Genomic variance of the 2019‐nCoV coronavirus

Abstract

There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and severe acute respiratory syndrome. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hypervariable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.

The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China

“…Recently, two mutations of the S protein and N protein SARS-CoV-2 may explain its zoonotic transmission [32]. Genomic alignment of 54 SARS-CoV-2 genomes identified two hotspots of hypervariability at positions 8789 (synonymous variant) and 28,151(Ser/ Leu change), located in the polyprotein and ORF8 genes respectively [33].…”

Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species

“…To date, a large number of studies have proved the pathogen of COVID-19 is a novel coronavirus, which belongs to the Coronavirus family, Betacoronavirus genus and Sarbecovirus subgenus, with a linear single-stranded positive-strand RNA genome of about 30 kb (Ceraolo and Giorgi, 2020;Jiang and Shi, 2020;Lai et al, 2020;Li et al, 2020;Lu et al, 2020;Zhou et al, 2020). However, so far, there are still controversies about the source of the virus and its intermediate host.…”

“…Notably, although the whole genome sequence of SARS-CoV-2 is almost identical, with a similarity rate of 99.9% (Ceraolo and Giorgi, 2020;Li et al, 2020;Lu et al, 2020;Paraskevis et al, 2020), the virus begins to mutate in patients . Mutations of different SARS-CoV-2 isolates mainly occurs in five genes, including S, N, ORF8, ORF3a, and ORF1ab, with about 42% of the variations are non-synonymous mutation ).…”

Codon usage and evolutionary rates of the 2019-nCoV genes

“…Z-score is calculated for two codon bias indexes ENC and CAI. We show in figure that a lot of coronavirus have a codon usage major than the average value of the family (Z-score 3). For what concerns 2019-nCoV, it presents average CAI and ENC higher than the average too.…”