Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria.

Disparities in SARS-CoV-2 genomic surveillance have limited our understanding of the viral population dynamics and may delay identification of globally important variants. Despite being the most populated country in Africa, Nigeria has remained critically under sampled. Here, we report sequences from 378 SARS-CoV-2 isolates collected in Oyo State, Nigeria between July 2020 and August 2021. In early 2021, most isolates belonged to the Alpha "variant of concern" (VOC) or the Eta lineage. Eta outcompeted Alpha in Nigeria and across West Africa, persisting in the region even after expansion of an otherwise rare Delta sub-lineage. Spike protein from the Eta variant conferred increased infectivity and decreased neutralization by convalescent sera in vitro. Phylodynamic reconstructions suggest that Eta originated in West Africa before spreading globally and represented a VOC in early 2021. These results demonstrate a distinct distribution of SARS-CoV-2 lineages in Nigeria, and emphasize the need for improved genomic surveillance worldwide.

Coincident rapid expansion of two SARS-CoV-2 lineages with enhanced infectivity in Nigeria.

The emergence of new SARS-CoV-2 variants with enhanced transmissibility or decreased susceptibility to immune responses is a major threat to global efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Disparities in viral genomic surveillance capabilities and efforts have resulted in gaps in our understanding of the viral population dynamics across the globe. Nigeria, despite having the largest population of any nation in Africa, has had relatively little SARS-CoV-2 sequence data made publicly available. Here we report the whole-genome sequences of 74 SARS-CoV-2 isolates collected from individuals in Oyo State, Nigeria in January 2021. Most isolates belonged to either the B.1.1.7 Alpha "variant of concern" or the B.1.525 Eta lineage, which is currently considered a "variant of interest" containing multiple spike protein mutations previously associated with enhanced transmissibility and possible immune escape. Nigeria has the highest reported frequency of the B.1.525 lineage globally with phylogenetic characteristics consistent with a recent monophyletic origin and rapid expansion. Spike protein from the B.1.525 lineage displayed both increased infectivity and decreased neutralization by convalescent sera compared to Spike proteins from other clades. These results, along with indications that the virus is outpacing the B.1.1.7 lineage in Nigeria, suggest that the B.1.525 lineage represents another "variant of concern" and further underline the importance of genomic surveillance in undersampled regions across the globe.

Anti-Schistosoma IgG responses in Schistosoma haematobium single and concomitant infection with malaria parasites.

Areas prone to schistosomiasis are also at risk of malaria transmission. The interaction between the causal agents of the two diseases could modulate immune responses tailored toward protecting or aggravating morbidity dynamics and impair Schistosoma diagnostic precision. This study aimed at assessing the effect of Plasmodium spp. in concomitant infection with Schistosoma haematobium in modulation of anti-Schistosoma IgG antibodies. The school-based cross-sectional study recruited a total of 322 children screened for S. haematobium and Plasmodium spp. Levels of IgG against S. haematobium-soluble egg antigen (SEA) in single S. haematobium/malaria parasites infection and co-infection of the two parasites in schoolchildren were determined. Data were analyzed using χ(2), Fisher's exact test, and Tukey's multiple comparison test analyses. The prevalence of single infection by S. haematobium, Plasmodium spp., and concurrent infection due to the two pathogens was 27.7, 41.0, and 9.3%, respectively (p < 0.0001). Anti-Schistosoma IgG production during co-infection of the two pathogens (1.950 ± 0.742 AU) was significantly higher than the value recorded for single malaria parasites' infection (1.402 ± 0.670 AU) (p < 0.01) but not in S. haematobium infection (1.591 ± 0.604 AU) (p > 0.05). The anti-Schistosoma IgG production in co-infection status was however dependent on the intensity of Plasmodium spp. with individuals having high intensity of malaria parasites recording lower anti-Schistosoma IgG. This study has implication for diagnosis of schistosomiasis where anti-Schistosoma IgG is used as an indicator of infection. Efforts should be made to control the two infections simultaneously in order not to undermine the efforts targeted toward the control of one.