SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic
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Abstract
Objectives
Pakistan has a high infectious disease burden with about 265,000 reported cases of COVID-19. We investigated the genomic diversity of SARS-CoV-2 strains and present the first data on viruses circulating in the country.
Methods
We performed whole-genome sequencing and data analysis of SARS-CoV-2 eleven strains isolated in March and May.
Results
Strains from travelers clustered with those from China, Saudi Arabia, India, USA and Australia. Five of eight SARS-CoV-2 strains were GH clade with Spike glycoprotein D614G, Ns3 gene Q57H, and RNA dependent RNA polymerase (RdRp) P4715L mutations. Two were S (ORF8 L84S and N S202N) and three were L clade and one was an I clade strain. One GH and one L strain each displayed Orf1ab L3606F indicating further evolutionary transitions.
Conclusions
This data reveals SARS-CoV-2 strains of L, G, S and I have been circulating in Pakistan from March, at the start of the pandemic. It indicates viral diversity regarding infection in this populous region. Continuing molecular genomic surveillance of SARS-CoV-2 in the context of disease severity will be important to understand virus transmission patterns and host related determinants of COVID-19 in Pakistan.
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SciScore for 10.1101/2020.08.04.234153: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Ethical approval: This study was approved by the Ethical Review Committee at the Aga Khan University (AKU), Karachi, Pakistan. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Diagnostic testing for SARS-CoV-2: Nasopharyngeal swab specimens were tested for SARS-CoV-2 by reverse transcription (RT) polymerase chain reaction (PCR) at the Section of Molecular Pathology, Clinical Laboratory, Clinical Laboratorysuggested: NoneVariant calling and Phylogenetic analysis: FASTQ files were aligned to the SARS-CoV-2 virus reference genome Wuhan-1 … SciScore for 10.1101/2020.08.04.234153: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Ethical approval: This study was approved by the Ethical Review Committee at the Aga Khan University (AKU), Karachi, Pakistan. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Diagnostic testing for SARS-CoV-2: Nasopharyngeal swab specimens were tested for SARS-CoV-2 by reverse transcription (RT) polymerase chain reaction (PCR) at the Section of Molecular Pathology, Clinical Laboratory, Clinical Laboratorysuggested: NoneVariant calling and Phylogenetic analysis: FASTQ files were aligned to the SARS-CoV-2 virus reference genome Wuhan-1 (NC_045512.2) by BWA (13). BWAsuggested: (BWA, RRID:SCR_010910)PICARD tools (http://broadinstitute.github.io/picard/) were used to remove redundant alignments and calculating alignment statistics. PICARDsuggested: (Picard, RRID:SCR_006525)Variants were identified by Genome Analysis Toolkit (GATK) (14). Genome Analysis Toolkitsuggested: NoneGATKsuggested: (GATK, RRID:SCR_001876)The MSA was subsequently used to generate a Maximum Likelihood (ML) phylogenetic tree using PhyML 3.0 (http://www.atgc-montpellier.fr/phyml/) with a GTR-based nucleotide substitution model and aLRT SH-Like branch support. PhyMLsuggested: (PhyML, RRID:SCR_014629)The tree was visualized and edited in Figtree software (http://tree.bio.ed.ac.uk/software/figtree/). Figtreesuggested: (FigTree, RRID:SCR_008515)The mean and individual pairwise distance between 7 SARS-CoV-2 sequences from our study and 3 previously deposited Pakistani SARS-CoV-2 sequences was calculated using MEGA 7 (18). MEGAsuggested: (Mega BLAST, RRID:SCR_011920)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.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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