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

Jamirah Nazziwa,Holly Rawizza,Patrick Dakum,Phyllis Kanki,Nicaise Ndembi,Alash’Le Abimiku,Man Charurat,Beth Chaplin,Nuno Rodrigues Faria,Joakim Esbjörnsson

doi:10.1038/s41598-020-59944-x

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 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.

Highlights

Nigeria has the highest number of AIDS-related deaths in the world
We analyzed 1442 HIV-1 pol sequences collected from four geopolitical zones in Nigeria between 1999 and 2013 (Table 1)
The distribution of different subtypes/circulating recombinant form (CRF) varied within these regions/states with fewer

Summary

Introduction

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. It has been suggested that targeted HIV-1 prevention may be a cost-effective way to decrease the number of new HIV-1 infections – not least in low-and-middle-income countries[13]. Nigeria is the most populous country in Sub-Saharan Africa, has the second highest number of HIV-1 infected persons in the world, and the highest number of annual AIDS-related deaths[14,15]. The estimates of each strain’s contribution to the Nigerian HIV-1 epidemic have varied considerably, with frequency estimates ranging from 22–50% for subtype G, and 19–60% for the CRF02_AG18–25 These variations could have several reasons, Department of Translational Medicine, Lund University, Lund, Sweden.

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Conclusion