Emergence of a unique recombinant form of HIV-1 from Manipur (India).
BACKGROUND
The AIDS epidemic in Manipur, India, manifests unique features, having co-circulation of B and C HIV-1 subtypes along with recombinant forms. Manipur has the highest incidence of HIV-1 infection compared to the other states of India, but limited information is available regarding the full-length sequence of HIV-1 recombinants.


OBJECTIVE
To characterize the near full-length genome of a novel recombinant HIV-1 strain from an injecting drug user of Manipur.


METHODS
Viral RNA, extracted from the plasma of a male injecting drug user aged 35, was diagnosed with HIV-1 infection. Near full-length genome was amplified by polymerase chain reaction using primer walking approach. Phylogenetic relationships were determined with neighbor-joining trees. The recombination break points were detected using boot scan and Simplot analyses.


RESULTS
This recombinant predominantly had subtype C genome and exhibited mosaic structures with subtype B insertions at three different positions of HIV-1 genome. Simplot analysis of near full-length genome sequence from the recombinant HIV-1 strain, MAN86 exhibited similarity with the sequence of C.IN.93.93IN905 in its subtype C backbone, while the subtype B insertions showed resemblance with the sequence of B.TH.99.99(TH)_C1416.


CONCLUSIONS
This study confirms the presence of a unique recombinant HIV-1 strain, emerging as a result of recombination between HIV-1 strains from India and Thailand.
HIV/AIDS Laboratory, Division of Virology, National Institute of Cholera & Enteric Diseases, Kolkata 700 010, India.
Roni
R
Sarkar
Kamalesh
K
Sarkar
N
N
Brajachand Singh
Y
Y
Manihar Singh
Debashis
D
Mitra
Sekhar
S
Chakrabarti
D000328:Adult; D016000:Cluster Analysis; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007194:India; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D015819:Substance Abuse, Intravenous / Q000150:complications
D012367:RNA, Viral