Almost all emerging viruses have genomes consisting RNA rather than DNA (Holmes and Rambaut 2004). As RNA viruses mutate and recombine at much faster rates than DNA viruses this strongly implies that viruses emerge as a result of changes occurring over time. Within the last three deacdes many apparently novel coronavirus have emerged that infect both humans and domestic animals. These include Bovine coronavirus (BCoV), human coronavirus OC43 (HCoV-OC43), human coronavirus 229E (HCoV-229E), canine coronavirus (CCoV), feline coronavirus (FCoV), porcine coronavirus (PCoV), and transmissible gastroenteritis virus (TGEV) (Graham and Baric 2010). The earliest descriptions of two human CoVs (HCoV-229E and OC43) were in the 1960s. In the SARS aftermath NL63 and HKU1 were detected by 2005. In 2012, a highly pathogenic sixth HCoV, termed Middle East respiratory syndrome (MERS)-CoV was found in the Arabian peninsula (Drexler, Corman, and Drosten 2014)
Coronaviruses consist of the largest single-stranded RNA genomes currently known, reaching 32 kb in length. This pushes the boundaries for effective replication. When coronaviruses replicate they use a rather unique mechanism that leads to synthesis of both genomic and multiple subgenomic RNA fragments before the assembly of the progeny virions (Masters 2006). If these fragments differed from the original RNA through random mutations due to poor fidelity of RNA polymerases this could result in the cells containing a quasispecies (sometimes termed a mutant swarm) of slightly differing variants of the virus (Lauring and Andino 2010). This is well known as occuring in the case of hepatitis C and HIV. Coronaviruses are considered to be rather more stable than would be expected given the length of their genome as a result of their possession of a proof reading mechanism (E. C. Smith and Denison 2013). However quasispecies have been reported to occur over long periods of infection with SARS (Xu, Zhang, and Wang 2004).
The unique mechanism of replication suggests that another mechanism may play a major role in the evoloution of coronaviruses. This is recombination.
Prior to 2014 there were typically limitations to reconstructing relationships based on PCR assays, as they tended to only target parts of the ORF1ab, typically the RdRp with amplicon sizes range from as little as 121 to around 404 base-pairs. However the diversity of coronaviruses was clear. Many of the partial sequences were found to branch deeply in the phylogenetic tree and likely represent not just new species, but even new genetic clades. (Drexler, Corman, and Drosten 2014).
A sequence obtained from a South African bat was more closely related to MERS-CoV than any other known virus and differed only 1 aa exchange (0.3%) in the translated 816-nt RdRp gene fragment.(Hashemi-Shahraki et al. 2013)
Recombination analysis shows evidence of frequent recombination events within the S gene and around the ORF8 between these SARSr-CoVs including strains with spike proteins that can all use the receptor ofSARS-CoV in humans (ACE2) for cell entry in Rhinolophus ferrumequinum, Rhinolophus affinis and from Aselliscus stoliczkanus (Hu et al. 2017)
We identified five SARS-related CoVs (SARSr-CoVs) in Rhinolophus bats from Sichuan and Yunnan and confirmed that angiotensin-converting enzyme 2 usable SARSr-CoVs were continuously circulating in Rhinolophus spp. in Yunnan.(Han et al. 2019)
Twelve out of 504 bats in Europe were found to be infected by a coronavirus (Monchatre-Leroy et al. 2017)
According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV- 229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. (Corman et al. 2015)
No SARS-like betacoronaviruses were found in a study in Australia despite targeting rhinolophid bats (C. S. Smith et al. 2016)
(Drexler, Corman, and Drosten 2014) present evidence for a zoonotic origin of four of the six known human CoVs (HCoV), three of which likely involved bats, namely SARS-CoV, MERS-CoV and HCoV-229E; compare the available data on CoV pathogenesis in bats to that in other mammalian hosts; and discuss hypotheses on the putative insect origins of CoV ancestors
The RBD of European rhinolophid bat SARS-related coronaviruses was more related to that of the human SARS-CoV than the RBD from Chinese bat viruses (Drexler et al. 2010), recombination may have played a role in the emergence of the human pathogenic virus
In a study on a maternal colony of Rhinolophus ferrumequinum in an unused building in the historical centre of Barrea (L’Aquila) in Central Itialy, cats were found to enter the roost especially when young bats were present, and bat remains found in 30% of the cat scats we examined. (Ancillotto, Venturi, and Russo 2019)
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