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

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

doi:10.1038/s41598-020-59944-x

Cited by 15 publications

(21 citation statements)

References 68 publications

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“…Diverse HIV‐1 subtypes and recombinant forms (CRF02_AG, G, A, B, C, D, CRF06_cpx, URFs, etc.) have been previously characterized in the country 7 . Several HIV‐1 high‐risk groups such as commercial sex workers, 8,9 voluntary blood donors, 10,11 long‐distance drivers, 12–14 mammy markets contiguous to military facilities, 15 etc., have also been identified.…”

Section: Introductionmentioning

confidence: 99%

New infections and HIV‐1 subtypes among febrile persons and blood donors in Oyo State, Nigeria

Olusola

Olaleye

Odaibo

2021

Journal of Medical Virology

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Purpose There were approximately 37.9 million persons infected with HIV in 2018 globally, resulting in 770,000 deaths annually. Over 50% of this infection and deaths occur in sub‐Saharan Africa, with countries like Nigeria being seriously affected. Nigeria has one of the highest rates of new infections globally. To control HIV infection in Nigeria, there is a need to continually screen high‐risk groups for early HIV infection and subtypes using very sensitive methods. In this study, new HIV‐1 infection and circulating HIV‐1 subtypes among febrile persons and blood donors were determined. Performance characteristics of three commercial EIA kits were also evaluated. Methods In total, 1028 participants were recruited for the study. New HIV‐1 infection and subtypes were determined using enzyme immunoassays and molecular techniques, respectively. Sensitivity, specificity, predictive values, and agreements were compared among the EIA kits using PCR‐confirmed HIV‐positive and negative samples. Results The overall prevalence of HIV infection in this study was 5.35%. The rate of new HIV infection was significantly different (p < .03674) among 1028 febrile persons (Ibadan: 2.22%; Saki: 1.36%) and blood donors (5.07%) studied. Three subtypes, CRF02_AG, A, and G, were found among those with new HIV infection. Whereas the commercial ELISA kits had very high specificities (94.12%, 100%, and 100%) for HIV‐1 detection, Alere Determine HIV‐1 antibody rapid kit had the lowest sensitivity score (50%). Conclusion Genetic diversity of HIV‐1 strains among infected individuals in Oyo State, Nigeria, is still relatively high. This high level of diversity of HIV‐1 strains may impact the reliability of diagnosis of the virus in Nigeria and other African countries where many of the virus strains co‐circulate.

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Section: Introductionmentioning

confidence: 99%

New infections and HIV‐1 subtypes among febrile persons and blood donors in Oyo State, Nigeria

Olusola

Olaleye

Odaibo

2021

Journal of Medical Virology

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“…Subtypes A and G have also been previously reported as circulating in Oyo state as well as in other parts of Nigeria. A recent study identified CRF02_AG, as well as subtypes G and A as the predominant circulating HIV-1 strains in Ibadan, Nigeria 6 .…”

Section: Discussionmentioning

confidence: 99%

“…Findings in this study observed more subtypes in Ibadan metropolis (urban settlement) compared to Saki town (rural settlement). Recent studies using phylodynamic tools have suggested that HIV-1 strains originate and expand in urban areas before migrating to smaller rural centers 6 . There is the need to describe the phylodynamics of HIV-1 subtypes in other states of the country as this will shed further light into the diversity of the virus.…”

Section: Discussionmentioning

confidence: 99%

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Detection of Early HIV-1 Infection among Febrile Persons and Blood Donors in Oyo State, Nigeria

Olusola

Odaibo

2020

Preprint

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About 37.9 million persons are infected with HIV globally resulting in 770,000 deaths. Over 50% of this infection and deaths occur in Sub-Saharan Africa with countries like Nigeria greatly affected. The country also has one of the highest rates of new infections globally. Diverse HIV-1 subtypes have been identified in the country. Febrile persons and blood donors pose a great transmission risk in the country especially during the early stages of infection. HIV-1 rapid kits are routinely used for diagnosis among the general population and high-risk groups. However, there is limited information on the usefulness of HIV rapid kits for early detection especially in areas where diverse HIV-1 subtypes circulate. In this study, the prevalence of early HIV-1 infection as well as circulating HIV-1 subtypes among febrile persons and blood donors were determined. Furthermore, the sensitivity of a widely used HIV-1 rapid antibody kit was compared with those of Antigen/Antibody ELISA based methods. Participants were recruited from selected hospitals in Ibadan and Saki, Nigeria. The prevalence of early HIV infection among 1028 febrile persons (Ibadan: 2.22%; Saki: 1.36%) and blood donors (5.07%) studied were significantly different (P<0.03674). CRF02_AG was the predominant subtype detected with more diverse HIV-1 subtypes observed among febrile persons compared to blood donors. About 1.2% of the samples detected on Antibody-based ELISA methods were undetectable on the HIV-1 rapid antibody kit. Genetic diversity of HIV-1 strains among infected individuals in Oyo State, Nigeria is still relatively high. This diversity is likely impacting on the diagnosis.

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“…We reconstructed the viral diffusion patterns between locations in SPREAD [56] and examined the viral migration profiles within and outside the GPC. A Bayes Factor (BF) test was applied to determine significant non-zero transition rates and a cut-off of BF = 3 was used [41,56,57].…”

Section: Bayesian Phylogeographic Analysismentioning

confidence: 99%

The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda

Ssemwanga

Bbosa

Nsubuga

et al. 2020

Viruses

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The General Population Cohort (GPC) in south-western Uganda has a low HIV-1 incidence rate (<1%). However, new infections continue to emerge. In this research, 3796 HIV-1 pol sequences (GPC: n = 1418, non-GPC sites: n = 1223, Central Uganda: n = 1010 and Eastern Uganda: n = 145) generated between 2003–2015 were analysed using phylogenetic methods with demographic data to understand HIV-1 transmission in this cohort and inform the epidemic response. HIV-1 subtype A1 was the most prevalent strain in the GPC area (GPC and non-GPC sites) (39.8%), central (45.9%) and eastern (52.4%) Uganda. However, in the GPC alone, subtype D was the predominant subtype (39.1%). Of the 524 transmission clusters identified by Cluster Picker, all large clusters (≥5 individuals, n = 8) involved individuals from the GPC. In a multivariate analysis, clustering was strongly associated with being female (adjusted Odds Ratio, aOR = 1.28; 95% CI, 1.06–1.54), being >25 years (aOR = 1.52; 95% CI, 1.16–2.0) and being a resident in the GPC (aOR = 6.90; 95% CI, 5.22–9.21). Phylogeographic analysis showed significant viral dissemination (Bayes Factor test, BF > 3) from the GPC without significant viral introductions (BF < 3) into the GPC. The findings suggest localized HIV-1 transmission in the GPC. Intensifying geographically focused combination interventions in the GPC would contribute towards controlling HIV-1 infections.

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

Cited by 15 publications

References 68 publications

New infections and HIV‐1 subtypes among febrile persons and blood donors in Oyo State, Nigeria

New infections and HIV‐1 subtypes among febrile persons and blood donors in Oyo State, Nigeria

Detection of Early HIV-1 Infection among Febrile Persons and Blood Donors in Oyo State, Nigeria

The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda

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