Molecular Epidemiology of SARS-CoV-2 in Greece Reveals Low Rates of Onward Virus Transmission after Lifting of Travel Restrictions Based on Risk Assessment during Summer 2020

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1. Version published to 10.1128/msphere.00180-21

   Jun 30, 2021
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.01.31.21250868: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The study was approved by the Ethics and Bioethics Committee of the Medical School, of the National and Kapodistrian University of Athens (protocol #300/25-05-2020).
   Randomization	Our data consisted of: i) five datasets of 3,000 randomly selected sequences until September 30, 2020 sampled from the GISAID database plus the best hits identified by a BLAST search using as queries all sequences of our study population against the GISAID database sampled at the same time period, and ii) a dataset of 15,000 randomly selected sequences sampled until September 30, 2020 plus the best hits identified by a BLAST search.
   Blinding	not detected.
   Power Analysis	not detected.
   Se…

   SciScore for 10.1101/2021.01.31.21250868: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The study was approved by the Ethics and Bioethics Committee of the Medical School, of the National and Kapodistrian University of Athens (protocol #300/25-05-2020).
   Randomization	Our data consisted of: i) five datasets of 3,000 randomly selected sequences until September 30, 2020 sampled from the GISAID database plus the best hits identified by a BLAST search using as queries all sequences of our study population against the GISAID database sampled at the same time period, and ii) a dataset of 15,000 randomly selected sequences sampled until September 30, 2020 plus the best hits identified by a BLAST search.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   The quality of FASTQ files was assessed using FastQC (version 0.11.9) [17].	FastQC suggested: (FastQC, RRID:SCR_014583)
   Adapter and poor-quality base trimming were performed with TrimGalore (version 0.6.6) [18], which also deploys Cutadapt (version 2.8) [19], keeping reads with length of at least 50 bp.	TrimGalore suggested: None
   Subsequently, the remaining paired short reads were normalized to 100x uniform coverage using BBnorm from the BBmap suite [20] and then subjected to guided de novo genome assembly using SPAdes (version 3.14.1) [21] with the --careful option.	BBmap suggested: (BBmap, RRID:SCR_016965) SPAdes suggested: (SPAdes, RRID:SCR_000131)
   The quality of the assemblies was assessed using QUAST (version 5.0.2) [23].	QUAST suggested: (QUAST, RRID:SCR_001228)
   The short reads were also mapped to the SARS-CoV-2 genome retrieved from UCSC using BWA (version 0.7.17) [25] in order to further assess the quality of the virus sequencing and visually inspect coverage and potential virus mutations.	BWA suggested: (BWA, RRID:SCR_010910)
   BLAST reported pairwise 20,517 hits matching at different regions.	BLAST suggested: (BLASTX, RRID:SCR_001653)
   Multiple sequence alignments were performed using the multithreaded version of MAFFT program [26].	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Phylogenetic analyses were carried out by the maximum likelihood (ML) method using the IQ-Tree (version 2.1.1) [27] and the FastTree (version 2) programs [28].	IQ-Tree suggested: (IQ-TREE, RRID:SCR_017254)
   The resulting phylogenies were visualized and annotated by the FigTree (version1.4) and the Dendroscope (version 3.7.2) programs.	FigTree suggested: (FigTree, RRID:SCR_008515)
   Phylogeographic analysis was performed on the ML tree reconstructed by phylogenetic analysis conducted on the FastTree program in the previous step of analysis.	FastTree suggested: (FastTree, RRID:SCR_015501)
   Hypothesis testing was performed by character reconstruction using the criterion of parsimony on the Mesquite (version 3.61) program [30].	Mesquite suggested: (Mesquite, RRID:SCR_017994)

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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 study has several limitations. Our sampling was not representative and was not performed across Greece. On the other hand, as discussed above, our analysis was based on 389 full-length genomes collected at different time points from Attica, suggesting that our results reflect a large proportion of the population. Moreover, our study data included a dense sample of diagnosed cases during the first and second phases; sampling proportion was lower in the third period, but this was due to the enhanced testing performed over time. Regarding the putative limitation of non-sampling from tourist destinations during the third phase, if SARS-CoV-2 was continuously transmitted from viral lineages imported during the summertime in Greece, we would be able to detect them in Attica residents, a large proportion of whom visit many different places in Greece during the summertime. Our findings suggest that imported cases did not contribute substantially to SARS-CoV-2 local spread between July and September 2020. Importantly, our results on the effects of virus importation correlated with those estimated from surveillance data, thus enhancing the robustness of our findings. We should note that our findings are relevant to the summer period in the Mediterranean region and may not be generalizable for areas with different climatic conditions. In conclusion, our molecular epidemiology study showed that the estimated proportion of imported cases during the first pandemic wave in Greece was 41...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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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 10.1101/2021.01.31.21250868v1 on medRxiv

   Feb 2, 2021