Abstract
Coronavirus disease – 2019 (COVID-19) pandemic, due to severe acute respiratory syndrome–coronavirus-2 (SARS-CoV-2), is posing a severe bio threat to the entire world. Nucleocapsids of SARS-CoV-2 and the related viruses were studied for gene and amino acid sequence homologies. In this study, we established similarities and differences in nucleocapsids in SARS-CoV-2, severe acute respiratory syndrome – coronavirus-1 (SARS-CoV-1), bat coronavirus (bat-CoV) and Middle East respiratory syndrome – coronavirus (MERS-CoV). We conducted a detailed analysis of the nucleocapsid protein amino acid and gene sequence encoding it, found in various coronavirus strains. After thoroughly screening the different nucleocapsids, we observed a close molecular homology between SARS-CoV-1 and SARS-CoV-2. More than 95% sequence similarity was observed between the two SARS-CoV strains. Bat-CoV and SARS-CoV-2 showed 92% sequence similarity. MERS-CoV and SARS-CoV-2 nucleocapsid analysis indicated only 65% identity. Molecular characterization of nucleocapsids from various coronaviruses revealed that SARS-CoV 2 is more related to SARS-CoV 1 and bat-CoV. SARS-CoV 2 exhibited less resemblance with MERS-CoV. SARS-CoV 2 showed less similarity to MERS-CoV. Thus, either SARS-CoV-1 or bat-CoV may be the source of SARS-CoV-2 evolution. Moreover, the existing differences in nucleocapsid molecular structures in SARS-CoV-2 make this virus more virulent and highly infectious, which means that the non-identical SARS-CoV-2 genes (which are absent in SARS-CoV-1 and bat-CoV) are responsible for COVID-19 severity. We observed that SARS-CoV-2 nucleocapsid from different locations varied in amino acid sequences. This revealed that there are many SARS-CoV-2 subtypes/subsets currently circulating globally. This study will help to develop antiviral vaccine and drugs, study viral replication and immunopathogenesis, and synthesize monoclonal antibodies that can be used for precise COVID-19 diagnosis, without false-positive/false-negative results.
Highlights
Coronaviruses are a relatively large (125 nm), diverse group of RNA viruses infecting many mammals, amphibians, reptiles, and birds[1,2]
When the nucleocapsids of SARS-CoV-2, SARS-CoV-1, bat coronavirus, and MERS-CoV amino acid sequences were analyzed, we found 95% homology existing between SARS-CoV-2 and SARS-CoV-1 (Fig. 1, Fig. 2)
Additional to the above were analyzed, we found that SARS-CoV-1 and bat coronavirus have close similarity (96%) with SARS-CoV-2
Summary
Coronaviruses are a relatively large (125 nm), diverse group of RNA viruses infecting many mammals, amphibians, reptiles, and birds[1,2]. Recent case studies have revealed that many patients with coronavirus disease-2019 (COVID-19) have died of myocardial infarction, stroke, and renal failure[11,12,13] This suggests that after viremia, SARS-CoV-2, in addition to severe lung infection, can infect other body sites. Coronavirus possesses a nucleocapsid (N) protein, which is very important for its replication, antigenesis, pathogenesis, virulence, infection and, dissemination[14]. We analyzed the molecular composition and amino acid sequence of N present in SARS-CoV-2 and other related viruses like SARSCoV-1, bat-CoV, and Middle East respiratory syndrome- coronavirus (MERS-CoV) This will help virologists to study viral replication, viral-host immunopathogenesis, and vaccine development to combat the current COVID-19 pandemic. This study emphasizes and suggests ways to contain and combat COVID-19
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