Method for Analysing Protein Structure of SARS-COV-2 M Protein for Possible Clues Regarding Virion Stability, Longevity and Transmission

Background

The SARS-CoV-2 Novel corona virus has been the cause of a worldwide pandemic in 2020. The novel strain, originating from Wuhan, China has, as of the 25^th April World Health Organization report, infected over 2.7 million people and led to the deaths of over 187,000 individuals worldwide (Coronavirus disease (COVID-2019) situation report-96, 2020). It has led to considerable disruptions in the economic and psychological welfare of the world population, on top of the continuously increasing loss of life (Chen et al., 2020). Efforts at identifying possible solutions to combating the virus have thus far ranged from basic precautionary awareness campaigns to the suggestions of nucleotide based drugs currently being tested for other diseases as possible therapeutic agents (Martinez, 2020). The genome of the SARS-CoV-2 novel coronavirus has been decoded and its expected proteome already established (RefSeq ID: NC_045512.2). However up until this point, to the best of our knowledge not much progress has been made in terms of identifying unique molecular features that are exclusive to this strain of the Coronavirus. Hence, in this study we made an attempt at studying the protein sequences of the major SARS-CoV-2 architectural protein in order to identify unique advantageous features. We chose to focus our efforts on the M Protein as it is the most abundant protein in the viral nucleocapsid and is believed to be responsible for maintaining the virion in its characteristic shape (Nal, 2005). This forms the basis of our investigative rationale; is there any particular feature that aids the spread of this strain. The percentage of infected patients who have died from this virus has been estimated to be approximately 6.9% percent as of this writing (WHO, 2020b). Furthermore the primary susceptible groups are the immunocompromised. This leads us to believe that the primary focus needs to be on the mechanism of spreading, as the rapid rates at which this strain has infected communities across the world has arguably been its most dangerous aspect. The coronaviruses are known to contain four main structural proteins, the S, M, E, and N proteins (Fehr and Perlman, 2015). The S or the spike protein is responsible for gaining entry into the endoplasmic reticulum following infection (Delmas and Hurst, 2009; Beniac et al., 2006). The N protein resides inside the nucleocapsid and is an RNA binding protein (Chang et al., 2005; Hurst et al., 2009). The M and E proteins are both transmembrane proteins. The M protein, a 3 pass transmembrane protein is particularly significant as it is believed to be responsible for maintaining and giving the virion its shape (Armstrong et al., 1984). The reasoning behind developing this protocol lies in the similarity in structure and function between SARS-CoV and SARS-CoV-2. The former was shown to be ineffective at transmission, thus limiting the epidemic caused by it (Peiris et al., 2003). As virion structure is a vital factor in determining how long a virus can survive free of a host and thus spread, we believe a comparison between the key architectural protein within the two viruses can provide important clues towards understanding SARS-CoV-2’s more efficient mechanism of transmission.