Host range projection of SARS-CoV-2: South Asia perspective
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Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causing agent of Coronavirus Disease-2019 (COVID-19), is likely to be originated from bat and transmitted through intermediate hosts. However, the immediate source species of SARS-CoV-2 has not yet been confirmed. Here, we used diversity analysis of the angiotensin I converting enzyme 2 (ACE2) that serves as cellular receptor for SARS-CoV-2 and transmembrane protease serine 2 (TMPRSS2), which has been proved to be utilized by SARS-CoV-2 for spike protein priming. We also simulated the structure of receptor binding domain of SARS-CoV-2 spike protein (SARS-CoV-2 S RBD) with the ACE2s to investigate their binding affinity to determine the potential intermediate animal hosts that could spread the SARS-CoV-2 virus to humans in South Asia. We identified cow, buffalo, goat and sheep, which are predominant species in the household farming system in South Asia that can potentially be infected by SARS-CoV-2. All the bird species studied along with rat and mouse were considered less potential to interact with SARS-CoV-2. The interaction interfaces of SARS-CoV-2 S RBD and ACE2 protein complex suggests pangolin as a potential intermediate host in SARS-CoV-2. Our results provide a valuable resource for the identification of potential hosts for SARS-CoV-2 in South Asia and henceforth reduce the opportunity for a future outbreak of COVID-19.
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SciScore for 10.1101/2020.09.30.320242: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Multiple comparisons were conducted using ClustalW multiple sequence alignment program incorporated in MEGA□X. ClustalWsuggested: (ClustalW, RRID:SCR_017277)MEGA□Xsuggested: NoneHomology-based structure simulation of ACE2□RBD complex: The recently solved crystal structure of SARS-CoV-2 S RBD12 bound to the cell receptor ACE2 was used as template (PDB: 6M0J) for homology modeling to simulate the interaction interfaces of SARS-COV-2 S RBD and ACE2 of human, pangolin, intermediate horseshoe bat, cow, goat, cat and dog using MODELLER28 incorporated in Chimera software version 1.14. Chimerasugges…SciScore for 10.1101/2020.09.30.320242: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Multiple comparisons were conducted using ClustalW multiple sequence alignment program incorporated in MEGA□X. ClustalWsuggested: (ClustalW, RRID:SCR_017277)MEGA□Xsuggested: NoneHomology-based structure simulation of ACE2□RBD complex: The recently solved crystal structure of SARS-CoV-2 S RBD12 bound to the cell receptor ACE2 was used as template (PDB: 6M0J) for homology modeling to simulate the interaction interfaces of SARS-COV-2 S RBD and ACE2 of human, pangolin, intermediate horseshoe bat, cow, goat, cat and dog using MODELLER28 incorporated in Chimera software version 1.14. Chimerasuggested: (Chimera, RRID:SCR_002959)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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