“Our findings demonstrate that under experimental conditions cattle show low susceptibility to SARS-CoV-2 infection. The wide distribution of BCoV is of special interest, especially because the presence of a pre-existing coronavirus did not protect from infection with another betacoronavirus in this study. Double infections of individual animals might lead to recombination events between SARS-CoV-2 and BCoV, a phenomenon already described for other pandemic coronaviruses. A resulting chimeric virus, comprising characteristics of both viruses, could threaten human and livestock populations and should therefore be monitored.”
“Spike analysis reveals that the current SARS-CoV-2 variants of concern have sampled only 36% of the possible spikes changes which have occurred historically in Sarbecovirus evolution. It is likely that new SARS-CoV-2 variants with changes in these regions are compatible with virus replication and are to be expected in the coming months, unless global viral replication is severely reduced.”
“The more global analysis of spike regions in SARS-CoV-2 genomes revealed the changes that have occurred across the Sarbecovirues. Combined with the current VOC spike changes, the patterns suggest that SARS-CoV-2 has a great deal of evolutionary possibilities to avoid immune pressure.”
“Spike changes in SARS-CoV-2 compared to a large set of known Sarbecovirus indicate that the immediate zoonotic source of SARS-CoV-2 is yet to be identified and reinforces the unique nature of the SARS-CoV-2 genome.”
Biorxiv Preprint – Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses
In this work, we reconstruct the evolutionary events that have accompanied the emergence of SARS-CoV-2, with a special emphasis on the RBD and its adaptation for binding to its receptor, human ACE2 (hACE2). In particular, we identify a specific recombination event which involved ancestral lineages to both SARS-CoV and SARS-CoV-2. By reconstruction of ancestral states of the Spike gene, we find that this ancestral recombination event is associated with an increased binding affinity towards hACE2. Through structure-based binding affinity predictions, we infer that affinity further increased in the lineages leading to SARS-CoV and SARS-CoV-2. These observations suggest that RBD recombination provides the backbone for CoV adaptation to humans, with subsequent point mutations further permitting high affinity RBD-hACE2 binding
A survey of SARS-CoV-2 genome sequences from the UK has detected a number of variants that had been assigned to the B.1.1.7 lineage but which do not contain the full set of B.1.1.7 ‘lineage defining’ mutations. Examination of these sequences revealed that some genome sections carry mutations characteristic of B.1.1.7, whilst other sections carry mutations specific to another lineage. Long runs of mutations along the SARS-CoV-2 that match different lineages are strongly indicative of virus recombination*.
In four instances (recombinant groups A-D) the same mosaic genome structure is observed in multiple closely-related genomes sampled from different infected people (Figure S1). These sequences are therefore highly unlikely to be artefactual (see discussion below). Additionally, we detected a further four mosaic virus genomes, each represented by only one genome sequence (Figure S2). These are also likely to be recombinants, but with a lower level of confidence
* Recombination involves the exchange of genetic material between two related viruses during coinfection of a host cell.
We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively.
WSJ: “The World Health Organization team investigating the origins of Covid-19 is planning to scrap an interim report on its recent mission to China amid mounting tensions between Beijing and Washington over the investigation and an appeal from one international group of scientists for a new probe. A group of two dozen scientists is calling in an open letter on Thursday for a new international inquiry. They say the WHO team that last month completed a mission to Wuhan—the Chinese city where the first known cases were found—had insufficient access to adequately investigate possible sources of the new coronavirus, including whether it slipped from a laboratory.”
Open Letter Link “Call for a Full and Unrestricted International Forensic Investigation into the Origins of COVID-19”
A multivariant of the British, South African, and Brazilian corona variant has been detected in a sample taken from a person who came to Trondheim from abroad.
There has been no further spread, municipal chief medical officer Tove Røsstad told newspaper Nidaros.
“We were informed of this after the person in question had finished his isolation period. It was a person who came from abroad and who tested positive at the border,” Røsstad noted.
According to Røsstad, the virus sample had some elements from the Brazilian variant, from the British variant, and the South African variant.
“..the most immediate threat to public health is recombination of other coronaviruses with SARS-CoV-2. Such recombination could readily produce further novel viruses with both the infectivity of SARS-CoV-2 and additional pathogenicity or viral tropism from elsewhere in the Coronaviridae”
The most prominent result for a SARS-CoV-2 recombination host is the domestic pig (Sus scrofa), having the most predicted associations of all included non-human mammals. The pig is a major known mammalian coronavirus host, harbouring both a large number of observed coronaviruses, as well as a wide diversity. Given the large number of predicted viral associations presented here, the pig’s close association to humans, its known reservoir status for many other zoonotic viruses, and its involvement in genetic recombination of some of these viruses, the pig is predicted to be one of the foremost candidates an important recombination host.
Two variants of the SARS-CoV-2 coronavirus that causes covid-19 have combined their genomes to form a heavily mutated hybrid version of the virus. The “recombination” event was discovered in a virus sample in California, provoking warnings that we may be poised to enter a new phase of the pandemic.
The hybrid virus is the result of recombination of the highly transmissible B.1.1.7 variant discovered in the UK and the B.1.429 variant that originated in California and which may be responsible for a recent wave of cases in Los Angeles because it carries a mutation making it resistant to some antibodies.
The implications of the finding aren’t yet clear because very little is known about the recombinant’s biology. However, it does carry a mutation from B.1.1.7, called Δ69/70, which makes the UK virus more transmissible, and another from B.1.429, called L452R, which can confer resistance to antibodies.