Study of a SARS-CoV-2 Outbreak in a Belgian Military Education and Training Center in Maradi, Niger

Abstract

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compromises the ability of military forces to fulfill missions. At the beginning of May 2020, 22 out of 70 Belgian soldiers deployed to a military education and training center in Maradi, Niger, developed mild COVID-19 compatible symptoms. Immediately upon their return to Belgium, and two weeks later, all seventy soldiers were tested for SARS-CoV-2 RNA (RT-qPCR) and antibodies (two immunoassays). Nine soldiers had at least one positive COVID-19 diagnostic test result. Five of them exhibited COVID-19 symptoms (mainly anosmia, ageusia, and fever), while four were asymptomatic. In four soldiers, SARS-CoV-2 viral load was detected and the genomes were sequenced. Conventional and genomic epidemiological data suggest that these genomes have an African most recent common ancestor and that the Belgian military service men were infected through contact with locals. The medical military command implemented testing of all Belgian soldiers for SARS-CoV-2 viral load and antibodies, two to three days before their departure on a mission abroad or on the high seas, and for specific missions immediately upon their return in Belgium. Some military operational settings (e.g., training camps in austere environments and ships) were also equipped with mobile infectious disease (COVID-19) testing capacity.

Symptomatic SARS-CoV-2 re-infection of a health care worker in a Belgian nosocomial outbreak despite primary neutralizing antibody response

“…Whole genome sequencing was performed on an Oxford Nanopore MinION device using R9.4 flow cells (Oxford Nanopore Technologies, UK) after a multiplex PCR with an 800bp SARS-CoV-2 primer scheme as previously described [25]. Sequence reads were basecalled in high accuracy mode and demultiplexed using the Guppy algorithm v3.6.…”

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

“…To analyze possible patterns of spread, especially among the small clusters of SARS-CoV-2-positive soldiers returning from Niger [ 16 ] and Mali, and to analyze the possible introduction of new SARS-CoV-2 variants in Belgium, we further determined the whole-genome sequences of the SARS-CoV-2 isolates. Nineteen complete genome sequences were obtained from the 21 RT-qPCR-positive samples.…”

“…Quantitative RT-PCR (RT-qPCR) was performed on the samples using two methods. Until October 2020, the Novel Coronavirus (2019-nCoV) Nucleic Acid Diagnostic Kit and Sample Release Reagent (both Sansure Biotech Inc., China) were used, according to the manufacturer’s instructions, including some modifications to cater for a LightCycler 2.0 instrument (Roche Diagnostics, Diegem, Belgium) [ 16 ]. The RT-qPCR assay amplifies the ORF1ab and N genes, which encode a well-conserved replicase polyprotein and the nucleocapsid protein, respectively.…”

“…Samples with sufficiently high virus concentrations (RT-qPCR Ct values < 35) were selected for sequencing on a MinION device using R9.4 flow cells (Oxford Nanopore Technologies, Oxford, UK), as previously described [ 16 , 17 ]. Briefly, using a Maxwell RSC instrument, RNA was extracted from 200 μL of UTM transport medium and eluted in 80 μL of water.…”

Special Issue “Emerging Viruses 2020: Surveillance, Prevention, Evolution and Control”

“…The discussed mechanisms included the hijack of antigen-presenting cells to virus dissemination through mucosal tissues; escape from RNA sensors by shielding RNA intermediates in replication organelles and 2′-O-methylation modification of virus RNA; antagonization of interferon-mediated signal transduction, and inhibition of interferon stimulated genes (ISG). Pirnay et al [ 5 ] characterized a SARS-CoV-2 outbreak in a Belgian military education and training center in Maradi, Niger. Viral load could be detected in symptomatic and asymptomatic individuals, and analysis of the genome sequences suggested that the soldiers and trainers were infected in Africa.…”