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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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2
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González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes (Basel) 2023; 14:407. [PMID: 36833334 PMCID: PMC9956206 DOI: 10.3390/genes14020407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10-3-10-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.
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Affiliation(s)
- Luis Daniel González-Vázquez
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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3
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Fischer C, Maponga TG, Yadouleton A, Abílio N, Aboce E, Adewumi P, Afonso P, Akorli J, Andriamandimby SF, Anga L, Ashong Y, Beloufa MA, Bensalem A, Birtles R, Boumba ALM, Bwanga F, Chaponda M, Chibukira P, Chico RM, Chileshe J, Chongwe G, Cissé A, D'Alessandro U, de Lamballerie XN, de Morais JFM, Derrar F, Dia N, Diarra Y, Doumbia L, Drosten C, Dussart P, Echodu R, Eggers Y, Eloualid A, Faye O, Feldt T, Frühauf A, Halatoko A, Ilouga PV, Ismael N, Jambou R, Jarju S, Kamprad A, Katowa B, Kayiwa J, King'wara L, Koita O, Lacoste V, Lagare A, Landt O, Lekana-Douki SE, Lekana-Douki JB, Iipumbu E, Loemba H, Lutwama J, Mamadou S, Maman I, Manyisa B, Martinez PA, Matoba J, Mhuulu L, Moreira-Soto A, Mwangi J, N Dilimabaka N, Nassuna CA, Ndiath MO, Nepolo E, Njouom R, Nourlil J, Nyanjom SG, Odari EO, Okeng A, Ouoba JB, Owusu M, Owusu Donkor I, Phadu KK, Phillips RO, Preiser W, Ruhanya V, Salah F, Salifou S, Sall AA, Sylverken AA, Tagnouokam-Ngoupo PA, Tarnagda Z, Tchikaya FO, Tufa TB, Drexler JF. RETRACTED: Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa. Science 2022; 378:eadd8737. [PMID: 36454863 DOI: 10.1126/science.add8737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.
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Affiliation(s)
- Carlo Fischer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Tongai Gibson Maponga
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Anges Yadouleton
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Nuro Abílio
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Praise Adewumi
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Pedro Afonso
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Jewelna Akorli
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Latifa Anga
- Institut Pasteur du Maroc, Casablanca, Morocco
| | - Yvonne Ashong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Aicha Bensalem
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Richard Birtles
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Anicet Luc Magloire Boumba
- Faculty of Health Sciences, Marien Ngouabi University, Pointe-Noire, Congo.,Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo
| | - Freddie Bwanga
- MBN Clinical Laboratories, Kampala, Uganda.,Makerere University College of Health Sciences, Kampala, Uganda
| | - Mike Chaponda
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Paradzai Chibukira
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | - Justin Chileshe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Gershom Chongwe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Assana Cissé
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | - Umberto D'Alessandro
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | | | | | - Fawzi Derrar
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Ndongo Dia
- Institut Pasteur de Dakar (IPD), Dakar, Senegal
| | - Youssouf Diarra
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Lassina Doumbia
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Richard Echodu
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Yannik Eggers
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Torsten Feldt
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Frühauf
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | | | | | | | - Ronan Jambou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Sheikh Jarju
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Antje Kamprad
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Ben Katowa
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Leonard King'wara
- National Public Health Reference Laboratory, Ministry of Health, Nairobi, Kenya
| | - Ousmane Koita
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | | | - Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | | | | | - Etuhole Iipumbu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Hugues Loemba
- Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo.,Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Santou Mamadou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | - Brendon Manyisa
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | - Pedro A Martinez
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Japhet Matoba
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Lusia Mhuulu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Andres Moreira-Soto
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Judy Mwangi
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Nadine N Dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Mamadou Ousmane Ndiath
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Emmanuel Nepolo
- School of Medicine, University of Namibia, Windhoek, Namibia
| | | | | | - Steven Ger Nyanjom
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eddy Okoth Odari
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | | | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Irene Owusu Donkor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karabo Kristen Phadu
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.,National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa
| | - Vurayai Ruhanya
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | | | | | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.,Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana
| | | | - Zekiba Tarnagda
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | | | - Tafese Beyene Tufa
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Felix Drexler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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4
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Theron E, Erasmus HC, Wylie C, Khan W, Geduld H, Stassen W. The lived experiences of emergency care personnel in the Western Cape, South Africa during the COVID-19 pandemic: A longitudinal hermeneutic phenomenological study. Afr J Emerg Med 2022; 12:410-7. [PMID: 36062254 DOI: 10.1016/j.afjem.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 12/03/2022] Open
Abstract
In March 2020, the World Health Organisation declared COVID-19 a global pandemic. Shortly after the first case of COVID-19 was reported in South Africa, the Western Cape province experienced a rapid growth in the number of cases, establishing it as the epicentre of the disease in South Africa. The aim of this study was to explore emergency care personnel's lived experiences and their perceptions thereof within the context of the COVID-19 pandemic in the Western Cape province. This study followed a longitudinal hermeneutic phenomenological approach. The convenience sample included prehospital and emergency centre medical personnel. Data were collected over a 4-month period using both one-on-one interviews and participant recorded voice recordings. Data were analysed following Ricoeur's theory of interpretation. Four themes were generated during the data analysis: 1) In the beginning, waiting for the unknown; 2) Next, change and adaptation in the workplace; 3) My COVID-19 feelings; 4) Support and connection. Participants discussed the uncertainty associated with responding to an unknown threat and a need to keep up with constant change in an overburdened work environment. Results showed high levels of uncertainty, restriction, fear, anxiety, and exhaustion. Despite these difficulties, participants demonstrated resilience and commitment to caring for patients. A need for support was also highlighted. Results indicated that change, over time, resulted in adaptation to a new way of practising and keeping safe. Healthcare workers experienced intersecting consequences as frontline healthcare workers and members of the public, all of which impacted their well-being. The importance of compassion and encouragement as forms of support was highlighted in the study. Robust and sustained support structures in a time of change, low mood, and exhaustion are essential.
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5
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Grobbelaar LM, Kruger A, Venter C, Burger EM, Laubscher GJ, Maponga TG, Kotze MJ, Kwaan HC, Miller JB, Fulkerson D, Huff W, Chang E, Wiarda G, Bunch CM, Walsh MM, Raza S, Zamlut M, Moore HB, Moore EE, Neal MD, Kell DB, Pretorius E. Relative Hypercoagulopathy of the SARS-CoV-2 Beta and Delta Variants when Compared to the Less Severe Omicron Variants Is Related to TEG Parameters, the Extent of Fibrin Amyloid Microclots, and the Severity of Clinical Illness. Semin Thromb Hemost 2022; 48:858-868. [PMID: 36174604 DOI: 10.1055/s-0042-1756306] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Earlier variants of SARS-CoV-2 have been associated with plasma hypercoagulability (as judged by thromboelastography) and an extensive formation of fibrin amyloid microclots, which are considered to contribute to the pathology of the coronavirus 2019 disease (COVID-19). The newer Omicron variants appear to be far more transmissible, but less virulent, even when taking immunity acquired from previous infections or vaccination into account. We here show that while the clotting parameters associated with Omicron variants are significantly raised over those of healthy, matched controls, they are only raised to levels significantly lower than those seen with more severe variants such as beta and delta. We also observed that individuals infected with omicron variants manifested less extensive microclot formation in platelet-poor plasma compared with those harboring the more virulent variants. The measurement of clotting effects between the different variants acts as a kind of "internal control" that demonstrates the relationship between the extent of coagulopathies and the virulence of the variant of interest. This adds to the evidence that microclots may play an important role in reflecting the severity of symptoms observed in COVID-19.
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Affiliation(s)
- Lize M Grobbelaar
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa
| | - Arneaux Kruger
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa
| | - Chantelle Venter
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa
| | | | | | - Tongai G Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Hau C Kwaan
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Joseph B Miller
- Departments of Emergency Medicine and Internal Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Daniel Fulkerson
- Department of Neurosurgery, St. Joseph Regional Medical Center, Mishawaka, Indiana
| | - Wei Huff
- Department of Neurosurgery, St. Joseph Regional Medical Center, Mishawaka, Indiana
| | - Eric Chang
- Indiana University School of Medicine - South Bend, Notre Dame, Indiana
| | - Grant Wiarda
- Department of Internal Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana
| | - Connor M Bunch
- Departments of Emergency Medicine and Internal Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Mark M Walsh
- Indiana University School of Medicine - South Bend, Notre Dame, Indiana.,Department of Internal Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana.,Department of Emergency Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana
| | - Syed Raza
- Department of Critical Care Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana
| | - Mahmud Zamlut
- Department of Critical Care Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana
| | - Hunter B Moore
- Division of Transplant Surgery, Department of Surgery, Denver Health and University of Colorado Health Sciences Center, Denver, Colorado
| | - Ernest E Moore
- Department of Surgery, Ernest E. Moore Shock Trauma Center at Denver Health and University of Colorado Health Sciences Center, Denver, Colorado
| | - Matthew D Neal
- Pittsburgh Trauma Research Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Douglas B Kell
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa.,Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, England, United Kingdom.,The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa.,The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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6
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Maponga TG, Jeffries M, Tegally H, Sutherland A, Wilkinson E, Lessells RJ, Msomi N, van Zyl G, de Oliveira T, Preiser W. Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection With accumulation of mutations in a patient with poorly controlled Human Immunodeficiency Virus infection. Clin Infect Dis 2022; 76:e522-e525. [PMID: 35793242 PMCID: PMC9278209 DOI: 10.1093/cid/ciac548] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/03/2022] [Accepted: 06/30/2022] [Indexed: 12/12/2022] Open
Abstract
A 22-year-old woman with uncontrolled advanced human immunodeficiency virus (HIV) infection was persistently infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) beta variant for 9 months, the virus accumulating >20 additional mutations. Antiretroviral therapy suppressed HIV and cleared SARS-CoV-2 within 6 to 9 weeks. Increased vigilance is warranted to benefit affected individuals and prevent the emergence of novel SARS-CoV-2 variants.
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Affiliation(s)
- Tongai G Maponga
- Correspondence to Tongai G. Maponga, Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, Tygerberg, 7505, Cape Town, South Africa,
| | - Montenique Jeffries
- Department of Medicine, Stellenbosch University and Tygerberg Academic Hospital, Cape Town, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Andrew Sutherland
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu–Natal, Durban, South Africa
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa,National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa,Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa,Department of Global Health, University of Washington, Seattle, WA, USA
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa,National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
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7
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Flores-Alanis A, Delgado G, Espinosa-Camacho LF, Rodríguez-Gómez F, Cruz-Rangel A, Sandner-Miranda L, Cravioto A, Morales-Espinosa R. Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern. Front Microbiol 2022; 13:886585. [PMID: 35865920 PMCID: PMC9294468 DOI: 10.3389/fmicb.2022.886585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/07/2022] [Indexed: 01/09/2023] Open
Abstract
Background The advance of the COVID-19 pandemic and spread of SARS-CoV-2 around the world has generated the emergence of new genomic variants. Those variants with possible clinical and therapeutic implications have been classified as variants of concern (VOCs) and variants of interest (VOIs). Objective This study aims to describe the COVID-19 pandemic and build the evolutionary and demographic dynamics of SARS-CoV-2 populations in Mexico, with emphasis on VOCs. Methods 30,645 complete genomes of SARS-CoV-2 from Mexico were obtained from GISAID databases up to January 25, 2022. A lineage assignment and phylogenetic analysis was completed, and demographic history for Alpha, Gamma, Delta and Omicron VOCs, and the Mexican variant (B.1.1.519) was performed. Results 148 variants were detected among the 30,645 genomes analyzed with the Delta variant being the most prevalent in the country, representing 49.7% of all genomes. Conclusion The COVID-19 pandemic in Mexico was caused by several introductions of SARS-CoV-2, mainly from the United States of America and Europe, followed by local transmission. Regional molecular epidemiological surveillance must implement to detect emergence, introductions and spread of new variants with biologically important mutations.
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Affiliation(s)
- Alejandro Flores-Alanis
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gabriela Delgado
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis F. Espinosa-Camacho
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Flor Rodríguez-Gómez
- Laboratorio de Análisis de la Biodiversidad y Genómica, Departamento de Bioingeniería Traslacional, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara, Mexico
| | - Armando Cruz-Rangel
- Laboratorio de Bioquímica de Enfermedades Crónicas, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Luisa Sandner-Miranda
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alejandro Cravioto
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Rosario Morales-Espinosa,
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Rowe BR, Canosa A, Meslem A, Rowe F. Increased airborne transmission of COVID-19 with new variants, implications for health policies. Build Environ 2022; 219:109132. [PMID: 35578697 PMCID: PMC9095081 DOI: 10.1016/j.buildenv.2022.109132] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
New COVID-19 variants, either of higher viral load such as delta or higher contagiousness like omicron, can lead to higher airborne transmission than historical strains. This paper highlights their implications for health policies, based on a clear analytical understanding and modeling of the airborne contamination paths, of the dose following exposure, and the importance of the counting unit for pathogens, itself linked to the dose-response law. Using the counting unit of Wells, i.e. the quantum of contagium, we develop the conservation equation of quanta which allows deriving the value of the quantum concentration at steady state for a well-mixed room. The link with the monitoring concentration of carbon dioxide is made and used for a risk analysis of a variety of situations for which we collected CO2 time-series observations. The main conclusions of these observations are that 1) the present norms of ventilation, are both insufficient and not respected, especially in a variety of public premises, leading to high risk of contamination and that 2) air can often be considered well-mixed. Finally, we insist that public health policy in the field of airborne transmission should be based on a multi parameter analysis such as the time of exposure, the quantum production rate, mask wearing and the infector proportion in the population in order to evaluate the risk, considering the whole complexity of dose evaluation. Recognizing airborne transmission requires thinking in terms of time of exposure rather than in terms of proximal distance.
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Affiliation(s)
- Bertrand R Rowe
- Rowe Consulting, 22 chemin des moines, 22750 Saint Jacut de la Mer, France
| | - André Canosa
- CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Université de Rennes, 35000 Rennes, France
| | - Amina Meslem
- Université de Rennes, LGCGM, 3 Rue du Clos Courtel, BP 90422, 35704, Rennes, CEDEX 7, France
| | - Frantz Rowe
- Nantes Université, LEMNA, Nantes, France
- SKEMA Business School, KTO, Sophia-Antipolis, France
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9
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Wang Y, Chen D, Zhu C, Zhao Z, Gao S, Gou J, Guo Y, Kong X. Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing. Front Immunol 2022; 13:814806. [PMID: 35444655 PMCID: PMC9013895 DOI: 10.3389/fimmu.2022.814806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread and poses a major threat to public health worldwide. The whole genome sequencing plays a crucial role in virus surveillance and evolutionary analysis. In this study, five genome sequences of SARS-CoV-2 were obtained from nasopharyngeal swab samples from Zhengzhou, China. Following RNA extraction and cDNA synthesis, multiplex PCR was performed with two primer pools to produce the overlapped amplicons of ~1,200 bp. The viral genomes were obtained with 96% coverage using nanopore sequencing. Forty-five missense nucleotide mutations were identified; out of these, 5 mutations located at Nsp2, Nsp3, Nsp14, and ORF10 genes occurred with a <0.1% frequency in the global dataset. On the basis of mutation profiles, five genomes were clustered into two sublineages (B.1.617.2 and AY.31) or subclades (21A and 21I). The phylogenetic analysis of viral genomes from several regions of China and Myanmar revealed that five patients had different viral transmission chains. Taken together, we established a nanopore sequencing platform for genetic surveillance of SARS-CoV-2 and identified the variants circulating in Zhengzhou during August 2021. Our study provided crucial support for government policymaking and prevention and control of COVID-19.
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Affiliation(s)
- Yanan Wang
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Duo Chen
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chaofeng Zhu
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shanshan Gao
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianjun Gou
- Department of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongjun Guo
- Department of Pathology, Henan Academy of Medical Sciences, Zhengzhou, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Affiliation(s)
- Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service (NHLS) Tygerberg, Cape Town 8000, South Africa.
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service (NHLS) Tygerberg, Cape Town 8000, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service (NHLS) Tygerberg, Cape Town 8000, South Africa
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Prasetyoputri A, Dharmayanthi AB, Iryanto SB, Andriani A, Nuryana I, Wardiana A, Ridwanuloh AM, Swasthikawati S, Hariyatun H, Nugroho HA, Idris I, Indriawati I, Noviana Z, Oktavia L, Yuliawati Y, Masrukhin M, Hasrianda EF, Sukmarini L, Fahrurrozi F, Yanthi ND, Fathurahman AT, Wulandari AS, Setiawan R, Rizal S, Fathoni A, Kusharyoto W, Lisdiyanti P, Ningrum RA, Saputra S. The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. PeerJ 2022; 10:e13132. [PMID: 35341058 PMCID: PMC8953504 DOI: 10.7717/peerj.13132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 11/11/2021] [Accepted: 02/26/2022] [Indexed: 01/12/2023] Open
Abstract
Background Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results We successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general. Conclusions We demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response.
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Affiliation(s)
- Anggia Prasetyoputri
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Anik B. Dharmayanthi
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Syam B. Iryanto
- Research Center for Informatics, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ade Andriani
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Isa Nuryana
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Andri Wardiana
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Asep M. Ridwanuloh
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Sri Swasthikawati
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Hariyatun Hariyatun
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Herjuno A. Nugroho
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Idris Idris
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Indriawati Indriawati
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Zahra Noviana
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Listiana Oktavia
- Research Center for Chemistry, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Yuliawati Yuliawati
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Masrukhin Masrukhin
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Erwin F. Hasrianda
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Linda Sukmarini
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Fahrurrozi Fahrurrozi
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Nova Dilla Yanthi
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Alfi T. Fathurahman
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ari S. Wulandari
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ruby Setiawan
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Syaiful Rizal
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ahmad Fathoni
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Wien Kusharyoto
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ratih A. Ningrum
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Sugiyono Saputra
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
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12
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Chouikha A, Fares W, Laamari A, Haddad-Boubaker S, Belaiba Z, Ghedira K, Kammoun Rebai W, Ayouni K, Khedhiri M, Ben Halima S, Krichen H, Touzi H, Ben Dhifallah I, Guerfali FZ, Atri C, Azouz S, Khamessi O, Ardhaoui M, Safer M, Ben Alaya N, Guizani I, Kefi R, Gdoura M, Triki H. Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19. Viruses 2022; 14:624. [PMID: 35337031 PMCID: PMC8956073 DOI: 10.3390/v14030624] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 12/17/2022] Open
Abstract
Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains.
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Affiliation(s)
- Anissa Chouikha
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Wasfi Fares
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Asma Laamari
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
| | - Sondes Haddad-Boubaker
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Zeineb Belaiba
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia;
| | - Wafa Kammoun Rebai
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia; (W.K.R.); (R.K.)
| | - Kaouther Ayouni
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Marwa Khedhiri
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Samar Ben Halima
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
| | - Henda Krichen
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
| | - Henda Touzi
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Imen Ben Dhifallah
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Fatma Z. Guerfali
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII) (LR16IPT02), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia; (F.Z.G.); (C.A.)
| | - Chiraz Atri
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII) (LR16IPT02), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia; (F.Z.G.); (C.A.)
| | - Saifeddine Azouz
- Genomics Plateform, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia;
| | - Oussema Khamessi
- Laboratoire de Venins et Biomolécules Thérapeutiques (LR16IPT08), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia;
| | - Monia Ardhaoui
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
- Laboratory of Molecular Epidemiology & Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia
| | - Mouna Safer
- National Observatory of New and Emergent Diseases, Tunis 1002, Tunisia; (M.S.); (N.B.A.)
| | - Nissaf Ben Alaya
- National Observatory of New and Emergent Diseases, Tunis 1002, Tunisia; (M.S.); (N.B.A.)
| | - Ikram Guizani
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
- Laboratory of Molecular Epidemiology & Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia; (W.K.R.); (R.K.)
| | - Mariem Gdoura
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Henda Triki
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
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Bianco L, Moser M, Silverj A, Micheletti D, Lorenzin G, Collini L, Barbareschi M, Lanzafame P, Segata N, Pindo M, Franceschi P, Rota-stabelli O, Rizzoli A, Fontana P, Donati C. On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy. Viruses 2022; 14:580. [PMID: 35336987 PMCID: PMC8951735 DOI: 10.3390/v14030580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Trentino is an Italian province with a tourism-based economy, bordering the regions of Lombardy and Veneto, where the two earliest and largest outbreaks of COVID-19 occurred in Italy. The earliest cases in Trentino were reported in the first week of March 2020, with most of the cases occurring in the winter sport areas in the Dolomites mountain range. The number of reported cases decreased over the summer months and was followed by a second wave in the autumn and winter of 2020. Methods: we performed high-coverage Oxford Nanopore sequencing of 253 positive SARS-CoV-2 swabs collected in Trentino between March and December 2020. Results: in this work, we analyzed genome sequences to trace the routes through which the virus entered the area, and assessed whether the autumnal resurgence could be attributed to lineages persisting undetected during summer, or as a consequence of new introductions. Conclusions: Comparing the draft genomes analyzed with a large selection of European sequences retrieved from GISAID we found that multiple introductions of the virus occurred at the early stage of the epidemics; the two epidemic waves were unrelated; the second wave was due to reintroductions of the virus in summer when traveling restrictions were uplifted.
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Campos FS, de Arruda LB, da Fonseca FG. Special Issue “Viral Infections in Developing Countries”. Viruses 2022; 14:405. [PMID: 35215998 PMCID: PMC8877050 DOI: 10.3390/v14020405] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/19/2022] Open
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Benslimane FM, Al Khatib HA, Al-Jamal O, Albatesh D, Boughattas S, Ahmed AA, Bensaad M, Younuskunju S, Mohamoud YA, Al Badr M, Mohamed AA, El-Kahlout RA, Al-Hamad T, Elgakhlab D, Al-Kuwari FH, Saad C, Jeremijenko A, Al-Khal A, Al-Maslamani MA, Bertollini R, Al-Kuwari EA, Al-Romaihi HE, Al-Marri S, Al-Thani M, Badji RM, Mbarek H, Al-Sarraj Y, Malek JA, Ismail SI, Abu-Raddad LJ, Coyle PV, Thani AAA, Yassine HM. One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar. Front Cell Infect Microbiol 2021; 11:768883. [PMID: 34869069 PMCID: PMC8637114 DOI: 10.3389/fcimb.2021.768883] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 09/01/2021] [Accepted: 10/19/2021] [Indexed: 01/03/2023] Open
Abstract
Qatar, a country with a strong health system and a diverse population consisting mainly of expatriate residents, has experienced two large waves of COVID-19 outbreak. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population’s genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number of mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. These findings raise the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor the SARS-CoV-2 profile and re-emergence in Qatar.
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Affiliation(s)
| | | | - Ola Al-Jamal
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Dana Albatesh
- Biomedical Research Center, Qatar University, Doha, Qatar
| | | | - Ayeda A Ahmed
- Genomics Laboratory, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
| | - Meryem Bensaad
- Genomics Laboratory, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
| | - Shameem Younuskunju
- Genomics Laboratory, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
| | - Yasmin A Mohamoud
- Genomics Laboratory, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
| | - Mashael Al Badr
- National Reference Laboratory Ministry of Public Health, Doha, Qatar
| | - Abdalla A Mohamed
- National Reference Laboratory Ministry of Public Health, Doha, Qatar
| | | | | | | | - Fatima H Al-Kuwari
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | | | | | | | | | | | | | | | | | - Radja M Badji
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Yasser Al-Sarraj
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Joel A Malek
- Genomics Laboratory, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar.,Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
| | - Said I Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Laith J Abu-Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar.,Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, United States.,World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine-Qatar, Doha, Qatar
| | | | | | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha, Qatar.,Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
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Chrysostomou AC, Vrancken B, Koumbaris G, Themistokleous G, Aristokleous A, Masia C, Eleftheriou C, Iοannou C, Stylianou DC, Ioannides M, Petrou P, Georgiou V, Hatziyianni A, Lemey P, Vandamme AM, Patsalis PP, Kostrikis LG. A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Viruses 2021; 13:1098. [PMID: 34207490 PMCID: PMC8227210 DOI: 10.3390/v13061098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 12/19/2022] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial outbreak on the island. In this study, we performed a comprehensive retrospective molecular epidemiological analysis (genetic, phylogenetic, phylodynamic and phylogeographic analyses) of SARS-CoV-2 isolates in Cyprus from April 2020 to January 2021, covering the first ten months of the SARS-CoV-2 infection epidemic on the island. The primary aim of this study was to assess the transmissibility of SARS-CoV-2 lineages in Cyprus. Whole SARS-CoV-2 genomic sequences were generated from 596 clinical samples (nasopharyngeal swabs) obtained from community-based diagnostic testing centers and hospitalized patients. The phylogenetic analyses revealed a total of 34 different lineages in Cyprus, with B.1.258, B.1.1.29, B.1.177, B.1.2, B.1 and B.1.1.7 (designated a Variant of Concern 202012/01, VOC) being the most prevalent lineages on the island during the study period. Phylodynamic analysis showed a highly dynamic epidemic of SARS-CoV-2 infection, with three consecutive surges characterized by specific lineages (B.1.1.29 from April to June 2020; B.1.258 from September 2020 to January 2021; and B.1.1.7 from December 2020 to January 2021). Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, ΔH69/V70, S898F, ΔY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. Phylogeographic analysis indicated that the majority of imports and exports were to and from the United Kingdom (UK), although many other regions/countries were identified (southeastern Asia, southern Europe, eastern Europe, Germany, Italy, Brazil, Chile, the USA, Denmark, the Czech Republic, Slovenia, Finland, Switzerland and Pakistan). Taken together, these findings demonstrate that the SARS-CoV-2 infection epidemic in Cyprus is being maintained by a continuous influx of lineages from many countries, resulting in the establishment of an ever-evolving and polyphyletic virus on the island.
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Affiliation(s)
- Andreas C. Chrysostomou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (B.V.); (P.L.); (A.-M.V.)
| | - George Koumbaris
- NIPD Genetics Limited, Nicosia 2409, Cyprus; (G.K.); (M.I.); (P.P.P.)
| | - George Themistokleous
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Christina Masia
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Christina Eleftheriou
- Department of Health and Safety, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus;
| | - Costakis Iοannou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Marios Ioannides
- NIPD Genetics Limited, Nicosia 2409, Cyprus; (G.K.); (M.I.); (P.P.P.)
| | - Panagiotis Petrou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Vasilis Georgiou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Amalia Hatziyianni
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (B.V.); (P.L.); (A.-M.V.)
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (B.V.); (P.L.); (A.-M.V.)
- Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
| | - Philippos P. Patsalis
- NIPD Genetics Limited, Nicosia 2409, Cyprus; (G.K.); (M.I.); (P.P.P.)
- Medical School, University of Nicosia, Nicosia 2417, Cyprus
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
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