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Gao L, Zheng C, Shi Q, Wang L, Tia A, Ngobeh J, Liu Z, Dong X, Li Z. Multiple introduced lineages and the single native lineage co-driving the four waves of the COVID-19 pandemic in West Africa. Front Public Health 2022; 10:957277. [PMID: 36187679 PMCID: PMC9521358 DOI: 10.3389/fpubh.2022.957277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/15/2022] [Indexed: 01/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has become a vast burden on public health and socioeconomics in West Africa, but the epidemic situation is unclear. Therefore, we conducted a retrospective analysis of the positive rate, death rate, and diversity of SARS-CoV-2. As of March 31, 2022, a total of 894,813 cases of COVID-19 have been recorded, with 12,028 deaths, both of which were distributed in all 16 countries. There were four waves of COVID-19 during this period. Most cases were recorded in the second wave, accounting for 34.50% of total cases. These data suggest that although West Africa seems to have experienced a low and relatively slow spread of COVID-19, the epidemic was ongoing, evolving with each COVID-19 global pandemic wave. Most cases and most deaths were both recorded in Nigeria. In contrast, the fewest cases and fewest deaths were reported, respectively, in Liberia and Sierra Leone. However, high death rates were found in countries with low incidence rates. These data suggest that the pandemic in West Africa has so far been heterogeneous, which is closely related to the infrastructure of public health and socioeconomic development (e.g., extreme poverty, GDP per capita, and human development index). At least eight SARS-CoV-2 variants were found, namely, Delta, Omicron, Eta, Alpha, Beta, Kappa, Iota, and Gamma, which showed high diversity, implicating that multiple-lineages from different origins were introduced. Moreover, the Eta variant was initially identified in Nigeria and distributed widely. These data reveal that the COVID-19 pandemic in the continent was co-driven by both multiple introduced lineages and a single native lineage. We suggest enhancing the quarantine measures upon entry at the borders and implementing a genome surveillance strategy to better understand the transmission dynamics of the COVID-19 pandemic in West Africa.
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Affiliation(s)
- Liping Gao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra Leone
| | - Canjun Zheng
- Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra Leone,Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qi Shi
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lili Wang
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Alie Tia
- Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra Leone
| | - Jone Ngobeh
- Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra Leone
| | - Zhiguo Liu
- Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra Leone,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,*Correspondence: Zhiguo Liu
| | - Xiaoping Dong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Xiaoping Dong
| | - Zhenjun Li
- Chinese Center for Disease Control and Prevention, Beijing, China,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Zhenjun Li
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Presser LD, Coffin J, Koivogui L, Campbell A, Campbell J, Barrie F, Ngobeh J, Souma Z, Sorie S, Harding D, Camara A, Tohonamou P, Traore B, Hamill FA, Bogan J, Altmann S, Ross C, Mansheim J, Hegerty R, Poynter S, Shearrer S, Asbun C, Karlstrand B, Davis P, Alam J, Roberts D, Stamper PD, Ndjomou J, Wauquier N, Koroma M, Munu A, McClintock J, Mar M, Burns T, Krcha S. The deployment of mobile diagnostic laboratories for Ebola virus disease diagnostics in Sierra Leone and Guinea. Afr J Lab Med 2021; 10:1414. [PMID: 34858796 PMCID: PMC8603149 DOI: 10.4102/ajlm.v10i1.1414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/18/2021] [Indexed: 11/03/2022] Open
Abstract
Background Ebola virus emerged in West Africa in December 2013. The ease of mobility, porous borders, and lack of public health infrastructure led to the largest Ebola virus disease (EVD) outbreak to date. Intervention The 2013 EVD outbreak signalled the need for laboratory diagnostic capabilities in areas without strong public health systems. As part of the United States' Department of Defense response, MRIGlobal was contracted to design, fabricate, equip, deploy, and operate two mobile diagnostic laboratories (MDLs). The first laboratory analysed blood samples from patients in an adjacent Ebola Treatment Centre (ETC) and buccal swabs from the deceased in the community in Moyamba, Sierra Leone. The second laboratory was deployed to support an ETC in Conakry, Guinea. The Department of Defense provided real-time quantitative reverse transcription polymerase chain reaction assays that were deployed and validated on-site. Lessons Learnt Prompt and accurate molecular diagnostics reduced sample turn-around times from over 24 h to under 4 h. Experienced laboratory staff tested up to 110 samples per day and on-site engineering proved necessary for MDL setup and operation. As the Ebola response slowed, the sustainment of the MDLs' operations was prioritised, including staff training and the transition of the MDLs to local governments. Training programmes for local staff were prepared in Sierra Leone and Guinea. Recommendations The MRIGlobal MDL team significantly contributed to establishing increased laboratory capacity during the EVD outbreak in West Africa. Using the MDLs for molecular diagnosis is highly recommended until more sustainable solutions can be provided.
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Affiliation(s)
- Lance D Presser
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Jeanette Coffin
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Lamine Koivogui
- Centre de Recherche et de Formation en Infectiologie de Guinée, Université Gamal Abdel Nasser de Conakry, Conakry, Guinea
| | - Allan Campbell
- Central Public Health Reference Laboratory, Freetown, Sierra Leone
| | - Julian Campbell
- Central Public Health Reference Laboratory, Freetown, Sierra Leone
| | - Fatmata Barrie
- Central Public Health Reference Laboratory, Freetown, Sierra Leone
| | - Jone Ngobeh
- Central Public Health Reference Laboratory, Freetown, Sierra Leone
| | - Zein Souma
- Central Public Health Reference Laboratory, Freetown, Sierra Leone
| | - Samuel Sorie
- Central Public Health Reference Laboratory, Freetown, Sierra Leone
| | - Doris Harding
- Central Public Health Reference Laboratory, Freetown, Sierra Leone
| | - Alimou Camara
- Institut National de Santé Publique, Conakry, Guinea
| | | | - Basala Traore
- Institut National de Santé Publique, Conakry, Guinea
| | - Frank A Hamill
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Joe Bogan
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Sharon Altmann
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Casey Ross
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Jay Mansheim
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Robert Hegerty
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Scott Poynter
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Scott Shearrer
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Carmen Asbun
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Brendan Karlstrand
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Phil Davis
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Jane Alam
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - David Roberts
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Paul D Stamper
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Jean Ndjomou
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Nadia Wauquier
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Mohamed Koroma
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Alhaji Munu
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Jason McClintock
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Mar Mar
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - True Burns
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
| | - Stephen Krcha
- Global Engagement Program, MRIGlobal, Gaithersburg, Maryland, United States
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