Both simulation and sequencing data reveal coinfections with multiple SARS-CoV-2 variants in the COVID-19 pandemic
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SciScore for 10.1101/2021.09.06.459196: (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 samples were sequenced on the MinIon sequencing platform (Oxford Nanopore Technologies, U.K.) MinIonsuggested: (MinION, RRID:SCR_017985)By applying NanoFilt (version 1.7.0) [32], we performed data filtration on the raw fastq data with the following criteria: the read lengths should be longer than 100 bp after removing the adapter sequences overall quality of reads should be higher than 10. NanoFiltsuggested: (NanoFilt, RRID:SCR_016966)Mutation detection with Nanopore data: We aligned the filtered and segmented reads to the SARS-CoV-2 reference genome (MN908947.3) with Minimap2 by … SciScore for 10.1101/2021.09.06.459196: (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 samples were sequenced on the MinIon sequencing platform (Oxford Nanopore Technologies, U.K.) MinIonsuggested: (MinION, RRID:SCR_017985)By applying NanoFilt (version 1.7.0) [32], we performed data filtration on the raw fastq data with the following criteria: the read lengths should be longer than 100 bp after removing the adapter sequences overall quality of reads should be higher than 10. NanoFiltsuggested: (NanoFilt, RRID:SCR_016966)Mutation detection with Nanopore data: We aligned the filtered and segmented reads to the SARS-CoV-2 reference genome (MN908947.3) with Minimap2 by applying the default parameters for Oxford Nanopore reads [33]. Mutation detection with Nanoporesuggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Although the findings implied the coinfection of multiple SARS-CoV-2 variants in patients from the perspectives of algorithm derivation and mutation detection, this study still has several limitations. In the simulation, we assumed that the first submitted sequence was the source of all SARS-COV-2 variants. While, in the pandemic, the first infective SARS-COV-2 variant should emerge long before being discovered. The study by Giovanni Apolone et al. proposed that SARS-CoV-2 RBD-specific antibodies can already be detected in the serum samples of Italian cohorts collected in March 2019, indicating that the source variants of all currently sequenced variants should appear earlier before [24]. Determining the virus’s origin is difficult, so we chose an exact time point during the simulation, but it does not affect our conclusions on the coinfection of multiple variants in hosts. Moreover, there was no guarantee considering the quality of the viral variants submitted to GISAID, which might influence the accuracy and potential phylogenetic study. Last but not least, the discovered heterozygous SNPs need to be verified with biological duplication, and we should identify the coinfected viral lineages in the COVID-19 patients in future study. In conclusion, our study proposed a computational simulating approach to decipher the number of the coinfected variants, declared the coinfection of multiple SARS-CoV-2 variants in COVID-19 patients, and reported the increased coinfected variants ...
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.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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