Identification and genomic characterisation of known and novel highly divergent sapoviruses in frugivorous and insectivorous bats in Nigeria

Abstract

Sapovirus (SaV) infections have been linked with moderate-to-severe acute gastroenteritis (AGE) in animals and humans and represent a significant risk to public health. SaVs from animals including pigs, chimpanzees, and rodents have been reported to be closely related with human SaVs, indicating the possibility of cross-species transmission. Divergent SaVs have been reported in various bat species across various continents including Asia, Europe, Oceania and Africa. However, little is known about the evolutionary history of SaVs across various bat species and their zoonotic potential. In this report, we describe the findings of a surveillance study across various bat species in Nigeria. Samples were pooled and subjected to metagenomics sequencing and analyses. Nine of 57 sample pools (containing 223 rectal swabs from five bat species) had SaV reads from which we assembled a total of four complete and three near-complete (having complete coding sequences) genomes. The bat SaV (BtSaV) strains from this study formed five distinct lineages of which four represented novel genogroups. BtSaV lineages clustered mainly according to bat families, which might suggest a likely virus-host-specific evolution. The BtSaV VP1 capsid protein structure prediction confirmed three main domains (S, P1, and P2) as reported for Human SaV (HuSaV). We found that the P2 subdomain of the VP1 protein contains a degree of homology to known immunoreactive epitopes suggesting these conserved regions may be valuable for diagnostics or medical countermeasure development. This study expands our understanding of reservoir hosts, provides information on the genetic diversity and continuous evolution of SaVs in bats.

Keywords: Nigeria; Sapovirus; VP1 protein; bats; metagenomic sequencing; new genogroups; protein modelling.

Figure 1.

Map of Africa highlighting Nigeria and the various geographical regions where bat samples were selected for sequencing in this study.

Figure 2.

Classification of SaV (GI to GXXI and GNA1 – GNA3) based on cutoff values for genogroup clusters defined as <0.503 and cutoff values for genotype clusters defined as <0.161 using SDT showing evidence of several tentative new genogroups. SaV contigs detected in this study are highlighted in red font with a question mark and a star while previously described SaVs are in black font.

Figure 3.

Maximum likelihood trees of SaV GI – GXXI and GNA1 – GNA3 based on A. complete VP1 gene and B. Complete genome sequences. All SaV genogroups were assigned a specific colour according to the legend provided. The BtSaV strains reported in this research are marked with an asterisk and highlighted in white font and black background while previously reported HuSaV from Nigeria are highlighted in black asterisk.

Figure 4.

Classification of BtSaV based on cutoff values for genogroup clusters defined as <0.503 and cutoff values for genotype clusters defined as <0.161 using SDT showing evidence of 17 distinct BtSaV lineages detected in various bat species. Tentative new genogroups are highlighted in red font with a question mark and red star while previously described BtSaVs are in black font.

Figure 5.

Maximum likelihood tree of All BtSaV based on A. complete VP1 gene and B. Complete RdRp gene, with 1000 bootstrap replications. Bat species are assigned a specific colour according to the legend provided. The BtSaV strains reported in this research are marked with an asterisk and highlighted in white.

Figure 6.

Predicted target sites for B cell binding across the VP1 domain with threshold set at 0.15. (A). Human SaV AB455803, (B) BtSaV/A2GB9/GBOKO/NGR/2020, (C) BtSaV/A11B14/OAU/NGR/2020, (D) BtSaV/A13B8/OAU/NGR/2020, (E) BtSaV/A26B14/OAU/NGR/2020 and (F) BtSaV/k141G10/IDANRE/NGR/2022. The hypervariable regions (HVR) located within the P2 subdomain in the VP1 are colour-coded as shown in the legend.

Figure 7.

Structure predictions of VP1 and VP2 propose conserved virion architecture and an important α-helix in VP2. (A) LocalColabFold prediction of a pentamer of VP1 from HuSaV AJ606694.2 (light green) reproduces the 5-fold axis from the HuSaV VLP structure⁴ (red). (B) The PAE plot of the pentamer structure in (A) shows protein-protein interactions. This heat map scheme is used for all subsequent PAE plots. (C) LocalColabFold predictions of a trimer of VP1 from HuSaV AJ606694.2 (light green) and BtSaV/A2GB9/GBOKO/NGR/2020 (green) reproduce the asymmetric unit from the HuSaV VLP structure⁴ (red). (D) The PAE plots of the trimers in (C) show protein-protein interactions. (E) AlphaFold 3 predictions of a dodecamer of VP2 from HuSaV AJ606694.2 (light blue) or BtSaV/A2GB9/GBOKO/NGR/2020 (blue) reproduces the VP2 portal barrel of cat FCV⁵ (pink). (F) The PAE plot of the dodecamers in (E) shows protein-protein interactions. (G) LocalColabFold prediction of the VP1-VP2 heterodimer (green and blue, respectively) from HuSaV AJ606694.2 and BtSaV/A2GB9/GBOKO/NGR/2020. (H) The PAE plots of the VP1-VP2 heterodimers in (G) predict an interaction of VP1 with an α-helix in VP2. This heterodimer was aligned to all 3 conformations of VP1 in the HuSaV VLP⁹ (red) (I) or both conformations of VP2 in cat FCV⁴⁸ (pink) (J). The interacting α-helix in VP2 is shown in dark blue.