Identification and genetic characterization of five novel bat coronaviruses from Yunnan, China

Abstract

Background: Coronaviruses (CoVs) represent a serious threat to human health and have become a major transmissible, endemic, and causative pathogen in humans; they represent a major health concern, given their ability to cause infectious diseases. Bats are natural hosts for diverse viruses. Many transmission events of CoVs and identification of multiple novel CoVs in bats has increased attention towards their capacity to serve as hosts for zoonotic viruses.

Results: In this study, 61 bats from Yunnan Province were analyzed, identifying seven CoVs, including three α- and two β-CoVs with full-genome sequences. Among the five identified alpha-CoVs, four belong to the Decacovirus subgenus and one to the Minunacovirus subgenus. Two beta-CoVs were also identified, both belonging to the Sarbecovirus subgenus.The genetic structures revealed similarities to known strains such as HKU10 and SARS-CoV-2, along with novel findings such as the Minunacovirus subgenus CoV YJ3c/f and unique ORF patterns. Our results demonstrated that strain JCC9 has a unique recombination pattern and shows a higher binding affinity to civet and pangolin ACE2 receptors, then the HpJC8xc strain transmits and recombines between hosts (bats), indicating a potential risk of crossing the interspecies barrier and infecting other animals.

Conclusions: The CoVs detected in the bats studied in this research exhibit high diversity. Genomic analysis revealed that CoVs in bats undergo frequent recombination events. Furthermore, recombination patterns and evolutionary analyses suggest that alpha-CoVs are more prone to cross-species transmission across different bat families/genera, whereas beta-CoVs demonstrate host specificity and tend to co-evolve with their bat hosts.Our finding suggest that bats, as hosts of CoVs, be constantly monitored to prevent outbreaks of new infections caused by viruses passing across interspecies barriers, and consequently, viral diseases in humans or livestock.

Keywords: Bats; Characterization; Coronaviruses; Transmission; Yunnan.

Fig. 1

Geographic distribution map of bat species in Yunnan. The gray background represents the state/city where the sampling originated from, and the different colors in the sector map indicate different bat species

Fig. 2

Neighbor-joining phylogenetic tree showing the homologous relationships of five CoVs strains. Phylogenetic tree of (A) α- and (B) β-CoVs constructed based on the complete nucleotide sequences of CoVs. Each reference strain is represented by serial number, strain name, and species origin. Each group is annotated. The red, pink, and blue markers refer to the CoVs detected in this study

Fig. 3

Full-length genomic sequence analysis of bats. The individual open reading frames of CoVs are indicated by different colors, and the respective lengths of the open reading frames correspond to the scale below. Login numbers for related viruses are detailed in the phylogenetic tree

Fig. 4

Recombination analysis in CoVs. Sequence similarity plots with a window size of 1000 bp and a step size of 100 bp. Reference strains are indicated using different colors, and the blue arrow at the top indicates the position of the ORF at the time of alignment. Potential restructuring breakpoints are marked below with a solid red line. The login numbers of related viruses are detailed in the phylogenetic tree

Fig. 5

Comparison of S protein. (A) Comparison of RBD Key Loci in Yunnan_Rp_JCC9_2020. Compared to the RBD and Flynn protease cleavage site regions, the RBD region corresponds to amino acid sequences 414–505 of the SARS-CoV-2 S protein, and the Flynn protease cleavage site region corresponds to 67–-707. The red triangles indicate the key amino acid residues and the red circles indicate the Flynn protease cleavage sites. (B) Structure and characterization of S protein subunit homology model in Yunnan_Rp_JCC9 and Yunnan_MP_YJ3C/F_2020 from β CoVs. The JCC9 homology to a representative β CoVs S protein subunit modeling structure and characterization. RBD has been marked with a large red circle, the two deletion loops are marked with small red circles, and the Flynn protease cleavage site is marked with a blue arrow

Fig. 6

Docking diagram of RBD, S protein, and related ACE2 protein. (A) Binding affinity of RBD of Yunnan_Rp_JCC9_2020 S protein with ACE2 of four species; (B) Binding affinity of RBD of SARS-CoV-2 S protein with ACE2 of four species