First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries
Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. While African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel li...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-01-01
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| Series: | International Journal of Infectious Diseases |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1201971220321962 |
| _version_ | 1818665662470422528 |
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| author | Edgar Simulundu Francis Mupeta Pascalina Chanda-Kapata Ngonda Saasa Katendi Changula Walter Muleya Simbarashe Chitanga Miniva Mwanza Paul Simusika Herman Chambaro Benjamin Mubemba Masahiro Kajihara Duncan Chanda Lloyd Mulenga Sombo Fwoloshi Aaron Lunda Shibemba Fred Kapaya Paul Zulu Kunda Musonda Mwaka Monze Nyambe Sinyange Mazyanga L. Mazaba Muzala Kapin’a Peter J. Chipimo Raymond Hamoonga Davie Simwaba William Ngosa Albertina N. Morales Nkomba Kayeyi John Tembo Mathew Bates Yasuko Orba Hirofumi Sawa Ayato Takada King S. Nalubamba Kennedy Malama Victor Mukonka Alimuddin Zumla Nathan Kapata |
| author_facet | Edgar Simulundu Francis Mupeta Pascalina Chanda-Kapata Ngonda Saasa Katendi Changula Walter Muleya Simbarashe Chitanga Miniva Mwanza Paul Simusika Herman Chambaro Benjamin Mubemba Masahiro Kajihara Duncan Chanda Lloyd Mulenga Sombo Fwoloshi Aaron Lunda Shibemba Fred Kapaya Paul Zulu Kunda Musonda Mwaka Monze Nyambe Sinyange Mazyanga L. Mazaba Muzala Kapin’a Peter J. Chipimo Raymond Hamoonga Davie Simwaba William Ngosa Albertina N. Morales Nkomba Kayeyi John Tembo Mathew Bates Yasuko Orba Hirofumi Sawa Ayato Takada King S. Nalubamba Kennedy Malama Victor Mukonka Alimuddin Zumla Nathan Kapata |
| author_sort | Edgar Simulundu |
| collection | DOAJ |
| description | Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. While African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 h of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient’s household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient’s SARS-CoV-2 strain showed that it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa. |
| first_indexed | 2024-12-17T05:52:12Z |
| format | Article |
| id | doaj.art-06bfdf10536349949822509f37a48f5f |
| institution | Directory Open Access Journal |
| issn | 1201-9712 |
| language | English |
| last_indexed | 2024-12-17T05:52:12Z |
| publishDate | 2021-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | International Journal of Infectious Diseases |
| spelling | doaj.art-06bfdf10536349949822509f37a48f5f2022-12-21T22:01:08ZengElsevierInternational Journal of Infectious Diseases1201-97122021-01-01102455459First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countriesEdgar Simulundu0Francis Mupeta1Pascalina Chanda-Kapata2Ngonda Saasa3Katendi Changula4Walter Muleya5Simbarashe Chitanga6Miniva Mwanza7Paul Simusika8Herman Chambaro9Benjamin Mubemba10Masahiro Kajihara11Duncan Chanda12Lloyd Mulenga13Sombo Fwoloshi14Aaron Lunda Shibemba15Fred Kapaya16Paul Zulu17Kunda Musonda18Mwaka Monze19Nyambe Sinyange20Mazyanga L. Mazaba21Muzala Kapin’a22Peter J. Chipimo23Raymond Hamoonga24Davie Simwaba25William Ngosa26Albertina N. Morales27Nkomba Kayeyi28John Tembo29Mathew Bates30Yasuko Orba31Hirofumi Sawa32Ayato Takada33King S. Nalubamba34Kennedy Malama35Victor Mukonka36Alimuddin Zumla37Nathan Kapata38Macha Research Trust, Choma, Zambia; University of Zambia, School of Veterinary Medicine, Lusaka, ZambiaMinistry of Health, Lusaka, ZambiaMinistry of Health, Lusaka, ZambiaUniversity of Zambia, School of Veterinary Medicine, Lusaka, ZambiaUniversity of Zambia, School of Veterinary Medicine, Lusaka, ZambiaUniversity of Zambia, School of Veterinary Medicine, Lusaka, ZambiaUniversity of Zambia, School of Health Sciences, Lusaka, Zambia; Hokkaido University, Research Centre for Zoonosis Control, Sapporo, JapanMinistry of Health, Lusaka, ZambiaMinistry of Health, Lusaka, ZambiaHokkaido University, Research Centre for Zoonosis Control, Sapporo, JapanCopperbelt University, School of Natural Resources, Kitwe, ZambiaHokkaido University, Research Centre for Zoonosis Control, Sapporo, JapanMinistry of Health, Lusaka, ZambiaMinistry of Health, Lusaka, ZambiaMinistry of Health, Lusaka, ZambiaMinistry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaMinistry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaZambia National Public Health Institute, Ministry of Health, Lusaka, ZambiaHerpeZ and UNZA-UCLMS Project, University Teaching Hospital, Lusaka, ZambiaHerpeZ and UNZA-UCLMS Project, University Teaching Hospital, Lusaka, ZambiaHokkaido University, Research Centre for Zoonosis Control, Sapporo, JapanUniversity of Zambia, School of Veterinary Medicine, Lusaka, ZambiaUniversity of Zambia, School of Veterinary Medicine, Lusaka, ZambiaUniversity of Zambia, School of Veterinary Medicine, Lusaka, ZambiaMinistry of Health, Lusaka, ZambiaDivision of Infection and Immunity, CCM, University College London, London, United KingdomDivision of Infection and Immunity, CCM, University College London, London, United Kingdom; University College London Hospitals NHS Foundation Trust NIHR Biomedical Research Centre, London, United KingdomZambia National Public Health Institute, Ministry of Health, Lusaka, Zambia; Corresponding author.Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. While African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 h of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient’s household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient’s SARS-CoV-2 strain showed that it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa.http://www.sciencedirect.com/science/article/pii/S1201971220321962ZambiaCOVID-19SARS-CoV-2Phylogenetic analysesDiagnosis |
| spellingShingle | Edgar Simulundu Francis Mupeta Pascalina Chanda-Kapata Ngonda Saasa Katendi Changula Walter Muleya Simbarashe Chitanga Miniva Mwanza Paul Simusika Herman Chambaro Benjamin Mubemba Masahiro Kajihara Duncan Chanda Lloyd Mulenga Sombo Fwoloshi Aaron Lunda Shibemba Fred Kapaya Paul Zulu Kunda Musonda Mwaka Monze Nyambe Sinyange Mazyanga L. Mazaba Muzala Kapin’a Peter J. Chipimo Raymond Hamoonga Davie Simwaba William Ngosa Albertina N. Morales Nkomba Kayeyi John Tembo Mathew Bates Yasuko Orba Hirofumi Sawa Ayato Takada King S. Nalubamba Kennedy Malama Victor Mukonka Alimuddin Zumla Nathan Kapata First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries International Journal of Infectious Diseases Zambia COVID-19 SARS-CoV-2 Phylogenetic analyses Diagnosis |
| title | First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries |
| title_full | First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries |
| title_fullStr | First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries |
| title_full_unstemmed | First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries |
| title_short | First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries |
| title_sort | first covid 19 case in zambia comparative phylogenomic analyses of sars cov 2 detected in african countries |
| topic | Zambia COVID-19 SARS-CoV-2 Phylogenetic analyses Diagnosis |
| url | http://www.sciencedirect.com/science/article/pii/S1201971220321962 |
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