Origin and dynamics of HIV-1 subtype c infection in India

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Shen, Chengli ^a,b   Craigo, Jodi ^c   Ding, Ming ^a   Chen, Yue ^a   Gupta, Phalguni ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b CAPITAL MEDICAL UNIVERSITY   (China)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; EFFECTIVE POPULATION SIZE; EPIDEMIC; HEALTH PROGRAM; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; INDIA; MICROBIAL POPULATION DYNAMICS; MOLECULAR CLOCK; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENETIC TREE; SEQUENCE ANALYSIS; TREATMENT PLANNING; VIROGENESIS; VIRUS TRANSMISSION; BAYES THEOREM; CLASSIFICATION; GENETICS; GEOGRAPHY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; PATHOGENICITY; PHYLOGENY; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

GLYCOPROTEIN GP 120; GP120 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1;

BAYES THEOREM; EVOLUTION, MOLECULAR; GEOGRAPHY; HIV ENVELOPE PROTEIN GP120; HIV INFECTIONS; HIV-1; HUMANS; INDIA; PHYLOGENY;

EID: 80053919437     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025956     Document Type: Article

References (34)

1. Simoes EA, Babu PG, John TJ, Nirmala S, Solomon S, et al. (1987) Evidence for HTLV-III infection in prostitutes in Tamil Nadu (India). Indian J Med Res 85: 335-338.
2. Delwart EL, Mullins JI, Gupta P, Learn GH Jr, Holodniy M, et al. (1998) Human immunodeficiency virus type 1 populations in blood and semen. J Virol 72: 617-623.
3. Maitra A, Singh B, Banu S, Deshpande A, Robbins K, et al. (1999) Subtypes of HIV type 1 circulating in India: partial envelope sequences. AIDS Res Hum Retroviruses 15: 941-944.
4. Mandal D, Jana S, Bhattacharya SK, Chakrabarti S, (2002) HIV type 1 subtypes circulating in eastern and northeastern regions of India. AIDS Res Hum Retroviruses 18: 1219-1227.
5. Mandal D, Jana S, Panda S, Bhattacharya S, Ghosh TC, et al. (2000) Distribution of HIV-1 subtypes in female sex workers of Calcutta, India. Indian J Med Res 112: 165-172.
6. Shankarappa R, Chatterjee R, Learn GH, Neogi D, Ding M, et al. (2001) Human immunodeficiency virus type 1 env sequences from Calcutta in eastern India: identification of features that distinguish subtype C sequences in India from other subtype C sequences. J Virol 75: 10479-10487.
7. Tripathy S, Renjifo B, Wang WK, McLane MF, Bollinger R, et al. (1996) Envelope glycoprotein 120 sequences of primary HIV type 1 isolates from Pune and New Delhi, India. AIDS Res Hum Retroviruses 12: 1199-1202.
8. Cassol S, Weniger BG, Babu PG, Salminen MO, Zheng X, et al. (1996) Detection of HIV type 1 env subtypes A, B, C, and E in Asia using dried blood spots: a new surveillance tool for molecular epidemiology. AIDS Res Hum Retroviruses 12: 1435-1441.
9. Beyrer C, Razak MH, Lisam K, Chen J, Lui W, et al. (2000) Overland heroin trafficking routes and HIV-1 spread in south and south-east Asia. AIDS 14: 75-83.
10. Grez M, Dietrich U, Balfe P, von Briesen H, Maniar JK, et al. (1994) Genetic analysis of human immunodeficiency virus type 1 and 2 (HIV-1 and HIV-2) mixed infections in India reveals a recent spread of HIV-1 and HIV-2 from a single ancestor for each of these viruses. J Virol 68: 2161-2168.
11. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
12. Posada D, (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
13. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
14. Price MN, Dehal PS, Arkin AP, (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.
15. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
16. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
17. Drummond AJ, Rambaut A, Shapiro B, Pybus OG, (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22: 1185-1192.
18. Luo CC, Tian C, Hu DJ, Kai M, Dondero T, et al. (1995) HIV-1 subtype C in China. Lancet 345: 1051-1052.
19. Kousiappa I, van de Vijver DA, Demetriades I, Kostrikis LG, (2009) Genetic analysis of HIV type 1 strains from newly infected untreated patients in cyprus: high genetic diversity and low prevalence of drug resistance. AIDS Res Hum Retroviruses 25: 23-35.
20. Liitsola K, Holmstrom P, Laukkanen T, Brummer-Korvenkontio H, Leinikki P, et al. (2000) Analysis of HIV-1 genetic subtypes in Finland reveals good correlation between molecular and epidemiological data. Scand J Infect Dis 32: 475-480.
21. Robbins KE, Lemey P, Pybus OG, Jaffe HW, Youngpairoj AS, et al. (2003) U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains. J Virol 77: 6359-6366.
22. Renjifo B, Chaplin B, Mwakagile D, Shah P, Vannberg F, et al. (1998) Epidemic expansion of HIV type 1 subtype C and recombinant genotypes in Tanzania. AIDS Res Hum Retroviruses 14: 635-638.
23. Van Harmelen JH, Van der Ryst E, Loubser AS, York D, Madurai S, et al. (1999) A predominantly HIV type 1 subtype C-restricted epidemic in South African urban populations. AIDS Res Hum Retroviruses 15: 395-398.
24. Carrion G, Eyzaguirre L, Montano SM, Laguna-Torres V, Serra M, et al. (2004) Documentation of subtype C HIV Type 1 strains in Argentina, Paraguay, and Uruguay. AIDS Res Hum Retroviruses 20: 1022-1025.
25. Castro E, Moreno M, Deibis L, de Perez G, Salmen S, et al. (2005) Trends of HIV-1 molecular epidemiology in Venezuela: introduction of subtype C and identification of a novel B/C mosaic genome. J Clin Virol 32: 257-258.
26. Dilernia DA, Gomez AM, Lourtau L, Marone R, Losso MH, et al. (2007) HIV type 1 genetic diversity surveillance among newly diagnosed individuals from 2003 to 2005 in Buenos Aires, Argentina. AIDS Res Hum Retroviruses 23: 1201-1207.
27. Mahanta J, Medhi GK, Paranjape RS, Roy N, Kohli A, et al. (2008) Injecting and sexual risk behaviours, sexually transmitted infections and HIV prevalence in injecting drug users in three states in India. AIDS 22 (Suppl 5): S59-68.
28. Mullick R, Sengupta S, Sarkar K, Chakrabarti S, (2010) Molecular characterization of tat gene and long terminal repeat region of human immunodeficiency virus type-1 detected among the injecting drug users (IDUs) of Manipur, India: identification of BC recombinants. Virus Res 147: 195-201.
29. Fontella R, Soares MA, Schrago CG, (2008) On the origin of HIV-1 subtype C in South America. AIDS 22: 2001-2011.
30. Bello G, Passaes CP, Guimaraes ML, Lorete RS, Matos Almeida SE, et al. (2008) Origin and evolutionary history of HIV-1 subtype C in Brazil. AIDS 22: 1993-2000.
31. Dietrich U, Grez M, von Briesen H, Panhans B, Geissendorfer M, et al. (1993) HIV-1 strains from India are highly divergent from prototypic African and US/European strains, but are linked to a South African isolate. AIDS 7: 23-27.
32. Korber B, Muldoon M, Theiler J, Gao F, Gupta R, et al. (2000) Timing the ancestor of the HIV-1 pandemic strains. Science 288: 1789-1796.
33. Leitner T, Escanilla D, Franzen C, Uhlen M, Albert J, (1996) Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci U S A 93: 10864-10869.
34. Dalai SC, de Oliveira T, Harkins GW, Kassaye SG, Lint J, et al. (2009) Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe. AIDS 23: 2523-2532.