AA111a_WG11 -C---A-T-A--A..--------------------------------T.------------TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 175 01_AE.TH.90.CM240 -C---A-T-A--A..----------C-------------------CA-TC-----------TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 304 01_AE.VN.98.98VNND15 .........................................................................................................................................................................C 1 02_AG.CM.08.DE00208CM001 ..........................T--------------------........--G---TTAATAGGGACTCGAAAGCGAAAGTT------A...--A---------.---G..---------------......-G-T--..A----------------A-CG...- 119 02_AG.ES.06.P1261 -C---A-TTA---A.--------------------------------........--G---TTAATAGGGACTCGAAAGCGAAAGTT------A...------------.---G..---------------......-G-T--..A---A------------A-CG...- 191 02_AG.FR.91.DJ263 ...................................................GG-C--G---CTAATAGGGACTCGAAAGCGAAAGTT------A...--A---------.---G..---------------......-G-T--..A-G-A------------A-CG...- 102 02_AG.GH.03.03GH181AG -G---A-T----AA.--------------------------------........-TG--ATTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---A..---------------......-G-T--..A-G-A------------A-CG...- 775 02_AG.LR.x.POC44951 -C---A-T--A-A..--------------------------------........TTG---ATAATAGGGACTCGAAAGCGAAAGTT----G-A...GCTCTCTC.---.---G..A--------------......-G-T--..A-G-A------------A-CG...- 749 02_AG.NG.x.IBNG -C---A-T----A..-----------------------------AC.........TTG-C-GTAATAGGGACTCGAAAGCGAAAGTT------A...--A---------.---A..---------------......-G-T--..----A------------A-CG...- 279 02_AG.SN.98.98SE_MP1211 .......................................................................................................................................................................... 0 02_AG.US.06.502_2696_FL01 .......................................................................................................................................................................... 0 02_AG.UZ.02.02UZ0683 .......................................................................................................................................................................... 0 03_AB.RU.97.KAL153_2 .......................................................................................................................................................................... 0 04_cpx.CY.94.94CY032_3 ................................................T------T-----TT.AATAGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 103 05_DF.BE.x.VI1310 ..................-----------------------------T.-----A------.....................TAG--------A...--AA--------.---...---------------......------..---A----------------T...A 112 06_cpx.AU.96.BFP90 -C---A------A..--------------------------------T.------------TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 768 07_BC.CN.98.98CN009 ................................................T------------.....................TA-G--------...--A---------.---...---------------......---T--..A-T--------------A-CGGC.. 84 08_BC.CN.06.nx2 -G-G-CAGTGTG-..------------------------------G-A.A----AG----A.....................T--G---C----...G-A-T---T---.---...---------------......---T--..A-T--------------A--GGC.. 694 09_cpx.GH.96.96GH2911 .......................................................................................................................................................................... 0 10_CD.TZ.96.96TZ_BF061 .................CC--------------------------TA-C------------.....................TAG---------...--A---------.---...---------------......------..----A----------------...A 114 11_cpx.CM.95.95CM_1816 ...............T--------------------------------.C-----------.....................TA-G-------A...--T---------.---...---------------......-G-T--..A-G-A------------A-CG...- 115 12_BF.AR.99.ARMA159 -C------------.--------------------------------T.------------.....................TAG---------...--A---------.---...---------------......------..-----------------A---...- 756 13_cpx.CM.96.96CM_1849 ................-------------------------------G.------------......................CT--------A...--T---------.---...---------------......-GCGC...----A----------------...- 112 14_BG.ES.05.X1870 -C----TGT---A..--------------------------------T.------------TTAACAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------AAAGGTGC......A----------------A-CG.... 215 15_01B.TH.99.99TH_MU2079 ..--A-TC-CCCT..T--------------------------------.-T----T-----TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 147 16_A2D.KR.97.97KR004 .................................................C-T--AGTG--AGTAATAGGGACTTGAAAGCGAAAGTT------A...--A---------.---...---------------......----....---------------------...- 101 17_BF.AR.99.ARMA038 .......................................................................................................................................................................... 0 18_cpx.CU.99.CU76 .....................................................................................................--------.---...---------------......-G-T--..A---A------------A-CG...- 54 19_cpx.CU.99.CU7 .......................................................................................................................................................................... 0 20_BG.CU.99.Cu103 -C---A------A..--------------------------------T.------T-----TTAAAAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 212 21_A2D.KE.99.KER2003 .......................................................................................................................................................................... 0 22_01A1.CM.01.01CM_0001BBY .......................................................................................................................................................................... 0 23_BG.CU.03.CB118 -C---A------A..--------------------------------T.------------TTAAAAGGGACTCGAAAGCGGAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 186 24_BG.ES.08.X2456_2 -C---A------A..--------------------------------T.------------TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A-------------A--...- 197 25_cpx.CM.02.1918LE .......................................................................................................................................................................... 0 26_AU.CD.02.02CD_MBTB047 -C---GT-----A..---------------------------------.-T----------T.AAAAGGGACTCGAAAGCGGAAGTT------A....AGA--------.---...---------------......-GTGC...A---A-------------A--...- 753 27_cpx.FR.04.04CD_FR_KZS --------------.--------------------------------T.------------.......................T--------A...--T---------.---...---------------......---T--..A-----------------A--...- 737 28_BF.BR.99.BREPM12609 .......................-C----------------------T.------------.....................TAG---------...------------.---...---------------......------..---------------------...- 107 29_BF.BR.01.BREPM16704 .......................------------------------T.--TG--------.....................TTG----T----...------------.---...---------------......------..----A---------C------...C 107 31_BC.BR.04.04BR142 ---T----------.--------------------------------G.C-----------.....................T--G--------...--A---------.---...---------------......---T--..A-T--------------A-CG...- 193 32_06A1.EE.01.EE0369 -----A------A..---------------------------------.-----A------TTAATAGGGACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......---T--..A----------------A-CG...- 388 33_01B.ID.07.JKT189_C .......................................................................................................------.---...---------------......-G-T--..A---A------------A---...- 52 34_01B.TH.99.OUR2478P .......................................................................................................................................................................... 0 35_AD.AF.07.169H .......................................................................................................................................................................... 0 36_cpx.CM.00.00CMNYU830 .......................................................................................................................................................................... 0 37_cpx.CM.00.00CMNYU926 .......................................................................................................................................................................... 0 38_BF1.UY.03.UY03_3389 --------------.---------------------------------.------------.....................TAG--------A...--A---------.---...---------------......------..--G-A------------A-CG...- 165 39_BF.BR.04.04BRRJ179 --------------.---------------------------------.------------.....................TAG---------...--A---------.---...---------------......------..---------------------...- 213 40_BF.BR.05.05BRRJ055 --------------.---------------------------------.------------.....................TAG---------...------------.---...---------------......--AGCGC.--G-A----------------...- 215 42_BF.LU.03.luBF_05_03 -------C------.--------------------------------Y.------------.....................TAG---------...------------.---...---------------......---T--..---------------------...- 268 43_02G.SA.03.J11223 -C---A-G----A..--------------------------------T.------T-----TTAATAGGGACTCGAAAGCGRAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 272 44_BF.CL.00.CH80 --------------.--------------------------------T.------------.....................TAG---------...--A---------.---...---------------......---T--..A----------------A--G...- 177 45_cpx.FR.04.04FR_AUK -C---G-G----A..------------------------------.........................ACTCGAAAGCGAAAGTT------A...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 732 46_BF.BR.07.07BR_FPS625 -------C-A----.--------------------------------T.------------.....................TAG--------A...--A---------.---...---------------......---T--..A----------------A-CG...- 192 47_BF.ES.08.P1942 --AGTCAGTGTG-A.---------------------------------.C-----------.....................TAG--------A...------------.---...---------------......------..--T------------------...- 181 48_01B.MY.07.07MYKT021 .......................................................................................................................................................................... 0 49_cpx.GM.03.N26677 -C---A-G----A..--------------------------------T.C----A------.....................TA-GG-----AA...--A---------.---...---------------......---T--..A----------------A-CG...- 170 51_01B.SG.11.11SG_HM021 .......................................................................................................................................................................... 0 52_01B.MY.03.03MYKL018_1 ....................................................................................................---------.---...---------Y-----......-G-T--..A---A-----------RA-CG...- 55 53_01B.MY.11.11FIR164 ...................................................................GGGACTCGAAAGCGRAAGTT-------...--T---------.---...---------------......-G-T--..A---A------------A-CG...- 85 54_01B.MY.09.09MYSB023 ...............T-------------------------------T.-----ATA----TTATTAGGGACTCGAAAGCGGAAGTTGG----A...--T---------.---...---------------......---T--GC----A------------A-CG...- 138 55_01B.CN.10.HNCS102056 ....................................................................................................---------.---...---------------......-G-T--..A---A------------A-CG...- 55 O.BE.87.ANT70 --AGACTGAA-CA-.--------------------------------..-TG---T-----.....................T--------G-AAGA-AAC---C.---.---AC.--G--------AGC-......G--T--..A-C--CT----------A--AA..C 769 O.CM.91.MVP5180 --AGACTGAA-CA-.--------------------------------G.C-----T-----.....................T-G------G-AAGA-AAC---C.---.---AC.--G--------AGC-......G--T--..A-CT-CT----------A--AA..C 743 O.CM.98.98CMA104 G-AGACTGAA-CA-.---------------------------------.G-----A-----.....................T--------G-AAGA-AAC---C.---.---AC.--G--------AGC-......G--T--..A-C--CT----------A--AA..C 201 O.FR.92.VAU --AGACTGAA-CA-G--------------------------------........------.....................T--------G-AAGA-AAC---C.---.---AC.--G--------AGC-......G--T--..A-C--CT----------A--AA..C 277 O.SN.99.99SE_MP1299 G-AGACTGAG-CA-.---------------------------------.G-----A-----.....................T--------G-AAGA-AAC---C.---.---AC.--G--------AGC-......G--T--..A-C--CT----------A--AA..C 770 O.US.10.LTNP --AGACTGAA-CA-.--------------------------------..C-G---A-----.....................T--------G-AAGA-AAC---C.---.--GAC.--G--------AGC-......G--T--..A-C--CT----------A--A...C 691 O.US.97.97US08692A --AGACTGAGTSA-A--------------------------------T.------A-----.....................T--------G-AAGA-AAC---C.---.---AC.--G--------AGC-......G--T--..A-CT-CT----------A--AA..C 167 N.CM.02.DJO0131 C-GGACTGAGTGA..--------------------------------T.-----A------.....................TAG----G----CTG.AA---------.---...----------C-T--........-T--..A---A--G----------C-G.... 205 N.CM.04.04CM_1015_04 --GG-CTGAGTA-..--------------------------------T.-----A------.....................TAG----G----CTG-AA---------.---...----------C-T--.......G-T--..A---A--G----------C-G.... 207 N.CM.06.U14842 C-AGACTGAGTGA..--------------------------------K.Y----A------.....................TAG----G----CTG-ATCTCTC.-G-.--TA..----------C-T--........-T--..A---A--G----------C-G.... 206 N.CM.95.YBF30 C-AGACTGAGTGA..--------------------------------T.-----A------.....................TAG----G----CTG.AA---------.---...----------C-T--........-T--..A---A--G----------C-G.... 293 N.CM.97.YBF106 CA---A-T-A--A..-------------S------------------T.-----A------.....................TAG----G----CTG-ATCTCTC.---.---A..----------C-T--........-T--..A---A--G----------C-G.... 294 N.FR.11.N1_FR_2011 ..............................-----------------T.-----A------.....................TAG----G----CTG-ATCTCTC.---.---A..----------C-T--........-T--..A---A--G----------C-G.... 100 P.CM.06.U14788 ---TAG-C-A---A.---------------------------------.------...........................T--------TTTCTG-AAC---C.---.---C..--G-------CAGC-......G--T--..A-CT-CTG---------A--AAC.. 204 P.FR.09.RBF168 --CTAG-C-A----.--------------------------------T.------...........................T--------T-TCTG-ATC---C.---.---C..--G-------CAGC-......G--T--..A-CT-CTG---------A--AGAGC 762 CPZ.CD.06.BF1167 -GA--G-TAA-CA..----------C---------------------T.---...............................---G-AG-G-ACGCG-AA-C--T---.--CA..------------TGC.........T--..---ACA-------------...... 729 CPZ.CM.05.SIVcpzMT145 C-ATA-TGA-AGA..--------------------------------T.------T-----.....................TA-----G----CTG-ATCTCTC.---.---C..---------------.......--T--..A-G-A-------------C-GCGAC 285 CPZ.GA.88.GAB1 A---TAGTCAAG-..---------------------------------.----GTGA--GT........................----G----CTG-ATCTC-C.---.---C..---------------.......--T--..A---A-------------C-G.... 753 CPZ.TZ.06.SIVcpzTAN13 AG-G-G-TAA--A..----------C---------------------T.-................................-AGT-A---G-AACGC-GC-C--G---.--TT..------------.--.......-CA--G.CA-TCA------------C-GA..C 278 CPZ.US.85.US_Marilyn --A-AAGTAG---..--------------------------------T.-----A------.....................TAC---------CTG.AAA--TC----.--G...----------C----.......--T--..A---A--G----------C-AA..C 761
H IV-1/SIV
cpz C
om plete
G enom
es A
lignm ents
Gag p2 end Gag p7 nucleocapsid start Gag-Pol fusion TF protein start
B.FR.83.HXB2 ....AAT.........TCAGCTACC...ATA...ATGATGCAGAGAGGCAATTTTAGG...AACCAA...AGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAG 2047 Gag __.__N__.__.__.__S__A__T__.__I__.__M__M__Q__R__G__N__F__R__.__N__Q__.__R__K__I__V__K__C__F__N__C__G__K__E__G__H__T__A__R__N__C__R__A__P__R__K__K__G__C__W__K__C__G__K__E__ A1.AU.03.PS1044_Day0 ....C-A...............--AAGC---...-----------------C------GGCGG---G...-A--G-...A----------T--C--------------A---CT------------------------------------------------G-----G- 1255 A1.CH.03.HIV_CH_BID_V3538 ....C--...............--AAAC---...----------------------A-...GG---G...-----A...A-------------C--------------A---CT------------------------------------------------G------- 1252 A1.ES.06.X2110 ....C--...............C-AAAC---...------------------------...GG---G...-A-GGA...A----------T--C--------------A--TCT-----A------------------A-----------------------G--A--G- 1285 A1.IT.02.60000 ....--G...............--AAAC---...----------A------------A...GG--CG...-A--GA...A-------------C--------------A---CT-------------------------------------------------------- 2052 A1.KE.06.06KECst_001 ....---...............--AAAC---...------------------------...GG---G...-A--G-...A-------------C-----T--------A---CT--------------------------------------------------G---G- 1253 A1.RU.11.11RU6950 ....---...............G-AAAC---...----------A-A-T---------...GG--C-...-A--GA...A-------------C-----T--------A--TCT-----------------------------------------G-------------- 1571 A1.RW.07.pR463F ....---...............--AAAC---ATG----------------------A-...GG----...-----A...A-------------C--------------A---CT-----A---C-----------C--------------------------G------- 2062 A1.SE.95.SE8538 ....C-G...............C--AAC---...--------------------C--A...GG----...----G-...A----------T--C--------------A---CT-----A------------------------------------------G------- 1246 A1.TZ.01.A341 ....C--............A-A-A-AAC---...--------------------C---...GG---G...-A--GA...A----------T--C--------------A---CT---------------------

HIV Sequence Compendium 2013

Documents

Transcript of HIV Sequence Compendium 2013