@article{fdi:010072077,
  title = {{D}ivergent {HIV}-1 strains ({CRF}92_{C}2{U} and {CRF}93_cpx) co-circulating in the {D}emocratic {R}epublic of the {C}ongo : {P}phylogenetic insights on the early evolutionary history of subtype {C}},
  author = {{A}renas, {C}. {J}. {V}. and {V}idal, {N}icole and {M}undeke, {S}. {A}. and {M}uwonga, {J}. and {S}errano, {L}. and {M}uyembe, {J}. {J}. and {B}oillot, {F}. and {D}elaporte, {E}. and {P}eeters, {M}artine},
  editor = {},
  language = {{ENG}},
  abstract = {{M}olecular epidemiological studies revealed that the epicenter of the {HIV} pandemic was {K}inshasa, the capital city of the {D}emocratic {R}epublic of the {C}ongo ({DRC}) in {C}entral {A}frica. {A}ll known subtypes and numerous complex recombinant strains co-circulate in the {DRC}. {M}oreover, high intra-subtype diversity has been also documented. {D}uring two previous surveys on {HIV}-1 antiretroviral drug resistance in the {DRC}, we identified two divergent subtype {C} lineages in the protease and partial reverse transcriptase gene regions. {W}e sequenced eight near full-length genomes and classified them using boot scanning and likelihood-based phylogenetic analyses. {F}our strains are more closely related to subtype {C} although within the range of inter sub-subtype distances. {H}owever, these strains also have small unclassified fragments and thus were named {CRF}92_{C}2{U}. {A}nother strain is a unique recombinant of {CRF}92_{C}2{U} with an additional small unclassified fragment and a small divergent subtype {A} fragment. {T}he three remaining strains represent a complex mosaic named {CRF}93_cpx. {CRF}93_cpx have two fragments of divergent subtype {C} sequences, which are not conventional subtype {C} nor the above described {C}2, and multiple divergent subtype {A}-like fragments. {W}e then inferred the time-scaled evolutionary history of subtype {C} following a {B}ayesian approach and a partitioned analysis using major genomic regions. {CRF}92_{C}2{U} and {CRF}93_cpx had the most recent common ancestor with conventional subtype {C} around 1932 and 1928, respectively. {A} {B}ayesian demographic reconstruction corroborated that the subtype {C} transition to a faster phase of exponential growth occurred during the 1950s. {O}ur analysis showed considerable differences between the newly discovered early-divergent strains and the conventional subtype {C} and therefore suggested that this virus has been diverging in humans for several decades before the {HIV}/{M} diversity boom in the 1950s.},
  keywords = {{HIV}-1 ; subtype {C} ; molecular epidemiology ; phylogeny ; democratic {R}epublic of the {C}ongo ; {REPUBLIQUE} {DEMOCRATIQUE} {DU} {CONGO} ; {KINSHASA}},
  booktitle = {},
  journal = {{V}irus {E}volution},
  volume = {3},
  numero = {2},
  pages = {vex032 [10 p.]},
  ISSN = {2057-1577},
  year = {2017},
  DOI = {10.1093/ve/vex032},
  URL = {https://www.documentation.ird.fr/hor/fdi:010072077},
}