Cross-neutralising antibodies to SARS-CoV-2 in sera from straw-coloured fruit bats (Eidolon helvum) in Nigeria.

Background: Straw-coloured fruit bats (Eidolon helvum; ) are widely distributed in Africa and are known reservoirs for viruses with zoonotic potential. These bats are widely hunted in West and Central Africa for human consumption as food source and medicine. This practice increases the potential for spillover of zoonotic disease to the human population. This study investigated the presence of neutralising antibodies against SARS-CoV-2 variants in serum samples (n = 142) from E. helvum bats captured between November 2017 and March 2019 in Makurdi, Nigeria. Faecal samples (n = 120) from the roost were collected in 2022 and screened for the presence of coronavirus RNA followed by genetic sequencing.

Results: Virus neutralisation tests revealed 7.04% of the bat sera neutralised 2019-nCoV/Italy-INMI1, while 17.57% of the bat sera neutralised a SARS-CoV-2 Omicron BA.1 isolate. Partial genome obtained by next generation sequencing identified a lineage D Betacoronavirus from one faecal sample with 98.16% nucleotide sequence identity to sequences from Eidolon helvum collected in Cameroon in 2013. Epitope analysis of the spike protein sequence from the faecal sample showed conserved antigenic determinants shared with SARS-CoV-2.

Conclusions: This study demonstrated that pre-pandemic sera collected from Eidolon helvum bats had neutralising activity against SARS-CoV-2 variants. Furthermore we detected the presence of lineage D betacoronavirus in this bat population that shared epitopes with SARS-CoV-2. This work contributes to our understanding of the complexities of coronavirus cross-reactivity. Characterizing bat coronaviruses is crucial to understand their zoonotic potential for spillover events due to bushmeat hunting practices.