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CovidReference.com
Genomic sequencing of lower respiratory tract samples from index patients in Wuhan, China, identified SARS-CoV-2 as a novel coronavirus. It was thus placed by the CSG within the Coronaviridae family [Lu 2020]. Phylogenetic analysis conducted to determine the relationship of SARS-CoV-2 to other CoV clustered it in the Betacoronavirus genus, Sarbecovirus subgenus [Tan W 2020, Zhu N 2020]. Notably there is 94,4% homology with SARS-CoV in the seven conserved replicase domains in ORF1ab forming a distinct clade within the Severe Acute respiratory syndrome related coronavirus species (SARSr-CoV). The SARSr-CoV species comprises of hundreds of known viruses predominantly isolated from humans and diverse bats. Understandably the reference to “SARS” can be misleading as SARS-CoV-2, along with other SARSr-CoV, do not cause SARS-like clinical disease. SARS-CoV was the prototype of a new viral species and thus the unique name was assigned to the species as per established viral taxonomic practise. Accordingly, virus nomenclature does not necessarily indicate SARS-like disease but refers to the phylogenetic grouping within the founding virus’s species (CSG ICTV 2020, Wu Y 2020).
Origin and Evolution There has been considerable discussion regarding the origin of SARS-CoV-2. Currently there are numerous articles in scientific journals, pre-publication servers, as well as conspiracy theories on social and popular media. The most controversial of theories center around a laboratory engineered virus or bioweaponry. One of the major contributors to this theory was a preprint article where authors (Pradhan 2020) reported disconcerting similarities between SARS-CoV-2 spike glycoprotein (S) and HIV-1 envelope glycoprotein gp120 and gag protein. The implication of the article was that SARS-CoV-2 may have been manufactured using gene fragments from the HIV-1 genome. The article received extensive scrutiny from various peers internationally. It was quickly refuted after extensive bioanalysis demonstrated that there was no evidence amino acid sequences within the s-glycoprotein were HIV-1 specific nor obtained from HIV-1 (Xiao C 2020). Other claims supporting a laboratory engineered virus was based on a study where construction of a chimeric mouse/bat CoV was capable of infecting human cells in vitro [Menachery 2015]. Investigation into these claims making use of whole genome sequencing compared SARS-CoV-2 to several artificial CoV. Significant divergence between their genomes was identified making it improbable that they are interrelated. Additionally, SARS-CoV-2 is not derived from a previously used virus backbone, and contains randomly occurring mutations favouring natural evolution rather than synthetic construction (Andersen 2020, Dalavilla 2020, Liu S 2020). Other concerns involve Kamps – Hoffmann
