Molecular Epidemiology of HIV-1 Subtypes in India: Origin and Evolutionary History of the Predominant Subtype C

PLoS ONE - Tập 7 Số 6 - Trang e39819
Ujjwal Neogi1,2, Irene Bontell2, Anita Shet3,4, Ayesha De Costa4, Soham Gupta1, Vishal Diwan5, Ranbir S. Laishram6, Ajay Wanchu7,8, Udaykumar Ranga9, Akhil C. Banerjea10, Anders Sönnerborg11,2
1Division of Clinical Virology, Department of Microbiology, St. John’s Medical College, Bangalore, Karnataka, India
2Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
3Department of Pediatrics, St. John’s Medical College Hospital, Bangalore, Karnataka, India
4Division of Global Health (IHCAR), Nobels Väg 9, Karolinska Institutet, Stockholm, Sweden
5Department of Public Health and Environment, R D Gardi Medical College, Ujjain, Madhya Pradesh, India
6Department of Pediatrics, Regional Institute of Medical Science, Imphal, Manipur, India
7Departnemt of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
8Division of Arthritis and Rheumatic Disease, Oregon Health and Science University, Portland Oregon, United States of America
9Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
10Virology-II, National Institute of Immunology, New Delhi, India
11Division of Clinical Virology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden

Tóm tắt

Từ khóa


Tài liệu tham khảo

EA Simoes, 1987, Evidence for HTLV-III infection in prostitutes in Tamil Nadu (India)., Indian J Med Res, 85, 335

U Neogi, 2009, Global HIV-1 molecular epidemiology with special reference to genetic analysis of HIV-1 subtypes circulating in North India: functional and pathogenic implications of genetic variation., Indian J Exp Biol, 47, 424

AJ Kandathil, 2005, Molecular epidemiology of HIV., Indian J Med Res, 121, 333

U Neogi, 2011, Genetic architecture of HIV-1 genes circulating in North India and their functional implications., Indian J Med Res, 134, 769, 10.4103/0971-5916.92624

U Neogi, 2012, Higher prevalence of predicted X4-tropic strains in perinatally-infected older children with HIV-1 subtype C in India., J Acquir Immune Defic Syndr, 59, 347, 10.1097/QAI.0b013e3182405c7b

DA Gadkari, 1998, Transmission of genetically diverse strains of HIV-1 in Pune, India., Indian J Med Res, 107, 1

D Mandal, 2002, HIV type 1 subtypes circulating in eastern and northeastern regions of India., AIDS Res Hum Retroviruses, 18, 1219, 10.1089/08892220260387968

AK Sahni, 2002, Genomic diversity of human immunodeficiency virus type-1 in India., Int J STD AIDS, 13, 115, 10.1258/0956462021924749

J Hemelaar, 2011, Global trends in molecular epidemiology of HIV-1 during 2000–2007., AIDS, 25, 679, 10.1097/QAD.0b013e328342ff93

AB Abecasis, 2009, Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution., J Virol, 83, 12917, 10.1128/JVI.01022-09

V Novitsky, 2010, HIV-1 Subtype C phylodynamics in the global epidemic., Viruses, 2, 33, 10.3390/v2010033

SA Travers, 2004, Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1., J Virol, 78, 10501, 10.1128/JVI.78.19.10501-10506.2004

G Bello, 2008, Origin and evolutionary history of HIV-1 subtype C in Brazil., AIDS, 22, 1993, 10.1097/QAD.0b013e328315e0aa

NM Véras, 2011, High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America., J Gen Virol, 92, 1698, 10.1099/vir.0.028951-0

SC Dalai, 2009, Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe., AIDS, 23, 2523, 10.1097/QAD.0b013e3283320ef3

DC Tully, 2010, Chronology and evolution of the HIV-1 subtype C epidemic in Ethiopia. AIDS., 24, 1577

T de Oliveira, 2010, The HIV-1 subtype C epidemic in South America is linked to the United Kingdom. PLoS One., 5, e9311

KK Tee, 2008, Temporal and spatial dynamics of human immunodeficiency virus type 1 circulating recombinant forms 08_BC and 07_BC in Asia., J Virol, 82, 9206, 10.1128/JVI.00399-08

C Shen, 2011, Origin and dynamics of HIV-1 subtype C infection in India., PLoS One, 6, e25956, 10.1371/journal.pone.0025956

AJ Drummond, 2007, BEAST: Bayesian evolutionary analysis by sampling trees., BMC Evol Bio, 7, 214, 10.1186/1471-2148-7-214

S Sengupta, 2005, Polymorphism of HIV-1 gag (p17) gene from female sex workers in Calcutta, India., Arch Virol, 150, 2117, 10.1007/s00705-005-0562-5

U Neogi, 2008, Novel HIV-1 long terminal repeat (LTR) sequences of subtype B and mosaic intersubtype B/C recombinants in North India., Arch Virol, 153, 1961, 10.1007/s00705-008-0210-y

KS Lole, 1999, Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination., J Virol, 73, 152, 10.1128/JVI.73.1.152-160.1999

NB Siddappa, 2005, Identification of unique B/C recombinant strains of HIV-1 in the southern state of Karnataka, India., AIDS, 19, 1426, 10.1097/01.aids.0000180795.49016.89

AS Bano, 2009, Genetic and functional characterization of HIV-1 VprC variants from North India: Presence of unique recombinants with mosaic genomes from B, C and D subtypes within the ORF of Vpr., J Gen Virol, 90, 2768, 10.1099/vir.0.011080-0

S Lakhashe, 2008, Evidence of a novel B/C recombinant exhibiting unique breakpoints of near full-length HIV type 1 genome from Northeastern India., AIDS Res Hum Retroviruses, 24, 229, 10.1089/aid.2007.0229

U Neogi, 2010, Naturally occurring polymorphisms and primary drug resistance profile among antiretroviral-naïve individuals in Bangalore, India., AIDS Res Hum Retroviruses, 26, 1097, 10.1089/aid.2010.0092

K Tamura, 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods., Mol Biol Evol, 28, 2731, 10.1093/molbev/msr121

MA Larkin, 2007, Clustal W and Clustal X version 2.0. Bioinformatics., 23, 2947

D Posada, 2008, jModelTest: phylogenetic model averaging., Mol Biol Evol, 25, 1253, 10.1093/molbev/msn083