Genomic surveillance of SARS-CoV-2 in US military compounds in Afghanistan reveals multiple introductions and outbreaks of Alpha and Delta variants

Irina Maljkovic Berry; Jun Hang; Christian Fung; Yu Yang; Marcus Chibucos; Adam Pollio; Jay Gandhi; Tao Li; Matthew A Conte; Grace M Lidl; Jay A Johannigman; Heather Friberg

doi:10.1186/s12864-022-08757-5

Genomic surveillance of SARS-CoV-2 in US military compounds in Afghanistan reveals multiple introductions and outbreaks of Alpha and Delta variants

BMC Genomics. 2022 Jul 15;23(1):513. doi: 10.1186/s12864-022-08757-5.

Authors

Affiliations

¹ Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA. Irina.maljkovicberry@nih.gov.
² Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA.
³ Uniformed Services University of the Health Sciences, Bethesda, MD, USA.

Abstract

Background: With the emergence and spread of SARS-CoV-2 variants, genomic epidemiology and surveillance have proven invaluable tools for variant tracking. Here, we analyzed SARS-CoV-2 samples collected from personnel located at the US/NATO bases across Afghanistan.

Results: Sequencing and phylogenetic analyses revealed at least 16 independent introductions of SARS-CoV-2 into four of these relatively isolated compounds during April and May 2021, including multiple introductions of Alpha and Delta variants. Four of the introductions resulted in sustained spread of the virus within, and in two cases between, the compounds. Three of these outbreaks, one Delta and two Alpha, occurred simultaneously.

Conclusions: Even in rigorously controlled and segregated environments, SARS-CoV-2 introduction and spread may occur frequently.

Keywords: Afghanistan; Military; Outbreaks; SARS-CoV-2.

MeSH terms

Afghanistan / epidemiology
COVID-19* / epidemiology
Disease Outbreaks
Genomics
Humans
Military Personnel*
Phylogeny
SARS-CoV-2 / genetics

Supplementary concepts

SARS-CoV-2 variants