@article{fdi:010092014,
  title = {{H}igh {HIV}-1 genetic diversity and low prevalence of transmitted drug resistance among treatment-naive people living with {HIV} in {M}adagascar},
  author = {{R}akotomalala, {F}. {A}. and {B}utel, {C}hristelle and {R}asamoelina, {T}. and {S}errano, {L}aetitia and {V}idal, {N}icole and {R}andriarimanana, {S}. {H}. {D}. and {M}aharavo, {L}. and {R}andriamananjara, {H}. {N}. and {F}ernandez-{N}uñez, {N}. and {R}abetokotany, {F}. {R}. and {R}akoto, {D}. {A}. {D}. and {D}elaporte, {E}. and {P}eeters, {M}artine and {B}abin, {F}. {X}. and {S}amison, {L}. {H}. and {N}errienet, {E}. and {A}youba, {A}hidjo},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground and objectives: {D}ata on {HIV} drug resistance in {M}adagascar are rare and outdated. {I}n this study, we assessed the prevalence of {HIV} drug resistance mutations to antiretrovirals ({ARV}s) and genetic diversity of circulating strains in treatment-naive people living with {HIV} ({PLHIV}) in {M}adagascar. {M}aterials and methods: {W}e amplified the protease ({PR}), fragments of the {R}everse {T}ranscriptase ({RT}) and {I}ntegrase ({IN}) genes according to the {F}rench {ANRS} protocol. {T}he amplicons were sequenced using next-generation sequencing technology on an {I}llumina platform ({M}i{S}eq). {W}e determined {HIV}-1 subtypes through phylogenetic analysis using maximum likelihood in {P}hy{ML}. {R}esistance interpretation was performed using the {S}tanford algorithm (version 9.5.1). {R}esults: {W}e included 239 {HIV}-infected adults and children, sampled between {J}anuary 2019 and {N}ovember 2023, with a median age of 30 years and a mean plasma {HIV} viral load of 6.3 {L}og copies/m{L}. {W}e sequenced at least one genomic fragment ({PR} or {RT} or {IN}) of the 239 samples, but 9 were excluded from analysis (mean depth < 10,000x). {P}hylogenetic analysis of 230 sequences revealed the presence of subtype {C} (33.91 %), {A}1 (11.30 %), {B} (11.30 %), {CRF}02_{AG} (9.56 %), subtype {G} (3.04 %), subtype {D} (0.43 %), {CRF}01_{AE} (0.43 %), and a significant proportion of unique recombinant forms ({URF}s) (30.30 %). {T}he prevalence of transmitted drug resistance ({TDR}) was 4.95% (10/202) among patients aged 15 years and older. {W}hen stratified by {ARV} class, this prevalence was 4.79 % for non-nucleoside reverse transcriptase inhibitors ({NNRTI}s), 0.59 % for {N}ucleoside {R}everse {T}ranscriptase inhibitors ({NRTI}s), and 0.50 % for integrase strand transfer inhibitors ({INSTI}s). {A}mong children under 15 years old (n = 28), the prevalence of {TDR} was 14.28 % (4/28), with all mutations conferring resistance to {NNRTI}s. {N}o mutation conferring resistance to protease inhibitors was found, neither in children nor in adults. {C}onclusion: {O}ur results show a low prevalence of {ARV} resistance mutations among adult treatment-naive {PLHIV} in {M}adagascar. {I}n children under 15 years old, 92 % were infants under two years old, the high resistance rate is likely related to mother-to-child transmission. {N}o resistance mutation to dolutegravir was detected. {W}e also observed high frequencies of subtypes {C}, {B}, {A}1 and a high proportion of {URF}s, highlighting an on going dynamic epidemic.},
  keywords = {{HIV} ; {G}enetic diversity ; {T}ransmitted drug resistance ; {A}ntiretrovirals ; {T}reatment-naive ; {PLHIV} ; {M}adagascar ; {MADAGASCAR}},
  booktitle = {},
  journal = {{I}nfection {G}enetics and {E}volution},
  volume = {125},
  numero = {},
  pages = {105679 [9 p.]},
  ISSN = {1567-1348},
  year = {2024},
  DOI = {10.1016/j.meegid.2024.105679},
  URL = {https://www.documentation.ird.fr/hor/fdi:010092014},
}