Molecular characterization of non-subtype C and recombinant HIV-1 viruses from Cape Town, South Africa
Date
2009-03
Authors
Wilkinson, Eduan
Journal Title
Journal ISSN
Volume Title
Publisher
Stellenbosch : University of Stellenbosch
Abstract
ENGLISH ABSTRACT: HIV-1 was first diagnosed within South Africa in 1982. In the 1980’s homosexual transmission dominated the HIV-1 epidemic within the country. In the late 1980’s the second HIV-1 epidemic was recognized amongst heterosexual individuals. Today heterosexual transmission of HIV-1 dominates the epidemic in South Africa. Subtype C HIV-1 is responsible for the overwhelming majority of heterosexual infections. An estimated 95% of all infections in the country are thought to be subtype C related. To date only a few papers have been published on non-subtype C HIV within the country. This study characterized subgenomic and near full-length sequences of non-subtype C HIV-1 viruses from the Cape Town area.
The gag p24, pol-integrase, and env gp41 regions of 11 of the 12 samples were characterized by amplification and direct sequencing. Phylogenetic analysis of the sequenced data, with online subtyping tools (REGA and jpHMM) and the drawing of NJ-trees revealed the presence of subtype A1, B, F1 and recombinant viral forms such as AD, AG and AC. One of the isolates was classified as a subtype C and was included for control purposes.
Near full-length characterization of four of the samples were attempted, through full genome PCR amplification and sequencing. Analysis of sequenced data with the use of subtyping-, recombination identification, and tree drawing tools revealed a subtype B, and A1 isolate. The other two isolates were identified as possible AC and AD recombinants.
The data that was generated will greatly improve our knowledge of non-subtype C isolates circulating within South Africa. Due to the possible impact that the high degree of genetic variation that HIV may have on vaccine design and development and ARV treatment and HIV diagnosis, ongoing research of the epidemiology and spread of HIV within South Africa are needed.
AFRIKAANSE OPSOMMING: MIV was in 1982 vir die eerste keer in Suid Afrika gediagnoseer en was hoofsaaklik deur homoseksuele kontak oorgedra. Aan die begin van die 1990’s is `n tweede MIV epidemie gewaar onder heteroseksuele individue. Heteroseksuele oordrag van die virus domineer tans die MIV epidemie in Suid Afrika en is meestal subtipe C verwant. Subtipe C, MIV-1 is verantwoordelik vir 95 persent van alle infeksies in die land. Tot hede is slegs `n paar publikasies oor die nie-subtipe C epidemie in die land gepubliseer. Die huidige studie was gemik op die karakterisering van subgenomiese en vollengte genome van nie-subtipe C MIV isolate van die Kaapstad omgewing. Die gag p24, pol-integrase en env gp41 subgenomiese fragmente van 12 monsters was gekarakteriseer deur amplifikasie en DNS nukleotied volgorde bepaling. Filogenetiese analise deur middel van subtipering (REGA en jpHMM aanlyn subtiperings programme) asook NJ-filogenetiese bome van die data het die teenwoordigheid van subtipe A1, B, en F1, asook verskeie rekombinante viruse insluitende AG, AD en AC vorme aangedui. Een van die isolate was geklassifiseer as `n subtipe C maar is in die studie ingevoeg vir kontrole doeleindes. Vollengte karakterisering van 4 uit die 12 isolate was ook gedoen deur vollengte genoom amplifikasie en DNS nukleotied volgorde bepaling. Tydens die analisering van die DNS volgorde data, deur middel van aanlyn subtipering, rekombinasie identifikasie (Simplot en RIP), en filogenetiese boom konstruksie programme is twee isolate geidentifiseer as subtipe B en A1 MIV-1 viruse. Die ander twee isolate was as moontlike AC en AD rekombinante geklassifiseer. Die data van nie-subtipe C MIV isolate sal ons kennis van die nie-subtipe C epidemie in Suid Afrika versterk. As gevolg van die impak wat die hoë graad van genetisie variasie van MIV op die ontwikkeling van entstowwe, sowel as die diagnose en behandeling van pasiente kan hê, is verdere navorsing in die epidemiologie van die MI-virus in Suid Afrika nodig.
AFRIKAANSE OPSOMMING: MIV was in 1982 vir die eerste keer in Suid Afrika gediagnoseer en was hoofsaaklik deur homoseksuele kontak oorgedra. Aan die begin van die 1990’s is `n tweede MIV epidemie gewaar onder heteroseksuele individue. Heteroseksuele oordrag van die virus domineer tans die MIV epidemie in Suid Afrika en is meestal subtipe C verwant. Subtipe C, MIV-1 is verantwoordelik vir 95 persent van alle infeksies in die land. Tot hede is slegs `n paar publikasies oor die nie-subtipe C epidemie in die land gepubliseer. Die huidige studie was gemik op die karakterisering van subgenomiese en vollengte genome van nie-subtipe C MIV isolate van die Kaapstad omgewing. Die gag p24, pol-integrase en env gp41 subgenomiese fragmente van 12 monsters was gekarakteriseer deur amplifikasie en DNS nukleotied volgorde bepaling. Filogenetiese analise deur middel van subtipering (REGA en jpHMM aanlyn subtiperings programme) asook NJ-filogenetiese bome van die data het die teenwoordigheid van subtipe A1, B, en F1, asook verskeie rekombinante viruse insluitende AG, AD en AC vorme aangedui. Een van die isolate was geklassifiseer as `n subtipe C maar is in die studie ingevoeg vir kontrole doeleindes. Vollengte karakterisering van 4 uit die 12 isolate was ook gedoen deur vollengte genoom amplifikasie en DNS nukleotied volgorde bepaling. Tydens die analisering van die DNS volgorde data, deur middel van aanlyn subtipering, rekombinasie identifikasie (Simplot en RIP), en filogenetiese boom konstruksie programme is twee isolate geidentifiseer as subtipe B en A1 MIV-1 viruse. Die ander twee isolate was as moontlike AC en AD rekombinante geklassifiseer. Die data van nie-subtipe C MIV isolate sal ons kennis van die nie-subtipe C epidemie in Suid Afrika versterk. As gevolg van die impak wat die hoë graad van genetisie variasie van MIV op die ontwikkeling van entstowwe, sowel as die diagnose en behandeling van pasiente kan hê, is verdere navorsing in die epidemiologie van die MI-virus in Suid Afrika nodig.
Description
Thesis (MScMedSc (Pathology. Medical Virology))--University of Stellenbosch, 2009.
Submitted in fulfilment for the degree MSc in BioMedical Science at Stellenbosch University.
Submitted in fulfilment for the degree MSc in BioMedical Science at Stellenbosch University.
Keywords
HIV-1, Molecular epidemiology, Recombinant, Cape Town, South Africa