Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

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1. Version published to 10.1126/science.abb9263

   Jul 31, 2020
2. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.03.27.20044925: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Ethics Statement: Clinical specimens were processed at the University of California San Francisco (UCSF) under protocols approved by the UCSF Institutional Review Board (protocol no. 10-01116, 11-05519).
   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
   Sequencing libraries were then sequenced on MiSeq, Nextseq, or HiSeq 1500 (Illumina Inc., San Diego, USA) as 1×150 single-end or 2×150 paired-end reads.	MiSeq suggested: (A5-miseq, RRID:SCR_012148)
   Genome assembly and consensus generation: Raw reads were first screened via BLASTn (BLAST+ …

   SciScore for 10.1101/2020.03.27.20044925: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Ethics Statement: Clinical specimens were processed at the University of California San Francisco (UCSF) under protocols approved by the UCSF Institutional Review Board (protocol no. 10-01116, 11-05519).
   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
   Sequencing libraries were then sequenced on MiSeq, Nextseq, or HiSeq 1500 (Illumina Inc., San Diego, USA) as 1×150 single-end or 2×150 paired-end reads.	MiSeq suggested: (A5-miseq, RRID:SCR_012148)
   Genome assembly and consensus generation: Raw reads were first screened via BLASTn (BLAST+ package 2.9.0) (23) for alignment to reference strain NC_045512.	BLASTn suggested: (BLASTN, RRID:SCR_001598) BLAST+ suggested: (Japan Bioinformatics, RRID:SCR_012250)
   They were then aligned to the reference with LASTZ version 1.04.03.	LASTZ suggested: (LASTZ, RRID:SCR_018556)
   SARS-CoV-2 reads were trimmed using Geneious version 11.1.3 by removal of 13 nucleotides (nt) (the length of the MSSPE primer) and low-quality reads from the ends, followed by removal of duplicate reads.	Geneious suggested: (Geneious, RRID:SCR_010519)
   Phylogenetic analysis and genomic comparison: Sequences were aligned using MAFFT v7.427 (24) under default settings and multiple sequence alignments were manually corrected.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Phylogenetic trees were constructed in PhyML v3.3 (25) under an HKY+Γ4 substitution model (26, 27).	PhyML suggested: (PhyML, RRID:SCR_014629)
   The location of SNPs and gaps were extracted from alignments using a custom Python script and visualized using a custom R-script.	Python suggested: (IPython, RRID:SCR_001658)
   Submission of the genomes and raw sequence data to NIH GenBank and Sequence Read Archive (SRA) is pending.	Sequence Read Archive suggested: (DDBJ Sequence Read Archive, RRID:SCR_001370)

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   Our epidemiological and genomic survey of SARS-CoV-2 has several limitations. First, this initial analysis represents relatively sparse sampling of cases. Undersampling of virus genomes is due in part to the high proportion of cases (80%) with asymptomatic or mild disease (3, 4, 20) and limited diagnostic testing for COVID-19 infection to date in California and throughout the United States. Second, the majority of samples analyzed were obtained from public health laboratories and thus may not be representative of the general population. Finally, phylogenetic clustering of viruses from different locations, such as Washington State and California in the same clade, does not prove directionality of spread. Despite this, our study shows that more robust insights into COVID-19 transmission are achievable if virus genomic diversity is combined and jointly interpreted with detailed epidemiological case data. Public health containment measures such as prompt isolation and contact tracing, as performed in the Solano County and Santa Clara County clusters, become more difficult to maintain once a lineage becomes established in the community. Our data suggest concerning trends in this direction, such as the association between the WA1 lineage and community-acquired COVID-19 cases in several counties of Northern California, travel-associated introduction of SARS-CoV-2 into the San Francisco Bay Area from New York state, and a virus from the lineage associated with a Santa Clara County cl...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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3. 

   Version published to 10.1101/2020.03.27.20044925v1 on medRxiv

   Mar 30, 2020