One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar

Abstract

Qatar, a country with a strong health system and a diverse population consisting mainly of expatriate residents, has experienced two large waves of COVID-19 outbreak. 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 of mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. These findings raise the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor the SARS-CoV-2 profile and re-emergence in Qatar.

Keywords: COVID19; N481K; Qatar; SARS-CoV-2; variant analysis.

Figure 1

Demographics and virological characteristics of Qatar study cohort. (A) Demographics, swab collection dates and virological parameters of the study cohort are demonstrated in an alluvial diagram with the display of relatedness among features of each two neighboring nodes. (B) SARS-CoV-2 major lineages distribution over the one-year study period from March 2020 to March 2021. Arrows represent when the designated lineages were reported worldwide. The white line demonstrates the daily COVID19 positive cases in Qatar. The international and national restrictions implemented by the country is presented below the stacked area chart.

Figure 2

Whole genome SARS-COV-2 mutation analysis. Mutations with at least 1% frequency are presented in bars and their evolution during the studied one-year period is presented in the heat map. SARS-COV-2 gene annotation is shown in colors. ORF, Open reading frame; S, Spike; E, Envelope; N, Nucleocapsid.

Figure 3

SARS-COV-2 lineage specific mutation analysis. Mutation in highly prevalent lineages are presented based on their prevalence. In solid lines, mutations that were detected at a frequency of at least 1% from the study cohort. Mutation in dotted lines did not pass the 1% cutoff in the study cohort but were present in at least 1% of the sequences in a particular lineage. The grey area represents the evolution of each lineage across the studied period. Variant of concern are identified with asterisk.

Figure 4

Maximum likelihood tree of high-coverage SARS-CoV-2 genomes included in this study. Phylogenetic tree was generated using 1,452 high-coverage genomes (>90%) sequenced during the period from March 2020 to March 2021. SARS-CoV-2 lineages are indicated in colors as follows: A in light green, B in light blue, B.1 in dark green, B.1.1 in grey, B.40 in in dark blue, B.1.1.75 in light brown, B.1.1.7 in bright red and B.1.351 in yellow. All other lineages are colored in black.

Figure 5

Maximum likelihood trees of SARS-CoV-2 variants of concern detected in this cohort. Phylogenetic tree of B.1.1.7 genomes (A) and B.1.351 genomes (B) were generated using 134 and 112 local sequences, respectively. Global genomes representative of the two clades with collection dates from November 2020 to March 2021 were included in the phylogenetic tress. Global genomes are indicated in black, local genomes are colored in blue, and imported samples are colored in yellow. The first genome detected locally is colored in red.