Journal
VIRUSES-BASEL
Volume 14, Issue 9, Pages -Publisher
MDPI
DOI: 10.3390/v14091918
Keywords
SARS-CoV-2; bioinformatics; genomics; surveillance; Djibouti
Categories
Funding
- Armed Forces Health Surveillance Division (AFHSD)
- Global Emerging Infections Surveillance (GEIS) Branch [P0013_AH_01.01, P0166_20_NM, P0099_22_NM, P0187_22_NM]
- NavyWork Unit Number (WUN) [A1417]
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This study contributes to the knowledge base of circulating SARS-CoV-2 lineages in the under-sampled country of Djibouti, and reveals circulating variants of concern, mutations of interest, and emerging spike mutations.
The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the disparity between developed and developing countries for infectious disease surveillance and the sequencing of pathogen genomes. The majority of SARS-CoV-2 sequences published are from Europe, North America, and Asia. Between April 2020 and January 2022, 795 SARS-CoV-2-positive nares swabs from individuals in the U.S. Navy installation Camp Lemonnier, Djibouti, were collected, sequenced, and analyzed. In this study, we described the results of genomic sequencing and analysis for 589 samples, the first published viral sequences for Djibouti, including 196 cases of vaccine breakthrough infections. This study contributes to the knowledge base of circulating SARS-CoV-2 lineages in the under-sampled country of Djibouti, where only 716 total genome sequences are available at time of publication. Our analysis resulted in the detection of circulating variants of concern, mutations of interest in lineages in which those mutations are not common, and emerging spike mutations.
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