Eco-epidemiology and complete genome comparison of bat SARS coronavirus in China reveal bats as reservoir for frequent recombination

Abstract

OBJECTIVE: Despite the identification of SARS-CoV-like viruses in horseshoe bats in China, the evolutionary and possible recombination origin of SARS-CoV remains undetermined. To better define the epidemiology and evolution of bat-SARS-CoV in China and their role as recombination origin of SARS-CoV in civet, a four-year study on coronaviruses in Chinese horseshoe bats in Hong Kong and Guangdong province of southern China was conducted. METHODS: Respiratory and alimentary samples were collected from 1401 Chinese horseshoe bats captured in Hong Kong and Guangdong province of southern China over a four-year period and were detected for coronaviruses by reverse-transcriptase polymerase chain reaction. Five hundred and eleven bats from Hong Kong were also tagged to study the migration pattern of bats and viral persistence. The complete genomes of 10 strains of bat-SARS-CoV obtained at different time were sequenced and compared to the previously characterized genomes. RESULTS: Bat-SARS-CoV was detected in alimentary specimens from 130 (9.3%) bats, with peak activity during spring. Bats carrying the viruses appeared healthy, with viral clearance occurring between two weeks to four months. Tagging exercise showed that migration distances of Chinese horseshoe bats in Hong Kong range from 1.86 to 17 km. Complete genome sequencing of 10 strains of bat-SARS-CoV revealed frequent recombination between different strains, especially among the bat viruses in China. Recombination was detected between bat-SARS-CoV Rp3 from Guangxi and Rf1 from Hubei in the possible generation of civet SARS-CoV SZ3, with breakpoint at nsp16/spike region. CONCLUSION: Bat-SARS-CoV causes acute, self-limiting infection in horseshoe bats which serve as reservoir for recombination between virus strains from different geographical locations within reachable foraging range. Civet SARS-CoV is likely a recombinant virus arising from bat-SARS-CoV strains closely related to Rp3 and Rf1. Such frequent recombination in these animals may have accounted for the cross-species transmission and emergence of SARS.