Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh
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Abstract
Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13,324X. We identified 564 high-quality SARS-CoV-2 variants, out of which 15 are novel. A total of 18 variants mapped to RT-PCR primer/probe sites, and 4 variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (94%), while 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.
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SciScore for 10.1101/2021.01.22.427775: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The study is in compliance with relevant laws and institutional guidelines and in accordance with the ethical standards of the Declaration of Helsinki and approved by Institutional Human Ethics Committee (RC.No.03/IHC/kmcknl/2020, dated 03/08/2020).
Consent: The patient consent has been waived by the ethics committee.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 Briefly, raw FASTQ files underwent quality control with average Phred score quality of Q30 and read length of 30 bps with adapter trimming using Trimmomatic (version 0.39)6. P…SciScore for 10.1101/2021.01.22.427775: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The study is in compliance with relevant laws and institutional guidelines and in accordance with the ethical standards of the Declaration of Helsinki and approved by Institutional Human Ethics Committee (RC.No.03/IHC/kmcknl/2020, dated 03/08/2020).
Consent: The patient consent has been waived by the ethics committee.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 Briefly, raw FASTQ files underwent quality control with average Phred score quality of Q30 and read length of 30 bps with adapter trimming using Trimmomatic (version 0.39)6. Phredsuggested: (Phred, RRID:SCR_001017)Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)The primer and probe sequences were mapped to the Wuhan-Hu-1 reference genome using BLAST to get their genomic loci. BLASTsuggested: (BLASTX, RRID:SCR_001653)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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