PMC:7103735 / 10603-17083 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7103735","sourcedb":"PMC","sourceid":"7103735","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7103735","text":"Animal hosts of HCoVs\nThe animal origin of HCoVs is supported by similarities in genome organization and phylogenetic relatedness of animal CoVs and HCoVs as well as the geographical coincidence of these viruses and plausible routes of cross-species transmission such as petting, butchering and close contact. Error-prone RNA-dependent RNA polymerase creates diversity in the CoV genome, enabling them to jump across the species barrier. However, HCoVs encode a proofreading exoribonuclease (ExoN) that plays a crucial role in RNA synthesis and replication fidelity [22]. This serves to reduce errors in RNA replication. The inactivation of ExoN causes a mutator phenotype and the resultant virus is either attenuated or inviable. In addition, other structural and non-structural genes might also contribute to the genomic diversity of CoVs by modulating polymerase and ExoN activity [23]. In addition to mutations, recombination and deletion also play an important role in host switching and adaptation. Among SARS-CoV, SARS-CoV-2, and MERS-CoV, a mutation rate as high as 0.80–2.38 × 10−3 nucleotide substation per base per year has been documented for SARS-CoV [24]. This is comparable to those of primate lentiviruses, including HIVs. Compared to SARS-CoV, the variabilities in SARS-CoV-2 and MERS-CoV genomes are much less dramatic. It will be of interest to clarify how this might relate to their host adaptability. In this regard, adaptive mutations in the S protein of SARS-CoV have been found during the outbreak to result in better binding with the ACE2 receptor. Cryo-EM analysis has provided structural evidence that S protein of SARS-CoV-2 binds with ACE2 with higher affinity. It will be of interest to see whether SARS-CoV-2 might be further adapted to ACE2 in the near future. Since the receptor-binding domain also contains predominant neutralizing epitopes, variations in this domain are only relevant to the development of a vaccine against SARS-CoV-2 [25].\nAll HCoVs have a zoonotic origin. Whereas bats are the evolutionary reservoir host of 229E, NL63, SARS-CoV, MERS-CoV, and SARS-CoV-2, parental viruses of OC43 and HKU1 have been found in rodents. Intermediate and amplifying hosts of HCoVs were also found in domestic and wild mammals. Ancestors of OC43 were identified in domestic animals such as cattle and swine. The switch of hosts from cattle or pigs to humans might have occurred in the context of a pandemic of respiratory disease recorded around 1890 in human history [26]. Similar to MERS-CoV, 229E could be acquired by humans from dromedary camels. However, the direction of this cross-species transmission remains to be determined and the possibility cannot be excluded that both humans and camels might have acquired 229E from an unidentified host including bats [27].\nIn an effort to identify the direct animal source of SARS-CoV, SARS-CoV-related CoVs (SARS-rCoV), which share 99.8% sequence homology at the nucleotide level with SARS-CoV, were isolated in 2003 from workers working in a live animal market where animal meats were sold and from animals in the same market [28], including Himalayan palm civets and a raccoon dog. Palm civets were once thought to be the natural host of SARS-CoV as anti-SARS-CoV antibody was detected in civets in the market. In experimental infection, civets were equally susceptible to SARS-CoV and SARS-rCoV. Infected animals displayed clinical symptoms. However, no anti-SARS-CoV antibodies were detected in any wild or farmed civets [29], raising the possibility that they are not a natural host of SARS-CoV and SARS-rCoVs. In 2005, horseshoe bats were identified as a natural host of SARS-rCoVs [30,31]. These bat SARS-rCoVs serve as the gene pool and an evolutionary origin of SARS-CoV. It is particularly noteworthy that a SARS-rCoV using the same ACE2 receptor as SARS-CoV was also found in bats [32]. Their genomes share 95% nucleotide sequence homology. Presumably, palm civets and other mammals in the market were transiently infected, and they transmitted the virus to humans. It remains to be clarified whether another stable and natural reservoir host of SARS-CoV, exactly like dromedary camels for MERS-CoV, might exist.\nThe genomic sequence of MERS-CoV was closely related to bat CoVs HKU4 and HKU5 [18]. Bat CoVs that are evolutionarily closer to MERS-CoV, sharing ∼75% nucleotide sequence homology and using the same DPP4 receptor, were also identified [32]. Although bats are the evolutionary reservoir host and bat CoVs serve as the gene pool of MERS-CoV, humans acquire MERS-CoV from diseased dromedary camels, but not directly from bats. These camels are the natural reservoir host of MERS-CoV. MERS-CoVs isolated from dromedaries are identical to those found in humans. Experimental infection of dromedary camels with MERS-CoV results in mild disease, shedding large quantities of the virus from the upper respiratory tract [33]. In addition, other non-camelid domestic animals in close contact with infected camels, including sheep, goats, a cow, and donkeys, are also infected by MERS-CoV [34]. These domestic animals could also pose a risk to humans and should, therefore, be included in the MERS-CoV surveillance programme.\nSARS-CoV-2 was found to share 96.2% nucleotide homology with a bat CoV RaTG13 found in Rhinolophus affinis bats [35]. However, their receptor-binding domains in the S proteins differ significantly. Some of the earliest patients infected with SARS-CoV-2 were linked to the Huanan Seafood Wholesale Market and other live animal markets in Wuhan, Hubei, China [36]. SARS-CoV-2 was detected from the working environment of the market, supporting the existence of a live animal source. Bamboo rats in the family of Rhizomyidae and civets are the prime suspects of an intermediate host of SARS-CoV-2, although no concrete evidence is available. Metagenomic analysis of CoV sequences indicates that pangolins, which are a group of endangered small mammals, carry betacoronaviruses at a high rate [37], including some sharing ∼90% nucleotide homology with SARS-CoV-2. The pangolin betacoronaviruses are phylogenetically related to both SARS-CoV-2 and RaTG13. Existing evidence suggests that neither RaTG13 nor pangolin betacoronaviruses might be the immediate ancestor of SARS-CoV-2. Further investigations are required to determine whether pangolins and other animals might harbour parental viruses of SARS-CoV-2 and serve as its intermediate and amplifying 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