Molecular epidemiology and genetic characterization of SARS-CoV-2 in Kuwait: A descriptive study

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been fatal to human health, affecting almost the entire world. Here we reported, for the first time, characterization of the genetic variants of SARS-CoV-2 circulating in Kuwait to understand their genetic diversity and monitor the accumulation of mutations over time. This study randomly enrolled 209 COVID-19 patients whose nasopharyngeal swabs were positive for SARS-CoV-2 between February 2020 and June 2021 using RT-PCR. The whole genomes of SARS-CoV-2 from the nasopharyngeal swabs were sequenced using the Oxford Nanopore sequencing technology following the ARTIC network protocol. Whole-genome sequencing has identified different clades/sub-clades circulating in Kuwait, mimicking the virus's global spread. Clade 20A was dominant from February 2020 until January 2021, and then clade 20I (Alpha, V1) emerged and dominated. In June 2021, the number of cases infected with clades 21I, 21A, and 21 J (Delta) increased and dominated. We detected several known clade-defining missense and synonymous mutations and other missense mutations in the genes encoding important viral proteins, including ORF1a, S, ORF3a, ORF8 regions and a novel mutation in the N region. ORF1ab region harbored more mutations and deletions (n = 62, 49.2%) compared to the other 12 gene regions, and the most prevalent missense mutations were P314L (97%) in ORF1b and D614G (97%) in the S glycoprotein regions. Detecting and analyzing mutations and monitoring the evolution of SARS-CoV-2 over time is essential to help better understand the spread of various clades/strains of SARS-CoV-2 and their implications for pathogenesis. In addition, knowledge of the circulating variants and genome sequence variability of SARS-CoV-2 may potentially influence the development of vaccines and antiviral drugs to control the COVID-19 pandemic.

Keywords: Kuwait; Nanopore sequencing technology; SARS-CoV-2; molecular epidemiology; variants.

Figure 1

Maximum likelihood tree of 209 SARS-CoV-2 genomes sequenced in Kuwait from February 2020 to June 2021. Each line indicates a sample coloured by the dominant viral clades, annotated with the clade’s definitive genetic variation. Reference strain (NC_045512) is coloured in black.

Figure 2

Relative prevalence of SARS-CoV-2 clades circulating in Kuwait from February 2020 to June 2021. Error bars represent a 95% confidence interval.

Figure 3

Time-resolved phylogenetic tree representing 6,169 genomes sampled between February 2020 and June 2021. The Whole-genome of 209 SARS-CoV-2 isolates in Kuwait and high coverage genomes from 16 countries in the Middle East from February 2020 to June 2021 available in GSAID were included. The phylogeny was estimated using IQTree under the GTR substitution model and visualized with auspice. The tree was rooted with the reference strain NC_045512.

Figure 4

Maximum likelihood IQ TREE of 6,169 SARS-CoV-2 genomes from Middle East countries and Kuwait from February 2020 to June 2021. Kuwaiti clades are in different colours. Bootstrap values are in red.

Figure 5

Graphical representation of the SARS-CoV-2 mutation diversity in Kuwait. A scaled genetic map shows the location of genomic mutations and deletions on the complete nucleotide sequence of SARS-CoV-2 isolated in Kuwait. Vertical arrows represent recurrent mutations and deletions. Del, deletions.

Figure 6

Heatmap demonstrates the percentage of each mutation and deletion in SARS-CoV-2 genes among different variants detected in Kuwait (n = 209). The colour scale indicates the significance of the correlation, with blue and white colours indicating the highest and lowest correlation, respectively.