Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

Article activity feed

1. Version published to 10.1016/j.ijid.2020.11.128

   Feb 1, 2021
2. 

   ScreenIT

   Jun 9, 2020

   SciScore for 10.1101/2020.05.29.20116376: (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
   SARS-CoV-2 whole genome amplification by multiplex PCR was carried out using primers designed on Primal Scheme (http://primal.zibraproject.org/) to generate 400bp amplicons with an overlap of 70bp that Remnant samples from nasopharyngeal and oropharyngeal swabs collected from symptomatic patients, were used for SARS-CoV-2 WGS.	SARS-CoV-2 suggested: (Active Motif Cat# 91351, RRID:AB_2847848) WGS suggested: None
   Bioinformatics assembly of genomes: Raw reads coming from both Nanopore and Illumina sequencing were assembled using Genome Detective 1·126 (https://www.genomedetective.com/) and the …

   SciScore for 10.1101/2020.05.29.20116376: (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
   SARS-CoV-2 whole genome amplification by multiplex PCR was carried out using primers designed on Primal Scheme (http://primal.zibraproject.org/) to generate 400bp amplicons with an overlap of 70bp that Remnant samples from nasopharyngeal and oropharyngeal swabs collected from symptomatic patients, were used for SARS-CoV-2 WGS.	SARS-CoV-2 suggested: (Active Motif Cat# 91351, RRID:AB_2847848) WGS suggested: None
   Bioinformatics assembly of genomes: Raw reads coming from both Nanopore and Illumina sequencing were assembled using Genome Detective 1·126 (https://www.genomedetective.com/) and the Coronavirus Typing Tool (26, 27).	Nanopore suggested: None
   All mutations were confirmed visually with bam files using Geneious software (Biomatters Ltd, New Zealand).	Geneious suggested: (Geneious, RRID:SCR_010519)
   The resulting phylogeny was viewed and annotated in FigTree and ggtree.	FigTree suggested: (FigTree, RRID:SCR_008515)
   To infer support for the splits in this tree topology we inferred an additional 100 bootstrap trees in IQ-Tree under the same model parameters as NextStrain.	IQ-Tree suggested: (IQ-TREE, RRID:SCR_017254)
   In short, sequences were aligned in mafft v7.313 and visualized and manually edited in Geneious software (Biomatters Ltd, New Zealand) as previously described.	mafft suggested: (MAFFT, RRID:SCR_011811)
   Resulting tree topologies were analyzed in TempEst software suite for temporal clock signal (Supplementary Figure S4).	TempEst suggested: (TempEst, RRID:SCR_017304)
   Coalescent molecular clock analyses were performed in BEAST v1·8.	BEAST suggested: (BEAST, RRID:SCR_010228)

   ---

   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: We detected the following sentences addressing limitations in the study:

   This paper has some important limitations. The first is related to estimation of R0 from COVID-19 a limited number of deaths in a heterogeneous epidemic. The second is a lack of well set up genomics laboratories that can sequence the virus in Africa. This is also amplified by the difficulty of acquiring reagents that are in high demand, coupled with the disruption of air freight. It is therefore a high priority for our consortium, SANGS-COVID, to evaluate and share protocols among national laboratories in South Africa that could generate sequences of high-quality and capacitate our laboratories with the protocols and bioinformatics pipelines to properly investigate virus introduction and to validate the call of variants with a detailed and reliable bioinformatics system. SANGS-COVID is also working with the Africa Center for Disease Control (CDC) and the World Health Organization (WHO) to strengthen genomics surveillance in the African continent. In this paper, we provide an early analysis of COVID-19 pandemic in South Africa, showing very heterogeneuos epidemics in the different provinces. We also estiamted SARS-CoV-2 genetic diversity in KZN using the first twenty one genomes from some of the first cases in the country. We find that KZN had many distinct introductions of SARS-CoV-2, but also had early evidence of nosocomial transmission. The pandemic at the local level is still developing and the objective of SANGS-COVID is to clarify the dynamics of the epidemic in South A...

   ---

   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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2020.05.29.20116376v1 on medRxiv

   May 30, 2020