key: cord-0964557-5wli2dxz
authors: younes, M.; Hamze, K.; Osman, K. L.; Carter, D. P.; Pullan, S. T.; Caroll, M.; Vipond, R. T.; Mohamad, N.; nassar, h.; Ghaddar, M.; Makki, M.; Nguewa, P.; Abdel Sater, f.
title: B.1.1.7 became the dominant variant in Lebanon.
date: 2021-03-17
journal: nan
DOI: 10.1101/2021.03.17.21253782
sha: 2c35a92aa9d3faa80a78f3f471790624443df770
doc_id: 964557
cord_uid: 5wli2dxz

Recently, a new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) designated VOC 202012/01 (or B.1.1.7 lineage) has become highly prevalent in several countries, after first being described in the United Kingdom (UK). Its rate of transmission has been estimated to be increased compared to other lineages. In the present study, we show the emergence, dominance and the rapid spread of the B.1.1.7 lineage in Lebanon.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 17, 2021. ; https://doi.org/10.1101/2021.03.17.21253782 doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was, and remains, the most rapidly spreading emerging disease of the year. Recently, a new variant of this virus called SARS-CoV-2 VOC 202012/01 (or B.1.1.7) has been described in the United Kingdom (UK). 1 It has become highly prevalent in parts of the UK and is emerging in more than 50 countries. This variant was predicted to potentially be 50 to 70% more rapidly transmissible than other SARS-COV-2 variants circulating in the UK. 2 The analysis of sequences showed that the new variant had accumulated a large number of mutations that together caused 17 amino acid changes in viral proteins. This variant harbors eight mutations in the spike protein. One of spike mutations is the Δ69-70 deletion in the S1 N-terminal domain (NTD), which has been associated with decreased sensitivity to convalescent plasma. 3 Other mutations within the spike protein are Δ144, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H. While the others occur in other regions of the genome

Recently, the European CDC recommended that multi-target RT-PCR assays that included an S gene target affected by the deletions could be used as a signal for the presence of the Δ69-70 mutation to help track these mutant variants. 4 Multi-target RT-PCR tests using S gene regions impacted by the Δ69-70 mutation are quicker and cheaper than sequencing especially if sequencing capacity is limited. The Applied Biosystems™ TaqPath™ COVID-19 assay allows the detection of this mutation. 5 In a patient infected with a variant harboring the Δ69-70mutation, there will be an S gene "drop out". The sequencing of diagnostic PCR amplicon products from S gene dropout samples showed that the S gene target contained the 6-nucleotide deletion (21,765-21,770) encoding the Δ69-70 amino acid deletion within the amplicon. The authors inferred the S gene dropout must be due to a failure of the qPCR probe to bind as a result of the deletion . 6

On December 9, a local patient was diagnosed as COVID -19 positive by PCR using TaqPath 2019-nCoV real-time PCR kit. RDRP and N genes of SARS-COV-2 were detected with a Ct value 18 while S gene was not detected. Two days later, the same profile was detected in two further patients from the same family. The 3 samples were retested using Kylt® SARS-CoV-2 Complete RTU, . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. They imposed a countrywide lockdown to combat the spread of COVID-19. The study was conducted between December 9, 2020 and February 6, 2021. Nasopharyngeal swab samples were collected from 34,978 patients. 6,264 of patients were reported as positive.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 17, 2021. ; https://doi.org/10.1101/2021.03.17.21253782 doi: medRxiv preprint

To confirm the lineage present in these patient samples, genomic sequencing was performed on nine samples displaying the S-dropout, collected between 9/12/2020 and 8/01/2021. Samples were sequenced using the ARTIC network methodology (https://artic.network/) with the V3 amplicon scheme , V3-LoCost library prep method (Quick 2020) and consensus sequences were generated using the bioinformatics SOP (https://artic.network/ncov-2019/ncov2019-bioinformaticssop.html) in Nanopolish mode. 8, 9 Consensus sequences were assigned a lineage using pangolin . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted March 17, 2021. ; https://doi.org/10.1101/2021.03.17.21253782 doi: medRxiv preprint

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. medRxiv

Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom

Thermo Fisher's COVID-19 tests: designed with virus mutations in mind

Two-step strategy for the identification of SARS-CoV-2 variants co-occurring with spike deletion H69-V70

A Rapid and Low-Cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-Based RT-qPCR. medRxiv

Quick Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Josh Quick2020. nCoV-2019 sequencing protocol v3 (LoCost). protocols.io https://protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye; . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted March 17, 2021. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)The copyright holder for this preprint this version posted March 17, 2021. ; https://doi.org/10.1101/2021.03.17.21253782 doi: medRxiv preprint