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

Abstract

More than a year after the first identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent of the 2019 coronavirus disease (COVID-19) in China, the emergence and spread of genomic variants of this virus through travel raise concerns regarding the introduction of lineages in previously unaffected regions, requiring adequate containment strategies. Concomitantly, such introductions fuel worries about a possible increase in transmissibility and disease severity, as well as a possible decrease in vaccine efficacy. Military personnel are frequently deployed on missions around the world. As part of a COVID-19 risk mitigation strategy, Belgian Armed Forces that engaged in missions and operations abroad were screened (7683 RT-qPCR tests), pre- and post-mission, for the presence of SARS-CoV-2, including the identification of viral lineages. Nine distinct viral genotypes were identified in soldiers returning from operations in Niger, the Democratic Republic of the Congo, Afghanistan, and Mali. The SARS-CoV-2 variants belonged to major clades 19B, 20A, and 20B (Nextstrain nomenclature), and included “variant of interest” B.1.525, “variant under monitoring” A.27, as well as lineages B.1.214, B.1, B.1.1.254, and A (pangolin nomenclature), some of which are internationally monitored due to the specific mutations they harbor. Through contact tracing and phylogenetic analysis, we show that isolation and testing policies implemented by the Belgian military command appear to have been successful in containing the influx and transmission of these distinct SARS-CoV-2 variants into military and civilian populations.

Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants

“…Belgian Armed Forces that engaged in missions and operations around the world were systematically screened, pre- and post-mission, for the presence of SARS-CoV-2, including the identification of viral lineages. A study by Pirnay et al [ 32 ] showed that nine distinct viral genotypes were identified in soldiers returning from operations in Niger, Congo, Afghanistan, and Mali. The SARS-CoV-2 lineages identified included the variant of interest (VOI) B.1.525, the variant under monitoring (VUM) A.27, as well as lineages B.1.214, B.1, B.1.1.254, and A.…”

“…The SARS-CoV-2 lineages identified included the variant of interest (VOI) B.1.525, the variant under monitoring (VUM) A.27, as well as lineages B.1.214, B.1, B.1.1.254, and A. Through contact tracing and phylogenetic analysis, Pirnay et al [ 32 ] showed that the isolation and testing policies implemented by the Belgian military command appear to have been successful in containing the influx and transmission of these distinct SARS-CoV-2 variants into both military and civilian populations. In a follow-up study dedicated to the A.27 SARS-CoV-2 lineage, Kaleta et al [ 33 ] performed Bayesian phylogeographic analyses obtained from national and international databases to reveal an origin of this lineage in Western Africa, and multiple introductions from there initiated a global spread of this lineage.…”

Antibody escape and global spread of SARS-CoV-2 lineage A.27

“…A similar pattern of concerning mutations in an emerging A-derived lineage has so far only been described for the A.23/A.23.1 lineage first discovered in Uganda and Rwanda 39 , 40 . The early detection in multiple countries in Western Africa in late December 2020, an outbreak in January 2021 in Mayotte and A.27 infections of Belgian military personnel returning from Mali pointed to a suspected origin in the African continent 41 , 42 . Through carefully crafted phylogeographic analyses that exploit individual travel histories of patients infected with A.27, we here provide support for the origin of A.27 in Western Africa.…”

Early SARS-CoV-2 reinfections within 60 days highlight the need to consider antigenic variations together with duration of immunity in defining retesting policies

“…Results of SARS-CoV-2 screening and vaccination status in the patient and his family. All samples were analyzed using reverse transcription polymerase chain reaction, whole genome sequencing was performed on SARS-CoV-2 positive samples in the Belgian National Reference Center for Respiratory Pathogens (10).…”