Molecular detection & genetic characterization of coronavirus from Bat sample in Nipah prone areas of Bangladesh

Abstract

Bats are considered key natural carriers of Nipah virus and various zoonotic coronaviruses. In recent years, human activities have significantly contributed to the emergence of zoonotic diseases, leading to virus outbreaks like SARS-CoV-2. This virus results from human contact that promotes interactions between wild animals, livestock, and humans. The Coronaviridae family includes viruses with positive-sense RNA genomes, and SARS-CoV-2, classified as a β-CoV, shares genetic similarities with bat-derived coronaviruses. Both SARS-CoV and MERS-CoV originated from bats, with intermediate hosts playing a role in their transmission to humans. Additionally, the Nipah virus, belonging to the Paramyxoviridae family, also utilizes bats as hosts, raising concerns about cross-species transmission and potential viral recombination. Viral coinfection can be influenced by both host and virus factors, which affect transmission dynamics and pathogenicity. Investigating the interactions and host switching among bat species that carry these viruses is crucial, as it may lead to the emergence of new viral strains or changes in viral pathogenicity. The objective of this study was to categorically detect and analyze bat coronavirus samples from Nipah-prone areas as they have a higher probability of viral transmission, coinfection and cross-species transmission leading to recombination mutation in the RdRp region. A total of 1625 bat samples collected from five nipah-prone areas in Bangladesh were observed, where 16 samples tested positive for Coronaviridae targeting the conserved region of RdRp (RNA Dependent RNA Polymerase) by semi-nested PCR. 10 out of the 16 samples were successfully retrieved after Sanger sequencing through a specific protocol. Among them, nine of the positive samples were obtained by the pathogen discovery protocol suggested by (Watanabe et al., 2010) (Protocol004-Used for bat coronavirus identification) and one (OHL-BAT-003) through (Maganga et al., 2014) (Protocol-003-Used for human coronavirus identification). While the Coronavirus Typing Tool (CTT) assisted in identifying reference sequences for eight samples, the two samples designated OHL-BAT-001 and OHL-BAT-004 remain unidentified following molecular analysis. Mutational analysis for these two strains was conducted to identify mutations in the RdRp region. Further correlation was established between RdRp mutations and host switch, cross-species transmission, and multiple Bat-CoV coexistence by constructing a tanglegram (co-phylogenetic analysis). For future prospects of such investigative studies, full genome sequencing should be done to confirm the novel mutations and viral recombination due to cross-species transmission. This approach would enhance our understanding of the molecular evolution and zoonotic potential of bat coronaviruses in Nipah-prone areas.