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Equestre M, Marcantonio C, Marascio N, Centofanti F, Martina A, Simeoni M, Suffredini E, La Rosa G, Bonanno Ferraro G, Mancini P, Veneri C, Matera G, Quirino A, Costantino A, Taffon S, Tritarelli E, Campanella C, Pisani G, Nisini R, Spada E, Verde P, Ciccaglione AR, Bruni R. Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy. Microorganisms 2023; 11:2711. [PMID: 38004723 PMCID: PMC10672769 DOI: 10.3390/microorganisms11112711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
We investigated SARS-CoV-2 variants circulating, from November 2020 to March 2022, among military and civilian personnel at an Air Force airport in Italy in order to classify viral isolates in a potential hotspot for virus spread. Positive samples were subjected to Next-Generation Sequencing (NGS) of the whole viral genome and Sanger sequencing of the spike coding region. Phylogenetic analysis classified viral isolates and traced their evolutionary relationships. Clusters were identified using 70% cut-off. Sequencing methods yielded comparable results in terms of variant classification. In 2020 and 2021, we identified several variants, including B.1.258 (4/67), B.1.177 (9/67), Alpha (B.1.1.7, 9/67), Gamma (P.1.1, 4/67), and Delta (4/67). In 2022, only Omicron and its sub-lineage variants were observed (37/67). SARS-CoV-2 isolates were screened to detect naturally occurring resistance in genomic regions, the target of new therapies, comparing them to the Wuhan Hu-1 reference strain. Interestingly, 2/30 non-Omicron isolates carried the G15S 3CLpro substitution responsible for reduced susceptibility to protease inhibitors. On the other hand, Omicron isolates carried unusual substitutions A1803V, D1809N, and A949T on PLpro, and the D216N on 3CLpro. Finally, the P323L substitution on RdRp coding regions was not associated with the mutational pattern related to polymerase inhibitor resistance. This study highlights the importance of continuous genomic surveillance to monitor SARS-CoV-2 evolution in the general population, as well as in restricted communities.
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Affiliation(s)
- Michele Equestre
- Department of Neurosciences, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Cinzia Marcantonio
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Nadia Marascio
- Clinical Microbiology Unit, Department of Health Sciences, “Magna Grecia” University, 88100 Catanzaro, Italy; (G.M.); (A.Q.)
| | - Federica Centofanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Antonio Martina
- Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.M.); (M.S.); (G.P.)
| | - Matteo Simeoni
- Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.M.); (M.S.); (G.P.)
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.L.R.); (G.B.F.); (P.M.); (C.V.)
| | - Giusy Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.L.R.); (G.B.F.); (P.M.); (C.V.)
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.L.R.); (G.B.F.); (P.M.); (C.V.)
| | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.L.R.); (G.B.F.); (P.M.); (C.V.)
| | - Giovanni Matera
- Clinical Microbiology Unit, Department of Health Sciences, “Magna Grecia” University, 88100 Catanzaro, Italy; (G.M.); (A.Q.)
| | - Angela Quirino
- Clinical Microbiology Unit, Department of Health Sciences, “Magna Grecia” University, 88100 Catanzaro, Italy; (G.M.); (A.Q.)
| | - Angela Costantino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Stefania Taffon
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Elena Tritarelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Carmelo Campanella
- Clinical Analysis and Molecular Biology Laboratory Rome, Institute of Aerospace Medicine, 00185 Rome, Italy;
| | - Giulio Pisani
- Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.M.); (M.S.); (G.P.)
| | - Roberto Nisini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Enea Spada
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Paola Verde
- Aerospace Medicine Department, Aerospace Test Division, Militay Airport Mario De Bernardi, Pratica di Mare, 00040 Rome, Italy;
| | - Anna Rita Ciccaglione
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
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Atik MD, Lüleci D, Çifci AG, Demiral GA, Demiral Y. Which Jobs are Unlucky against the Biologic and the Economic Risks Caused by the Covid-19 Pandemic? Indian J Occup Environ Med 2023; 27:9-16. [PMID: 37303995 PMCID: PMC10257239 DOI: 10.4103/ijoem.ijoem_85_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/11/2022] [Accepted: 05/24/2022] [Indexed: 06/13/2023] Open
Abstract
Context Beyond the biological impact of the pandemic in working life, socioeconomic consequences is also important for workers. This study aimed to investigate both biologic and economic impacts of the pandemic. Methods In this cross-sectional study, a structured questionnaire were applied by telephone to 233 workers who were diagnosed with coronavirus disease-2019 (Covid-19) at hospital. A pretest was applied before the data collection. The outcomes of the study were work-related Covid-19 transmission (WRCT) and pandemic-related economic worsening (PREW). Descriptive statistics is presented. Chi-square test is used in comparison of proportions. Results Of the 233 workers, 52% were male (n = 120) and the mean age was 37.7 (±9.2) years. WRCT was observed in 73% of health care workers. PREW was 6.7 times higher in private sector (95% confidence interval = 3.1-14.5), especially in self-employed and small business owners. Drivers and sales workers were the unluckiest. Because they were affected in terms of both the WRCT and PREW. Conclusions Within the framework of occupational health, the economic destructive effects of the Covid-19 pandemic as well as the biological impacts should be considered with a holistic perspective. Protective policies should be developed especially for economically fragile groups against the pandemic such as self-employed, small business owners, and private sector workers.
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Affiliation(s)
- Merve D. Atik
- Department of Occupational Medicine, Dokuz Eylül University, Faculty of Medicine, Izmir, Turkey
| | - Duygu Lüleci
- Department of Occupational Medicine, Dokuz Eylül University, Faculty of Medicine, Izmir, Turkey
| | - Aylin G. Çifci
- Department of Occupational Medicine, Dokuz Eylül University, Faculty of Medicine, Izmir, Turkey
| | - Gökçen A. Demiral
- Department of Occupational Medicine, Katip Celebi University Atatürk Education and Research Hospital, Izmir, Turkey
| | - Yücel Demiral
- Department of Public Health, Dokuz Eylül University, Faculty of Medicine, Izmir, Turkey
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Hasan T, Thach PN, Anh NT, Hien LTT, An NTM, Thuy DT, Van Duyet L, Dung NT, Diep TT, Van Huynh H, Toelle BG, Marks GB, Fox GJ. The prevalence of SARS-CoV-2 antibodies in quarantine workers and high-risk communities in Vietnam. IJID REGIONS 2022; 2:137-140. [PMID: 35721423 PMCID: PMC8665841 DOI: 10.1016/j.ijregi.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 11/04/2022]
Abstract
A low prevalence (2%) of SARS-CoV-2 antibodies was found among quarantine workers. A low prevalence of SARS-CoV-2 antibodies was found in communities with COVID-19. Vietnam had controlled the COVID-19 pandemic until mid-2021. This study preceded the widespread outbreak in Vietnam in mid-2021.
Objective The aim of this study was to determine the seroprevalence of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) antibodies in high-risk communities and quarantine workers in Vietnam. Methods The prevalence of SARS-CoV-2 antibodies was measured in household contacts, close contacts, community members, and migrant workers from two sub-communes in which COVID-19 outbreaks occurred in early 2021: Bac Ma 1 and Tien. The prevalence of SARS-CoV-2 antibodies was also evaluated among quarantine workers at two facilities responsible for quarantining of contacts of COVID-19 cases. Results Among 2069 participants from the two sub-communes, six individuals (0.3%) had detectable SARS-CoV-2 antibodies despite no history of COVID-19. This included one Vietnamese migrant worker, two community members, two household contacts, and one close contact of known COVID-19 cases. Among 50 workers at two COVID-19 quarantine facilities, including 15 health care workers (HCWs), one of the HCWs tested positive for SARS-CoV-2 antibodies (1/50, 2.0%) despite no known disease. Conclusion The prevalence of SARS-CoV-2 antibodies was low in Vietnamese ‘hotspots’, suggesting limited community transmission.
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Sah P, Fitzpatrick MC, Zimmer CF, Abdollahi E, Juden-Kelly L, Moghadas SM, Singer BH, Galvani AP. Asymptomatic SARS-CoV-2 infection: A systematic review and meta-analysis. Proc Natl Acad Sci U S A 2021; 118:e2109229118. [PMID: 34376550 PMCID: PMC8403749 DOI: 10.1073/pnas.2109229118] [Citation(s) in RCA: 274] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Quantification of asymptomatic infections is fundamental for effective public health responses to the COVID-19 pandemic. Discrepancies regarding the extent of asymptomaticity have arisen from inconsistent terminology as well as conflation of index and secondary cases which biases toward lower asymptomaticity. We searched PubMed, Embase, Web of Science, and World Health Organization Global Research Database on COVID-19 between January 1, 2020 and April 2, 2021 to identify studies that reported silent infections at the time of testing, whether presymptomatic or asymptomatic. Index cases were removed to minimize representational bias that would result in overestimation of symptomaticity. By analyzing over 350 studies, we estimate that the percentage of infections that never developed clinical symptoms, and thus were truly asymptomatic, was 35.1% (95% CI: 30.7 to 39.9%). At the time of testing, 42.8% (95% prediction interval: 5.2 to 91.1%) of cases exhibited no symptoms, a group comprising both asymptomatic and presymptomatic infections. Asymptomaticity was significantly lower among the elderly, at 19.7% (95% CI: 12.7 to 29.4%) compared with children at 46.7% (95% CI: 32.0 to 62.0%). We also found that cases with comorbidities had significantly lower asymptomaticity compared to cases with no underlying medical conditions. Without proactive policies to detect asymptomatic infections, such as rapid contact tracing, prolonged efforts for pandemic control may be needed even in the presence of vaccination.
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Affiliation(s)
- Pratha Sah
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT 06520
| | - Meagan C Fitzpatrick
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT 06520
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Charlotte F Zimmer
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT 06520
| | - Elaheh Abdollahi
- Agent-Based Modelling Laboratory, York University, Toronto, ON M3J 1P3, Canada
| | - Lyndon Juden-Kelly
- Agent-Based Modelling Laboratory, York University, Toronto, ON M3J 1P3, Canada
| | - Seyed M Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, ON M3J 1P3, Canada
| | - Burton H Singer
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610
| | - Alison P Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT 06520
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