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Title: Primate immunodeficiency virus classification and nomenclature: Review

Abstract

The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. As a result, this review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written in 2000.

Authors:
 [1];  [1];  [2];  [3]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. National and Kapodistrian Univ. of Athens, Athens (Greece)
  3. Univ. of Montpellier, Montpellier (France); IBC, Computational Biology Institute, Montpellier (France)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
National Institutes of Health (NIH); USDOE
OSTI Identifier:
1331286
Report Number(s):
LA-UR-16-24498
Journal ID: ISSN 1567-1348
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Infection, Genetics and Evolution
Additional Journal Information:
Journal Volume: 46; Journal ID: ISSN 1567-1348
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological Science; Immunodeficiency; HIV; Lentivirus; Nomenclature; Classification

Citation Formats

Foley, Brian T., Leitner, Thomas, Paraskevis, Dimitrios, and Peeters, Martine. Primate immunodeficiency virus classification and nomenclature: Review. United States: N. p., 2016. Web. doi:10.1016/j.meegid.2016.10.018.
Foley, Brian T., Leitner, Thomas, Paraskevis, Dimitrios, & Peeters, Martine. Primate immunodeficiency virus classification and nomenclature: Review. United States. https://doi.org/10.1016/j.meegid.2016.10.018
Foley, Brian T., Leitner, Thomas, Paraskevis, Dimitrios, and Peeters, Martine. Mon . "Primate immunodeficiency virus classification and nomenclature: Review". United States. https://doi.org/10.1016/j.meegid.2016.10.018. https://www.osti.gov/servlets/purl/1331286.
@article{osti_1331286,
title = {Primate immunodeficiency virus classification and nomenclature: Review},
author = {Foley, Brian T. and Leitner, Thomas and Paraskevis, Dimitrios and Peeters, Martine},
abstractNote = {The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. As a result, this review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written in 2000.},
doi = {10.1016/j.meegid.2016.10.018},
journal = {Infection, Genetics and Evolution},
number = ,
volume = 46,
place = {United States},
year = {Mon Oct 24 00:00:00 EDT 2016},
month = {Mon Oct 24 00:00:00 EDT 2016}
}

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Cited by: 28 works
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Works referenced in this record:

Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E
journal, November 2000


Evidence for continuing cross-species transmission of SIVsmm to humans: characterization of a new HIV-2 lineage in rural Côte d’Ivoire
journal, January 2013


Hybrid Origin of SIV in Chimpanzees
journal, June 2003


New Simian Immunodeficiency Virus Infecting De Brazza's Monkeys ( Cercopithecus neglectus ): Evidence for a Cercopithecus Monkey Virus Clade
journal, July 2004


Identification of an env G subtype and heterogeneity of HIV-1 strains in the Russian Federation and Belarus
journal, January 1994


Spatial Epidemiology of Recently Acquired HIV Infections across Rural and Urban Areas of North Carolina
journal, February 2014


The Serologic Significance Of F Viral Genotype For Human Immunodeficiency Virus Type 1 Epidemic
journal, October 1994


Identification of human immunodeficiency virus subtypes with distinct patterns of sensitivity to serum neutralization.
journal, April 1988

  • Cheng-Mayer, C.; Homsy, J.; Evans, L. A.
  • Proceedings of the National Academy of Sciences, Vol. 85, Issue 8
  • DOI: 10.1073/pnas.85.8.2815

Origin of the HIV-1 group O epidemic in western lowland gorillas
journal, March 2015

  • D’arc, Mirela; Ayouba, Ahidjo; Esteban, Amandine
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 11
  • DOI: 10.1073/pnas.1502022112

Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models
journal, March 2015

  • Duchêne, Sebastián; Ho, Simon YW; Holmes, Edward C.
  • BMC Evolutionary Biology, Vol. 15, Issue 1
  • DOI: 10.1186/s12862-015-0312-6

Gene Loss and Adaptation to Hominids Underlie the Ancient Origin of HIV-1
journal, July 2013


The Role of the Antiviral APOBEC3 Gene Family in Protecting Chimpanzees against Lentiviruses from Monkeys
journal, September 2015


The early spread and epidemic ignition of HIV-1 in human populations
journal, October 2014


Distinct Evolutionary Pressures Underlie Diversity in Simian Immunodeficiency Virus and Human Immunodeficiency Virus Lineages
journal, October 2012

  • Fischer, W.; Apetrei, C.; Santiago, M. L.
  • Journal of Virology, Vol. 86, Issue 24
  • DOI: 10.1128/JVI.01862-12

Hiv-1 Infection in Norwegian Family Before 1970
journal, June 1988


Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes
journal, February 1999

  • Gao, Feng; Bailes, Elizabeth; Robertson, David L.
  • Nature, Vol. 397, Issue 6718
  • DOI: 10.1038/17130

Endogenous Lentiviral Elements in the Weasel Family (Mustelidae)
journal, April 2012


An African primate lentivirus (SIVsmclosely related to HIV-2
journal, June 1989

  • Hirsch, Vanessa M.; Olmsted, Robert A.; Murphey-Corb, Michael
  • Nature, Vol. 339, Issue 6223
  • DOI: 10.1038/339389a0

Epidemic History and Iatrogenic Transmission of Blood-borne Viruses in Mid-20th Century Kinshasa
journal, January 2016

  • Hogan, Catherine A.; Iles, James; Frost, Eric H.
  • Journal of Infectious Diseases, Vol. 214, Issue 3
  • DOI: 10.1093/infdis/jiw009

Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index
journal, September 2008

  • Hraber, Peter; Kuiken, Carla; Waugh, Mark
  • Journal of General Virology, Vol. 89, Issue 9
  • DOI: 10.1099/vir.0.83657-0

Genetic organization of a chimpanzee lentivirus related to HIV-1
journal, May 1990

  • Huet, Thierry; Cheynier, Rémi; Meyerhans, Andreas
  • Nature, Vol. 345, Issue 6273
  • DOI: 10.1038/345356a0

HIV-2 CRF01_AB: First Circulating Recombinant Form of HIV-2
journal, January 2010

  • Ibe, Shiro; Yokomaku, Yoshiyuki; Shiino, Teiichiro
  • JAIDS Journal of Acquired Immune Deficiency Syndromes, Vol. 54, Issue 3
  • DOI: 10.1097/QAI.0b013e3181dc98c1

Infection of a yellow baboon with simian immunodeficiency virus from African green monkeys: evidence for cross-species transmission in the wild
journal, December 1994


Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1
journal, July 2006


Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz
journal, July 2009

  • Keele, Brandon F.; Jones, James Holland; Terio, Karen A.
  • Nature, Vol. 460, Issue 7254
  • DOI: 10.1038/nature08200

A Lymph Node-Derived Cytopathic Simian Immunodeficiency Virus Mne Variant Replicates in Nonstimulated Peripheral Blood Mononuclear Cells
journal, January 1998


Short Communication: Molecular Epidemiology of HIV Type 1 Infection in Kazakhstan: CRF02_AG Prevalence Is Increasing in the Southeastern Provinces
journal, August 2014

  • Lapovok, Ilya; Kazennova, Elena; Laga, Vita
  • AIDS Research and Human Retroviruses, Vol. 30, Issue 8
  • DOI: 10.1089/aid.2013.0291

Sequence Diversity among Chimpanzee Simian Immunodeficiency Viruses (SIVcpz) Suggests that SIVcpz Pts Was Derived from SIVcpz Ptt through Additional Recombination Events
journal, September 2007

  • Leitner, Thomas; Dazza, Marie-Christine; Ekwalanga, Michel
  • AIDS Research and Human Retroviruses, Vol. 23, Issue 9
  • DOI: 10.1089/aid.2007.0071

Eastern Chimpanzees, but Not Bonobos, Represent a Simian Immunodeficiency Virus Reservoir
journal, July 2012

  • Li, Y.; Ndjango, J. -B.; Learn, G. H.
  • Journal of Virology, Vol. 86, Issue 19
  • DOI: 10.1128/JVI.01498-12

HIV-1 genetic subtype A/B recombinant strain causing an explosive epidemic in injecting drug users in Kaliningrad
journal, January 1998


An AB Recombinant and Its Parental HIV Type 1 Strains in the Area of the Former Soviet Union: Low Requirements for Sequence Identity in Recombination
journal, July 2000

  • Liitsola, Kirsi; Holm, Kirsi; Bobkov, Aleksei
  • AIDS Research and Human Retroviruses, Vol. 16, Issue 11
  • DOI: 10.1089/08892220050075309

Immunogenetics: Genome-Wide Association of Non-Progressive HIV and Viral Load Control: HLA Genes and Beyond
journal, January 2013


Reanalysis of the HIV-1 Circulating Recombinant Form A/E (CRF01_AE): Evidence of A/E/G Recombination
journal, January 2002

  • Magiorkinis, Gkikas; Paraskevis, Dimitris; Magiorkinis, Emmanouil
  • JAIDS Journal of Acquired Immune Deficiency Syndromes, Vol. 30, Issue 1
  • DOI: 10.1097/00042560-200205010-00017

Genetic Variants of HIV-1 in Thailand
journal, November 1992

  • McCUTCHAN, Francine E.; Hegerich, Patricia A.; Brennan, Terrence P.
  • AIDS Research and Human Retroviruses, Vol. 8, Issue 11
  • DOI: 10.1089/aid.1992.8.1887

The impact of host genetic variation on infection with HIV-1
journal, May 2015

  • McLaren, Paul J.; Carrington, Mary
  • Nature Immunology, Vol. 16, Issue 6
  • DOI: 10.1038/ni.3147

Distinct Human Immunodeficiency Virus Type 1 Subtype A Virus Circulating in West Africa: Sub-Subtype A3
journal, November 2004


Identification of a Novel Clade of Human Immunodeficiency Virus Type 1 in Democratic Republic of Congo
journal, July 2002

  • Mokili, John L. K.; Rogers, Melissa; Carr, Jean K.
  • AIDS Research and Human Retroviruses, Vol. 18, Issue 11
  • DOI: 10.1089/08892220260139567

CRF06-cpx: A New Circulating Recombinant Form of HIV-1 in West Africa Involving Subtypes A, G, K, and J
journal, January 2002

  • Montavon, Celine; Toure-Kane, Coumba; Nkengasong, John N.
  • JAIDS Journal of Acquired Immune Deficiency Syndromes, Vol. 29, Issue 5
  • DOI: 10.1097/00126334-200204150-00014

V3 Region Polymorphisms in HIV-1 from Brazil: Prevalence of Subtype B Strains Divergent from North American/European Prototype and Detection of Subtype F
journal, May 1994

  • Morgado, Mariza G.; Sabino, Ester C.; Shpaer, Eugene G.
  • AIDS Research and Human Retroviruses, Vol. 10, Issue 5
  • DOI: 10.1089/aid.1994.10.569

The Emergence of Simian/Human Immunodeficiency Viruses
journal, March 1992

  • Myers, Gerald; MacINNES, Kersti; Korber, Bette
  • AIDS Research and Human Retroviruses, Vol. 8, Issue 3
  • DOI: 10.1089/aid.1992.8.373

Molecular Analysis of the Full-Length Genome of HIV Type 1 Subtype I: Evidence of A/G/I Recombination
journal, May 1999

  • Nasioulas, G.; Paraskevis, D.; Magiorkinis, E.
  • AIDS Research and Human Retroviruses, Vol. 15, Issue 8
  • DOI: 10.1089/088922299310836

Recombination Rate and Selection Strength in HIV Intra-patient Evolution
journal, January 2010


IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
journal, November 2014

  • Nguyen, Lam-Tung; Schmidt, Heiko A.; von Haeseler, Arndt
  • Molecular Biology and Evolution, Vol. 32, Issue 1
  • DOI: 10.1093/molbev/msu300

SIV from stump-tailed macaques: Molecular characterization of a highly transmissible primate lentivirus
journal, February 1992


Emerging Viruses in the Felidae: Shifting Paradigms
journal, February 2012

  • O’Brien, Stephen J.; Troyer, Jennifer L.; Brown, Meredith A.
  • Viruses, Vol. 4, Issue 2
  • DOI: 10.3390/v4020236

Role of Trim5α in the Suppression of Cross-Species Transmission and its Defence Against Human Immunodeficiency Virus
journal, April 2014


Complete nucleotide sequence of the AIDS virus, HTLV-III
journal, January 1985

  • Ratner, Lee; Haseltine, William; Patarca, Roberto
  • Nature, Vol. 313, Issue 6000
  • DOI: 10.1038/313277a0

HIV-1 Nomenclature Proposal
journal, April 2000


Nucleotide sequence and expression of an AIDS-associated retrovirus (ARV-2)
journal, February 1985


Amplification of a Complete Simian Immunodeficiency Virus Genome from Fecal RNA of a Wild Chimpanzee
journal, February 2003


The evolution of HIV-1 and the origin of AIDS
journal, August 2010

  • Sharp, Paul M.; Hahn, Beatrice H.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 365, Issue 1552
  • DOI: 10.1098/rstb.2010.0031

The phylogenetic history of immunodeficiency viruses
journal, June 1988

  • Smith, T. F.; Srinivasan, A.; Schochetman, G.
  • Nature, Vol. 333, Issue 6173
  • DOI: 10.1038/333573a0

X-chromosomal window into the evolutionary history of the guenons (Primates: Cercopithecini)
journal, July 2005

  • Tosi, Anthony J.; Detwiler, Kate M.; Disotell, Todd R.
  • Molecular Phylogenetics and Evolution, Vol. 36, Issue 1
  • DOI: 10.1016/j.ympev.2005.01.009

Near-Full-Length Genome Sequencing of Divergent African HIV Type 1 Subtype F Viruses Leads to the Identification of a New HIV Type 1 Subtype Designated K
journal, January 2000

  • Triques, Karine; Bourgeois, Anke; Vidal, Nicole
  • AIDS Research and Human Retroviruses, Vol. 16, Issue 2
  • DOI: 10.1089/088922200309485

FIV diversity: FIVPle subtype composition may influence disease outcome in African lions
journal, October 2011

  • Troyer, Jennifer L.; Roelke, Melody E.; Jespersen, Jillian M.
  • Veterinary Immunology and Immunopathology, Vol. 143, Issue 3-4
  • DOI: 10.1016/j.vetimm.2011.06.013

Genetic diversity and phylogeographic clustering of SIVcpzPtt in wild chimpanzees in Cameroon
journal, November 2007


Simian immunodeficiency viruses (SIVs) from eastern and southern Africa: detection of a SIVagm variant from a chacma baboon.
journal, July 1998


Identification and Molecular Characterization of Subsubtype A4 in Central Africa
journal, February 2006

  • Vidal, N.; Mulanga, C.; Bazepeo, S. Edidi
  • AIDS Research and Human Retroviruses, Vol. 22, Issue 2
  • DOI: 10.1089/aid.2006.22.182

Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2
journal, May 2009


Characterization of novel recombinant HIV-1 genomes using the branching index
journal, November 2003


Island Biogeography Reveals the Deep History of SIV
journal, September 2010


HIV-1 Genetic Diversity and Genotypic Drug Susceptibility in the Republic of Georgia
journal, May 2006

  • Zarandia, Maia; Tsertsvadze, Tengiz; Carr, Jean K.
  • AIDS Research and Human Retroviruses, Vol. 22, Issue 5
  • DOI: 10.1089/aid.2006.22.470

The Epidemic Dynamics of Four Major Lineages of HIV-1 CRF01_AE Strains After Their Introduction into China
journal, May 2016

  • Zeng, Haiyan; Li, Tingting; Wang, Yan
  • AIDS Research and Human Retroviruses, Vol. 32, Issue 5
  • DOI: 10.1089/aid.2015.0212

The role of recombination in the emergence of a complex and dynamic HIV epidemic
journal, March 2010


Works referencing / citing this record:

Prevalence and Structure of Hiv-1 drug Resistance Among Treatment NaÏVe Patients Since the Introduction of Antiretroviral Therapy in the Russian Federation
journal, July 2019


Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences
journal, July 2018


Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineages
journal, January 2018

  • Tongo, Marcel; Harkins, Gordon W.; Dorfman, Jeffrey R.
  • Virus Evolution, Vol. 4, Issue 1
  • DOI: 10.1093/ve/vey003

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis
journal, December 2019


Molecular Surveillance of HIV-1 Infection in Krasnoyarsk Region, Russia: Epidemiology, Phylodynamics and Phylogeography
journal, September 2019


Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences
journal, July 2018


Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain
journal, April 2019


Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis
journal, December 2019