Coexistence of different genotypes in the same bat and serological characterization of Rousettus bat coronavirus HKU9 belonging to a novel Betacoronavirus subgroup.
Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9), a recently identified coronavirus of novel Betacoronavirus subgroup D, from Leschenault's rousette, was previously found to display marked sequence polymorphism among genomes of four strains. Among 10 bats with complete RNA-dependent RNA polymerase (RdRp), spike (S), and nucleocapsid (N) genes sequenced, three and two sequence clades for all three genes were codetected in two and five bats, respectively, suggesting the coexistence of two or three distinct genotypes of Ro-BatCoV HKU9 in the same bat. Complete genome sequencing of the distinct genotypes from two bats, using degenerate/genome-specific primers with overlapping sequences confirmed by specific PCR, supported the coexistence of at least two distinct genomes in each bat. Recombination analysis using eight Ro-BatCoV HKU9 genomes showed possible recombination events between strains from different bat individuals, which may have allowed for the generation of different genotypes. Western blot assays using recombinant N proteins of Ro-BatCoV HKU9, Betacoronavirus subgroup A (HCoV-HKU1), subgroup B (SARSr-Rh-BatCoV), and subgroup C (Ty-BatCoV HKU4 and Pi-BatCoV HKU5) coronaviruses were subgroup specific, supporting their classification as separate subgroups under Betacoronavirus. Antibodies were detected in 75 (43%) of 175 and 224 (64%) of 350 tested serum samples from Leschenault's rousette bats by Ro-BatCoV HKU9 N-protein-based Western blot and enzyme immunoassays, respectively. This is the first report describing coinfection of different coronavirus genotypes in bats and coronavirus genotypes of diverse nucleotide variation in the same host. Such unique phenomena, and the unusual instability of ORF7a, are likely due to recombination which may have been facilitated by the dense roosting behavior and long foraging range of Leschenault's rousette.
Lau
Susanna K P
SK
State Key Laboratory of Emerging Infectious Diseases, Research Centre of Infection and Immunology, Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, China.
Poon
Rosana W S
RW
Wong
Beatrice H L
BH
Wang
Ming
M
Huang
Yi
Y
Xu
Huifang
H
Guo
Rongtong
R
Li
Kenneth S M
KS
Gao
Kai
K
Chan
Kwok-Hung
KH
Zheng
Bo-Jian
BJ
Woo
Patrick C Y
PC
Yuen
Kwok-Yung
KY
D000818:Animals; D000914:Antibodies, Viral / Q000097:blood; D001483:Base Sequence; D002685:Chiroptera / Q000821:virology*; D015897:Comorbidity; D017934:Coronavirus / Q000145:classification* / Q000235:genetics*; D016678:Genome; D005838:Genotype; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D012698:Serologic Tests / Q000379:methods
D000914:Antibodies, Viral