One year of SARS-CoV-2: Genomic characterization of COVID-19 outbreak in Qatar

Abstract

The state of Qatar has emerged as a major transit hub connecting all parts of the globe, making it as a hotspot for infectious disease introduction and providing an ideal setting to monitor the emergence and spread of variants. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population's genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number in the mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. This raises the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor SARS-CoV-2 profile and re-emergence in Qatar.

Molecular epidemiology of SARS-CoV-2 in Cyprus

“…Similar studies have been reported from a plethora of countries around the world including the UK, Ireland, Russia, India, Qatar etc. [26,[33][34][35][36]. These studies provide valuable information on the routes of importation of new strains and the emergence of critical mutations that change key parameters such as transmissibility or virulence, as was recently highlighted by the discovery of the B.1.617 variant and its B.1.617.2 sub-lineage in India [37], which led to a surge of SARS-CoV-2 infections in Delhi.…”

BNT162b2 and mRNA-1273 COVID-19 vaccine effectiveness against the SARS-CoV-2 Delta variant in Qatar

“…Extended Data Figs. [1][2][3] show flowcharts depicting the selection of study populations to estimate effectiveness of BNT162b2 (Extended Data Fig. 1), mRNA-1273 vaccine (Extended Data Fig.…”

“…In comparing estimates for Beta to those for Delta, it must be noted that the median PCR diagnosis date was 15 April 2021 for Beta cases, but was 2 August 2021 for Delta cases. Beta dominated transmission earlier in the study, whereas Delta dominated transmission later in the study [1][2][3][4][5] . From 1 August 2021 to 7 September 2021, 83.6% of the RT-qPCR-genotyped cases were Delta cases (Methods).…”

“…A ppreciable community transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta (B.1.617.2) variant was first noted in Qatar by end of March 2021 (refs. [1][2][3] ). Although Delta incidence has increased along with a recent surge in cases and hovered at about 200 cases per day in the summer of 2021, it remains low compared to earlier variant incidences with no signal for an epidemic wave materializing as of 19 September 2021.…”

“…Delta dominance was, however, preceded by two large consecutive SARS-CoV-2 Alpha (B.1.1.7) and Beta (B.1.351) waves earlier in 2021 (refs. [1][2][3][4][5] ). The rapid scale-up of Coronavirus Disease 2019 (COVID-19) vaccination in Qatar may have impeded efficient Delta transmission.…”