Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
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Abstract
The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 % of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks.
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SciScore for 10.1101/2021.08.10.21261847: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization Samples: For this study a total of 905 SARS-CoV-2 positive samples were collected from Lebanon, selected at random from clinical diagnostic samples, to provide a representative view of regions within Lebanon as shown in Supplementary Figure 1. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The raw reads were demultiplexed using bcl2fastq (v2.20). bcl2fastqsuggested: (bcl2fastq , RRID:SCR_015058)Briefly, the reads had adapters trimmed with TrimGalore (Krueger [2016] 2020) and were aligned to the WuhanHu-1 reference genome (accession MN908947.3) using BWA-MEM (v0.7.17) … SciScore for 10.1101/2021.08.10.21261847: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization Samples: For this study a total of 905 SARS-CoV-2 positive samples were collected from Lebanon, selected at random from clinical diagnostic samples, to provide a representative view of regions within Lebanon as shown in Supplementary Figure 1. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The raw reads were demultiplexed using bcl2fastq (v2.20). bcl2fastqsuggested: (bcl2fastq , RRID:SCR_015058)Briefly, the reads had adapters trimmed with TrimGalore (Krueger [2016] 2020) and were aligned to the WuhanHu-1 reference genome (accession MN908947.3) using BWA-MEM (v0.7.17) (Li 2013); the ARTIC amplicons were trimmed and a consensus built using iVAR (v.1.3.0) (Grubaugh et al. 2019). BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
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).
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.
Results from scite Reference Check: We found no unreliable references.
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