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Characterisation of HIV-1 Molecular Epidemiology in Nigeria : Origin, Diversity, Demography and Geographic Spread

Nazziwa, Jamirah LU orcid ; Faria, Nuno Rodrigues ; Chaplin, Beth ; Rawizza, Holly ; Kanki, Phyllis ; Dakum, Patrick ; Abimiku, Alash'le ; Charurat, Man ; Ndembi, Nicaise and Esbjörnsson, Joakim LU orcid (2020) In Scientific Reports 10.
Abstract

Nigeria has the highest number of AIDS-related deaths in the world. In this study, we characterised the HIV-1 molecular epidemiology by analysing 1442 HIV-1 pol sequences collected 1999-2014 from four geopolitical zones in Nigeria using state-of-the-art maximum-likelihood and Bayesian phylogenetic analyses. The main circulating forms were the circulating recombinant form (CRF) 02_AG (44% of the analysed sequences), CRF43_02G (16%), and subtype G (8%). Twenty-three percent of the sequences represented unique recombinant forms (URFs), whereof 37 (11%) could be grouped into seven potentially novel CRFs. Bayesian phylodynamic analysis suggested that five major Nigerian HIV-1 sub-epidemics were introduced in the 1960s and 1970s, close to the... (More)

Nigeria has the highest number of AIDS-related deaths in the world. In this study, we characterised the HIV-1 molecular epidemiology by analysing 1442 HIV-1 pol sequences collected 1999-2014 from four geopolitical zones in Nigeria using state-of-the-art maximum-likelihood and Bayesian phylogenetic analyses. The main circulating forms were the circulating recombinant form (CRF) 02_AG (44% of the analysed sequences), CRF43_02G (16%), and subtype G (8%). Twenty-three percent of the sequences represented unique recombinant forms (URFs), whereof 37 (11%) could be grouped into seven potentially novel CRFs. Bayesian phylodynamic analysis suggested that five major Nigerian HIV-1 sub-epidemics were introduced in the 1960s and 1970s, close to the Nigerian Civil War. The analysis also indicated that the number of effective infections decreased in Nigeria after the introduction of free antiretroviral treatment in 2006. Finally, Bayesian phylogeographic analysis suggested gravity-like dynamics in which virus lineages first emerge and expand within large urban centers such as Abuja and Lagos, before migrating towards smaller rural areas. This study provides novel insight into the Nigerian HIV-1 epidemic and may have implications for future HIV-1 prevention strategies in Nigeria and other severely affected countries.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Scientific Reports
volume
10
article number
3468
publisher
Nature Publishing Group
external identifiers
  • pmid:32103028
  • scopus:85080102374
ISSN
2045-2322
DOI
10.1038/s41598-020-59944-x
language
English
LU publication?
yes
id
fc753362-5fee-4185-9e33-97c80f2454d2
date added to LUP
2020-05-08 14:59:55
date last changed
2024-08-21 20:27:43
@article{fc753362-5fee-4185-9e33-97c80f2454d2,
  abstract     = {{<p>Nigeria has the highest number of AIDS-related deaths in the world. In this study, we characterised the HIV-1 molecular epidemiology by analysing 1442 HIV-1 pol sequences collected 1999-2014 from four geopolitical zones in Nigeria using state-of-the-art maximum-likelihood and Bayesian phylogenetic analyses. The main circulating forms were the circulating recombinant form (CRF) 02_AG (44% of the analysed sequences), CRF43_02G (16%), and subtype G (8%). Twenty-three percent of the sequences represented unique recombinant forms (URFs), whereof 37 (11%) could be grouped into seven potentially novel CRFs. Bayesian phylodynamic analysis suggested that five major Nigerian HIV-1 sub-epidemics were introduced in the 1960s and 1970s, close to the Nigerian Civil War. The analysis also indicated that the number of effective infections decreased in Nigeria after the introduction of free antiretroviral treatment in 2006. Finally, Bayesian phylogeographic analysis suggested gravity-like dynamics in which virus lineages first emerge and expand within large urban centers such as Abuja and Lagos, before migrating towards smaller rural areas. This study provides novel insight into the Nigerian HIV-1 epidemic and may have implications for future HIV-1 prevention strategies in Nigeria and other severely affected countries.</p>}},
  author       = {{Nazziwa, Jamirah and Faria, Nuno Rodrigues and Chaplin, Beth and Rawizza, Holly and Kanki, Phyllis and Dakum, Patrick and Abimiku, Alash'le and Charurat, Man and Ndembi, Nicaise and Esbjörnsson, Joakim}},
  issn         = {{2045-2322}},
  language     = {{eng}},
  month        = {{02}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Scientific Reports}},
  title        = {{Characterisation of HIV-1 Molecular Epidemiology in Nigeria : Origin, Diversity, Demography and Geographic Spread}},
  url          = {{http://dx.doi.org/10.1038/s41598-020-59944-x}},
  doi          = {{10.1038/s41598-020-59944-x}},
  volume       = {{10}},
  year         = {{2020}},
}