Sequence analysis for SNP detection and phylogenetic reconstruction of SARS-cov-2 isolated from Nigerian COVID-19 cases
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SciScore for 10.1101/2020.09.25.310078: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
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Software and Algorithms Sentences Resources The genomes were initially aligned with MAUVE to check for large scale genomic changes including large deletions, gene inversion, and genome rearrangements. MAUVEsuggested: (Mauve, RRID:SCR_012852)Then, the sequences were re-aligned in MAFFT (Fig.1) to produce aligned sequences that were fed into DnaSP for SNP and haplotype analysis and subsequently into Jalview 2.11.1.0 for visualization and automatic determination of allelic frequency of SNPs. DnaSPsuggested: (DnaSP, RRID:SCR_003067)Jalviewsuggested: (Jalview, RRID:SCR_006459)Phylogenetic Analysis: Maximum likelihood phylogenetic tree … SciScore for 10.1101/2020.09.25.310078: (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 The genomes were initially aligned with MAUVE to check for large scale genomic changes including large deletions, gene inversion, and genome rearrangements. MAUVEsuggested: (Mauve, RRID:SCR_012852)Then, the sequences were re-aligned in MAFFT (Fig.1) to produce aligned sequences that were fed into DnaSP for SNP and haplotype analysis and subsequently into Jalview 2.11.1.0 for visualization and automatic determination of allelic frequency of SNPs. DnaSPsuggested: (DnaSP, RRID:SCR_003067)Jalviewsuggested: (Jalview, RRID:SCR_006459)Phylogenetic Analysis: Maximum likelihood phylogenetic tree construction was implemented in MEGA X using sequences that had been aligned by MAFFT employing Tamura-Nei evolutionary model under assumption of uniform nucleotide substitution [21, 22]. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)MAFFTsuggested: (MAFFT, RRID:SCR_011811)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:A limitation of this study is the small sample size of eighteen genome sequences used in this study, which we consider too small for detection of all SARS-CoV-2 SNPs in Nigeria. In subsequent studies, it will be of interest to see if distribution of SNPs and conserved regions identified in this study are peculiar to Nigerian SARS-CoV-2 or have complete overlap with genomes of SARS-CoV-2 found elsewhere. If there are regions of non-overlap, any attempt to produce testing kits with high sensitivity for Nigeria’s COVID-19 cases should take note of the conserved regions and SNP distribution in the genomes of SARS-CoV-2 detected in this study. The frequency of SNPs observed in the Nigerian SARS-CoV-2 genome is higher than twice the frequency of SNPs in human genome which is generally taken to be 1 SNP per 1000 bps. The UTRs, especially 3’UTR, are mutation hot spots in Nigerian SARS-CoV-2 genome. This is expected because UTRs, unlike coding sequences, are generally under more relaxed or neutral selection pressure which allow mutations to accumulate at a higher rate in that region [25]. Relatively high SNP densities were also recorded in some of the coding regions of Nigerian SARS-CoV-2. An example is ORF 10 region with a SNP density of 8.55 SNPs/1000 nts. Although coronaviridae have proofreading capability due to their exonuclease activity during nucleotide replication, mutation rate of SARS-CoV-2 was estimated at ∼6 × 10− 4 nucleotides/genome/year with the capacity to mutate durin...
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