Insights into SARS-CoV-2 evolution, potential antivirals, and vaccines

Abstract

SARS-CoV-2 is a novel coronavirus, spread among humans, and to date, more than 100 million of laboratory-confirmed cases have been reported worldwide. The virus demonstrates 96% similarity to a coronavirus from a horseshoe bat and most probably emerged from a spill over from bats or wild animal(s) to humans. Currently, two variants are circulating in the UK and South Africa and spread to many countries around the world. The impact of mutations on virus replication, virulence and transmissibility should be monitored carefully. Current data suggest recurrent infection with SARS-CoV-2 correlated to the level of neutralising antibodies and with sustained memory responses following infection. Recently, remdesivir was FDA approved for treatment of COVID-19, however many potential antivirals are currently in different clinical trials. Clinical data and experimental studies indicated that licenced vaccines are helpful in controlling the disease. However, the current vaccines should be evaluated against the emerging variants of SARS-CoV-2.

Keywords: 2019-nCoV; Bats; Betacoronaviruses; COVID-19; COVID-19 antivirals; COVID-19 vaccine; Coronavirus disease; Interspecies transmission; Viral zoonosis.

Fig. 1

Deduced amino acids of the SARS-CoV-2 receptor binding domain in comparison to SARS-CoV-2 like bat and pangolin viruses. Amino acid residues that were found critical for ACE-2 binding are shaded in grey.

Fig. 2

Phylogenetic tree of SARS-CoV-2 with SARS-CoV-2 similar viruses from bats and pangolins. a) Receptor binding domain b) Full-length spike protein (S) c) Full-length genome. The phylogenetic tree was constructed using MEGA 5.2. Maximum likelihood with 1000 bootstrap replications using Jones-Taylor-Thornton (JTT) model was used for amino acids and Tamura-Nei model with uniform rates for nucleotides. ML heuristic method with the Nearest-Neighbor-Interchange was used as tree interface. Bat viruses are in green colour, pangolin viruses in black colour while human SARS-CoV-2 virus is in red colour.

Fig. 3

Phylogentic tree of the full-length spike protein from different clades and lineages of the SARS-CoV-2. Maximum likelihood with 1000 bootstrap replications using Jones-Taylor-Thornton (JTT) model with uniform rates. ML heuristic method with the Nearest-Neighbor-Interchange was used as tree interface. Strains of the same clade are presented with the same colour. Amino acid substitutions except D614G were represented by grey highlight. Most of the sequences in the tree showed D614G substitution so not highlighted. Strains related to variant 1, that emerged in UK in 2020, were highlighted in cyan while strains related to variant 2, that emerged in South Africa in 2020, were highlighted in yellow.