Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations

Abstract

The 2019 coronavirus disease (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded RNA beta- coronavirus with a genome 29,903 nucleotides long [1]. First identified at the end of 2019 in Wuhan, China, it spread rapidly and caused the ongoing global pandemic. Even though the disease predominantly causes lung damage, other organs such as the heart can also be affected [2]. At the time of writing (17 April 2021), 175,987,176 confirmed COVID-19 cases, including 3,811,561 deaths, had been reported to the World Health Organization (WHO) worldwide [3]. Although coronaviruses have a genetic proofreading mechanism, viral mutations occur and can spread and increase in frequency, mainly due to natural selection of beneficial mutations. SARS-CoV-2 protein sequence diversity may be associated with pathogenicity and/or transmission of the virus, and certain SARS-CoV-2 genotypes or variants were found to be specific to geographical locations [4]. Therefore, it has been suggested that genomic, epidemiological, and clinical data should be combined to better understand the infectivity and pathogenicity of SARS-CoV-2 [5]. Today, the risk associated with the international spread of new SARS-CoV-2 variants (via travel) is a matter of great concern. In November 2020, a new SARS-CoV-2 variant, named B.1.1.7 or 20I/501Y.V1 (depending on the nomenclature used), was identified in the United Kingdom (UK) [6,7]. In December 2020, it was reported that the transmission rate of this variant could be up to 71% higher than for other variants [7]. This new variant was subsequently identified in several other countries and has become globally dominant today. It was recently suggested that the B.1.1.7 variant causes higher COVID-19 mortality [8], and it was found to be associated with higher viral load and younger age of infected patients [9]. Another highly transmissible SARS-CoV-2 variant named B.1.351 (or 20H/501Y.V2) likely emerged from the first wave of the South African COVID-19 epidemic and then spread quickly to its neighboring country of Botswana in December 2020, as well as several other countries across the world in January 2021 [10]. There are concerns that certain mutations in the spike protein (e.g., K417N, E484K, N501Y) could decrease the effectiveness of COVID-19 vaccines. An increased resistance of variant B.1.351, but also B.1.1.7, to antibody neutralization has been reported [11]. More recently, Wang et al. reported that an emergent variant from Brazil, named P.1 or 20J/501Y.V3, was also more resistant to neutralization by convalescent plasma and vaccine sera [12]. Even though a small study examining the impact of the N501Y mutation on the Pfizer-BioNTech vaccine did not show any loss of antibody neutralization efficacy, further studies examining the impact of other mutations (e.g., K417N, E484K, . . . ), and involving the other COVID-19 vaccines, are required [13].