Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CLpro targeting repurposed drug candidates

Abstract

Background Severe acute respiratory syndrome (SARS) has been initiating pandemics since the beginning of the century. In December 2019, the world was hit again by a devastating SARS episode that has so far infected almost four million individuals worldwide, with over 200,000 fatalities having already occurred by mid-April 2020, and the infection rate continues to grow exponentially. SARS coronavirus 2 (SARS-CoV-2) is a single stranded RNA pathogen which is characterised by a high mutation rate. It is vital to explore the mutagenic capability of the viral genome that enables SARS-CoV-2 to rapidly jump from one host immunity to another and adapt to the genetic pool of local populations. Methods For this study, we analysed 2301 complete viral sequences reported from SARS-CoV-2 infected patients. SARS-CoV-2 host genomes were collected from The Global Initiative on Sharing All Influenza Data (GISAID) database containing 9 genomes from pangolin-CoV origin and 3 genomes from bat-CoV origin, Wuhan SARS-CoV2 reference genome was collected from GeneBank database. The Multiple sequence alignment tool, Clustal Omega was used for genomic sequence alignment. The viral replicating enzyme, 3-chymotrypsin-like cysteine protease (3CLpro) that plays a key role in its pathogenicity was used to assess its affinity with pharmacological inhibitors and repurposed drugs such as anti-viral flavones, biflavanoids, anti-malarial drugs and vitamin supplements. Results Our results demonstrate that bat-CoV shares > 96% similar identity, while pangolin-CoV shares 85.98% identity with Wuhan SARS-CoV-2 genome. This in-depth analysis has identified 12 novel recurrent mutations in South American and African viral genomes out of which 3 were unique in South America, 4 unique in Africa and 5 were present in-patient isolates from both populations. Using state of the art in silico approaches, this study further investigates the interaction of repurposed drugs with the SARS-CoV-2 3CLpro enzyme, which regulates viral replication machinery. Conclusions Overall, this study provides insights into the evolving mutations, with implications to understand viral pathogenicity and possible new strategies for repurposing compounds to combat the nCovid-19 pandemic.

Stability of SARS-CoV-2 phylogenies

“…Because many tests of recombination assume that all mutations can only occur once at each site, recurrent mutation and systematic errors can confound signatures of recombination [7,27,36]. Finally, recurrent mutations have been identified as a possible signature of elevated mutation rates or natural selection in SARS-CoV-2 [9,14,24,26,27,30,34,36,42], but some of these apparent instances of selection may be due to systematic errors in the sequences. Confusion about recurrent mutations and recombination affects our understanding of host response and influences our decisions about which viral molecular processes or specific immune epitopes we might want to target in vaccine development.…”

“…Extremely rapid whole-genome sequencing has enabled nearly real-time tracing of the evolution of the SARS-CoV-2 pandemic [1][2][3][4][5][6]. By leveraging sequence data produced by labs throughout the world, researchers can trace the transmission of the virus across human populations [7][8][9][10][11][12][13][14][15]. Typically, viral evolution is encapsulated by a phylogenetic tree relating all of the virus samples in a large set to one another [6,[16][17][18][19][20].…”

The Pathophysiology, Diagnosis and Treatment of Corona Virus Disease 2019 (COVID-19)

“…One study identified 12 novel recurrent mutations in South American and African viral genomes, among which 3 were exclusively in South America, 4 in Africa and 5 were present in-patient isolates from both populations [11].…”

“…Using all accessible genomic information, the phylogenetic tree investigation has ascertained the high sequence similarity (> 99%) between all the existing sequenced SARS-CoV-2 genomes, with the closest as Bat coronavirus (BCoV) sequence resembling 96.2% sequence identity [ 10 ], while pangolin-CoV shares 85.98% identity [ 11 ], authenticating the conception of a zoonotic origin of 2019-nCoV [ 10 ]. Other studies including full genome sequencing of strains from China, Japan, USA, Finland and Korea showed more than 99.9% sequence homology [ 12 , 13 ].…”

World-wide Sequence Variant and Non-synonymous Amino Acid Substitution Signature in SARS-COV-2 Structural Proteins

“…Several other studies on SARS-COV-2 have shown that a mutation can trigger protein structure alteration, dynamics and function while binding with human receptor protein (ACE2) [39,40,41,42]. Therefore, these studies are important to understand the clinical presentation and spread of the disease, and also useful for antiviral drug design [43,44].…”