Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, in late December 2019. Due to SARS-CoV-2's high infectivity, it spread rapidly across the world. In less than three months, the World Health Organization (WHO) declared the outbreak as the COVID-19 pandemic.
To date, over 41 million cases are reported, with over 1.1 million deaths. Genomic structures and phylogenomic studies reveal that SARS-CoV-2 belongs to genera beta coronavirus (includes SARS-CoV and MERS-CoV (Middle East respiratory syndrome-related coronavirus). However, there are important differences in the genotypic and phenotypic levels that influence their pathogenesis.
While there are variations in severity and lethality of coronaviruses, the infectivity of SARS-CoV-2 is higher than SARS-CoV or MERS-CoV, even though the fatality rate is higher in the latter infections. It is essential to understand the molecular mechanism of SARS-CoV-2 infection to devise therapeutic strategies. In this context, resistant mutations need to be explored to improve any strategy adopted to arrest the infection progression or transmission.
However, there is little focus on mapping the mutations on the important protein components of SARS-CoV-2. Souradip Basu et al. recently published a study exploring clade-specific mutations and their impact on SARS-CoV-2 proteins.
In their bioRxiv* preprint paper, the researchers focus on mapping the clade-specific mutations' effects on the protein structures' conformation and stability. They identified the mutations in the set of seven proteins - orf8, nsp2, nsp4, nsp6, nucleocapsid protein (N), and Spike protein (S).
The SARS-CoV-2 contains a single-stranded positive-sense RNA encapsulated in a nucleoprotein matrix. The RNA genome of SARS-CoV-2 consists of approximately 29,800 nucleotides, encoding for 29 known proteins. Four proteins make up the viral structure.
With the help of a list with prevalent mutations and the NCBI Genome Browser, the researchers created a list of clade-specific mutations in the major pathogenesis proteins of SARS-CoV-2 and their protein sequences. They created two data sets: 1) wild type protein sequences - which were directly the ones from the Wuhan strain, and 2) Mutant Data Set - which consisted of the protein sequences carrying the mutations in them.
Researchers analyzed the physicochemical properties of the proteins. They discuss the secondary structure, accessible surface area, and intrinsic disorder of the protein post mutation in detail. All mutations involved structural changes in the protein, mostly abolishing specific structures such as helices and beta sheets in the proteins.
In this study, the ORF3a protein exhibits decreased disorderedness in its mutant form. This indicates a change in the structural conformation and rigidity of the protein. Also, a maximum change in accessible surface area is observed in S protein. Since the intrinsic disorder was observed to decrease significantly in ORF3a, the role of S protein's functional interaction along with ORF3a is also affected.
The researchers also predict the epitopes in the viral proteins. Epitopes elicit immune responses in the host. These may serve as potent vaccine candidates. Post mutation, they observe a suggestive change in binding efficiencies. This study predicts the possible drug binding sites, along with the druggability of these proteins. The conformational epitopes of B cell, T cell, MHC -I, and MHC –II alleles were also identified.
The authors note that any mutation leads to the structural and functional change in the protein - impairing protein stability.
Using a binary scoring scheme, the authors identify L84S mutation in ORF8 as the most disruptive of the virus's mutations.
Most of us in this pandemic are asymptomatic carriers. With no advanced and assured way of identifying the asymptomatic carriers, there is a high possibility of the successful escape of mutations in the virus's genome. It is imperative to study these mutations and understand its possible impact on infection and response to vaccines and therapeutic agents. This study analyses the effect of prevalent mutations in the SARS-CoV-2 proteins that are primarily related to pathogenesis in humans. The researchers discuss the effects of those mutations on the structural stability of the proteins.
On a positive note, the authors observe 'that the virus is under the influence of an evolutionary phenomenon similar to Muller's ratchet where the continuous accumulation of these mutations makes the virus less virulent, which may also explain the reduction in fatality rates worldwide.'
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.
- Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins, Souradip Basu, Suparba Mukhopadhyay, Rajdeep Das, Sarmishta Mukhopadhyay, Pankaj Kumar Singh, Sayak Ganguli, bioRxiv 2020.10.20.347021; DOI: https://doi.org/10.1101/2020.10.20.347021