Characterization of novel emerging coronaviruses : evolutionary origin and potential zoonotic transmission

Abstract

Since the emergence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in 2012, human and dromedary camels are known for being the host reservoirs for this CoV. However, MERS-CoV was absent in the archived camels’ samples of retrospective studies and no MERS related cases were reported before 2012. It is hypothesized that animals other than camels are the ultimate host reservoir of MERS-CoV. In this study, available MERS-CoV genomes obtained from database were studied using phylogenetic and recombination analyses. Possible recombination events were observed from lineages B3, B4 and B5. Highest rate of amino acid (aa) substitution was detected in spike (S) protein with codon 1020 experiencing positive selection in clade B viral strains. The most recent common ancestor of MERS-CoV strains was predicted to be around 2010, suggesting camels are the intermediate host of MERS-CoV.

Several bat Merbecoviruses were discovered in Africa and China with close genetic relatedness to MERS-CoV, suggesting MERS-CoV is originated from bats. Yet, none of these CoVs carries receptor binding domain (RBD) resembling that of MERS-CoV and hence they are unlikely the progenitor of MERS-CoV. Intriguingly, Ty-BatCoV HKU4 consists of the closest RBD to that of MERS-CoV. Therefore, it is hypothesized that bat Merbecoviruses, which are closely related to MERS-CoV, may display similar phenotypes and the potential for zoonotic transmission. Ty-BatCoV HKU4 was successfully isolated in this study. Cellular tropism and dipeptidyl peptidase 4 (DPP4) usage were studied and suggested Ty-BatCoV HKU4 can utilize human and camel DPP4 but not Tylonycteris pachypus DPP4 for viral entry, suggesting Ty-BatCoV HKU4 may be able to jump from bats to humans directly. Unrecognized receptor may be used in its natural host. Interferons α/β were shown to be potential antiviral candidates for Ty-BatCoV HKU4 infection. This notwithstanding, the progenitor of MERS-CoV is yet to be found and the evolutionary gap of MERS-CoV remains unanswered. It is proposed that unidentified bat CoVs, which are the origin of MERS-CoV, may exist in the wild. Therefore, possible ancestral viruses of MERS-CoV were searched from diverse bats but no novel Merbecoviruses was discovered. However, two novel alphacoronaviruses, Rs-BatCoV HKU32 and Ty-BatCoV HKU33, were discovered from Rhinolophus and Tylonycteris bats and they were known to harbor Sarbecoviruses and Merbecoviruses respectively. Genomic analyses revealed Rs-BatCoV HKU32 carried the SARSr-CoV ORF7a-like accessory protein, suggesting a common evolutionary origin and the potential of recombination between alphacoronaviruses and betacoronaviruses. Further study on its emergence potential is needed. The recently emerged SARS-CoV-2 was a novel strain of SARSr-CoV causing the COVID-19 pandemic and it shares close genetic relatedness to bat Sarbecoviruses, especially BatCoV-RaTG13 from horseshoe bats except RBD. Similarly, its progenitor is yet to be identified. It is hypothesized SARS-CoV-2 is a recombinant virus with bat origin and displays similar phenotypes as SARS-CoV does. However, bat cells susceptibility test revealed differential tropism of SARS-CoV and SARS-CoV-2. SARS-CoV could replicate in its natural host kidney cells but not for SARS-CoV-2, suggesting different evolutionary origin. Structural modeling provided clues to the different tropisms of these two viruses through receptor binding interface investigation.