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Table 1 Summary of subtype assignments by phylogenetic, REGA and jPHMM HIV subtyping and recombination analyses of 08MB26ZA

From: A putative HIV-1 subtype C/CRF11_cpx unique recombinant from South Africa

Gene

Phylogenetic analysis

REGA

jPHMM

gag

HIV-1 subtype C

HIV subtype C

HIV-1 subtype C

PR

HIV-1 CRF11_cpx

HIV subtype J

HIV-1 subtype J

RT

HIV-1 CRF11_cpx

HIV-1 CRF11_cpx

HIV-1 subtype J/C

IN

Outlier to HIV-1 subtype C

HIV-1 subtype C

HIV-1 subtype C/A1

pol

HIV CRF11_cpx

CRF11_cpx/HIV-1 subtype C

HIV-1 subtype J/C/K

nef

HIV-1 subtype C

HIV-1 subtype C

HIV-1 subtype C

env (C2-V5)

Outlier to HIV-1 subtype C

HIV-1 subtype C

HIV-1 subtype C

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