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Sow MS, Togo J, Simons LM, Diallo ST, Magassouba ML, Keita MB, Somboro AM, Coulibaly Y, Ozer EA, Hultquist JF, Murphy RL, Maiga AI, Maiga M, Lorenzo-Redondo R. Genomic characterization of SARS-CoV-2 in Guinea, West Africa. PLoS One 2024; 19:e0299082. [PMID: 38446806 PMCID: PMC10917296 DOI: 10.1371/journal.pone.0299082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
SARS-CoV-2 has claimed several million lives since its emergence in late 2019. The ongoing evolution of the virus has resulted in the periodic emergence of new viral variants with distinct fitness advantages, including enhanced transmission and immune escape. While several SARS-CoV-2 variants of concern trace their origins back to the African continent-including Beta, Eta, and Omicron-most countries in Africa remain under-sampled in global genomic surveillance efforts. In an effort to begin filling these knowledge gaps, we conducted retrospective viral genomic surveillance in Guinea from October 2020 to August 2021. We found that SARS-CoV-2 clades 20A, 20B, and 20C dominated throughout 2020 until the coincident emergence of the Alpha and Eta variants of concern in January 2021. The Alpha variant remained dominant throughout early 2021 until the arrival of the Delta variant in July. Surprisingly, despite the small sample size of our study, we also found the persistence of the early SARS-CoV-2 clade 19B as late as April 2021. Together, these data help fill in our understanding of the SARS-CoV-2 population dynamics in West Africa early in the COVID-19 pandemic.
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Affiliation(s)
- Mamadou Saliou Sow
- Service de Maladie Infectieuse du Centre Hospitalier de Donka, Conakry, Guinée
| | - Josue Togo
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Département de Biologie médicale, Centre Hospitalier Universitaire Gabriel Toure, Bamako, Mali
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
| | | | | | - Mamadou Bhoye Keita
- Département de laboratoire, Institut National de la Santé Publique, Conakry, Guinée
- Département de biologie, Université Gamal Abdel Nasser de Conakry, Conakry, Guinée
| | - Anou Moise Somboro
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Youssouf Coulibaly
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
| | - Judd F. Hultquist
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
| | - Robert Leo Murphy
- Institute for Global Health, Northwestern University, Chicago, IL, United States of America
| | - Almoustapha Issiaka Maiga
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Département de Biologie médicale, Centre Hospitalier Universitaire Gabriel Toure, Bamako, Mali
| | - Mamoudou Maiga
- Institute for Global Health, Northwestern University, Chicago, IL, United States of America
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
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Davids M, Johnstone S, Mendes A, Brecht G, Avenant T, du Plessis N, de Villiers M, Page N, Venter M. Changes in Prevalence and Seasonality of Pathogens Identified in Acute Respiratory Tract Infections in Hospitalised Individuals in Rural and Urban Settings in South Africa; 2018-2022. Viruses 2024; 16:404. [PMID: 38543769 PMCID: PMC10974059 DOI: 10.3390/v16030404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 05/23/2024] Open
Abstract
Severe acute respiratory tract infections (SARIs) has been well described in South Africa with seasonal patterns described for influenza and respiratory syncytial virus (RSV), while others occur year-round (rhinovirus and adenovirus). This prospective syndromic hospital-based surveillance study describes the prevalence and impact of public interventions on the seasonality of other respiratory pathogens during the coronavirus disease-19 (COVID-19) pandemic. This occurred from August 2018 to April 2022, with 2595 patients who met the SARS case definition and 442 controls, from three sentinel urban and rural hospital sites in South Africa. Naso/oro-pharyngeal (NP/OP) swabs were tested using the FastTrack Diagnostics® Respiratory pathogens 33 (RUO) kit. Descriptive statistics, odds ratios, and univariate/multivariate analyses were used. Rhinovirus (14.80%, 228/1540) and Streptococcus pneumoniae (28.50%, 439/1540) were most frequently detected in NP/OP swabs and in children <1 years old (35%, 648/1876). Among others, pathogens associated with SARI cases causing disease were influenza A&B, HRV, RSV, hCoV 229e, Haemophilus influenzae, Staphylococcus aureus, and Streptococcus pneumoniae. Pre-COVID-19, seasonal trends of these pathogens correlated with previous years, with RSV and influenza A seasons only resuming after the national lockdown (2021). It is evident that stringent lockdown conditions have severe impacts on the prevalence of respiratory tract infections.
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Affiliation(s)
- Michaela Davids
- Centre for Emerging Respiratory and Arbovirus Research, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa
| | - Siobhan Johnstone
- Centre for Enteric Diseases, Virology, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa; (S.J.); (N.P.)
| | - Adriano Mendes
- Centre for Emerging Respiratory and Arbovirus Research, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa
| | - Gadean Brecht
- Centre for Emerging Respiratory and Arbovirus Research, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa
| | - Theunis Avenant
- Department of Paediatrics, Kalafong Provincial Tertiary Hospital, University of Pretoria, Pretoria 0084, South Africa
| | - Nicolette du Plessis
- Department of Paediatrics, Kalafong Provincial Tertiary Hospital, University of Pretoria, Pretoria 0084, South Africa
| | - Maryke de Villiers
- Department of Internal Medicine, Kalafong Provincial Tertiary Hospital, University of Pretoria, Pretoria 0084, South Africa
| | - Nicola Page
- Centre for Enteric Diseases, Virology, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa; (S.J.); (N.P.)
- Centre of Enteric Diseases, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa
| | - Marietjie Venter
- Centre for Emerging Respiratory and Arbovirus Research, Department of Medical Virology, University of Pretoria, Pretoria 0084, South Africa
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Kia P, Katagirya E, Kakembo FE, Adera DA, Nsubuga ML, Yiga F, Aloyo SM, Aujat BR, Anguyo DF, Katabazi FA, Kigozi E, Joloba ML, Kateete DP. Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing. Sci Rep 2023; 13:20507. [PMID: 37993530 PMCID: PMC10665338 DOI: 10.1038/s41598-023-47379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023] Open
Abstract
SARS-CoV-2 undergoes frequent mutations, affecting COVID-19 diagnostics, transmission and vaccine efficacy. Here, we describe the genetic diversity of 49 SARS-CoV-2 samples from Uganda, collected during the COVID-19 waves of 2020/2021. Overall, the samples were similar to previously reported SARS-CoV-2 from Uganda and the Democratic Republic of Congo (DRC). The main lineages were AY.46 and A.23, which are considered to be Delta SARS-CoV-2 variants. Further, a total of 268 unique single nucleotide variants and 1456 mutations were found, with more than seventy percent mutations in the ORF1ab and S genes. The most common mutations were 2042C>G (83.4%), 14143C>T (79.5%), 245T>C (65%), and 1129G>T (51%), which occurred in the S, ORF1ab, ORF7a and N genes, respectively. As well, 28 structural variants-21 insertions and 7 deletions, occurred in 16 samples. Our findings point to the possibility that most SARS-CoV-2 infections in Uganda at the time arose from local spread and were not newly imported. Moreover, the relatedness of variants from Uganda and the DRC reflects high human mobility and interaction between the two countries, which is peculiar to this region of the world.
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Affiliation(s)
- Praiscillia Kia
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fredrick Elishama Kakembo
- The African Centers of Excellence in Bioinformatics and Date Intensive Sciences, Infectious Disease Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Doreen Ato Adera
- Multifunctional Research Laboratories, Gulu University, Gulu, Uganda
| | - Moses Luutu Nsubuga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fahim Yiga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sharley Melissa Aloyo
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Brendah Ronah Aujat
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
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Gwarinda HB, Tessema SK, Raman J, Greenhouse B, Birkholtz LM. Population structure and genetic connectivity of Plasmodium falciparum in pre-elimination settings of Southern Africa. FRONTIERS IN EPIDEMIOLOGY 2023; 3:1227071. [PMID: 38455947 PMCID: PMC10910941 DOI: 10.3389/fepid.2023.1227071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/17/2023] [Indexed: 03/09/2024]
Abstract
To accelerate malaria elimination in the Southern African region by 2030, it is essential to prevent cross-border malaria transmission. However, countries within the region are highly interconnected due to human migration that aids in the movement of the parasite across geographical borders. It is therefore important to better understand Plasmodium falciparum transmission dynamics in the region, and identify major parasite source and sink populations, as well as cross-border blocks of high parasite connectivity. We performed a meta-analysis using collated parasite allelic data generated by microsatellite genotyping of malaria parasites from Namibia, Eswatini, South Africa, and Mozambique (N = 5,314). The overall number of unique alleles was significantly higher (P ≤ 0.01) in Namibia (mean A = 17.3 ± 1.46) compared to South Africa (mean A = 12.2 ± 1.22) and Eswatini (mean A = 13.3 ± 1.27, P ≤ 0.05), whilst the level of heterozygosity was not significantly different between countries. The proportion of polyclonal infections was highest for Namibia (77%), and lowest for Mozambique (64%). A was significant population structure was detected between parasites from the four countries, and patterns of gene flow showed that Mozambique was the major source area and Eswatini the major sink area of parasites between the countries. This study showed strong signals of parasite population structure and genetic connectivity between malaria parasite populations across national borders. This calls for strengthening the harmonization of malaria control and elimination efforts between countries in the southern African region. This data also proves its potential utility as an additional surveillance tool for malaria surveillance on both a national and regional level for the identification of imported cases and/or outbreaks, as well as monitoring for the potential spread of anti-malarial drug resistance as countries work towards malaria elimination.
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Affiliation(s)
- Hazel B. Gwarinda
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Sofonias K. Tessema
- EppiCenter, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Jaishree Raman
- Laboratory for Antimalarial Resistance Monitoring and Malaria Operational Research (ARMMOR), Centre for Emerging Zoonotic and Parasitic Diseases, A Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, Wits Research Institute for Malaria, University of Witwatersrand, Johannesburg, South Africa
| | - Bryan Greenhouse
- EppiCenter, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Lyn-Marié Birkholtz
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
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Kuzmina A, Korovin D, Cohen Lass I, Atari N, Ottolenghi A, Hu P, Mandelboim M, Rosental B, Rosenberg E, Diaz-Griffero F, Taube R. Changes within the P681 residue of spike dictate cell fusion and syncytia formation of Delta and Omicron variants of SARS-CoV-2 with no effects on neutralization or infectivity. Heliyon 2023; 9:e16750. [PMID: 37292300 PMCID: PMC10238279 DOI: 10.1016/j.heliyon.2023.e16750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
The rapid spread and dominance of the Omicron SARS-CoV-2 lineages have posed severe health challenges worldwide. While extensive research on the role of the Receptor Binding Domain (RBD) in promoting viral infectivity and vaccine sensitivity has been well documented, the functional significance of the 681PRRAR/SV687 polybasic motif of the viral spike is less clear. In this work, we monitored the infectivity levels and neutralization potential of the wild-type human coronavirus 2019 (hCoV-19), Delta, and Omicron SARS-CoV-2 pseudoviruses against sera samples drawn four months post administration of a third dose of the BNT162b2 mRNA vaccine. Our findings show that in comparison to hCoV-19 and Delta SARS-CoV-2, Omicron lineages BA.1 and BA.2 exhibit enhanced infectivity and a sharp decline in their sensitivity to vaccine-induced neutralizing antibodies. Interestingly, P681 mutations within the viral spike do not play a role in the neutralization potential or infectivity of SARS Cov-2 pseudoviruses carrying mutations in this position. The P681 residue however, dictates the ability of the spike protein to promote fusion and syncytia formation between infected cells. While spike from hCoV-19 (P681) and Omicron (H681) promote only modest cell fusion and formation of syncytia between cells that express the spike-protein, Delta spike (R681) displays enhanced fusogenic activity and promotes syncytia formation. Additional analysis shows that a single P681R mutation within the hCoV-19 spike, or H681R within the Omicron spike, restores fusion potential to similar levels observed for the Delta R681 spike. Conversely, R681P point mutation within the spike of Delta pseudovirus abolishes efficient fusion and syncytia formation. Our investigation also demonstrates that spike proteins from hCoV-19 and Delta SARS-CoV-2 are efficiently incorporated into viral particles relative to the spike of Omicron lineages. We conclude that the third dose of the Pfizer-BNT162b2 provides appreciable protection against the newly emerged Omicron sub-lineages. However, the neutralization sensitivity of these new variants is diminished relative to that of the hCoV-19 or Delta SARS-CoV-2. We further show that the P681 residue within spike dictates cell fusion and syncytia formation with no effects on the infectivity of the specific viral variant and on its sensitivity to vaccine-mediated neutralization.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Dina Korovin
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Ido Cohen Lass
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Nofar Atari
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Aner Ottolenghi
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Israel
| | - Pan Hu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Israel
| | | | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
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Maposa I, Welch R, Ozougwu L, Arendse T, Mudara C, Blumberg L, Jassat W. Using generalized structured additive regression models to determine factors associated with and clusters for COVID-19 hospital deaths in South Africa. BMC Public Health 2023; 23:830. [PMID: 37147648 PMCID: PMC10161152 DOI: 10.1186/s12889-023-15789-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 04/30/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND The first case of COVID-19 in South Africa was reported in March 2020 and the country has since recorded over 3.6 million laboratory-confirmed cases and 100 000 deaths as of March 2022. Transmission and infection of SARS-CoV-2 virus and deaths in general due to COVID-19 have been shown to be spatially associated but spatial patterns in in-hospital deaths have not fully been investigated in South Africa. This study uses national COVID-19 hospitalization data to investigate the spatial effects on hospital deaths after adjusting for known mortality risk factors. METHODS COVID-19 hospitalization data and deaths were obtained from the National Institute for Communicable Diseases (NICD). Generalized structured additive logistic regression model was used to assess spatial effects on COVID-19 in-hospital deaths adjusting for demographic and clinical covariates. Continuous covariates were modelled by assuming second-order random walk priors, while spatial autocorrelation was specified with Markov random field prior and fixed effects with vague priors respectively. The inference was fully Bayesian. RESULTS The risk of COVID-19 in-hospital mortality increased with patient age, with admission to intensive care unit (ICU) (aOR = 4.16; 95% Credible Interval: 4.05-4.27), being on oxygen (aOR = 1.49; 95% Credible Interval: 1.46-1.51) and on invasive mechanical ventilation (aOR = 3.74; 95% Credible Interval: 3.61-3.87). Being admitted in a public hospital (aOR = 3.16; 95% Credible Interval: 3.10-3.21) was also significantly associated with mortality. Risk of in-hospital deaths increased in months following a surge in infections and dropped after months of successive low infections highlighting crest and troughs lagging the epidemic curve. After controlling for these factors, districts such as Vhembe, Capricorn and Mopani in Limpopo province, and Buffalo City, O.R. Tambo, Joe Gqabi and Chris Hani in Eastern Cape province remained with significantly higher odds of COVID-19 hospital deaths suggesting possible health systems challenges in those districts. CONCLUSION The results show substantial COVID-19 in-hospital mortality variation across the 52 districts. Our analysis provides information that can be important for strengthening health policies and the public health system for the benefit of the whole South African population. Understanding differences in in-hospital COVID-19 mortality across space could guide interventions to achieve better health outcomes in affected districts.
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Affiliation(s)
- Innocent Maposa
- Division of Epidemiology & Biostatistics, School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
- Division of Epidemiology & Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, Cape Town, South Africa.
| | - Richard Welch
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
| | - Lovelyn Ozougwu
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
| | - Tracy Arendse
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
| | - Caroline Mudara
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lucille Blumberg
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
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Mukoma G, Bosire EN, Hardy-Johnson P, Barker M, Norris SA. ' We were not allowed to gather even for Christmas.' Impact of COVID-19 on South African young people: Exploring messaging and support. Glob Public Health 2023; 18:2264968. [PMID: 37801722 DOI: 10.1080/17441692.2023.2264968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/21/2023] [Indexed: 10/08/2023]
Abstract
COVID-19 prevention measures including lockdowns, school closures, and restricted movement disrupted young people's lives. This longitudinal qualitative study conducted in Soweto, South Africa aimed to explore young people's knowledge and perceptions of COVID-19, vaccination, and the impact of infections. A convenience sample of 30 young black people (n = 15 men; n = 15 women, aged 16-21 years) from Soweto participated in 24 focus group discussions (FGDs), conducted in six phases - each phase had four FGDs stratified by gender and age. Young people's understanding of COVID-19 deepened throughout the study, however, did not always translate into adherence (following the government's COVID-19 prevention measures). Although deemed inadequate, TV and radio were preferred over internet COVID-19 information. Parents, teachers, and schools were trusted sources of information. Vaccines and limited access to information attributed to low-risk perception, while new COVID-19 variants attributed to high-risk perception. A low-risk perception and conspiracy theories contributed to non-adherence (disregarding COVID-19 preventative measures provided by the government), particularly among young men. Accessing reliable information that considers young people's lives and their living context is important. Communities, scientists, and policymakers must learn from the COVID-19 experience and implement localised preventive strategies for education, awareness, and economic support in future emergencies.
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Affiliation(s)
- Gudani Mukoma
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Biokinetics, Recreation and Sports Science, Faculty of Health Sciences, University of Venda, Thohoyandou, South Africa
| | - Edna N Bosire
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Brain and Mind Institute, Aga Khan University, Nairobi, Kenya
| | - Polly Hardy-Johnson
- Medical Research Council Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
- Primary Care Population Sciences and Medical Education (PPM), Faculty of Medicine, University of Southampton, Southampton, UK
| | - Mary Barker
- Medical Research Council Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
- School of Health Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Shane A Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute for Developmental Science and Global Health Research Institute, School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
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Strydom A, Mellet J, Van Rensburg J, Viljoen I, Athanasiadis A, Pepper MS. Open access and its potential impact on public health - A South African perspective. Front Res Metr Anal 2022; 7:975109. [PMID: 36531754 PMCID: PMC9755351 DOI: 10.3389/frma.2022.975109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/15/2022] [Indexed: 09/19/2023] Open
Abstract
Traditionally, access to research information has been restricted through journal subscriptions. This means that research entities and individuals who were unable to afford subscription costs did not have access to journal articles. There has however been a progressive shift toward electronic access to journal publications and subsequently growth in the number of journals available globally. In the context of electronic journals, both open access and restricted access options exist. While the latter option is comparable to traditional, subscription-based paper journals, open access journal publications follow an "open science" publishing model allowing scholarly communications and outputs to be publicly available online at no cost to the reader. However, for readers to enjoy open access, publication costs are shifted elsewhere, typically onto academic institutions and authors. SARS-CoV-2, and the resulting COVID-19 pandemic have highlighted the benefits of open science through accelerated research and unprecedented levels of collaboration and data sharing. South Africa is one of the leading open access countries on the African continent. This paper focuses on open access in the South African higher education research context with an emphasis on our Institution and our own experiences. It also addresses the financial implications of open access and provides possible solutions for reducing the cost of publication for researchers and their institutions. Privacy in open access and the role of the Protection of Personal Information Act (POPIA) in medical research and secondary use of data in South Africa will also be discussed.
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Affiliation(s)
| | | | | | | | | | - Michael S. Pepper
- SAMRC Extramural Unit for Stem Cell Research and Therapy, Department of Immunology, Faculty of Health Sciences, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
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Ibe C, Otu AA, Mnyambwa NP. Advancing disease genomics beyond COVID-19 and reducing health disparities: what does the future hold for Africa? Brief Funct Genomics 2022; 22:241-249. [DOI: 10.1093/bfgp/elac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/03/2022] [Accepted: 10/14/2022] [Indexed: 11/27/2022] Open
Abstract
Abstract
The COVID-19 pandemic has ushered in high-throughput sequencing technology as an essential public health tool. Scaling up and operationalizing genomics in Africa is crucial as enhanced capacity for genome sequencing could address key health problems relevant to African populations. High-quality genomics research can be leveraged to improve diagnosis, understand the aetiology of unexplained illnesses, improve surveillance of infectious diseases and inform efficient control and therapeutic methods of known, rare and emerging infectious diseases. Achieving these within Africa requires strong commitment from stakeholders. A roadmap is needed to guide training of scientists, infrastructural development, research funding, international collaboration as well as promote public–private partnerships. Although the COVID-19 pandemic has significantly boosted genomics capacity in Africa, the continent still lags other regions. Here, we highlighted key initiatives in genomics research and efforts to address health challenges facing the diverse and fast-growing populations on the continent. We explore the scalability of genomic tools and techniques to tackle a broader range of infectious diseases in Africa, a continent that desperately requires a boost from genomic science.
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Affiliation(s)
- Chibuike Ibe
- Abia State University Department of Microbiology, Faculty of Biological Sciences, , Uturu, Nigeria
| | | | - Nicholaus P Mnyambwa
- National Institute for Medical Research , Muhimbili Research Centre, Dar es Salaam , Tanzania
- Alliance for Africa Health and Research (A4A), Dar es Salaam , Tanzania
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10
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Osman I, Singaram V. Using PhotoVoice to understand mindfulness in health care practitioners. Health SA 2022; 27:1942. [PMID: 36262926 PMCID: PMC9575345 DOI: 10.4102/hsag.v27i0.1942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/15/2022] [Indexed: 11/07/2022] Open
Abstract
Background The disruptions of the coronavirus disease 2019 (COVID-19) pandemic have placed added stress on health care practitioners’ (HCPs) mental health. Mindfulness-based interventions (MBIs) have been reported to increase the awareness of burnout and promote self-care practices that enhance mental well-being. Aim To gain insight into the use of mindfulness through the lens of PhotoVoice on how HCPs reflected on their stressors and sense of self whilst working as frontline workers during the COVID-19 pandemic. Setting This study was conducted online with HCPs working in South Africa during the first wave of COVID-19. Method A four-week MBI intervention was implemented using Zoom. An exploratory qualitative analysis was conducted using a PhotoVoice methodology. Interpretative phenomenological analysis was used to generate themes. Fifty-five HCPs consented to participate in this study. Results The major themes identified were operating on autopilot, feeling a sense of overwhelm because of COVID-19, using faith to cope and being able to attain a sense of self-compassion by the end of the intervention. Conclusions Using visual representations, HCPs were able to share the development of their reperceived lived experiences of increased self-compassion as they navigated the dilemmas and disruptions of the pandemic. Contribution A brief online MBI was impactful enough to show a reappraisal of the stressors of COVID-19, such that HCPs felt calmer, more competent and more compassionate. PhotoVoice methodology is recommended for future studies and mindfulness courses. It facilitates a deeper understanding of the practice of imbuing mindfulness and its impact on stressors and the self.
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Affiliation(s)
- Iram Osman
- Department of Clinical Medicine, Faculty of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Veena Singaram
- Department of Clinical Medicine, Faculty of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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11
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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] [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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12
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Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nat Rev Genet 2022; 23:547-562. [PMID: 35459859 PMCID: PMC9028907 DOI: 10.1038/s41576-022-00483-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 01/05/2023]
Abstract
Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.
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Affiliation(s)
- Stephen W Attwood
- Department of Zoology, University of Oxford, Oxford, UK.
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK.
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13
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Kuja JO, Kanoi BN, Balboa RF, Shiluli C, Maina M, Waweru H, Gathii K, Mungai M, Masika M, Anzala O, Mwau M, Clark TG, Waitumbi J, Gitaka J. Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya. BMC Genomics 2022; 23:627. [PMID: 36050650 PMCID: PMC9434529 DOI: 10.1186/s12864-022-08853-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/19/2022] [Indexed: 11/10/2022] Open
Abstract
Genomic surveillance and identification of COVID-19 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SARS-CoV-2. Genomic surveillance provides insights into circulating infections, and the robustness and design of vaccines and other infection control approaches. We sequenced 57 SARS-CoV-2 isolates from a Kenyan clinical population, of which 55 passed quality checks using the Ultrafast Sample placement on the Existing tRee (UShER) workflow. Phylo-genome-temporal analyses across two regions in Kenya (Nairobi and Kiambu County) revealed that B.1.1.7 (Alpha; n = 32, 56.1%) and B.1 (n = 9, 15.8%) were the predominant lineages, exhibiting low Ct values (5-31) suggesting high infectivity, and variant mutations across the two regions. Lineages B.1.617.2, B.1.1, A.23.1, A.2.5.1, B.1.596, A, and B.1.405 were also detected across sampling sites within target populations. The lineages and genetic isolates were traced back to China (A), Costa Rica (A.2.5.1), Europe (B.1, B.1.1, A.23.1), the USA (B.1.405, B.1.596), South Africa (B.1.617.2), and the United Kingdom (B.1.1.7), indicating multiple introduction events. This study represents one of the genomic SARS-CoV-2 epidemiology studies in the Nairobi metropolitan area, and describes the importance of continued surveillance for pandemic control.
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Affiliation(s)
- Josiah O Kuja
- Mount Kenya University, Thika, Kenya.
- University of Copenhagen, Copenhagen, Denmark.
| | | | | | | | | | | | - Kimita Gathii
- United States Army Medical Research Directorate, Kisumu, Kenya
| | - Mary Mungai
- Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Omu Anzala
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Matilu Mwau
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Taane G Clark
- London School of Hygiene & Tropical Medicine, London, UK
| | - John Waitumbi
- United States Army Medical Research Directorate, Kisumu, Kenya
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14
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Yang W, Shaman JL. COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron). eLife 2022; 11:e78933. [PMID: 35943138 PMCID: PMC9363123 DOI: 10.7554/elife.78933] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/21/2022] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have been key drivers of new coronavirus disease 2019 (COVID-19) pandemic waves. To better understand variant epidemiologic characteristics, here we apply a model-inference system to reconstruct SARS-CoV-2 transmission dynamics in South Africa, a country that has experienced three VOC pandemic waves (i.e. Beta, Delta, and Omicron BA.1) by February 2022. We estimate key epidemiologic quantities in each of the nine South African provinces during March 2020 to February 2022, while accounting for changing detection rates, infection seasonality, nonpharmaceutical interventions, and vaccination. Model validation shows that estimated underlying infection rates and key parameters (e.g. infection-detection rate and infection-fatality risk) are in line with independent epidemiological data and investigations. In addition, retrospective predictions capture pandemic trajectories beyond the model training period. These detailed, validated model-inference estimates thus enable quantification of both the immune erosion potential and transmissibility of three major SARS-CoV-2 VOCs, that is, Beta, Delta, and Omicron BA.1. These findings help elucidate changing COVID-19 dynamics and inform future public health planning.
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Affiliation(s)
- Wan Yang
- Department of Epidemiology, Mailman School of Public Health, Columbia UniversityNew YorkUnited States
| | - Jeffrey L Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia UniversityNew YorkUnited States
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15
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Yang W, Shaman J. COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022. [PMID: 34981071 DOI: 10.1101/2021.12.19.21268073] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have been key drivers of new coronavirus disease 2019 (COVID-19) pandemic waves. To better understand variant epidemiologic characteristics, here we apply a model-inference system to reconstruct SARS-CoV-2 transmission dynamics in South Africa, a country that has experienced three VOC pandemic waves (i.e. Beta, Delta, and Omicron). We estimate key epidemiologic quantities in each of the nine South African provinces during March 2020 â€" Feb 2022, while accounting for changing detection rates, infection seasonality, nonpharmaceutical interventions, and vaccination. Model validation shows that estimated underlying infection rates and key parameters (e.g., infection-detection rate and infection-fatality risk) are in line with independent epidemiological data and investigations. In addition, retrospective predictions capture pandemic trajectories beyond the model training period. These detailed, validated model-inference estimates thus enable quantification of both the immune erosion potential and transmissibility of three major SARS-CoV-2 VOCs, i.e., Beta, Delta, and Omicron. These findings help elucidate changing COVID-19 dynamics and inform future public health planning.
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16
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El-Attar EA, Helmy Elkaffas RM, Aglan SA, Naga IS, Nabil A, Abdallah HY. Genomics in Egypt: Current Status and Future Aspects. Front Genet 2022; 13:797465. [PMID: 35664315 PMCID: PMC9157251 DOI: 10.3389/fgene.2022.797465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Egypt is the third most densely inhabited African country. Due to the economic burden and healthcare costs of overpopulation, genomic and genetic testing is a huge challenge. However, in the era of precision medicine, Egypt is taking a shift in approach from “one-size-fits all” to more personalized healthcare via advancing the practice of medical genetics and genomics across the country. This shift necessitates concrete knowledge of the Egyptian genome and related diseases to direct effective preventive, diagnostic and counseling services of prevalent genetic diseases in Egypt. Understanding disease molecular mechanisms will enhance the capacity for personalized interventions. From this perspective, we highlight research efforts and available services for rare genetic diseases, communicable diseases including the coronavirus 2019 disease (COVID19), and cancer. The current state of genetic services in Egypt including availability and access to genetic services is described. Drivers for applying genomics in Egypt are illustrated with a SWOT analysis of the current genetic/genomic services. Barriers to genetic service development in Egypt, whether economic, geographic, cultural or educational are discussed as well. The sensitive topic of communicating genomic results and its ethical considerations is also tackled. To understand disease pathogenesis, much can be gained through the advancement and integration of genomic technologies via clinical applications and research efforts in Egypt. Three main pillars of multidisciplinary collaboration for advancing genomics in Egypt are envisaged: resources, infrastructure and training. Finally, we highlight the recent national plan to establish a genome center that will aim to prepare a map of the Egyptian human genome to discover and accurately determine the genetic characteristics of various diseases. The Reference Genome Project for Egyptians and Ancient Egyptians will initialize a new genomics era in Egypt. We propose a multidisciplinary governance system in Egypt to support genomic medicine research efforts and integrate into the healthcare system whilst ensuring ethical conduct of data.
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Affiliation(s)
- Eman Ahmed El-Attar
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
- *Correspondence: Eman Ahmed El-Attar,
| | | | - Sarah Ahmed Aglan
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Iman S. Naga
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Amira Nabil
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Hoda Y. Abdallah
- Medical Genetics Unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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17
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Generation of human tonsil epithelial organoids as an ex vivo model for SARS-CoV-2 infection. Biomaterials 2022; 283:121460. [PMID: 35286852 PMCID: PMC8901203 DOI: 10.1016/j.biomaterials.2022.121460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 12/14/2022]
Abstract
The palatine tonsils (hereinafter referred to as “tonsils”) serve as a reservoir for viral infections and play roles in the immune system's first line of defense. The aims of this study were to establish tonsil epithelial cell–derived organoids and examine their feasibility as an ex vivo model for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The tonsil organoids successfully recapitulated the key characteristics of the tonsil epithelium, including cellular composition, histologic properties, and biomarker distribution. Notably, the basal layer cells of the organoids express molecules essential for SARS-CoV-2 entry, such as angiotensin-converting enzyme 2 (ACE2), transmembrane serine protease 2 (TMPRSS2) and furin, being susceptible to the viral infection. Changes in the gene expression profile in tonsil organoids revealed that 395 genes associated with oncostatin M signaling and lipid metabolism were highly upregulated within 72 h after SARS-CoV-2 infection. Notably, remdesivir suppressed the viral RNA copy number in organoid culture supernatants and intracellular viral protein levels in a dose-dependent manner. Here, we suggest that tonsil epithelial organoids could provide a preclinical and translational research platform for investigating SARS-CoV-2 infectivity and transmissibility or for evaluating antiviral candidates.
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Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-Kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. iScience 2022; 25:103880. [PMID: 35156006 PMCID: PMC8817759 DOI: 10.1016/j.isci.2022.103880] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/29/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
There is a dearth of information on COVID-19 disease dynamics in Africa. To fill this gap, we investigated the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in the continent. We retrieved 5229 complete genomes collected in 33 African countries from the GISAID database. We investigated the circulating diversity, reconstructed the viral evolutionary divergence and history, and studied the case and death trends in the continent. Almost a fifth (144/782, 18.4%) of Pango lineages found worldwide circulated in Africa, with five different lineages dominating over time. Phylogenetic analysis revealed that African viruses cluster more closely with those from Europe. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the epidemiological and evolutionary dynamics of the circulating viral diversity in Africa. They also emphasize the need to expand surveillance efforts in Africa to help inform and implement better public health measures. SARS-CoV-2 viruses from Africa cluster predominantly with European strains Lower viral diversity observed in Africa is likely due to genomic under-surveillance Number of cases, deaths, and testing show substantial heterogeneity across Africa Two motifs could function as integrin-binding sites and N-glycosylation domains
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Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria.,Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-Kwashie
- Department of Medical Microbiology, Clinical Virology Unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria.,Helix Biogen Institute, Ogbomoso, Nigeria
| | - Louis Odinakaose Ezediuno
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin,1515 P.M.B, Ilorin, Nigeria
| | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria.,Division of Microbiology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield Pretoria 0028, South Africa
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Medical Microbiology and Parasitology, University of Ilorin 1515, P.M.B, Ilorin, Nigeria
| | - David J Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria
| | - Nídia S Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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19
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Katey D, Abass K, Garsonu EK, Gyasi RM. Depopulation or vaccination? Tackling the COVID-19 crisis in prisons in Africa. HEALTH & JUSTICE 2022; 10:12. [PMID: 35247123 PMCID: PMC8897616 DOI: 10.1186/s40352-022-00176-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 02/20/2022] [Indexed: 05/05/2023]
Abstract
Several attempts have been made by the global public health efforts and national governments to contain the spread and vulnerabilities to COVID-19. Evidence, however, shows a disproportionate upsurge in COVID-19 cases in correctional facilities such as prisons, particularly, in low- and middle-income countries (LMICs). The poor adherence to COVID-19 preventive protocols in these settings has raised a serious "moral panic" among the public. There are public health concerns about the most effective and state-of-the-art approach to tackling the continuous spread of the virus in prisons. This paper discusses the feasibility of depopulation and vaccination rollouts in combating COVID-19 in correctional facilities with a particular focus on African prisons. The paper proposes selective and strategic depopulation of prisoners, effective prioritization of vaccination among prisoners, and general sensitization of prisoners toward vaccine disbursement in this total institution.
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Affiliation(s)
- Daniel Katey
- Department of Geography and Rural Development, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kabila Abass
- Department of Geography and Rural Development, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emmanuel Kofi Garsonu
- Department of Geography and Rural Development, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Razak M. Gyasi
- African Population and Health Research Centre, Nairobi, Kenya
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20
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Aggarwal D, Page AJ, Schaefer U, Savva GM, Myers R, Volz E, Ellaby N, Platt S, Groves N, Gallagher E, Tumelty NM, Le Viet T, Hughes GJ, Chen C, Turner C, Logan S, Harrison A, Peacock SJ, Chand M, Harrison EM. Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nat Commun 2022; 13:1012. [PMID: 35197443 PMCID: PMC8866425 DOI: 10.1038/s41467-022-28371-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/18/2022] [Indexed: 01/16/2023] Open
Abstract
Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16-20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement.
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Affiliation(s)
- Dinesh Aggarwal
- University of Cambridge, Department of Medicine, Cambridge, UK. .,Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. .,Cambridge University Hospital NHS Foundation Trust, Cambridge, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Ulf Schaefer
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Richard Myers
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Erik Volz
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
| | - Nicholas Ellaby
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Steven Platt
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Natalie Groves
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | | | - Niamh M Tumelty
- University of Cambridge, Cambridge University Libraries, Cambridge, UK
| | - Thanh Le Viet
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Gareth J Hughes
- Public Health England National Infections Service, Field Service, Leeds, UK
| | - Cong Chen
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Charlie Turner
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Sophie Logan
- Public Health England, National Infections Service, Field Service, Nottingham, UK
| | - Abbie Harrison
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | | | - Sharon J Peacock
- University of Cambridge, Department of Medicine, Cambridge, UK.,Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK.,Cambridge University Hospital NHS Foundation Trust, Cambridge, UK.,Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Meera Chand
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Ewan M Harrison
- University of Cambridge, Department of Medicine, Cambridge, UK. .,Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,University of Cambridge, Department of Public Health and Primary Care, Cambridge, UK.
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21
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Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. Microorganisms 2022; 10:microorganisms10010099. [PMID: 35056548 PMCID: PMC8778844 DOI: 10.3390/microorganisms10010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/25/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
In the initial phase of the novel coronavirus disease (COVID-19) pandemic, a large-scale cluster on the cruise ship Diamond Princess (DP) emerged in Japan. Genetic analysis of the DP strains has provided important information for elucidating the possible transmission process of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on a cruise ship. However, genome-based analyses of SARS-CoV-2 detected in large-scale cruise ship clusters other than the DP cluster have rarely been reported. In the present study, whole-genome sequences of 94 SARS-CoV-2 strains detected in the second large cruise ship cluster, which emerged on the Costa Atlantica (CA) in Japan, were characterized to understand the evolution of the virus in a crowded and confined place. Phylogenetic and haplotype network analysis indicated that the CA strains were derived from a common ancestral strain introduced on the CA cruise ship and spread in a superspreading event-like manner, resulting in several mutations that might have affected viral characteristics, including the P681H substitution in the spike protein. Moreover, there were significant genetic distances between CA strains and other strains isolated in different environments, such as cities under lockdown. These results provide new insights into the unique evolution patterns of SARS-CoV-2 in the CA cruise ship cluster.
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22
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Chan CTM, Leung JSL, Lee LK, Lo HWH, Wong EYK, Wong DSH, Ng TTL, Lao HY, Lu KK, Jim SHC, Yau MCY, Lam JYW, Ho AYM, Luk KS, Yip KT, Que TL, To KKW, Siu GKH. A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. J Virol Methods 2022; 299:114333. [PMID: 34656702 PMCID: PMC8516123 DOI: 10.1016/j.jviromet.2021.114333] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022]
Abstract
The increasing prevalence of N501Y variants of SARS-CoV-2 has kindled global concern due to their enhanced transmissibility. Genome sequencing is the gold standard method to identify the emerging variants of concern. But it is time-consuming and expensive, limiting the widespread deployment of genome surveillance in some countries. Health authorities surge the development of alternative assay to expand screening capacity with reduced time and cost. In this study, we developed an in-house TaqMan minor groove binder (MGB) probe-based one-step RT-qPCR assay to detect the presence of N501Y mutation in SARS-CoV-2. A total of 168 SARS-CoV-2 positive respiratory specimens were collected to determine diagnostic accuracy of the RT-qPCR assay. As a reference standard, PANGO lineages and the mutation patterns of all samples were characterised by whole-genome sequencing. The analytical sensitivity and the ability of the assay to detect low frequency of N501Y variants were also evaluated. A total of 31 PANGO lineages were identified from 168 SARS-CoV-2 positive cases, in which 34 samples belonged to N501Y variants, including B.1.1.7 (n = 20), B.1.351 (n = 12) and P.3 (n = 2). The N501Y RT-qPCR correctly identified all 34 samples as N501Y-positive and the other 134 samples as wildtype. The limit-of-detection of the assay consistently achieved 1.5 copies/μL on four different qPCR platforms. N501Y mutation was successfully detected at an allele frequency as low as 10 % in a sample with mixed SARS-CoV-2 lineage. The N501Y RT-qPCR is simple and inexpensive (US$1.6 per sample). It enables robust high-throughput screening for surveillance of SARS-CoV-2 variants of concern harbouring N501Y mutation.
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Affiliation(s)
- Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Hazel Wing-Hei Lo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Evelyn Yin-Kwan Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Denise Sze-Hang Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Kelvin Keru Lu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Stephanie Hoi-Ching Jim
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Miranda Chong-Yee Yau
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong Special Administrative Region
| | - Jimmy Yiu-Wing Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong Special Administrative Region
| | - Alex Yat-Man Ho
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region
| | - Kristine Shik Luk
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region
| | - Kam-Tong Yip
- Department of Clinical Pathology, Tuen Mun Hospital, Hong Kong Special Administrative Region
| | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Hong Kong Special Administrative Region
| | - Kelvin Kai-Wang To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region.
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23
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Kuzmina A, Wattad S, Khalaila Y, Ottolenghi A, Rosental B, Engel S, Rosenberg E, Taube R. SARS CoV-2 Delta variant exhibits enhanced infectivity and a minor decrease in neutralization sensitivity to convalescent or post-vaccination sera. iScience 2021; 24:103467. [PMID: 34805783 PMCID: PMC8591850 DOI: 10.1016/j.isci.2021.103467] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/19/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022] Open
Abstract
Since their identification, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Kappa and Delta have rapidly spread to become globally dominant. However, their infectivity and sensitivity to administered vaccines have not been documented. We monitored the neutralization potential of convalescent or BNT162b2 post-vaccination sera against Kappa and Delta SARS-CoV-2 pseudoviruses. We show that both variants were successfully neutralized by convalescent and post-vaccination sera, exhibiting a mild decrease in their neutralization sensitivity. Of the two variants, Delta presented enhanced infectivity levels compared with Kappa or wild-type SARS-CoV-2. Nevertheless, both variants were not as infectious or resistant to post-vaccination sera as the Beta variant of concern. Interestingly, the Delta plus variant (AY.1/B.1.617.2.1) exhibited high resistance to post-vaccination sera, similar to that of the Beta SARS-CoV-2. However, its infectivity levels were close to those of wild-type SARS-CoV-2. These results account for the worldwide prevalence of Delta variant of concern and confirm the efficacy of the BNT162b2 vaccine against circulating other Delta variants.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Seraj Wattad
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Aner Ottolenghi
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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24
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Peng XL, Cheng JSY, Gong HL, Yuan MD, Zhao XH, Li Z, Wei DX. Advances in the design and development of SARS-CoV-2 vaccines. Mil Med Res 2021; 8:67. [PMID: 34911569 PMCID: PMC8674100 DOI: 10.1186/s40779-021-00360-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 11/15/2021] [Indexed: 01/18/2023] Open
Abstract
Since the end of 2019, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. The RNA genome of SARS-CoV-2, which is highly infectious and prone to rapid mutation, encodes both structural and nonstructural proteins. Vaccination is currently the only effective method to prevent COVID-19, and structural proteins are critical targets for vaccine development. Currently, many vaccines are in clinical trials or are already on the market. This review highlights ongoing advances in the design of prophylactic or therapeutic vaccines against COVID-19, including viral vector vaccines, DNA vaccines, RNA vaccines, live-attenuated vaccines, inactivated virus vaccines, recombinant protein vaccines and bionic nanoparticle vaccines. In addition to traditional inactivated virus vaccines, some novel vaccines based on viral vectors, nanoscience and synthetic biology also play important roles in combating COVID-19. However, many challenges persist in ongoing clinical trials.
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Affiliation(s)
- Xue-Liang Peng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Ji-Si-Yu Cheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Hai-Lun Gong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Meng-Di Yuan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Xiao-Hong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
| | - Zibiao Li
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634 Singapore
| | - Dai-Xu Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Department of Life Sciences and Medicine, Northwest University, Xi’an, 710069 China
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25
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Nxumalo CT, Mchunu GG. A qualitative study to explore primary health care practitioners' perceptions and understanding regarding the COVID-19 pandemic in KwaZulu-Natal, South Africa. Afr J Prim Health Care Fam Med 2021; 13:e1-e11. [PMID: 34879694 PMCID: PMC8661111 DOI: 10.4102/phcfm.v13i1.3084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) is a novel virus that has rapidly spread across countries globally, and has been declared a pandemic by the World Health Organization (WHO). In South Africa, more that 1 million cases have been confirmed since case zero was detected in March 2020. South Africa is currently leading in the sub-Saharan African region in terms of COVID-19-related mortality and morbidity rates. AIM The aim of this study was to explore primary health care practitioners' perceptions and understanding regarding the COVID-19 pandemic in KwaZulu-Natal, South Africa. SETTING The study was conducted at two selected primary health care facilities (a community health centre and satellite clinic) within a low-income rural context in KwaZulu-Natal, South Africa. METHODS A qualitative study was conducted to explore and describe perceptions and understanding of primary health care practitioners regarding the COVID-19 pandemic in KwaZulu-Natal (KZN), South Africa. Data were collected from a purposive sample of 15 participants at two different clinics situated in rural KZN, South Africa. Participants comprised of nurses, physiotherapists, pharmacists, community care givers, social workers and clinical associates. The participants were both men and women who were all above the age of 20. Data were collected through individual, in-depth face-to-face interviews using a semi-structured interview guide. An audiotape was used to collect data, which were transcribed verbatim. Data were analysed manually by thematic analysis following Tech's steps of data analysis. RESULTS Participants reported pre-pandemic and pandemic perceptions of fear, denial, expectancy and a perceived poor preparation for the COVID-19 outbreak. The findings also revealed participants' misperceptions regarding the nature of the COVID-19 pandemic and unrealistic expectations of occupational compensations for working during the outbreak. CONCLUSION The findings of this study suggest that primary health care practitioners generally have negative perceptions and understanding regarding the pandemic because of misinformation obtained from social media. Interventions to support health care practitioners are necessary to mitigate the potentially negative implications of health practitioners' misconceptions on service delivery and their mental health.
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Affiliation(s)
- Celenkosini T Nxumalo
- School of Nursing and Public Health, College of Health Sciences, University of KwaZulu-Natal, Durban.
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26
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Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri ARN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang’a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O’Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LDO, Tyers L, Ramuth M, Mastouri M, Aouni M, el Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science 2021; 374:423-431. [PMID: 34672751 PMCID: PMC7613315 DOI: 10.1126/science.abj4336] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023]
Abstract
The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
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Affiliation(s)
- Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, 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
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diego Cuadros
- Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abechi Priscilla
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Adedotun-Sulaiman Kemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Adeyemi O. O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Adnène Hammami
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Ahmad Sayed
- Genomics Research Program, Children’s Cancer Hospital, Cairo, Egypt
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Aida Elargoubi
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ajogbasile F. Victoria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Ali A. Yahaya
- World Health Organization, Africa Region, Brazzaville Congo
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France
| | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Kone
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amel Chtourou
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | | | - Anika Vinze
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arnold Lambisia
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Audu Rosemary
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | | | - Bronwyn Kleinhans
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Bryan Tegomoh
- The Biotechnology Center of the University of Yaoundé I, Cameroon and CDC Foundation, Yaounde, Cameroon
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | | | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - D. James Nokes
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Danny Park
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | | | - Deelan Doolabh
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diarra Bassirou
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edgar Simulundu
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Elmostafa El Fahime
- Functional Genomic Platform/National Centre for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | | | - Faida Ajili
- Research Unit of Autoimmune Diseases UR17DN02, Military Hospital of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fakayode O. Enoch
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Fares Wasfi
- Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | | | - Fawzi Derrar
- National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria
| | - Feriel Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Fowotade Adeola
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Frank Tanser
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | | | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Gugu P. Maphalala
- Institution and Department, Ministry Of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hajar Lemriss
- Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Happi Anise
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela H. Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | - Hesham A. Elgahzaly
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas B. Ayed
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, 1006 Tunis, Tunisia
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Imed Gaaloul
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Inbal Gazy
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Innocent Mudau
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Jean B. Lekana-Douk
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jingjing Li
- Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Q. Mends
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - John M. Morobe
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnathan A. Edwards
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | - Khadija M. Said
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Kim Hae-Young
- New York University Grossman School of Medicine, New York City, NY, USA
| | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Lahcen Belyamani
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Ministry of Health and Wellness, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Mahmoud el Hefnawi
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo Egypt
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Manel Turki
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Marietou Paye
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Maureen W. Mburu
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Maximillian Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Institute, Dar-es-Salaam, Tanzania
| | - Mba Nwando
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Mirabeau T. Youtchou
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Mohamed G. Seadawy
- Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, Egypt
| | | | - Mooko Sekhele
- National Reference Laboratory Lesotho, Maseru, Lesotho
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | | | | | - Mushal Allam
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nalia Ismael
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nedio Mabunda
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngoy Nsenga
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | | | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oguzie Judith
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olawoye Idowu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Omoruyi E. Chukwuma
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Chika K. Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Peter K. Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Reuben Ayivor-Djanie
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Saâd El Kabbaj
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Salako B. Lawal
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Samar Kassim
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Metha
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Sami Kammoun
- CHU Hedi Chaker Sfax, Service de Pneumologie, Tunis, Tunisia
| | - Sanaâ Lemriss
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Sara H. A. Agwa
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | | | | | - Seydou Doumbia
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Sheila M. Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Sobajo Tope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Steve A. Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwanibe Jessica
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - William K. Ampofo
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Bourema Kouriba
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | | | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ngonda Saasa
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | | | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, 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
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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Sun Q, McMahon DE, Ugwu-Dike PO, Sun Q, Tang K, Zhang H, Suchonwanit P, Oh CC, Chong AH, Willems A, Galván C, Dodiuk-Gad RP, Fantini F, Recalcati S, Avancini J, Miyamoto D, Sanches JA, Raboobee N, Bravo F, Freeman EE. How Coronavirus Disease 2019 Changed Dermatology Practice in 1 Year Around the World: Perspectives from 11 Countries. Dermatol Clin 2021; 39:639-651. [PMID: 34556253 PMCID: PMC8452267 DOI: 10.1016/j.det.2021.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qisi Sun
- Department of Dermatology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Devon E McMahon
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA
| | - Pearl O Ugwu-Dike
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA
| | - Qiuning Sun
- Department of Dermatology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 9 Dongdan 3rd Alley, Dong Dan, Dongcheng Qu, Beijing Shi, China
| | - Keyun Tang
- Department of Dermatology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 9 Dongdan 3rd Alley, Dong Dan, Dongcheng Qu, Beijing Shi, China
| | - Hanlin Zhang
- Department of Dermatology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 9 Dongdan 3rd Alley, Dong Dan, Dongcheng Qu, Beijing Shi, China
| | - Poonkiat Suchonwanit
- Division of Dermatology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Thanon Rama VI, Khwaeng Thung Phaya Thai, Khet Ratchathewi, Krung Thep Maha Nakhon 10400, Thailand
| | - Choon Chiat Oh
- Department of Dermatology, Singapore General Hospital, Singapore, Outram Rd, Singapore 169608, Singapore
| | - Alvin H Chong
- Skin Health Institute, level 1/80 Drummond St, Carlton, VIC 3053, Australia; Department of Medicine (Dermatology), St Vincent's Hospital Melbourne, University of Melbourne, Parkville, VIC 3010, Australia
| | - Anneliese Willems
- Skin Health Institute, level 1/80 Drummond St, Carlton, VIC 3053, Australia
| | - Cristina Galván
- Department of Dermatology, Hospital Universitario de Móstoles, Calle Río Júcar, S/N, 28935 Móstoles, Madrid, Spain
| | - Roni P Dodiuk-Gad
- Bruce Rappaport Faculty of Medicine, Technion - Institute of Technology, Haifa, 3200003, Israel; Department of Dermatology, Emek Medical Center, Yitshak Rabin Boulevard 21, Afula, 1834111, Israel; Division of Dermatology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada
| | - Fabrizio Fantini
- Department of Dermatology, Dermatology Unit, ASST Lecco, Alessandro Manzoni Hospital, Via dell'Eremo, 9/11, 23900 Lecco LC, Italy
| | - Sebastiano Recalcati
- Department of Dermatology, Dermatology Unit, ASST Lecco, Alessandro Manzoni Hospital, Via dell'Eremo, 9/11, 23900 Lecco LC, Italy
| | - Joao Avancini
- Department of Dermatology, Hospital das Clínicas of the University of Sao Paulo, Rua, Av. Dr. Enéas Carvalho de Aguiar, 255-Cerqueira César, São Paulo-SP, 05403-000, Brazil
| | - Denise Miyamoto
- Department of Dermatology, Hospital das Clínicas of the University of Sao Paulo, Rua, Av. Dr. Enéas Carvalho de Aguiar, 255-Cerqueira César, São Paulo-SP, 05403-000, Brazil
| | - Jose A Sanches
- Department of Dermatology, Hospital das Clínicas of the University of Sao Paulo, Rua, Av. Dr. Enéas Carvalho de Aguiar, 255-Cerqueira César, São Paulo-SP, 05403-000, Brazil
| | - Noufal Raboobee
- Department of Dermatology, Westville Hospital, 7 Harry Gwala Rd, Westville, Durban, 3630, South Africa
| | - Francisco Bravo
- Department of Dermatology, Universidad Peruana Cayetano Heredia, Hospital Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porres 15102, Peru; Department of Pathology, Universidad Peruana Cayetano Heredia, Hospital Cayetano Heredia, 1 CV Zac, Av. Honorio Delgado 262, San Martín de Porres 15102, Peru
| | - Esther E Freeman
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA.
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Could live attenuated vaccines better control COVID-19? Vaccine 2021; 39:5719-5726. [PMID: 34426024 PMCID: PMC8354792 DOI: 10.1016/j.vaccine.2021.08.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/23/2022]
Abstract
In an effort to control the COVID-19 pandemic, large-scale vaccination is being implemented in various countries using anti-SARS-CoV-2 vaccines based on mRNAs, adenovirus vectors, and inactivated viruses. However, there are concerns regarding adverse effects, such as the induction of fever attributed to mRNA vaccines and pre-existing immunity against adenovirus vectored vaccines or their possible involvement in the development of thrombosis. The induction of antibodies against the adenovirus vector itself constitutes another hindrance, rendering boosting vaccinations ineffective. Additionally, it has been questioned whether inactivated vaccines that predominantly induce humoral immunity are effective against newly arising variants, as some isolated strains were found to be resistant to the serum from COVID-19-recovered patients. Although the number of vaccinated people is steadily increasing on a global scale, it is still necessary to develop vaccines to address the difficulties and concerns mentioned above. Among the various vaccine modalities, live attenuated vaccines have been considered the most effective, since they closely replicate a natural infection without the burden of the disease. In our attempt to provide an additional option to the repertoire of COVID-19 vaccines, we succeeded in isolating temperature-sensitive strains with unique phenotypes that could serve as seeds for a live attenuated vaccine. In this review article, we summarize the characteristics of the currently approved SARS-CoV-2 vaccines and discuss their advantages and disadvantages. In particular, we focus on the novel temperature-sensitive variants of SARS-CoV-2 that we have recently isolated, and their potential application as live-attenuated vaccines. Based on a thorough evaluation of the different vaccine modalities, we argue that it is important to optimize usage not only based on efficacy, but also on the phases of the pandemic. Our findings can be used to inform vaccination practices and improve global recovery from the COVID-19 pandemic.
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McCarthy KM, Tempia S, Kufa T, Kleynhans J, Wolter N, Jassat W, Ebonwu J, von Gottberg A, Erasmus L, Muchengeti M, Walaza S, Ntshoe G, Shonhiwa AM, Manana PN, Pillay Y, Moonasar D, Muthivhi T, Mngemane S, Mlisana K, Chetty K, Blumberg LH, Cohen C, Govender NP. The importation and establishment of community transmission of SARS-CoV-2 during the first eight weeks of the South African COVID-19 epidemic. EClinicalMedicine 2021; 39:101072. [PMID: 34405139 PMCID: PMC8360332 DOI: 10.1016/j.eclinm.2021.101072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND We describe the epidemiology of COVID-19 in South Africa following importation and during implementation of stringent lockdown measures. METHODS Using national surveillance data including demographics, laboratory test data, clinical presentation, risk exposures (travel history, contacts and occupation) and outcomes of persons undergoing COVID-19 testing or hospitalised with COVID-19 at sentinel surveillance sites, we generated and interpreted descriptive statistics, epidemic curves, and initial reproductive numbers (Rt). FINDINGS From 4 March to 30 April 2020, 271,670 SARS-CoV-2 PCR tests were performed (462 tests/100,000 persons). Of these, 7,892 (2.9%) persons tested positive (median age 37 years (interquartile range 28-49 years), 4,568 (58%) male, cumulative incidence of 13.4 cases/100,000 persons). Hospitalization records were found for 1,271 patients (692 females (54%)) of whom 186 (14.6%) died. Amongst 2,819 cases with data, 489/2819 (17.3%) travelled internationally within 14 days prior to diagnosis, mostly during March 2020 (466 (95%)). Cases diagnosed in April compared with March were younger (median age, 37 vs. 40 years), less likely female (38% vs. 53%) and resident in a more populous province (98% vs. 91%). The national initial Rt was 2.08 (95% confidence interval (CI): 1.71-2.51). INTERPRETATION The first eight weeks following COVID-19 importation were characterised by early predominance of imported cases and relatively low mortality and transmission rates. Despite stringent lockdown measures, the second month following importation was characterised by community transmission and increasing disease burden in more populous provinces.
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Oude Munnink BB, Worp N, Nieuwenhuijse DF, Sikkema RS, Haagmans B, Fouchier RAM, Koopmans M. The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nat Med 2021; 27:1518-1524. [PMID: 34504335 DOI: 10.1038/s41591-021-01472-w] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/20/2021] [Indexed: 02/08/2023]
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.
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Affiliation(s)
- Bas B Oude Munnink
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Bart Haagmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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Rattanapisit K, Bulaon CJI, Khorattanakulchai N, Shanmugaraj B, Wangkanont K, Phoolcharoen W. Plant-produced SARS-CoV-2 receptor binding domain (RBD) variants showed differential binding efficiency with anti-spike specific monoclonal antibodies. PLoS One 2021; 16:e0253574. [PMID: 34379620 PMCID: PMC8357147 DOI: 10.1371/journal.pone.0253574] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/09/2021] [Indexed: 11/18/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the ongoing coronavirus disease (COVID-19) pandemic which is characterized by respiratory illness and severe pneumonia, and currently accounts for > 2.5 million deaths worldwide. Recently, diverse mutations in the spike protein of SARS-CoV-2 were reported in United Kingdom (Alpha) and South Africa (Beta) strains which raise concerns over the potential increase in binding affinity towards the host cell receptor and diminished host neutralization capabilities. In order to study the effect of mutation in the binding efficiency of SARS-CoV-2 receptor binding domain (RBD) with anti-SARS-CoV/CoV-2 monoclonal antibodies (mAbs), we have produced SARS-CoV-2 RBD and two variants SARS-CoV-2 RBD (Alpha RBD and Beta RBD) in Nicotiana benthamiana by transient expression. Plant-produced SARS-CoV-2 RBD-Fc, Alpha RBD-Fc and Beta RBD-Fc exhibited specific binding to human angiotensin converting enzyme 2 (ACE2) receptor determined by ELISA. Intriguingly, the binding of plant-produced SARS-CoV-2 RBD proteins to plant-produced mAbs CR3022, B38, and H4 was found to be different depending on the variant mutation. In contrary to the plant-produced SARS-CoV-2 RBD-Fc and Alpha RBD-Fc, Beta RBD-Fc variant showed weak binding affinity towards the mAbs. The result suggested that the Beta RBD variant might have acquired partial resistance to neutralizing antibodies compared to other variants. However, further studies with sera from convalescent or vaccinated individuals are required to confirm this finding.
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Affiliation(s)
| | - Christine Joy I. Bulaon
- Research Unit for Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Narach Khorattanakulchai
- Research Unit for Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp (GCE 6302823006-1), Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Molecular Crop Research Unit (GRU 6407023008-1), Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Waranyoo Phoolcharoen
- Research Unit for Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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32
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Lin Z, Qing H, Li R, Zheng L, Yao H. Evolution trace of SARS-CoV-2 from January 19 to March 12, 2020, in the United States. J Med Virol 2021; 93:6595-6604. [PMID: 34292617 PMCID: PMC8426869 DOI: 10.1002/jmv.27225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/13/2021] [Indexed: 01/18/2023]
Abstract
As a kind of human betacoronavirus, SARS‐CoV‐2 has endangered globally public health. As of January 2021, the virus had resulted in 2,209,195 deaths. By studying the evolution trend and characteristics of 265 SARS‐CoV‐2 strains in the United States from January to March, it is found that the strains can be divided into six clades, USA clade‐1, USA clade‐2, USA clade‐3, USA clade‐4, USA clade‐5, and USA clade‐6, in which US clade‐1 may be the most ancestral clade, USA clade‐2 is an interim clade of USA clade‐1 and USA clade‐3, the other three clades have similar codon usage pattern, while USA clade‐6 is the newest and most adaptable clade. Mismatch analysis and protein alignment showed that the evolution of the clades arises from some special mutations in viral proteins, which may help the strain to invade, replicate, transcribe and so on. Compared with previous research and classifications, we suggest that clade O in GISAID should not be an independent clade and Wuhan‐Hu‐1 (EPI_ISL_402125) should not be an ancestral reference sequence. Our study decoded the evolutionary dynamic of SARS‐CoV‐2 in the early stage from the United States, which give some clues to infer the current evolution trend of SARS‐CoV‐2 and study the function of viral mutational protein. Basing on decoding the characteristics and evolution process of SARS‐CoV‐2 in the early stage of the USA, it is suggested that the clade O in GISAID should not be as an independent evolutionary clade by phylogenetic analysis or protein alignment. Secondly, Wuhan‐Hu‐1 (EPI_ISL_402125) should not be as an ancestral reference sequence and its candidate should be EPI_ISL_529213. Thirdly, many unique mutation sites in viral proteins were found to lay foundation to study the function of the mutational protein and to reveal the evolution trend of SARS‐CoV‐2 in coming days.
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Affiliation(s)
- Ziying Lin
- College of Life Science, Sichuan Agriculture University, Ya'an, China
| | - Hua Qing
- College of Life Science, Sichuan Agriculture University, Ya'an, China
| | - Rui Li
- College of Life Science, Sichuan Agriculture University, Ya'an, China
| | | | - Huipeng Yao
- College of Life Science, Sichuan Agriculture University, Ya'an, China
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Yang CH, Li HC, Lee WH, Lo SY. Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. Pathogens 2021; 10:pathogens10070869. [PMID: 34358019 PMCID: PMC8308897 DOI: 10.3390/pathogens10070869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 12/03/2022] Open
Abstract
The COVID-19 pandemic was caused by SARS-CoV-2 infection. To prevent the spread of SARS-CoV-2, an effective vaccine is required. Two linear peptides from potential B-cell epitopes in the spike protein of SARS-CoV-2 (a.a. 440–460; a.a. 494–506) were synthesized and used to immunize rabbits. High-titer antibodies of IgG were produced, purified, and verified by Western blot analysis. Antibodies against these two epitopes could effectively neutralize SARS-CoV-2 pseudoviral particles with the spike proteins from not only the original strain (basal; wild-type), but also a strain with a single point mutation (D614G), and two other emerging variants (the Alpha and Beta variants) prevalent around the world, but not from SARS-CoV. In conclusion, antibodies against these two epitopes are protective. This information is important for the development of vaccines against SARS-CoV-2.
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Affiliation(s)
- Chee-Hing Yang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan; (C.-H.Y.); (W.-H.L.)
| | - Hui-Chun Li
- Department of Biochemistry, Tzu Chi University, Hualien 97004, Taiwan;
| | - Wen-Han Lee
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan; (C.-H.Y.); (W.-H.L.)
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan; (C.-H.Y.); (W.-H.L.)
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
- Correspondence: ; Tel.: +886-3-8565301 (ext. 2322)
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Oketch JW, Kamau E, Otieno JR, Mwema A, Lewa C, Isoe E, Nokes DJ, Agoti CN. Comparative analysis of spatial-temporal patterns of human metapneumovirus and respiratory syncytial virus in Africa using genetic data, 2011-2014. Virol J 2021; 18:104. [PMID: 34051792 PMCID: PMC8164071 DOI: 10.1186/s12985-021-01570-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are leading causes of viral severe acute respiratory illnesses in childhood. Both the two viruses belong to the Pneumoviridae family and show overlapping clinical, epidemiological and transmission features. However, it is unknown whether these two viruses have similar geographic spread patterns which may inform designing and evaluating their epidemic control measures. METHODS We conducted comparative phylogenetic and phylogeographic analyses to explore the spatial-temporal patterns of HMPV and RSV across Africa using 232 HMPV and 842 RSV attachment (G) glycoprotein gene sequences obtained from 5 countries (The Gambia, Zambia, Mali, South Africa, and Kenya) between August 2011 and January 2014. RESULTS Phylogeographic analyses found frequently similar patterns of spread of RSV and HMPV. Viral sequences commonly clustered by region, i.e., West Africa (Mali, Gambia), East Africa (Kenya) and Southern Africa (Zambia, South Africa), and similar genotype dominance patterns were observed between neighbouring countries. Both HMPV and RSV country epidemics were characterized by co-circulation of multiple genotypes. Sequences from different African sub-regions (East, West and Southern Africa) fell into separate clusters interspersed with sequences from other countries globally. CONCLUSION The spatial clustering patterns of viral sequences and genotype dominance patterns observed in our analysis suggests strong regional links and predominant local transmission. The geographical clustering further suggests independent introduction of HMPV and RSV variants in Africa from the global pool, and local regional diversification.
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Affiliation(s)
- John W. Oketch
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, Kenya
| | - Everlyn Kamau
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, Kenya
| | - James R. Otieno
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anthony Mwema
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, Kenya
| | - Clement Lewa
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, Kenya
| | - Everlyne Isoe
- School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - D. James Nokes
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, Kenya
- School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
- School of Life Sciences, and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N. Agoti
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, Kenya
- School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
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35
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Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.17.21257341. [PMID: 34031660 PMCID: PMC8142660 DOI: 10.1101/2021.05.17.21257341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent. To investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 African countries were retrieved from the GISAID database and analyzed. We investigated their diversity using various clade and lineage nomenclature systems, reconstructed their evolutionary divergence and history using maximum likelihood inference methods, and studied the case and death trends in the continent. We also examined potential repeat patterns and motifs across the sequences. In this study, we show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the evolutionary dynamics of the circulating viral strains in Africa, elucidate the functions of protein motifs present in the genome sequences, and emphasize the need to expand genomic surveillance efforts in the continent to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa.
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Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-kwashie
- Department of Medical Microbiology Clinical Virology unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | | | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, University of Ilorin, Nigeria
| | - David J. Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Nídia S. Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
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Mveang Nzoghe A, Padzys GS, Maloupazoa Siawaya AC, Kandet Yattara M, Leboueny M, Avome Houechenou RM, Bongho EC, Mba-Mezeme C, Mvoundza Ndjindji O, Biteghe-Bi-Essone JC, Boulende A, Essone PN, Ndong Sima CAA, Minkobame U, Zang Eyi C, Ndeboko B, Voloc A, Meye JF, Ategbo S, Djoba Siawaya JF. Dynamic and features of SARS-CoV-2 infection in Gabon. Sci Rep 2021; 11:9672. [PMID: 33958601 PMCID: PMC8102484 DOI: 10.1038/s41598-021-87043-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/23/2021] [Indexed: 12/20/2022] Open
Abstract
In a context where SARS-CoV-2 population-wide testing is implemented, clinical features and antibody response in those infected have never been documented in Africa. Yet, the information provided by analyzing data from population-wide testing is critical to understand the infection dynamics and devise control strategies. We described clinical features and assessed antibody response in people screened for SARS-CoV-2 infection. We analyzed data from a cohort of 3464 people that we molecularly screened for SARS-CoV-2 infection in our routine activity. We recorded people SARS-CoV-2 diagnosis, age, gender, blood types, white blood cells (WBC), symptoms, chronic disease status and time to SARS-CoV-2 RT-PCR conversion from positive to negative. We calculated the age-based distribution of SARS-CoV-2 infection, analyzed the proportion and the spectrum of COVID-19 severity. Furthermore, in a nested sub-study, we screened 83 COVID-19 patients and 319 contact-cases for anti-SARS-CoV-2 antibodies. Males and females accounted for respectively 51% and 49% of people screened. The studied population median and mean age were both 39 years. 592 out of 3464 people (17.2%) were diagnosed with SARS-CoV-2 infection with males and females representing, respectively, 53% and 47%. The median and mean ages of SARS-CoV-2 infected subjects were 37 and 38 years respectively. The lowest rate of infection (8%) was observed in the elderly (aged > 60). The rate of SARS-Cov-2 infection in both young (18–35 years old) and middle-aged adults (36–60 years old) was around 20%. The analysis of SARS-CoV-2 infection age distribution showed that middle-aged adults accounted for 54.7% of SARS-CoV-2 positive persons, followed respectively by young adults (33.7%), children (7.7%) and elderly (3.8%). 68% (N = 402) of SARS-CoV-2 infected persons were asymptomatic, 26.3% (N = 156) had influenza-like symptoms, 2.7% (N = 16) had influenza-like symptoms associated with anosmia and ageusia, 2% (N = 11) had dyspnea and 1% (N = 7) had respiratory failure, which resulted in death. Data also showed that 12% of SARS-CoV-2 infected subjects, had chronic diseases. Hypertension, diabetes, and asthma were the top concurrent chronic diseases representing respectively 58%, 25% and 12% of recorded chronic diseases. Half of SARS-CoV-2 RT-PCR positive patients were cured within 14 days following the initiation of the anti-COVID-19 treatment protocol. 78.3% of COVID-19 patients and 55% of SARS-CoV-2 RT-PCR confirmed negative contact-cases were positive for anti-SARS-CoV-2 antibodies. Patients with severe-to-critical illness have higher leukocytes, higher neutrophils and lower lymphocyte counts contrarily to asymptomatic patients and patients with mild-to-moderate illness. Neutrophilic leukopenia was more prevalent in asymptomatic patients and patients with mild-to-moderate disease for 4 weeks after diagnosis (27.1–42.1%). In Patients with severe-to-critical illness, neutrophilic leukocytosis or neutrophilia (35.6–50%) and lymphocytopenia (20–40%) were more frequent. More than 60% of participants were blood type O. It is also important to note that infection rate was slightly higher among A and B blood types compared with type O. In this African setting, young and middle-aged adults are most likely driving community transmission of COVID-19. The rate of critical disease is relatively low. The high rate of anti-SARS-CoV-2 antibodies observed in SARS-CoV-2 RT-PCR negative contact cases suggests that subclinical infection may have been overlooked in our setting.
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Affiliation(s)
- Amandine Mveang Nzoghe
- Unité de Recherche et Diagnostics Spécialisé, Service Laboratoire, CHU-Mère-EnfantFondation Jeanne EBORI, Libreville, Gabon
| | - Guy-Stephan Padzys
- Département de Biologie Cellulaire et Physiologie, Faculté Des Sciences, Université Des Sciences Et Techniques de Masuku, Franceville, Gabon
| | | | | | - Marielle Leboueny
- Unité de Recherche et Diagnostics Spécialisé, Service Laboratoire, CHU-Mère-EnfantFondation Jeanne EBORI, Libreville, Gabon
| | | | - Eliode Cyrien Bongho
- Unité de Recherche et Diagnostics Spécialisé, Service Laboratoire, CHU-Mère-EnfantFondation Jeanne EBORI, Libreville, Gabon
| | - Cedrick Mba-Mezeme
- Département de Biologie Cellulaire et Physiologie, Faculté Des Sciences, Université Des Sciences Et Techniques de Masuku, Franceville, Gabon
| | - Ofilia Mvoundza Ndjindji
- Unité de Recherche et Diagnostics Spécialisé, Service Laboratoire, CHU-Mère-EnfantFondation Jeanne EBORI, Libreville, Gabon
| | - Jean Claude Biteghe-Bi-Essone
- Unité de Recherche et Diagnostics Spécialisé, Service Laboratoire, CHU-Mère-EnfantFondation Jeanne EBORI, Libreville, Gabon
| | - Alain Boulende
- Unité de Recherche et Diagnostics Spécialisé, Service Laboratoire, CHU-Mère-EnfantFondation Jeanne EBORI, Libreville, Gabon
| | - Paulin N Essone
- Laboratoire National de Santé Publique, Libreville, Gabon.,Centre de Recherches Médicales de Lambaréné, BP 242, Lambaréné, Gabon
| | - Carene Anne Alene Ndong Sima
- Unité de Recherche et Diagnostics Spécialisé, Service Laboratoire, CHU-Mère-EnfantFondation Jeanne EBORI, Libreville, Gabon.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, 7505, South Africa
| | - Ulysse Minkobame
- Pôle mère, CHU- Mère-Enfant Fondation Jeanne EBORI, Libreville, Gabon
| | - Carinne Zang Eyi
- Pôle enfant, CHU- Mère-Enfant Fondation Jeanne EBORI, Libreville, Gabon
| | - Bénédicte Ndeboko
- Unité de Recherche et Diagnostics Spécialisé, Service Laboratoire, CHU-Mère-EnfantFondation Jeanne EBORI, Libreville, Gabon.,Département de Biologie Cellulaire and Moléculaire-Génétique, Faculté de Médecine, Université Des Sciences de La Santé, Libreville, Gabon
| | - Alexandru Voloc
- Pôle enfant, CHU- Mère-Enfant Fondation Jeanne EBORI, Libreville, Gabon
| | | | - Simon Ategbo
- Pôle enfant, CHU- Mère-Enfant Fondation Jeanne EBORI, Libreville, Gabon
| | - Joel Fleury Djoba Siawaya
- Unité de Recherche et Diagnostics Spécialisé, Service Laboratoire, CHU-Mère-EnfantFondation Jeanne EBORI, Libreville, Gabon.
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Li Q, Nie J, Wu J, Zhang L, Ding R, Wang H, Zhang Y, Li T, Liu S, Zhang M, Zhao C, Liu H, Nie L, Qin H, Wang M, Lu Q, Li X, Liu J, Liang H, Shi Y, Shen Y, Xie L, Zhang L, Qu X, Xu W, Huang W, Wang Y. SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Cell 2021; 184:2362-2371.e9. [PMID: 33735608 PMCID: PMC7901273 DOI: 10.1016/j.cell.2021.02.042] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 01/06/2023]
Abstract
The 501Y.V2 variants of SARS-CoV-2 containing multiple mutations in spike are now dominant in South Africa and are rapidly spreading to other countries. Here, experiments with 18 pseudotyped viruses showed that the 501Y.V2 variants do not confer increased infectivity in multiple cell types except for murine ACE2-overexpressing cells, where a substantial increase in infectivity was observed. Notably, the susceptibility of the 501Y.V2 variants to 12 of 17 neutralizing monoclonal antibodies was substantially diminished, and the neutralization ability of the sera from convalescent patients and immunized mice was also reduced for these variants. The neutralization resistance was mainly caused by E484K and N501Y mutations in the receptor-binding domain of spike. The enhanced infectivity in murine ACE2-overexpressing cells suggests the possibility of spillover of the 501Y.V2 variants to mice. Moreover, the neutralization resistance we detected for the 501Y.V2 variants suggests the potential for compromised efficacy of monoclonal antibodies and vaccines.
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Affiliation(s)
- Qianqian Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Jianhui Nie
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Jiajing Wu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Li Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Ruxia Ding
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Haixin Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Yue Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Tao Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Shuo Liu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Mengyi Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Chenyan Zhao
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Huan Liu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Lingling Nie
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Haiyang Qin
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Meng Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Qiong Lu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Xiaoyu Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Junkai Liu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Haoyu Liang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yuelei Shen
- Beijing Biocytogen Co., Ltd., Beijing 101111, China
| | - Liangzhi Xie
- Beijing Antibody Research Key Laboratory, Sino Biological Inc., Building 9, Jing Dong Bei Technology Park, No. 18 Ke Chuang 10th St., BDA, Beijing 100176, China
| | - Linqi Zhang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, and Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaowang Qu
- Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Chenzhou 423000, China.
| | - Wenbo Xu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China.
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China.
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38
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Kuzmina A, Khalaila Y, Voloshin O, Keren-Naus A, Boehm-Cohen L, Raviv Y, Shemer-Avni Y, Rosenberg E, Taube R. SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Cell Host Microbe 2021; 29:522-528.e2. [PMID: 33789085 PMCID: PMC7980135 DOI: 10.1016/j.chom.2021.03.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
Toward eradicating the COVID-19 pandemic, vaccines that induce high humoral and cellular immune responses are essential. However, SARS-CoV-2 variants have begun to emerge and raise concerns, as they may potentially compromise vaccine efficiency. Here, we monitored neutralization potency of convalescent or Pfizer-BTN162b2 post-vaccination sera against pseudoviruses displaying spike proteins derived from wild-type SARS-CoV-2, or its UK-B.1.1.7 and SA-B.1.351 variants. Compared to convalescent sera, vaccination induces high titers of neutralizing antibodies, which exhibit efficient neutralization potential against pseudovirus carrying wild-type SARS-CoV-2. However, while wild-type and UK-N501Y pseudoviruses were similarly neutralized, those displaying SA-N501Y/K417N/E484K spike mutations moderately resist neutralization. Contribution of single or combined spike mutations to neutralization and infectivity were monitored, highlighting mechanisms by which viral infectivity and neutralization resistance are enhanced by N501Y or E484K/K417N mutations. Our study validates the importance of the Pfizer vaccine but raises concerns regarding its efficacy against specific SARS-CoV-2 circulating variants.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
| | | | | | | | | | - Yael Raviv
- Soroka Medical Center, Beer Sheva, Israel
| | - Yonat Shemer-Avni
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel; Soroka Medical Center, Beer Sheva, Israel
| | | | - Ran Taube
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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El-Sayed A, Kamel M. Coronaviruses in humans and animals: the role of bats in viral evolution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:19589-19600. [PMID: 33655480 PMCID: PMC7924989 DOI: 10.1007/s11356-021-12553-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/14/2021] [Indexed: 04/15/2023]
Abstract
Bats act as a natural reservoir for many viruses, including coronaviruses, and have played a crucial epidemiological role in the emergence of many viral diseases. Coronaviruses have been known for 60 years. They are usually responsible for the induction of mild respiratory signs in humans. However, since 2002, the bat-borne virus started to induce fatal epidemics according to WHO reports. In this year, the first serious human coronavirus epidemic (severe acute respiratory syndrome; SARS) occurred (China, 8098 cases, 774 deaths [9.5% of the cases] in 17 countries). The case fatality was higher in elderly patients above 60 years and reached 50% of the cases. SARS epidemic was followed 10 years later by the emergence of the middle east respiratory syndrome (MERS) in Saudi Arabia (in 2012, 2260 cases, 803 deaths [35.5% of the cases] in 27 countries). Finally, in December 2019, a new epidemic in Wuhan, China, (corona virus disease 2019, COVID-19) emerged and could spread to 217 countries infecting more than 86,255,226 cases and killing 1,863,973 people by the end of 2020. There are many reasons why bats are ideal reservoir hosts for viral diseases such as the tolerance of their immune system to the invading viruses for several months. They can actively shed the viruses, although they develop no clinical signs (will be discussed in details later in the review). Bats were directly or indirectly involved in the three previous coronavirus epidemics. The indirect transmission takes place via intermediate hosts including civet cats for SARS and dromedary camels in the case of MERS. Although bats are believed to be the source of COVID-19 pandemic, direct pieces of evidence are still lacking. Therefore, coronaviruses' role in epidemics induction and the epidemiological role of bats are discussed. The current work also presents different evidence (phylogenetic data, animal experiments, bats artificial infection studies, and computerized models of SARS-CoV2 evolution) that underline the involvement of bats in the epidemiology of the pandemic.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt.
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40
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Engelbrecht S, Delaney K, Kleinhans B, Wilkinson E, Tegally H, Stander T, van Zyl G, Preiser W, de Oliveira T. Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. Viruses 2021; 13:v13030526. [PMID: 33810168 PMCID: PMC8005015 DOI: 10.3390/v13030526] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9-17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town.
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Affiliation(s)
- Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
- Tygerberg Business Unit, National Health Laboratory Service (NHLS), Cape Town 8000, South Africa;
- Correspondence: (S.E.); (T.d.O.); Tel.: +27-21-9389357 (S.E.)
| | - Kayla Delaney
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
| | - Bronwyn Kleinhans
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (E.W.); (H.T.)
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (E.W.); (H.T.)
| | - Tania Stander
- Tygerberg Business Unit, National Health Laboratory Service (NHLS), Cape Town 8000, South Africa;
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
- Tygerberg Business Unit, National Health Laboratory Service (NHLS), Cape Town 8000, South Africa;
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
- Tygerberg Business Unit, National Health Laboratory Service (NHLS), Cape Town 8000, South Africa;
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (E.W.); (H.T.)
- Centre for Aids Programme of Research in South Africa (CAPRISA), Durban 4000, South Africa
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Correspondence: (S.E.); (T.d.O.); Tel.: +27-21-9389357 (S.E.)
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Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 2021; 592:438-443. [PMID: 33690265 DOI: 10.1038/s41586-021-03402-9] [Citation(s) in RCA: 1068] [Impact Index Per Article: 356.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/26/2021] [Indexed: 12/15/2022]
Abstract
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance3-5. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu-Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data-which show rapid expansion and displacement of other lineages in several regions-suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape6-8.
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Genomic-informed pathogen surveillance in Africa: opportunities and challenges. THE LANCET. INFECTIOUS DISEASES 2021; 21:e281-e289. [PMID: 33587898 PMCID: PMC7906676 DOI: 10.1016/s1473-3099(20)30939-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022]
Abstract
The ongoing COVID-19 pandemic has highlighted the need to incorporate pathogen genomics for enhanced disease surveillance and outbreak management in Africa. The genomics of SARS-CoV-2 has been instrumental to the timely development of diagnostics and vaccines and in elucidating transmission dynamics. Global disease control programmes, including those for tuberculosis, malaria, HIV, foodborne pathogens, and antimicrobial resistance, also recommend genomics-based surveillance as an integral strategy towards control and elimination of these diseases. Despite the potential benefits, capacity remains low for many public health programmes in Africa. The COVID-19 pandemic presents an opportunity to reassess and strengthen surveillance systems and potentially integrate emerging technologies for preparedness of future epidemics and control of endemic diseases. We discuss opportunities and challenges for integrating pathogen genomics into public health surveillance systems in Africa. Improving accessibility through the creation of functional continent-wide networks, building multipathogen sequencing cores, training a critical mass of local experts, development of standards and policies to facilitate best practices for data sharing, and establishing a community of practice of genomics experts are all needed to use genomics for improved disease surveillance in Africa. Coordination and leadership are also crucial, which the Africa Centres for Disease Control and Prevention seeks to provide through its institute for pathogen genomics.
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Sixteen novel lineages of SARS-CoV-2 in South Africa. Nat Med 2021; 27:440-446. [PMID: 33531709 DOI: 10.1038/s41591-021-01255-3] [Citation(s) in RCA: 251] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/15/2021] [Indexed: 12/15/2022]
Abstract
The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020 (ref. 5).
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Lu L, Lycett S, Ashworth J, Mutapi F, Woolhouse M. What are SARS-CoV-2 genomes from the WHO Africa region member states telling us? BMJ Glob Health 2021; 6:bmjgh-2020-004408. [PMID: 33419930 PMCID: PMC7798429 DOI: 10.1136/bmjgh-2020-004408] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022] Open
Affiliation(s)
- Lu Lu
- Usher Institute, Ashworth Laboratories, Kings Buildings, The University of Edinburgh, Edinburgh, UK
| | - Samantha Lycett
- The University of Edinburgh The Roslin Institute, Roslin, Midlothian, UK
| | - Jordan Ashworth
- Usher Institute, Ashworth Laboratories, Kings Buildings, The University of Edinburgh, Edinburgh, UK
| | - Francisca Mutapi
- Institute of Immunology & Infection Research, The University of Edinburgh School of Biological Sciences, Edinburgh, UK .,NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), The University of Edinburgh, Edinburgh, UK
| | - Mark Woolhouse
- Usher Institute, Ashworth Laboratories, Kings Buildings, The University of Edinburgh, Edinburgh, UK.,NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), The University of Edinburgh, Edinburgh, UK
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Sander AL, Yadouleton A, Moreira-Soto A, Tchibozo C, Hounkanrin G, Badou Y, Fischer C, Krause N, Akogbeto P, F de Oliveira Filho E, Dossou A, Brünink S, Drosten C, Aïssi MAJ, Harouna Djingarey M, Hounkpatin B, Nagel M, Drexler JF. An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa. mSphere 2021; 6:e00979-20. [PMID: 33441410 PMCID: PMC7845609 DOI: 10.1128/msphere.00979-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/16/2020] [Indexed: 12/23/2022] Open
Abstract
Information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread in Africa is limited by insufficient diagnostic capacity. Here, we assessed the coronavirus disease (COVID-19)-related diagnostic workload during the onset of the pandemic in the central laboratory of Benin, Western Africa; characterized 12 SARS-CoV-2 genomes from returning travelers; and validated the Da An RT-PCR-based diagnostic kit that is widely used across Africa. We found a 15-fold increase in the monthly laboratory workload due to COVID-19, dealt with at the cost of routine activities. Genomic surveillance showed near-simultaneous introduction of distinct SARS-CoV-2 lineages termed A.4 and B.1, including the D614G spike protein variant potentially associated with higher transmissibility from travelers from six different European and African countries during March-April 2020. We decoded the target regions within the ORF1ab and N genes of the Da An dual-target kit by MinION-based amplicon sequencing. Despite relatively high similarity between SARS-CoV-2 and endemic human coronaviruses (HCoVs) within the ORF1ab target domain, no cross-detection of high-titered cell culture supernatants of HCoVs was observed, suggesting high analytical specificity. The Da An kit was highly sensitive, detecting 3.2 to 9.0 copies of target-specific in vitro transcripts/reaction. Although discrepant test results were observed in low-titered clinical samples, clinical sensitivity of the Da An kit was at least comparable to that of commercial kits from affluent settings. In sum, virologic diagnostics are achievable in a resource-limited setting, but unprecedented pressure resulting from COVID-19-related diagnostics requires rapid and sustainable support of national and supranational stakeholders addressing limited laboratory capacity.IMPORTANCE Months after the start of the COVID-19 pandemic, case numbers from Africa are surprisingly low, potentially because the number of SARS-CoV-2 tests performed in Africa is lower than in other regions. Here, we show an overload of COVID-19-related diagnostics in the central laboratory of Benin, Western Africa, with a stagnating average number of positive samples irrespective of daily sample counts. SARS-CoV-2 genomic surveillance confirmed a high genomic diversity in Benin introduced by travelers returning from Europe and other African countries, including early circulation of the D614G spike mutation associated with potentially higher transmissibility. We validated a widely used RT-PCR kit donated by the Chinese Jack Ma Foundation and confirmed high analytical specificity and clinical sensitivity equivalent to tests used in affluent settings. Our assessment shows that although achievable in an African setting, the burden from COVID-19-related diagnostics on national reference laboratories is very high.
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Affiliation(s)
- Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Anges Yadouleton
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
- Ecole Normale Supérieure de Natitingou, Université Nationale des Sciences, Technologies, Ingénierie et Mathématiques (UNSTIM), Natitingou, Benin
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Carine Tchibozo
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
| | - Gildas Hounkanrin
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
| | - Yvette Badou
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
| | - Carlo Fischer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nina Krause
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | - Edmilson F de Oliveira Filho
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | - Sebastian Brünink
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research (DZIF), associated partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Melchior A Joël Aïssi
- Conseil National de Lutte contre le VIH-Sida, la Tuberculose, le Paludisme, les IST et les Epidémies, Cotonou, Benin
| | | | | | - Michael Nagel
- Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH, Bonn, Germany
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research (DZIF), associated partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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Sanyaolu A, Okorie C, Marinkovic A, Haider N, Abbasi AF, Jaferi U, Prakash S, Balendra V. The emerging SARS-CoV-2 variants of concern. Ther Adv Infect Dis 2021; 8:20499361211024372. [PMID: 34211709 PMCID: PMC8216402 DOI: 10.1177/20499361211024372] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/24/2021] [Indexed: 12/21/2022] Open
Abstract
Since emerging from Wuhan, China, in December of 2019, the coronavirus (SARS-CoV-2) has been causing devastating severe respiratory infections in humans worldwide. With the disease spreading faster than the medical community could contain it, death tolls increased at an alarming rate worldwide, causing the World Health Organization to officially sanction the SARS-CoV-2 outbreak as a pandemic, leading to a state of worldwide lockdown for the majority of the year 2020. There have been reports of new strains of the virus emerging in various parts of the world, with some strains displaying even greater infectivity and transmissibility. Areas of the emerging variant of concern arise from countries like the United Kingdom, South Africa, Brazil, and India. These mutations carry a lineage from N501Y, D614G, N439K, Y453F, and others, which are globally dominated by clades 20A, 20B, and 20C. This literature review intends to identify and report SARS-CoV-2 variants that are currently evolving and their disease implications.
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Affiliation(s)
- Adekunle Sanyaolu
- Federal Ministry of Health, Department of Public Health, New Federal Secretariat Complex, Phase III, Ahmadu Bello Way, Central Business District, FCT, Abuja, Nigeria
| | - Chuku Okorie
- Union County College, Plainfield Campus, NJ, USA
| | | | | | | | - Urooj Jaferi
- All Saints University School of Medicine, Dominica
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Kouriba B, Dürr A, Rehn A, Sangaré AK, Traoré BY, Bestehorn-Willmann MS, Ouedraogo J, Heitzer A, Sogodogo E, Maiga A, Walter MC, Zimmermann F, Wölfel R, Antwerpen MH. First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region. Viruses 2020; 12:v12111251. [PMID: 33147840 PMCID: PMC7692263 DOI: 10.3390/v12111251] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 01/18/2023] Open
Abstract
We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019. From China, the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on 2 March 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequencing data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates, from which 21 whole genome sequences were generated. Our analysis shows that both the early A (19B) and the later observed B (20A/C) clade are present in Mali, indicating multiple and independent introductions of SARS-CoV-2 to the Sahel region.
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Affiliation(s)
- Bourema Kouriba
- Centre d’Infectiologie Charles Mérieux du Mali, BPE2283 Bamako, Mali; (B.K.); (A.K.S.); (B.Y.T.); (J.O.); (E.S.); (A.M.)
| | - Angela Dürr
- Bundeswehr Institute of Microbiology, D-80937 Munich, Germany; (A.D.); (A.R.); (M.S.B.-W.); (A.H.); (M.C.W.); (F.Z.); (R.W.)
| | - Alexandra Rehn
- Bundeswehr Institute of Microbiology, D-80937 Munich, Germany; (A.D.); (A.R.); (M.S.B.-W.); (A.H.); (M.C.W.); (F.Z.); (R.W.)
| | - Abdoul Karim Sangaré
- Centre d’Infectiologie Charles Mérieux du Mali, BPE2283 Bamako, Mali; (B.K.); (A.K.S.); (B.Y.T.); (J.O.); (E.S.); (A.M.)
| | - Brehima Y. Traoré
- Centre d’Infectiologie Charles Mérieux du Mali, BPE2283 Bamako, Mali; (B.K.); (A.K.S.); (B.Y.T.); (J.O.); (E.S.); (A.M.)
| | - Malena S. Bestehorn-Willmann
- Bundeswehr Institute of Microbiology, D-80937 Munich, Germany; (A.D.); (A.R.); (M.S.B.-W.); (A.H.); (M.C.W.); (F.Z.); (R.W.)
| | - Judicael Ouedraogo
- Centre d’Infectiologie Charles Mérieux du Mali, BPE2283 Bamako, Mali; (B.K.); (A.K.S.); (B.Y.T.); (J.O.); (E.S.); (A.M.)
| | - Asli Heitzer
- Bundeswehr Institute of Microbiology, D-80937 Munich, Germany; (A.D.); (A.R.); (M.S.B.-W.); (A.H.); (M.C.W.); (F.Z.); (R.W.)
| | - Elisabeth Sogodogo
- Centre d’Infectiologie Charles Mérieux du Mali, BPE2283 Bamako, Mali; (B.K.); (A.K.S.); (B.Y.T.); (J.O.); (E.S.); (A.M.)
| | - Abderrhamane Maiga
- Centre d’Infectiologie Charles Mérieux du Mali, BPE2283 Bamako, Mali; (B.K.); (A.K.S.); (B.Y.T.); (J.O.); (E.S.); (A.M.)
| | - Mathias C. Walter
- Bundeswehr Institute of Microbiology, D-80937 Munich, Germany; (A.D.); (A.R.); (M.S.B.-W.); (A.H.); (M.C.W.); (F.Z.); (R.W.)
| | - Fee Zimmermann
- Bundeswehr Institute of Microbiology, D-80937 Munich, Germany; (A.D.); (A.R.); (M.S.B.-W.); (A.H.); (M.C.W.); (F.Z.); (R.W.)
| | - Roman Wölfel
- Bundeswehr Institute of Microbiology, D-80937 Munich, Germany; (A.D.); (A.R.); (M.S.B.-W.); (A.H.); (M.C.W.); (F.Z.); (R.W.)
| | - Markus H. Antwerpen
- Bundeswehr Institute of Microbiology, D-80937 Munich, Germany; (A.D.); (A.R.); (M.S.B.-W.); (A.H.); (M.C.W.); (F.Z.); (R.W.)
- Correspondence:
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48
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Chaguza C, Nyaga MM, Mwenda JM, Esona MD, Jere KC. Using genomics to improve preparedness and response of future epidemics or pandemics in Africa. LANCET MICROBE 2020; 1:e275-e276. [PMID: 33345202 PMCID: PMC7729821 DOI: 10.1016/s2666-5247(20)30169-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.,Darwin College, University of Cambridge, Cambridge, UK.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Martin M Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Jason M Mwenda
- World Health Organization, Regional Office for Africa, Brazzaville, Congo
| | - Mathew D Esona
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Khuzwayo C Jere
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
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49
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Yang Y, Xiao Z, Ye K, He X, Sun B, Qin Z, Yu J, Yao J, Wu Q, Bao Z, Zhao W. SARS-CoV-2: characteristics and current advances in research. Virol J 2020; 17:117. [PMID: 32727485 PMCID: PMC7387805 DOI: 10.1186/s12985-020-01369-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection has spread rapidly across the world and become an international public health emergency. Both SARS-CoV-2 and SARS-CoV belong to subfamily Coronavirinae in the family Coronaviridae of the order Nidovirales and they are classified as the SARS-like species while belong to different cluster. Besides, viral structure, epidemiology characteristics and pathological characteristics are also different. We present a comprehensive survey of the latest coronavirus-SARS-CoV-2-from investigating its origin and evolution alongside SARS-CoV. Meanwhile, pathogenesis, cardiovascular disease in COVID-19 patients, myocardial injury and venous thromboembolism induced by SARS-CoV-2 as well as the treatment methods are summarized in this review.
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Affiliation(s)
- Yicheng Yang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Zhiqiang Xiao
- Department of clinical medicine, Zhengzhou university, 100 Science Avenue, Zhengzhou, 450001, China
| | - Kaiyan Ye
- Second Clinical Medical College, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoen He
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Bo Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Zhiran Qin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jianghai Yu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jinxiu Yao
- Yang Jiang Hospital, Yangjiang, 510515, Guangdong Province, China
| | - Qinghua Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Zhang Bao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Wei Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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