SARS-CoV-2 Infections in Vaccinated and Unvaccinated Populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022.
Catherine E Arnold, Logan J Voegtly, Emily K Stefanov, Matthew R Lueder, Andrea E Luquette, Robin H Miller, Haven L Miner, Andrew J Bennett, Lindsay Glang, Tara N McGinnis, Kristie E Reisinger, Jae W Dugan, Michael A Mangat, Daniel J Silberger, Rebecca L Pavlicek, Chaselynn M Watters, Gregory K Rice, Francisco Malagon, Regina Z Cer, Stephen M Eggan, Kimberly A Bishop-Lilly
Author Information
Catherine E Arnold: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA. ORCID
Logan J Voegtly: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA. ORCID
Emily K Stefanov: U.S. Naval Medical Research Unit No. 3 (NAMRU-3), 95030 Sigonella, Italy.
Matthew R Lueder: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Andrea E Luquette: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Robin H Miller: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Haven L Miner: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Andrew J Bennett: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Lindsay Glang: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Tara N McGinnis: Expeditionary Medical Facility, CLDJ-HOA, Camp Lemonnier 09622, Djibouti.
Kristie E Reisinger: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Jae W Dugan: Expeditionary Medical Facility, CLDJ-HOA, Camp Lemonnier 09622, Djibouti.
Michael A Mangat: U.S. Naval Medical Research Unit No. 3 (NAMRU-3), 95030 Sigonella, Italy.
Daniel J Silberger: Navy Environmental Preventive Medicine Unit-Two, Norfolk, VA 23511, USA.
Rebecca L Pavlicek: Expeditionary Medical Facility, CLDJ-HOA, Camp Lemonnier 09622, Djibouti. ORCID
Chaselynn M Watters: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Gregory K Rice: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Francisco Malagon: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA. ORCID
Regina Z Cer: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA.
Stephen M Eggan: U.S. Naval Medical Research Unit No. 3 (NAMRU-3), 95030 Sigonella, Italy.
Kimberly A Bishop-Lilly: Naval Medical Research Center, Fort Detrick, Frederick, MD 21702, USA. ORCID
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.
