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Su Z, Li Y, Xie Y, Huang Z, Cheng A, Zhou X, Li J, Qin R, Wei X, Liu Y, Xia X, Song Q, Zhao L, Liu Z, Xiao D, Wang C. Acute and long COVID-19 symptoms and associated factors in the omicron-dominant period: a nationwide survey via the online platform Wenjuanxing in China. BMC Public Health 2024; 24:2086. [PMID: 39090598 PMCID: PMC11295386 DOI: 10.1186/s12889-024-19510-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUNDS To our knowledge, there is no available nationwide data on omicron symptom patterns in China mainland. We aim to determine the acute and long COVID-19 symptoms in the omicron-dominant period and to evaluate its association with risk factors. METHODS We designed a cross-sectional nationwide study and data about self-reported symptoms were collected by an online platform named Wenjuanxing. Eligible participants were aged 25-65 years and were symptomatic. In this study, the ratios of the number of people of different ages and genders were weighted by the data from the Seventh National Census (2020 years), and validated by a published nationwide representative study through comparing smoking rates. Descriptive indicators were calculated for demographic characteristics, diagnosis ways, and duration time, acute symptoms, hospitalization, severity and long COVID-19 symptoms. And, the associations between risk factors and acute and long COVID-19 symptoms were analyzed by multivariable logistic regression models. RESULTS A total of 32,528 individuals diagnosed as COVID-19 infection from October 1, 2022 to February 21, 2023 were included. The first three acute symptoms of COVID-19 infection were fever (69.90%), headache (62.63%), and sore throat (54.29%), respectively. The hospitalization rate within 7 days was 3.07% and symptoms disappearance rate within 21 days was 68.84%, respectively. Among 3983 COVID-19 patients with 3 months or more time difference between first infection and participation into the study, the long COVID-19 rate was 19.68% and the primary symptoms were muscle weakness (19.39%), headache (17.98%) and smell/taste disorder (15.18%). Age groups, smoking, marriage status and vaccination were risk factors for numbers of acute phase symptoms and long COVID-19 symptoms. Lastly, female and current smokers also showed more numbers of symptoms during acute infection period. CONCLUSIONS In Chinese mainland, our respondent indicated that current smokers and women were associated with acute COVID-19 symptoms, which should be treated with caution due to the lack of representative.
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Affiliation(s)
- Zheng Su
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yinghua Li
- China Health Education Center, Beijing, China
| | - Ying Xie
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- School of Health Policy and Management, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhenxiao Huang
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- School of Health Policy and Management, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Anqi Cheng
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinmei Zhou
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jinxuan Li
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Capital Medical University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Rui Qin
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaowen Wei
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Capital Medical University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Yi Liu
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Xia
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qingqing Song
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Capital Medical University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Liang Zhao
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhao Liu
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Dan Xiao
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China.
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China.
- National Clinical Research Center for Respiratory Diseases, Beijing, China.
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China.
- National Center for Respiratory Medicine, Beijing, China.
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
| | - Chen Wang
- Department of Tobacco Control and Prevention of Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- WHO Collaborating Center for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- School of Health Policy and Management, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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2
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Ahmad SJ, Degiannis JR, Borucki J, Pouwels S, Rawaf DL, Lala A, Whiteley GS, Head M, Simpson A, Archid R, Ahmed AR, Soler JA, Wichmann D, Thangavelu M, Abdulmajed M, Elmousili M, Lin YR, Gelber E, Exadaktylos AK. Fatality Rates After Infection With the Omicron Variant (B.1.1.529): How Deadly has it been? A Systematic Review and Meta-Analysis. J Acute Med 2024; 14:51-60. [PMID: 38855048 PMCID: PMC11153312 DOI: 10.6705/j.jacme.202406_14(2).0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/15/2023] [Accepted: 09/05/2023] [Indexed: 06/11/2024]
Abstract
Background Since late 2019, the global community has been gripped by the uncertainty surrounding the SARS-CoV-2 pandemic. In November 2021, the emergence of the Omicron variant in South Africa added a new dimension. This study aims to assess the disease's severity and determine the extent to which vaccinations contribute to reducing mortality rates. Methods A systematic review and meta-analysis of the epidemiological implications of the omicron variant of SARS-CoV-2 were performed, incorporating an analysis of articles from November 2021that address mortality rates. Results The analysis incorporated data from 3,214,869 patients infected with omicron, as presented in 270 articles. A total of 6,782 deaths from the virus were recorded (0.21%). In the analysed articles, the pooled mortality rate was 0.003 and the pooled in-house mortality rate was 0.036. Vaccination is an effective step in preventing death (odds ratio: 0.391, p < 0.01). Conclusion The mortality rates for the omicron variant are lower than for the preceding delta variant. mRNA vaccination affords secure and effective protection against severe disease and death from omicron.
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Affiliation(s)
- Suhaib Js Ahmad
- Betsi Cadwaladr University Health Board Department of General Surgery Wales UK
- University Hospital of Bern Department of Emergency Medicine Inselspital Switzerland
| | - Jason R Degiannis
- University Hospital of Bern Department of Emergency Medicine Inselspital Switzerland
- University Hospital of Saarland Clinic of Neurosurgery Homburg Germany
| | - Joseph Borucki
- Norfolk and Norwich University Hospitals NHS Foundation Trust Department of General Surgery Norwich UK
| | - Sjaak Pouwels
- Abdominal and Minimally Invasive Surgery Department of General Helios Klinikum Krefeld Germany
| | - David Laith Rawaf
- Imperial College London WHO Collaborating Centre for Public Health Education & Training London UK
| | - Anil Lala
- Betsi Cadwaladr University Health Board Department of General Surgery Wales UK
| | - Graham S Whiteley
- Betsi Cadwaladr University Health Board Department of General Surgery Wales UK
| | - Marion Head
- Betsi Cadwaladr University Health Board Department of General Surgery Wales UK
| | - Angharad Simpson
- Betsi Cadwaladr University Health Board BCUHB Library Service Wales UK
| | - Rami Archid
- Visceral and Transplant Surgery Department of General Eberhard-Karls-University Hospital, Tuebingen Germany
| | - Ahmed R Ahmed
- Imperial College London Department of Bariatric and Metabolic Surgery London UK
| | - J Agustin Soler
- Betsi Cadwaladr University Health Board Department of Trauma and Orthopaedics Wales UK
| | - Doerte Wichmann
- Visceral and Transplant Surgery Department of General Eberhard-Karls-University Hospital, Tuebingen Germany
| | | | | | | | - Yan-Ren Lin
- Changhua Christian Hospital Department of Emergency and Critical Care Medicine Changhua Taiwan
- National Chung-Hsing University Department of Post Baccalaureate Medicine Taichung Taiwan
| | - Edgar Gelber
- Betsi Cadwaladr University Health Board Department of General Surgery Wales UK
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3
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Liao Y, Su J, Zhao J, Qin Z, Zhang Z, Gao W, Wan J, Liao Y, Zou X, He X. The effectiveness of booster vaccination of inactivated COVID-19 vaccines against susceptibility, infectiousness, and transmission of omicron BA.2 variant: a retrospective cohort study in Shenzhen, China. Front Immunol 2024; 15:1359380. [PMID: 38881892 PMCID: PMC11176464 DOI: 10.3389/fimmu.2024.1359380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/04/2024] [Indexed: 06/18/2024] Open
Abstract
Little studies evaluated the effectiveness of booster vaccination of inactivated COVID-19 vaccines against being infected (susceptibility), infecting others (infectiousness), and spreading the disease from one to another (transmission). Therefore, we conducted a retrospective cohort study to evaluate the effectiveness of booster vaccination of inactivated COVID-19 vaccines against susceptibility, infectiousness, and transmission in Shenzhen during an Omicron BA.2 outbreak period from 1 February to 21 April 2022. The eligible individuals were classified as four sub-cohorts according to the inactivated COVID-19 vaccination status of both the close contacts and their index cases: group 2-2, fully vaccinated close contacts seeded by fully vaccinated index cases (reference group); group 2-3, booster-vaccinated close contacts seeded by fully vaccinated index cases; group 3-2, fully vaccinated close contacts seeded by booster-vaccinated index cases; and group 3-3, booster-vaccinated close contacts seeded by booster-vaccinated index cases. Univariate and multivariate logistic regression analyses were applied to estimate the effectiveness of booster vaccination. The sample sizes of groups 2-2, 2-3, 3-2, and 3-3 were 846, 1,115, 1,210, and 2,417, respectively. We found that booster vaccination had an effectiveness against infectiousness of 44.9% (95% CI: 19.7%, 62.2%) for the adults ≥ 18 years, 62.2% (95% CI: 32.0%, 78.9%) for the female close contacts, and 60.8% (95% CI: 38.5%, 75.1%) for the non-household close contacts. Moreover, booster vaccination had an effectiveness against transmission of 29.0% (95% CI: 3.2%, 47.9%) for the adults ≥ 18 years, 38.9% (95% CI: 3.3%, 61.3%) for the female close contacts, and 45.8% (95% CI: 22.1%, 62.3%) for the non-household close contacts. However, booster vaccination against susceptibility did not provide any protective effect. In summary, this study confirm that booster vaccination of the inactivated COVID-19 vaccines provides low level of protection and moderate level of protection against Omicron BA.2 transmission and infectiousness, respectively. However, booster vaccination does not provide any protection against Omicron BA.2 susceptibility.
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Affiliation(s)
- Yuxue Liao
- Office of Emergency, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jiao Su
- Department of Biochemistry, Changzhi Medical College, Changzhi, China
| | - Jieru Zhao
- Department of Infectious Disease, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
| | - Zhen Qin
- Class of 2002 of the Department of Preventive Medicine, Changzhi Medical College, Changzhi, China
| | - Zhuo'Ao Zhang
- Class of 2002 of the Department of Preventive Medicine, Changzhi Medical College, Changzhi, China
| | - Wei Gao
- Office of Emergency, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jia Wan
- Office of Emergency, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yi Liao
- Office of Emergency, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xuan Zou
- Office of Emergency, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaofeng He
- Institute of Evidence-Based Medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
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4
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Ose NJ, Campitelli P, Modi T, Kazan IC, Kumar S, Ozkan SB. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 2024; 12:RP92063. [PMID: 38713502 PMCID: PMC11076047 DOI: 10.7554/elife.92063] [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] [Indexed: 05/08/2024] Open
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
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Affiliation(s)
- Nicholas James Ose
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - I Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple UniversityPhiladelphiaUnited States
- Department of Biology, Temple UniversityPhiladelphiaUnited States
- Center for Genomic Medicine Research, King Abdulaziz UniversityJeddahSaudi Arabia
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
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5
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Scovino AM, Dahab EC, Diniz-Lima I, de Senna Silveira E, Barroso SPC, Cardoso KM, Nico D, Makhoul GJ, da Silva-Junior EB, Freire-de-Lima CG, Freire-de-Lima L, da Fonseca LM, Valente N, Nacife V, Machado A, Araújo M, Vieira GF, Pauvolid-Corrêa A, Siqueira M, Morrot A. A Comparative Analysis of Innate Immune Responses and the Structural Characterization of Spike from SARS-CoV-2 Gamma Variants and Subvariants. Microorganisms 2024; 12:720. [PMID: 38674664 PMCID: PMC11052025 DOI: 10.3390/microorganisms12040720] [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: 09/05/2023] [Revised: 10/16/2023] [Accepted: 11/28/2023] [Indexed: 04/28/2024] Open
Abstract
The SARS-CoV-2 P.1 variant, responsible for an outbreak in Manaus, Brazil, is distinguished by 12 amino acid differences in the S protein, potentially increasing its ACE-2 affinity and immune evasion capability. We investigated the innate immune response of this variant compared to the original B.1 strain, particularly concerning cytokine production. Blood samples from three severe COVID-19 patients were analyzed post-infection with both strains. Results showed no significant difference in cytokine production of mononuclear cells and neutrophils for either variant. While B.1 had higher cytopathogenicity, neither showed viral replication in mononuclear cells. Structural analyses of the S protein highlighted physicochemical variations, which might be linked to the differences in infectivity between the strains. Our studies point to the increased infectivity of P.1 could stem from altered immunogenicity and receptor-binding affinity.
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Affiliation(s)
- Aline Miranda Scovino
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
| | - Elizabeth Chen Dahab
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
| | - Israel Diniz-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Etiele de Senna Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil; (E.d.S.S.)
| | - Shana Priscila Coutinho Barroso
- Laboratório de Biologia Molecular, Instituto de Pesquisa Biomédica, Hospital Naval Marcílio Dias, Marinha do Brazil, Rio de Janeiro 20725-090, Brazil; (S.P.C.B.); (K.M.C.)
- Biomanguinhos, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-900, Brazil
| | - Karina Martins Cardoso
- Laboratório de Biologia Molecular, Instituto de Pesquisa Biomédica, Hospital Naval Marcílio Dias, Marinha do Brazil, Rio de Janeiro 20725-090, Brazil; (S.P.C.B.); (K.M.C.)
| | - Dirlei Nico
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
| | - Gustavo José Makhoul
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Elias Barbosa da Silva-Junior
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Celio Geraldo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Leonardo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Leonardo Marques da Fonseca
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
- Curso de Medicina, Universidade Castelo Branco (UCB), Rio de Janeiro 21710-255, Brazil
| | - Natalia Valente
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Valeria Nacife
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Ana Machado
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Mia Araújo
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Gustavo Fioravanti Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil; (E.d.S.S.)
- PPGSDH—Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Canoas 92010-000, Brazil
| | - Alex Pauvolid-Corrêa
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
- Laboratório de Virologia Veterinária de Viçosa, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Marilda Siqueira
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Alexandre Morrot
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
- Escola de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
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6
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Cui G, Sun Y, Zou Y, Sun R, Gao Y, Liu X, Zhou Y, Zhang D, Wang X, Li Y, Liu L, Zhang G, Rao B, Yu Z, Ren Z. Dynamic changes of Bacterial Microbiomes in Oropharynx during Infection and Recovery of COVID-19 Omicron Variant. PLoS Pathog 2024; 20:e1012075. [PMID: 38568937 PMCID: PMC10990182 DOI: 10.1371/journal.ppat.1012075] [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: 08/13/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Oropharyngeal microbiomes play a significant role in the susceptibility and severity of COVID-19, yet the role of these microbiomes play for the development of COVID-19 Omicron variant have not been reported. A total of 791 pharyngeal swab samples were prospectively included in this study, including 297 confirmed cases of Omicron variant (CCO), 222 confirmed case of Omicron who recovered (CCOR), 73 confirmed cases of original strain (CCOS) and 199 healthy controls (HC). All samples completed MiSeq sequencing. The results showed that compared with HC, conditional pathogens increased in CCO, while acid-producing bacteria decreased. Based on six optimal oropharyngeal operational taxonomy units (OTUs), we constructed a marker microbial classifier to distinguish between patients with Omicron variant and healthy people, and achieved high diagnostic efficiency in both the discovery queue and the verification queue. At same time, we introduced a group of cross-age infection verification cohort and Omicron variant subtype XBB.1.5 branch, which can be accurately distinguished by this diagnostic model. We also analyzed the characteristics of oropharyngeal microbiomes in two subgroups of Omicron disease group-severity of infection and vaccination times, and found that the change of oropharyngeal microbiomes may affect the severity of the disease and the efficacy of the vaccine. In addition, we found that some genera with significant differences gradually increased or decreased with the recovery of Omicron variant infection. The results of Spearman analysis showed that 27 oropharyngeal OTUs were closely related to 6 clinical indexes in CCO and HC. Finally, we found that the Omicron variant had different characterization of oropharyngeal microbiomes from the original strain. Our research characterizes oropharyngeal microbiomes of Omicron variant cases and rehabilitation cases, successfully constructed and verified the non-invasive diagnostic model of Omicron variant, described the correlation between microbial OTUs and clinical indexes. It was found that the infection of Omicron variant and the infection of original strain have different characteristics of oropharyngeal microbiomes.
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Affiliation(s)
- Guangying Cui
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yawen Zou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ranran Sun
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanxia Gao
- Emergency Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaorui Liu
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongjian Zhou
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Donghua Zhang
- Anyang City Fifth People’s Hospital, Long An District, Anyang, China
| | - Xueqing Wang
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yonghong Li
- Anyang City Fifth People’s Hospital, Long An District, Anyang, China
| | - Liwen Liu
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guizhen Zhang
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Benchen Rao
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zujiang Yu
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Ose NJ, Campitelli P, Modi T, Can Kazan I, Kumar S, Banu Ozkan S. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557827. [PMID: 37745560 PMCID: PMC10515954 DOI: 10.1101/2023.09.14.557827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 Spike (S) protein. With this approach, we first identified Candidate Adaptive Polymorphisms (CAPs) of the SARS-CoV-2 Spike protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
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Affiliation(s)
- Nicholas J. Ose
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - I. Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S. Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
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Peng D, Yang L, Jin C, Feng J, Cao M, Liu Y. Effect of second booster vaccination on clinical outcomes of Omicron-variant breakthrough infection: A propensity score matching cohort study. Heliyon 2024; 10:e23344. [PMID: 38169898 PMCID: PMC10758784 DOI: 10.1016/j.heliyon.2023.e23344] [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: 05/30/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Objective To further explore the effect of vaccination regimen and frequency on clinical outcomes of breakthrough infections caused by the Omicron variant, as well as the durability of vaccine effectiveness. Methods A retrospective, propensity score matching, real-world cohort study was conducted. Vaccination frequency was categorized into regular vaccination, first booster, and second booster. Results A total of 7428 cases were included, with 3910 (53 %) being male. The median age was 39 years. BA.2 than BA.5/5.2 infection presented with more pulmonary symptoms and fewer influenza-like symptoms. Among the 3516 cases of BA.5/5.2 breakthrough infections, patients who received the second booster than the first booster or regular vaccination had higher first IgM and IgG titers and first cycle thredhold values for N gene on admission, a lower percentage of fever, lower peak body temperatures, and a higher percentage of asymptomatic cases. Patients who received the first booster vaccinated with homologous mRNA or heterologous inactivated plus mRNA vaccines than homologous inactivated vaccines had higher first IgM and IgG titers, a higher percentage of asymptomatic cases, and a lower percentage of fever. Moreover, significantly different first IgG titers were observed among patients receiving the second booster vaccinated with any of the three regimens. There was no statistical difference between booster regimens of homologous mRNA vaccines and heterologous inactivated plus mRNA vaccines. Patients in Month 7- than Month 0-6 after the first booster had lower first IgM and IgG titers and first cycle thredhold values, a lower percentage of asymptomatic cases, and a higher percentage of fever; and a higher percentage of pneumonia after the second booster. Conclusions Repeated booster vaccinations every six months, with priority given to heterologous mRNA vaccine booster regimens in countries previously primarily using inactivated vaccines, may provide protection for adult patients with Omicron-variant breakthrough infections and improve clinical outcomes.
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Affiliation(s)
- Denggao Peng
- Department of Emergency Medicine, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, 518112, China
| | - Liuqing Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Cheng Jin
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jiaqi Feng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Mengli Cao
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
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9
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Ahmed AI, Al Rifai M, Alahdab F, Saad JM, Han Y, Alfawara MS, Nayfeh M, Malahfji M, Nabi F, Mahmarian JJ, Cooke JP, Zoghbi WA, Al-Mallah MH. Coronary microvascular health in symptomatic patients with prior COVID-19 infection: an updated analysis. Eur Heart J Cardiovasc Imaging 2023; 24:1544-1554. [PMID: 37254693 PMCID: PMC10610774 DOI: 10.1093/ehjci/jead118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023] Open
Abstract
AIMS Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with endothelial dysfunction. We aimed to determine the effects of prior coronavirus disease 2019 (COVID-19) on the coronary microvasculature accounting for time from COVID-19, disease severity, SARS-CoV-2 variants, and in subgroups of patients with diabetes and those with no known coronary artery disease. METHODS AND RESULTS Cases consisted of patients with previous COVID-19 who had clinically indicated positron emission tomography (PET) imaging and were matched 1:3 on clinical and cardiovascular risk factors to controls having no prior infection. Myocardial flow reserve (MFR) was calculated as the ratio of stress to rest myocardial blood flow (MBF) in mL/min/g of the left ventricle. Comparisons between cases and controls were made for the odds and prevalence of impaired MFR (MFR < 2). We included 271 cases matched to 815 controls (mean ± SD age 65 ± 12 years, 52% men). The median (inter-quartile range) number of days between COVID-19 infection and PET imaging was 174 (58-338) days. Patients with prior COVID-19 had a statistically significant higher odds of MFR <2 (adjusted odds ratio 3.1, 95% confidence interval 2.8-4.25 P < 0.001). Results were similar in clinically meaningful subgroups. The proportion of cases with MFR <2 peaked 6-9 months from imaging with a statistically non-significant downtrend afterwards and was comparable across SARS-CoV-2 variants but increased with increasing severity of infection. CONCLUSION The prevalence of impaired MFR is similar by duration of time from infection up to 1 year and SARS-CoV-2 variants, but significantly differs by severity of infection.
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Affiliation(s)
- Ahmed Ibrahim Ahmed
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Mahmoud Al Rifai
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Fares Alahdab
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Jean Michel Saad
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Yushui Han
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Moath Said Alfawara
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Malek Nayfeh
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Maan Malahfji
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Faisal Nabi
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - John J Mahmarian
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - John P Cooke
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - William A Zoghbi
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Mouaz H Al-Mallah
- Houston Methodist DeBakey Heart & Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
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10
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He X, Zeng B, Wang Y, Pang Y, Zhang M, Hu T, Liang Y, Kang M, Tang S. Effectiveness of booster vaccination with inactivated COVID-19 vaccines against SARS-CoV-2 Omicron BA.2 infection in Guangdong, China: a cohort study. Front Immunol 2023; 14:1257360. [PMID: 37915583 PMCID: PMC10616523 DOI: 10.3389/fimmu.2023.1257360] [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: 07/12/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
The effectiveness of COVID-19 vaccines wanes over time and the emergence of the SARS-CoV-2 Omicron variant led to the accelerated expansion of efforts for booster vaccination. However, the effect and contribution of booster vaccination with inactivated COVID-19 vaccines remain to be evaluated. We conducted a retrospective close contacts cohort study to analyze the epidemiological characteristics and Omicron infection risk, and to evaluate the effectiveness of booster vaccination with inactivated COVID-19 vaccines against SARS-CoV-2 infection, symptomatic COVID-19, and COVID-19 pneumonia during the outbreaks of Omicron BA.2 infection from 1 February to 31 July 2022 in Guangdong, China. A total of 46,547 close contacts were identified while 6.3% contracted Omicron BA.2 infection, 1.8% were asymptomatic infection, 4.1% developed mild COVID-19, and 0.3% had COVID-19 pneumonia. We found that females and individuals aged 0-17 or ≥ 60 years old were more prone to SARS-CoV-2 infection. The vaccinated individuals showed lower infection risk when compared with the unvaccinated people. The effectiveness of booster vaccination with inactivated COVID-19 vaccines against SARS-CoV-2 infection and symptomatic COVID-19 was 28.6% (95% CI: 11.6%, 35.0%) and 39.6% (95% CI: 30.0, 47.9) among adults aged ≥ 18 years old, respectively when compared with full vaccination. Booster vaccination provided a moderate level of protection against SARS-CoV-2 infection (VE: 49.9%, 95% CI: 22.3%-67.7%) and symptomatic COVID-19 (VE: 62.6%, 95% CI: 36.2%-78.0%) among adults aged ≥ 60 years old. Moreover, the effectiveness of booster vaccination was 52.2% (95% CI: 21.3%, 70.9%) and 83.8% (95% CI: 28.1%, 96.3%) against COVID-19 pneumonia in adults aged ≥ 18 and ≥ 60 years old, respectively. The reduction of absolute risk rate of COVID-19 pneumonia in the booster vaccination group was 0·96% (95% CI: 0.33%, 1.11%), and the number needed to vaccinate to prevent one case of COVID-19 pneumonia was 104 (95% CI: 91, 303) in adults aged ≥ 60 years old. In summary, booster vaccination with inactivated COVID-19 vaccines provides a low level of protection against infection and symptomatic in adults of 18-59 years old, and a moderate level of protection in older adults of more than 60 years old, but a high level of protection against COVID-19 pneumonia in older adults.
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Affiliation(s)
- Xiaofeng He
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
- Institute of Evidence-Based Medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
| | - Biao Zeng
- Institute of Infectious Disease Control and Prevention, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ye Wang
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Yulian Pang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Meng Zhang
- Institute of Infectious Disease Control and Prevention, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ting Hu
- Institute of Infectious Disease Control and Prevention, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Yuanhao Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Min Kang
- Institute of Infectious Disease Control and Prevention, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
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11
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Giannitsioti E, Mavroudis P, Speggos I, Katsoulidou A, Pantazis N, Loupis T, Daniil I, Rekleiti N, Damianidou S, Louka C, Sidiropoulou C, Kranidiotis G, Velentza L, Stamati A, Kasidiaraki M, Efstratiadi E, Linardaki G, Chrysos G, Zarkotou O, Zoi K, Tryfinopoulou K, Gerakari S. Real life treatment experience and outcome of consecutively hospitalised patients with SARS-CoV-2 pneumonia by Omicron-1 vs Delta variants. Infect Dis (Lond) 2023; 55:706-715. [PMID: 37427461 DOI: 10.1080/23744235.2023.2232445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/11/2023] Open
Abstract
BACKGROUND Omicron-1 COVID-19 is less invasive in the general population than previous viral variants. However, clinical course and outcome of hospitalised patients with SARS-CoV-2 pneumonia during the shift of the predominance from Delta to Omicron variants are not fully explored. METHODS During January 2022 consecutively hospitalised patients with SARS-CoV-2 pneumonia were analysed. SARS-CoV-2 variants were identified by a 2-step pre-screening protocol and randomly confirmed by whole genome sequencing analysis. Clinical, laboratory and treatment data split by type of variant were analysed along with logistic regression of factors associated to mortality. RESULTS 150 patients [mean age (SD) 67.2(15.8) years, male 54%] were analysed. Compared to Delta (n = 46), Omicron-1 patients (n = 104) were older [mean age (SD): 69.5(15.4) vs 61.9(15.8) years, p = 0.007], with more comorbidities (89.4% vs 65.2%, p = 0.001), less obesity (BMI >30Kg/m2 in 24% vs 43.5%, p = 0.034) but higher vaccination rates for COVID-19 (52.9% vs 8.7%, p < 0.001). Severe pneumonia (48.7%), pulmonary embolism (4.7%), need for invasive mechanical ventilation (8%), administration of dexamethasone (76%) and 60-day mortality (22.6%) did not significantly differ. Severe SARS-CoV-2 pneumonia independently predicted mortality [OR 8.297 (CI95% 2.080-33.095), p = 0.003]. Remdesivir administration (n = 135) was protective from death both in unadjusted and adjusted models [OR 0.157 (CI95% 0.026-0.945), p = 0.043. CONCLUSIONS In a COVID-19 department the severity of pneumonia that did not differ between Omicron-1 and Delta variants predicted mortality whilst remdesivir remained protective in all analyses. Death rates did not differ between SARS-CoV-2 variants. Vigilance and consistency with prevention and treatment guidelines for COVID-19 is mandatory regardless of the predominant SARS-CoV-2 variant.
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Affiliation(s)
- Efthymia Giannitsioti
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Fourth Department of Internal Medicine, National and Kapodistrian University of Athens, ATTIKON University General Hospital, Athens, Greece
| | - Panagiotis Mavroudis
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Ioannis Speggos
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Antigoni Katsoulidou
- Central Public Health Laboratory, National Public Health Organization, Athens, Greece
| | - Nikos Pantazis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Theodoros Loupis
- Greek Genome Centre, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
- Haematology Research Laboratory, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Ioannis Daniil
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Nektaria Rekleiti
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Sofia Damianidou
- Central Public Health Laboratory, National Public Health Organization, Athens, Greece
| | - Christina Louka
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Chrysanthi Sidiropoulou
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Georgios Kranidiotis
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Lemonia Velentza
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Emergency Department, Tzaneio General Hospital, Piraeus, Greece
| | - Alexandra Stamati
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Maria Kasidiaraki
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Emergency Department, Tzaneio General Hospital, Piraeus, Greece
| | - Efrosini Efstratiadi
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Emergency Department, Tzaneio General Hospital, Piraeus, Greece
| | - Garyfallia Linardaki
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Georgios Chrysos
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Second Department of Internal Medicine, Tzaneio General Hospital, Piraeus, Greece
| | - Olympia Zarkotou
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Katerina Zoi
- Greek Genome Centre, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
- Haematology Research Laboratory, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Kyriaki Tryfinopoulou
- Central Public Health Laboratory, National Public Health Organization, Athens, Greece
| | - Styliani Gerakari
- COVID-19 Department, Tzaneio General Hospital, Piraeus, Greece
- Emergency Department, Tzaneio General Hospital, Piraeus, Greece
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12
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Yuan Z, Shao Z, Ma L, Guo R. Clinical Severity of SARS-CoV-2 Variants during COVID-19 Vaccination: A Systematic Review and Meta-Analysis. Viruses 2023; 15:1994. [PMID: 37896770 PMCID: PMC10611048 DOI: 10.3390/v15101994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Due to the variation in the SARS-CoV-2 virus, COVID-19 exhibits significant variability in severity. This presents challenges for governments in managing the allocation of healthcare resources and prioritizing health interventions. Clinical severity is also a critical statistical parameter for researchers to quantify the risks of infectious disease, model the transmission of COVID-19, and provide some targeted measures to control the pandemic. To obtain more accurate severity estimates, including confirmed case-hospitalization risk, confirmed case-fatality risk, hospitalization-fatality risk, and hospitalization-ICU risk, we conducted a systematic review and meta-analysis on the clinical severity (including hospitalization, ICU, and fatality risks) of different variants during the period of COVID-19 mass vaccination and provided pooled estimates for each clinical severity metric. All searches were carried out on 1 February 2022 in PubMed for articles published from 1 January 2020 to 1 February 2022. After identifying a total of 3536 studies and excluding 3523 irrelevant studies, 13 studies were included. The severity results show that the Delta and Omicron variants have the highest (6.56%, 0.46%, 19.63%, and 9.06%) and lowest severities (1.51%, 0.04%, 6.01%, and 3.18%), respectively, according to the four clinical severity metrics. Adults over 65 have higher severity levels for all four clinical severity metrics.
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Affiliation(s)
- Zhilu Yuan
- School of Architecture and Urban Planning, Research Institute for Smart Cities, Shenzhen University, Shenzhen 518060, China; (Z.Y.); (R.G.)
| | - Zengyang Shao
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Lijia Ma
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Renzhong Guo
- School of Architecture and Urban Planning, Research Institute for Smart Cities, Shenzhen University, Shenzhen 518060, China; (Z.Y.); (R.G.)
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13
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Li J, Zhang Q, Xu C, Zhang Y, Lu Y, Ai M, Tan X. Differences in clinical characteristics and liver injury between patients diagnosed with the Omicron subvariant BA.5.2 and the prototype of SARS-CoV-2: a single center retrospective study. BMC Gastroenterol 2023; 23:271. [PMID: 37553605 PMCID: PMC10408107 DOI: 10.1186/s12876-023-02907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND The purpose of this study was to investigate the differences between the clinical characteristics and the factors influencing liver injury in patients with the Omicron subvariant BA.5.2 (Omicron BA.5.2) and the prototype of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS Between December 30, 2019 and November 30, 2022, 157 patients infected with the SARS-CoV-2 prototype and 199 patients infected with the Omicron BA.5.2 were included in this case-control, single-center, retrospective study. Differences in clinical characteristics and liver injury between the Omicron BA.5.2 patients and the prototype patients were subsequently analyzed. RESULTS None of the Omicron BA.5.2 patients reached the critical state, and showed relatively milder symptoms including fever, cough, headache, muscle soreness, nausea or vomiting, diarrhea, anorexia and hypoxia. The Omicron BA.5.2 had a lower effect on body temperature (T), white blood cell (WBC) count, hematocrit (HCT), C-reactive protein (CRP) level, D-dimer, finger pulse oxygen saturation (SpO2) and lung lesions. The differences in liver injury between the two groups were related to the severity of the disease, T, blood oxygen levels, albumin (ALB), CRP, and medication usage. Gender, body mass index, and CRP levels influenced liver damage in the Omicron BA.5.2 patients. In particular, CRP was an independent risk factor for liver injury. Because the severity of liver function damage was considerably low, only a small number of Omicron BA.5.2 patients required liver-protective treatment. CONCLUSION Liver injury is expected in the COVID-19 patients. The Omicron BA.5.2 patients showed milder symptoms of liver injury than the prototype patients. However, dynamic monitoring of liver function is warranted, especially for individuals presenting with elevated levels of CRP.
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Affiliation(s)
- Jie Li
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Qing Zhang
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
- Clinical medical college, Jingzhou of Hubei Province, Yangtze University, Jingzhou, China
| | - Chao Xu
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Yan Zhang
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Yueyue Lu
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Minghua Ai
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Xiaoping Tan
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China.
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China.
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14
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Kim CY, Sardar Z, Ayele BA, Fleck‐Derderian S, Barrett CE, Sun Y, Clague M, Hurst HA, Boruah A, Zucker J, Maddox R, Sejvar J, Thakur KT. Neurological diagnoses in hospitalized COVID-19 patients during the B.1.1.529 surge. Ann Clin Transl Neurol 2023; 10:1433-1441. [PMID: 37350635 PMCID: PMC10424653 DOI: 10.1002/acn3.51833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
OBJECTIVE Emerging variants and sublineages of SARS-CoV-2 have differing disease severity, transmissibility, and immune evasion. The neurological conditions associated with the original strain of SARS-CoV-2 are well established. Our study assessed the neurological presentations specific to hospitalized patients during the B.1.1.529 (Omicron) variant surge in New York City. METHODS A total of 178 cases with positive RT-PCR result within 6 weeks before admission, and subsequent development of select neurological conditions during the SARS-CoV-2 B.1.1.529 (Omicron) surge between December 1, 2021 and February 28, 2022, were included from 12,800 SARS-CoV-2-positive hospital admissions. Clinical data from acute hospitalizations were compared to findings of inpatient neurological cases with COVID-19 infections from the initial surge in NYC in the same hospital system. RESULTS Compared to SARS-CoV-2 infections of the original strain, COVID-19 cases hospitalized during the Omicron surge (B.1.1.529) were associated with incidental and/or asymptomatic COVID-19 cases (96, 53.9%) and an increased incidence of pre-existing neurological and immunocompromising conditions. Encephalopathy, seizures, and stroke remained the most prevalent neurological conditions identified in hospitalized COVID-19 cases during the study period, reflecting a similar distribution of neurological presentations associated with the original strain. INTERPRETATION In our cohort of 178 admitted SARS-CoV-2-positive patients with select neurological conditions during the Omicron B.1.1.529 surge, 54% of COVID-19 cases were considered incidental and/or asymptomatic, and the identified neurological conditions resembled those associated with the original SARS-CoV-2 strain. Further studies characterizing neurological presentation in Omicron sublineages and other variants are warranted in an ongoing COVID-19 pandemic.
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Affiliation(s)
- Carla Y. Kim
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Zomer Sardar
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Biniyam A. Ayele
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | | | | | - Yifei Sun
- Department of BiostatisticsColumbia UniversityNew YorkNew YorkUSA
| | - Madison Clague
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Holly A. Hurst
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Abhilasha Boruah
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
- Case Western Reserve University School of MedicineClevelandOhioUSA
| | - Jason Zucker
- Department of Infectious DiseaseColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Ryan Maddox
- United States Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - James Sejvar
- United States Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Kiran T. Thakur
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
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15
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Gottlieb M, Wang RC, Yu H, Spatz ES, Montoy JCC, Rodriguez RM, Chang AM, Elmore JG, Hannikainen PA, Hill M, Huebinger RM, Idris AH, Lin Z, Koo K, McDonald S, O’Laughlin KN, Plumb ID, Santangelo M, Saydah S, Willis M, Wisk LE, Venkatesh A, Stephens KA, Weinstein RA. Severe Fatigue and Persistent Symptoms at 3 Months Following Severe Acute Respiratory Syndrome Coronavirus 2 Infections During the Pre-Delta, Delta, and Omicron Time Periods: A Multicenter Prospective Cohort Study. Clin Infect Dis 2023; 76:1930-1941. [PMID: 36705268 PMCID: PMC10249989 DOI: 10.1093/cid/ciad045] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/12/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Most research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants focuses on initial symptomatology with limited longer-term data. We characterized prevalences of prolonged symptoms 3 months post-SARS-CoV-2 infection across 3 variant time-periods (pre-Delta, Delta, and Omicron). METHODS This multicenter prospective cohort study of adults with acute illness tested for SARS-CoV-2 compared fatigue severity, fatigue symptoms, organ system-based symptoms, and ≥3 symptoms across variants among participants with a positive ("COVID-positive") or negative SARS-CoV-2 test ("COVID-negative") at 3 months after SARS-CoV-2 testing. Variant periods were defined by dates with ≥50% dominant strain. We performed multivariable logistic regression modeling to estimate independent effects of variants adjusting for sociodemographics, baseline health, and vaccine status. RESULTS The study included 2402 COVID-positive and 821 COVID-negative participants. Among COVID-positives, 463 (19.3%) were pre-Delta, 1198 (49.9%) Delta, and 741 (30.8%) Omicron. The pre-Delta COVID-positive cohort exhibited more prolonged severe fatigue (16.7% vs 11.5% vs 12.3%; P = .017) and presence of ≥3 prolonged symptoms (28.4% vs 21.7% vs 16.0%; P < .001) compared with the Delta and Omicron cohorts. No differences were seen in the COVID-negatives across time-periods. In multivariable models adjusted for vaccination, severe fatigue and odds of having ≥3 symptoms were no longer significant across variants. CONCLUSIONS Prolonged symptoms following SARS-CoV-2 infection were more common among participants infected during pre-Delta than with Delta and Omicron; however, these differences were no longer significant after adjusting for vaccination status, suggesting a beneficial effect of vaccination on risk of long-term symptoms. Clinical Trials Registration. NCT04610515.
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Affiliation(s)
- Michael Gottlieb
- Department of Emergency Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Ralph C Wang
- Department of Emergency Medicine, University of California, San Francisco, California, USA
| | - Huihui Yu
- Center for Outcomes Research and Evaluation, Yale School of Medicine, New Haven, Connecticut, USA
- Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Erica S Spatz
- Center for Outcomes Research and Evaluation, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Juan Carlos C Montoy
- Department of Emergency Medicine, University of California, San Francisco, California, USA
| | - Robert M Rodriguez
- Department of Emergency Medicine, University of California – San Francisco School of Medicine, San Francisco, California, USA
| | - Anna Marie Chang
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joann G Elmore
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, USA
| | - Paavali A Hannikainen
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mandy Hill
- Department of Emergency Medicine, UTHealth Houston, Houston, Texas, USA
| | - Ryan M Huebinger
- Department of Emergency Medicine, UTHealth Houston, Houston, Texas, USA
| | - Ahamed H Idris
- Department of Emergency Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zhenqiu Lin
- Center for Outcomes Research and Evaluation, Yale School of Medicine, New Haven, Connecticut, USA
- Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Katherine Koo
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
| | - Samuel McDonald
- Department of Emergency Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Clinical Informatics Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kelli N O’Laughlin
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Ian D Plumb
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michelle Santangelo
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
| | - Sharon Saydah
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael Willis
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Lauren E Wisk
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, USA
| | - Arjun Venkatesh
- Center for Outcomes Research and Evaluation, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Emergency Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Kari A Stephens
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Robert A Weinstein
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
- Department of Medicine, Division of Infectious Diseases, Cook County Hospital, Chicago, Illinois, USA
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16
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Abstract
PURPOSE OF REVIEW This is an expert overview on recent literature about the complex relationship between coronavirus disease 2019 (COVID-19) and headache. RECENT FINDINGS Long COVID is a clinical syndrome characterized by the presence of persistent symptoms following the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Headache is one of the most common symptoms and is described most often as throbbing pain, associated with photo and phonofobia and worsening with physical exercise. In acute COVID-19, headache is usually described as moderate or severe, diffuse and oppressive although sometimes it has been described with a migraine-like phenotype, especially in patients with a previous history of migraine. Headache intensity during acute phase seems to be the most important predictor of duration of headache over time. Some COVID-19 cases can be associated with cerebrovascular complications, and red flags of secondary headaches (e.g. new worsening or unresponsive headache, or new onset of neurological focal signs) should be urgently investigated with imaging. Treatment goals are the reduction of number and intensity of headache crises, and the prevention of chronic forms. SUMMARY This review can help clinicians to approach patients with headache and infection from SARS-CoV-2, with particular attention to persistent headache in long COVID.
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Affiliation(s)
- Claudio Tana
- Center of Excellence on Headache, Geriatrics and COVID-19 Clinic, SS Annunziata Hospital of Chieti, Chieti
| | - Maria Adele Giamberardino
- Center of Excellence on Headache, Geriatrics and COVID-19 Clinic, SS Annunziata Hospital of Chieti, Chieti
- Department of Medicine and Science of Aging and CAST, G. D'Annunzio University of Chieti
| | - Paolo Martelletti
- Internal Medicine and Emergency Medicine, Sant' Andrea Hospital, Sapienza University, Rome, Italy
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17
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Borse R, Karyakarte RP, Das R, Yanamandra S, Salvi S, Bhitkar H, Mundhe S, Ogale D, Radewad N, Joshi S, Karmodiya K. Clinical Characteristics of SARS-CoV-2 Omicron Cases in Pune, Maharashtra, India. Cureus 2023; 15:e37032. [PMID: 37143627 PMCID: PMC10153589 DOI: 10.7759/cureus.37032] [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] [Accepted: 04/02/2023] [Indexed: 05/06/2023] Open
Abstract
Background The SARS-CoV-2 Omicron variant, within two months of its detection, replaced the Delta variant to become the dominant circulating variant globally. Therefore, it is essential to understand the characteristics of the disease caused by the variant and its impact on vaccination. Methods A total of 165 confirmed Omicron cases attending a tertiary care hospital in Pune, Maharashtra, between December 2021 to February 2022 were studied. Their demographic, clinical, and immunization history was recorded. Results Among the 165 cases, 7.88% were B.1.1.529 Omicron cases, 25.45% were BA.1 Omicron cases, and 66.67% were BA.2 Omicron cases. Of these 165 patients, 146 (88.48%) were discharged after treatment, 12 (7.27%) died during hospitalization, and seven (4.24%) were brought dead. The presence of one or more comorbid conditions was seen in 15.15%, of which diabetes mellitus and hypertension (28% each) were the most common conditions. Older age (greater than 60 years), an important risk factor for poor outcomes, was present in 9.1% of cases. Among the 165 cases, vaccination with at least one dose of vaccine was found in 80.61% of cases. Out of 165 cases, clinical data was available for 158 cases. Of these 158 cases, 86.71% had symptoms, and 13.29% were asymptomatic. Fever, followed by cough, myalgia, runny nose, and headache, were the most common presenting symptoms. The mean duration of illness was 2.69 days, with 91.14% of cases having the illness for less than five days, and 89.24% of cases had a National Early Warning Score (NEWS) of 1-4, suggesting a good prognosis. In 93.90% of cases, the chest X-ray findings were normal. Of the 158 cases, 92.41% of cases recovered with supportive treatment, and only 7.59% of cases required oxygen therapy. Conclusion The current study shows that the Omicron variant caused mild disease with reduced need for hospital admission and oxygen therapy in India.
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Affiliation(s)
- Rohidas Borse
- Internal Medicine, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Rajesh P Karyakarte
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Rashmita Das
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Sushma Yanamandra
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Sonali Salvi
- Internal Medicine, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Harshal Bhitkar
- Internal Medicine, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Sanjay Mundhe
- Internal Medicine, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Dhananjay Ogale
- Internal Medicine, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Nagnath Radewad
- Internal Medicine, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Suvarna Joshi
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Pune, IND
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18
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Wang J, Chen Y, Huang J, Niu C, Zhang P, Yuan K, Zhu X, Jin Q, Ran S, Huang Z. Prevalence of taste and smell dysfunction in mild and asymptomatic COVID-19 patients during Omicron prevalent period in Shanghai, China: a cross-sectional survey study. BMJ Open 2023; 13:e067065. [PMID: 36944468 PMCID: PMC10032136 DOI: 10.1136/bmjopen-2022-067065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
OBJECTIVES COVID-19, which is caused by SARS-CoV-2, is a severe threat to human health and the economy globally. This study aimed to investigate the prevalence of taste and/or smell dysfunction and associated risk factors in mild and asymptomatic patients with Omicron infection in Shanghai, China.DesignThis was a questionnaire-based cross-sectional study. SETTING COVID-19 patients at the makeshift hospital in the Shanghai World Expo Exhibition and Convention Centre were recruited from March to April 2022. PARTICIPANTS In total, 686 COVID-19-infected patients who were defined as mild or asymptomatic cases according to the diagnostic criteria of New Coronavirus Pneumonia Prevention and Control Programme ninth edition (National Health Commission of China, 2022) were enrolled. MEASURES Data to investigate taste and smell loss and to characterise other symptoms were collected by the modified Chemotherapy-induced Taste Alteration Scale and Sino-Nasal Outcome Test-22 questionnaires. The risk factors for the severity of taste/smell dysfunction were analysed by binary logistic regression models. RESULTS 379 males (379/686, 55.2%) and 307 females (307/686, 44.8%) completed the questionnaires to record recent changes in taste and smell ability. A total of 302 patients (44%) had chemosensory dysfunction with Omicron infection, of which 22.7% (156/686) suffered from both taste and smell dysfunction. In addition, cough (60.2%), expectoration (40.5%), fever (33.2%) and sore throat (32.5%) were common symptoms during Omicron infection. The quality-of-life-related indicators were negatively associated with participants' self-reported taste and smell dysfunction. CONCLUSIONS The prevalence of taste or/and smell dysfunction in patients with Omicron infections was 44%. Individuals with chemosensory dysfunction had significantly higher rates of various upper respiratory influenza-like symptoms, xerostomia and bad breath. Moreover, smell dysfunction was a risk factor for the prevalence of taste dysfunction in patients with Omicron infection. TRIAL REGISTRATION NUMBER ChiCTR 2200059097.
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Affiliation(s)
- Jia Wang
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Chen
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Huang
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenguang Niu
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pengfei Zhang
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Keyong Yuan
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohan Zhu
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiaoqiao Jin
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shujun Ran
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengwei Huang
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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19
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Zhou R, Liu N, Li X, Peng Q, Yiu CK, Huang H, Yang D, Du Z, Kwok HY, Au KK, Cai JP, Fan-Ngai Hung I, Kai-Wang To K, Xu X, Yuen KY, Chen Z. Three-dose vaccination-induced immune responses protect against SARS-CoV-2 Omicron BA.2: a population-based study in Hong Kong. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2023; 32:100660. [PMID: 36591327 PMCID: PMC9786166 DOI: 10.1016/j.lanwpc.2022.100660] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
Abstract
Background The ongoing outbreak of SARS-CoV-2 Omicron BA.2 infections in Hong Kong, the model city of universal masking of the world, has resulted in a major public health crisis. Although the third vaccination resulted in strong boosting of neutralization antibody, vaccine efficacy and correlate of immune protection against the major circulating Omicron BA.2 remain to be investigated. Methods We investigated the vaccine efficacy against the Omicron BA.2 breakthrough infection among 470 public servants who had received different SARS-CoV-2 vaccine regimens including two-dose BNT162b2 (2 × BNT, n = 169), three-dose BNT162b2 (3 × BNT, n = 168), two-dose CoronaVac (2 × CorV, n = 34), three-dose CoronaVac (3 × CorV, n = 67) and third-dose BNT162b2 following 2 × CorV (2 × CorV+1BNT, n = 32). Humoral and cellular immune responses after three-dose vaccination were further characterized and correlated with clinical characteristics of BA.2 infection. Findings During the BA.2 outbreak, 27.7% vaccinees were infected. The timely third-dose vaccination provided significant protection with lower incidence rates of breakthrough infections (2 × BNT 46.2% vs 3 × BNT 13.1%, p < 0.0001; 2 × CorV 44.1% vs 3 × CorV 19.4%, p = 0.003). Investigation of immune responses on blood samples derived from 90 subjects in three-dose vaccination cohorts collected before the BA.2 outbreak revealed that the third-dose vaccination activated spike (S)-specific memory B cells and Omicron cross-reactive T cell responses, which correlated with reduced frequencies of breakthrough infections and disease severity rather than with types of vaccines. Moreover, the frequency of S-specific activated memory B cells was significantly lower in infected vaccinees than uninfected vaccinees before vaccine-breakthrough infection whereas IFN-γ+ CD4 T cells were negatively associated with age and viral clearance time. Critically, BA.2 breakthrough infection boosted cross-reactive memory B cells with enhanced cross-neutralizing antibodies to Omicron sublineages, including BA.2.12.1 and BA.4/5, in all vaccinees tested. Interpretation Our results imply that the timely third vaccination and immune responses are likely required for vaccine-mediated protection against Omicron BA.2 pandemic. Although BA.2 conferred the highest neutralization resistance compared with variants of concern tested before the emergence of BA.2.12.1 and BA.4/5, the third dose vaccination-activated S-specific memory B cells and Omicron cross-reactive T cell responses contributed to reduced frequencies of breakthrough infection and disease severity. Neutralizing antibody potency enhanced by BA.2 breakthrough infection in vaccinees with prior 3 doses of CoronaVac or BNT162b2 may reduce the risk of infection against ongoing BA.2.12.1 and BA.4/5. Funding Hong Kong Research Grants Council Collaborative Research Fund, Health and Medical Research Fund, Wellcome Trust, Shenzhen Science and Technology Program, the Health@InnoHK, Innovation and Technology Commission of Hong Kong, China, National Program on Key Research Project, Emergency Key Program of Guangzhou Laboratory, donations from the Friends of Hope Education Fund and the Hong Kong Theme-Based Research Scheme.
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Affiliation(s)
- Runhong Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Na Liu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Xin Li
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of a China
| | - Qiaoli Peng
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Cheuk-Kwan Yiu
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Haode Huang
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Dawei Yang
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Zhenglong Du
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hau-Yee Kwok
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ka-Kit Au
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Jian-Piao Cai
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of a China
| | - Xiaoning Xu
- Centre for Immunology & Vaccinology, Chelsea and Westminster Hospital, Department of Medicine, Imperial College London, London, United Kingdom
| | - Kwok-Yung Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of a China
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Zhiwei Chen
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
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Sha J, Meng C, Sun J, Sun L, Gu R, Liu J, Zhu X, Zhu D. Clinical and upper airway characteristics of 3715 patients with the Omicron variant of SARS-Cov-2 in Changchun, China. J Infect Public Health 2023; 16:422-429. [PMID: 36731245 PMCID: PMC9854235 DOI: 10.1016/j.jiph.2023.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/01/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVE The spread of the novel SARS-Cov-2 variant Omicron created a challenging public health situation in a number of countries. In March 2022, Omicron emerged in Changchun, China, and the number of patients infected rapidly increased. The prevalence of Omicron infection symptoms differs from that of Delta, with more upper airway clinical symptoms apparent. This study aimed to investigate the clinical and upper airway characteristics of the Omicron variant. MATERIALS AND METHODS In this retrospective study, we collected data from participants in Changchun who had tested positive for Omicron with quantitative polymerase chain reaction between 10 March and 30 May 2022 using telephone interviews. The questionnaire was designed by the research team based on the number of upper airway symptoms using the visual analogue scale. We also considered age, sex, vaccination status, general symptoms, and cure period. RESULTS A total of 3715 patients (2056 males and 1659 females) with mild COVID-19 from the Omicron variant were included. The patients had a mean age of 38.63 ( ± 13.97) years (range 2-86 years). The vaccine uptake rate was 91.33 % (8.66 %, 4.58 %, 65.33 %, and 21.43 % had received zero, one, two, and three doses, respectively). The incidence of upper airway symptoms, including throat and nasal symptoms, was 54.21 %. Throat symptoms were the most common during Omicron infection (49.12 %). Nasal symptoms were also common (20.08 %). The incidence of lower airway symptoms was 25.60 %, and gastrointestinal symptoms was 10.87 %. The incidence of general symptoms was 55.26 %. The cure period ranged from three to 37 days, with a mean of 10.24 ± 4.69 days. We compared the upper airway symptom severity for Omicron among different vaccination statuses and found no differences. CONCLUSIONS The main clinical characteristics of the SARS-Cov-2 Omicron variant are upper airway symptoms and general symptoms. Fever remains the most common symptom, followed by mild dry cough. There was no association between Omicron infection and COVID-19 vaccines, and the vaccination status might have been ineffective against upper airway symptom severity by Omicron.
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Affiliation(s)
- Jichao Sha
- Department of Otorhinolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Blvd, Changchun 130033, People's Republic of China.
| | - Cuida Meng
- Department of Otorhinolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Blvd, Changchun 130033, People's Republic of China.
| | - Jing Sun
- Department of Physical examination center, China-Japan Union Hospital of Jilin University, 126 Xiantai Blvd, Changchun 130033, People's Republic of China.
| | - Liwei Sun
- Department of Otorhinolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Blvd, Changchun 130033, People's Republic of China.
| | - Rui Gu
- Department of Orthopaedics, China-Japan Union Hospital of Jilin University, 126 Xiantai Blvd, Changchun 130033, People's Republic of China.
| | - Junzhi Liu
- China-Japan Union Hospital of Jilin University, 126 Xiantai Blvd, Changchun 130033, People's Republic of China.
| | - Xuewei Zhu
- Department of Otorhinolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Blvd, Changchun 130033, People's Republic of China.
| | - Dongdong Zhu
- Department of Otorhinolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Blvd, Changchun 130033, People's Republic of China.
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Kang W, Yang P, Dang B, Zhang W, Gang Y, Wang W, Ma C, Zhao Y, Zhang Y, Hao C, Quan H, Li J, Cao J, Kang W, Shang L. Dynamics of disease characteristics and viral RNA decay in patients with asymptomatic and mild infections during the Omicron wave in Shanghai, China: A retrospective cohort study. Int J Infect Dis 2023; 130:60-70. [PMID: 36849069 DOI: 10.1016/j.ijid.2023.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
OBJECTIVES Asymptomatic infections and mild diseases were more common during the Omicron outbreak in Shanghai, China in 2022. This study aimed to assess the characteristics and viral RNA decay between patients with asymptomatic and mild infections. METHODS A total of 55,111 patients infected with SARS-CoV-2 who were quarantined in the National Exhibition & Convention Center (Shanghai) Fangcang shelter hospital within 3 days after diagnosis from April 9 to May 23, 2022 were enrolled. The kinetics of cycle threshold (Ct) values of reverse transcription-polymerase chain reaction were assessed. The influencing factors for disease progression and the risk factors for the viral RNA shedding time (VST) were investigated. RESULTS On admission, 79.6% (43,852/55,111) of the cases were diagnosed with asymptomatic infections, and 20.4% were mild diseases. However, 78.0% of initially asymptomatic subjects developed mild diseases at the follow-up. The final proportion of asymptomatic infections was 17.5%. The median time of symptom onset, the duration of symptoms, and the VST were 2 days, 5 days, and 7 days, respectively. Female, age 19-40 years, underlying comorbidities with hypertension and diabetes, and vaccination were associated with higher risks of progressing to mildly symptomatic infections. In addition, mildly symptomatic infections were found to be associated with prolonged VST compared with asymptomatic infections. However, the kinetics of viral RNA decay and dynamics of Ct values were similar among asymptomatic subjects, patients with asymptomatic-to-mild infection, and patients with mild infection. CONCLUSION A large proportion of initially diagnosed asymptomatic Omicron infections is in the presymptomatic stage. The Omicron infection has a much shorter incubation period and VST than previous variants. The infectivity of asymptomatic infections and mildly symptomatic infections with Omicron is similar.
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Affiliation(s)
- Wen Kang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Peng Yang
- Department of Health Statistics, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Bianli Dang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Wenjing Zhang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Yi Gang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Wei Wang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Chunyan Ma
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Yanyan Zhao
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Ying Zhang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Chunqiu Hao
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Huiqin Quan
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Jing Li
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Jiaojiao Cao
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China
| | - Wenzhen Kang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China; The Third Branch of Fangcang Shelter Hospital of the National Exhibition and Convention Center, Shanghai, China.
| | - Lei Shang
- Department of Health Statistics, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an, China.
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22
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SARS-CoV-2 BA.2 (Omicron) variant infection in pediatric liver transplanted recipients and cohabitants during 2022 Shanghai outbreak: a prospective cohort. Virol J 2023; 20:28. [PMID: 36774503 PMCID: PMC9918817 DOI: 10.1186/s12985-023-01978-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/26/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND The Omicron variant BA.2 was the dominant variant in the COVID-19 outbreak in Shanghai since March 2022. We aim to investigate the characteristics of SARS-CoV-2 Omicron variant infection in pediatric liver-transplanted recipients. METHODS We conducted a single-center, prospective, observational, single-arm study. We enrolled pediatric liver-transplanted patients infected with the Omicron variant BA.2 from March 19th to October 1st, 2022 and analyzed their demographic, clinical, laboratory, and outcome data. The management of COVID-19 was conducted according to the 9th trial edition of the Chinese guideline. The immunosuppressive therapy was tailored considering the patients' infection developments and liver functions. RESULTS Five children were included. The primary diseases included Niemann-Pick disease, propionic acidemia, decompensated cirrhosis, biliary atresia, and Crigler-Najjar syndrome type I. All of the patients were onset with fever before or when getting RNA-positive results at the age of 3 (Range: 1-13) years. The infection duration was 29 (Range: 18-40) days. Three and two children were diagnosed with mild and moderate COVID-19 respectively. Two patients were tested RNA-positive within 14 days after having been tested negative. The immunosuppressants were paused or extenuated in four patients. Eight of all nine cohabitants were injected with at least two doses of inactivated SARS-CoV-2 vaccine. The disease courses were significantly longer than the patients (P < 0.05). CONCLUSIONS Post-transplant immunosuppression slows down the virus clearance and increases the risk of relapse but does not affect symptom duration or infection severity in pediatric patients. Patients can usually gain a favorable outcome and prognosis by extenuating immunosuppressants.
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23
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Setayeshgar S, Wilton J, Sbihi H, Zandy M, Janjua N, Choi A, Smolina K. Comparison of influenza and COVID-19 hospitalisations in British Columbia, Canada: a population-based study. BMJ Open Respir Res 2023; 10:10/1/e001567. [PMID: 36731922 PMCID: PMC9895913 DOI: 10.1136/bmjresp-2022-001567] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION We compared the population rate of COVID-19 and influenza hospitalisations by age, COVID-19 vaccine status and pandemic phase, which was lacking in other studies. METHOD We conducted a population-based study using hospital data from the province of British Columbia (population 5.3 million) in Canada with universal healthcare coverage. We created two cohorts of COVID-19 hospitalisations based on date of admission: annual cohort (March 2020 to February 2021) and peak cohort (Omicron era; first 10 weeks of 2022). For comparison, we created influenza annual and peak cohorts using three historical periods years to capture varying severity and circulating strains: 2009/2010, 2015/2016 and 2016/2017. We estimated hospitalisation rates per 100 000 population. RESULTS COVID-19 and influenza hospitalisation rates by age group were 'J' shaped. The population rate of COVID-19 hospital admissions in the annual cohort (mostly unvaccinated; public health restrictions in place) was significantly higher than influenza among individuals aged 30-69 years, and comparable to the severe influenza year (2016/2017) among 70+. In the peak COVID-19 cohort (mostly vaccinated; few restrictions in place), the hospitalisation rate was comparable with influenza 2016/2017 in all age groups, although rates among the unvaccinated population were still higher than influenza among 18+. Among people aged 5-17 years, COVID-19 hospitalisation rates were lower than/comparable to influenza years in both cohorts. The COVID-19 hospitalisation rate among 0-4 years old, during Omicron, was higher than influenza 2015/2016 and 2016/2017 and lower than 2009/2010 pandemic. CONCLUSIONS During first Omicron wave, COVID-19 hospitalisation rates were significantly higher than historical influenza hospitalisation rates for unvaccinated adults but were comparable to influenza for vaccinated adults. For children, in the context of high infection levels, hospitalisation rates for COVID-19 were lower than 2009/2010 H1N1 influenza and comparable (higher for 0-4) to non-pandemic years, regardless of the vaccine status.
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Affiliation(s)
- Solmaz Setayeshgar
- Data and Analytic Services, BC Centre for Disease Control, Vancouver, British Columbia, Canada
| | - James Wilton
- Data and Analytic Services, BC Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Hind Sbihi
- Data and Analytic Services, BC Centre for Disease Control, Vancouver, British Columbia, Canada,School of Population and Public Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Moe Zandy
- Public Health Surveillance Unit, Vancouver Coastal Health Authority, Vancouver, British Columbia, Canada
| | - Naveed Janjua
- Data and Analytic Services, BC Centre for Disease Control, Vancouver, British Columbia, Canada,School of Population and Public Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandra Choi
- Office of the Chief Medical Health Officer, Vancouver Coastal Health Authority, Vancouver, British Columbia, Canada
| | - Kate Smolina
- Data and Analytic Services, BC Centre for Disease Control, Vancouver, British Columbia, Canada,School of Population and Public Health, The University of British Columbia, Vancouver, British Columbia, Canada
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24
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Luo J, Zhang J, Tang HT, Wong HK, Ma Y, Xie D, Peng B, Lyu A, Cheung CH, Bian Z. Weekly symptom profiles of nonhospitalized individuals infected with SARS-CoV-2 during the Omicron outbreak in Hong Kong: A retrospective observational study from a telemedicine center. J Med Virol 2023; 95:e28447. [PMID: 36583471 PMCID: PMC9880749 DOI: 10.1002/jmv.28447] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Omicron BA.2.2 is the dominant variant in the Hong Kong outbreak since December 31, 2021. There is no study reporting the weekly symptom profile after infection. In this retrospective study, participants who tested positive for SARS-CoV-2 after December 31, 2021, and registered in the telemedicine system between March 14 and May 6, 2022, were analyzed. Among registered 12 950 self-quarantined COVID-19-positive patients, 11 776 symptomatic patients were included for weekly symptom profile analysis. A total of 4718 (40.1%) patients reported symptoms in the first week after a positive test, 2501 (21.2%) in the second week, 1498 (12.7%) in the third week, 1048 (8.9%) in the fourth week, and 2011 (17.1%) in over 4 weeks. Cough was the most common symptom in all participants. Patients in the first week had higher odds of reporting fever (0.206, 95% confidence interval [CI]: 0.161-0.263, p < 0.001) and sore throat (0.228, 95% CI: 0.208-0.252, p < 0.001). Patients in over 4 weeks had higher odds of reporting fatigue (1.263, 95% CI: 1.139-1.402, p < 0.001). Further, having at least two vaccine doses linked to lower odds of having fever (0.675, 95% CI: 0.562-0.811, p < 0.001), but not associated with the presence of cough and fatigue. Diabetic patients had higher odds of reporting diarrhea (1.637, 95% CI: 1.351-1.982, p < 0.001). Symptoms from Omicron infection may last for more than 4 weeks and symptom profiles vary from week to week. Vaccination and comorbidity affect the symptom profiles.
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Affiliation(s)
- Jingyuan Luo
- Hong Kong Chinese Medicine Clinical Study Centre, School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina,Centre for Chinese Herbal Medicine Drug DevelopmentHong Kong Baptist UniversityHong Kong SARChina
| | - Jialing Zhang
- Hong Kong Chinese Medicine Clinical Study Centre, School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina,Centre for Chinese Herbal Medicine Drug DevelopmentHong Kong Baptist UniversityHong Kong SARChina
| | - Hiu To Tang
- School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Hoi Ki Wong
- School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Yanfang Ma
- School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Duoli Xie
- School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Bo Peng
- School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Aiping Lyu
- Hong Kong Chinese Medicine Clinical Study Centre, School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina,School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Chun Hoi Cheung
- School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
| | - Zhaoxiang Bian
- Hong Kong Chinese Medicine Clinical Study Centre, School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina,Centre for Chinese Herbal Medicine Drug DevelopmentHong Kong Baptist UniversityHong Kong SARChina,School of Chinese MedicineHong Kong Baptist UniversityHong Kong SARChina
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25
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Wang Y, Chen Y, Gu L, Lou L, Zhang J, Zhang K. The clinical characteristics and risk factors for severe COVID-19 in patients with COVID-19 and tuberculosis coinfection. Front Microbiol 2022; 13:1061879. [PMID: 36619998 PMCID: PMC9817148 DOI: 10.3389/fmicb.2022.1061879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background Under the wave of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) variant Omicron epidemic, the number of infectious cases has increased dramatically in Jilin Province, China since March 2022.The clinical features and severity of SARS-CoV-2 Omicron variant infection in tuberculosis (TB) patients are not yet clear. Methods Data were obtained from 153 patients with the Omicron variant and TB coinfection and 153 non-TB COVID-19 patients who had been hospitalized at Changchun Infectious Disease Hospital from March to June 2022. Results Among these coinfection patients, 17 patients showed COVID-19-related pneumonia on chest imaging and 11 were diagnosed with severe COVID-19. The median duration of SARS-CoV-2 clearance was 13 days. The negative conversion time was associated with age, COVID-19-related pneumonia and antibody IgG. A higher white blood cell count, a lower lymphocyte percentage, a higher CRP level, and a higher D-dimer level were found in the severe group. Age and increased PCT were individual risk factors for the severity of COVID-19. Compared with the non-TB patients, the coinfection patients had higher severity of COVID-19 and the elder coinfection patients had a longer negative conversion time. Conclusion This study found an association between age, pneumonia, antibody IgG and RNA negative conversion time in COVID-19 and TB coinfection patients, and age and increased PCT were risk factors for the severity of COVID-19.
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Affiliation(s)
- Yang Wang
- Center of Infectious Disease and Pathogen Biology, Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Yanping Chen
- Department of Tuberculosis, Changchun Infectious Disease Hospital, Changchun, China
| | - Lina Gu
- Intensive Care Unit, The First Hospital of Jilin University, Changchun, China
| | - Lixin Lou
- Center of Infectious Disease and Pathogen Biology, Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jian Zhang
- Department of Infectious Diseases, Changchun Infectious Disease Hospital, Changchun, China,Jian Zhang,
| | - Kaiyu Zhang
- Center of Infectious Disease and Pathogen Biology, Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China,*Correspondence: Kaiyu Zhang,
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Feng Y, Shao H, Gong X, Song Z, Xie Y, Qi S, Shi L, Hu Y, Liu X, Liu X, Shen Q, Wu Q, Cheng T, Jiang W, Wu J, Chen J. 'Dynamic zero-COVID' policy and viral clearance during an omicron wave in Tianjin, China: a city-wide retrospective observational study. BMJ Open 2022; 12:e066359. [PMID: 36521897 PMCID: PMC9755905 DOI: 10.1136/bmjopen-2022-066359] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE To report how the Chinese mainland battled its first omicron wave, which happened in Tianjin, a metropolis with 14 million residents. We also sought to better understand how clinical features affected the timing of viral clearance. DESIGN A retrospective study of the omicron wave in Tianjin between 8 January 2022 and 3 March 2022. SETTING Except for the first cases on 8 January, all the omicron cases were identified through PCR mass testing in the residential communities. Residential quarantine and serial PCR mass testing were dynamically adjusted according to the trends of new cases. PARTICIPANTS All the 417 consecutive PCR-positive cases identified through mass screening of the entire city's 14 million residents. 45.3% of the cases were male, and the median age was 37 (range 0.3-90). 389 (93%) cases had complete data for analysing the correlation between clinical features and the timing of viral clearance. MAIN OUTCOME AND MEASURE Time to viral clearance. RESULTS Tianjin initiated the 'dynamic zero-COVID' policy very early, that is, when daily new case number was ≈0.4 cases per 1 000 000 residents. Daily new cases dropped to <5 after 3 February, and the number of affected residential subdivisions dropped to ≤2 after 13 February. 64% (267/417) of the cases had no or mild symptoms. The median interval from hospital admission to viral clearance was 10 days (range 3-28). An exploratory analysis identified a feature cluster associated with earlier viral clearance, with HRs of 3.56 (95% CI 1.66 to 7.63) and 3.15 (95% CI 1.68 to 5.91) in the training and validation sets, respectively. CONCLUSIONS The 'dynamic zero-COVID' policy can suppress an omicron wave within a month. It might be possible to predict in advance which cases will require shorter periods of isolation based on their clinical features.
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Affiliation(s)
- Yahui Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Hongxia Shao
- Department of Infectious Disease, Haihe Clinical School, Tianjin Medical University, Tianjin, China
| | - Xiaowen Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zhen Song
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yan Xie
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Tianjin, China
| | - Saibing Qi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Lixia Shi
- Department of Infectious Disease, Haihe Clinical School, Tianjin Medical University, Tianjin, China
| | - Yu Hu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xueou Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaolong Liu
- Department of Infectious Disease, Haihe Clinical School, Tianjin Medical University, Tianjin, China
| | - Qiujin Shen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Qi Wu
- School of Clinical Medicine, Medical College, Tianjin University, Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Wentao Jiang
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Tianjin, China
| | - Junping Wu
- Department of Infectious Disease, Haihe Clinical School, Tianjin Medical University, Tianjin, China
| | - Junren Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
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Lai A, Bergna A, Della Ventura C, Menzo S, Bruzzone B, Sagradi F, Ceccherini-Silberstein F, Weisz A, Clementi N, Brindicci G, Vicenti I, Sasset L, Caucci S, Corvaro B, Ippoliti S, Acciarri C, De Pace V, Lanfranchi L, Bellocchi MC, Giurato G, Ferrarese R, Lagioia A, Francisci D, Colombo ML, Lazzarin S, Ogliastro M, Cappelletti MR, Iannetta M, Rizzo F, Torti C, Fumi M, d’Avenia M, Brusa S, Greco F, Menchise A, Letizia V, Vaccaro E, Santoro CR, Fraccalvieri C, Testa S, Carioti L, Rocco T, Saracino A, Cattelan A, Clementi M, Sarmati L, Riva A, Galli M, Antinori S, Zehender G. Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April-December 2021 in Italy. Viruses 2022; 14:v14112508. [PMID: 36423117 PMCID: PMC9699621 DOI: 10.3390/v14112508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 is constantly evolving, leading to new variants. We analysed data from 4400 SARS-CoV-2-positive samples in order to pursue epidemiological variant surveillance and to evaluate their impact on public health in Italy in the period of April-December 2021. The main circulating strain (76.2%) was the Delta variant, followed by the Alpha (13.3%), the Omicron (5.3%), and the Gamma variants (2.9%). The B.1.1 lineages, Eta, Beta, Iota, Mu, and Kappa variants, represented around 1% of cases. There were 48.2% of subjects who had not been vaccinated, and they had a lower median age compared to the vaccinated subjects (47 vs. 61 years). An increasing number of infections in the vaccinated subjects were observed over time, with the highest proportion in November (85.2%). The variants correlated with clinical status; the largest proportion of symptomatic patients (59.6%) was observed with the Delta variant, while subjects harbouring the Gamma variant showed the highest proportion of asymptomatic infection (21.6%), albeit also deaths (5.4%). The Omicron variant was only found in the vaccinated subjects, of which 47% had been hospitalised. The diffusivity and pathogenicity associated with the different SARS-CoV-2 variants are likely to have relevant public health implications, both at the national and international levels. Our study provides data on the rapid changes in the epidemiological landscape of the SARS-CoV-2 variants in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
- Correspondence: ; Tel.: +39-0250319775
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Carla Della Ventura
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | | | - Fabio Sagradi
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | | | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Nicola Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | | | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Lolita Sasset
- Infectious Diseases Unit, Azienda Ospedale Università di Padova, 35128 Padova, Italy
| | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Benedetta Corvaro
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Silvia Ippoliti
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Carla Acciarri
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | | | - Leonardo Lanfranchi
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Maria C. Bellocchi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Roberto Ferrarese
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | | | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, Santa Maria della Misericordia Hospital, University of Perugia, 06123 Perugia, Italy
| | - Martina L. Colombo
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Samuel Lazzarin
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Matilde Ogliastro
- Department of Health Sciences (DISSAL), University of Genoa, 16126 Genoa, Italy
| | - Maria R. Cappelletti
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Marco Iannetta
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Carlo Torti
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Maurizio Fumi
- UOC Patologia Clinica, AO San Pio Benevento, 82100 Benevento, Italy
| | - Morena d’Avenia
- UOSVD di Citopatologia e Screening, Department of Laboratory Medicines, 70131 Bari, Italy
| | - Stefano Brusa
- Department of Translational Medical Sciences, Università Federico II, 80138 Naples, Italy
| | - Francesca Greco
- UOC Microbiologia e Virologia, PO Cosenza, 87100 Cosenza, Italy
| | - Angela Menchise
- Microbiology and Virology Laboratory, A.O.R. San Carlo Potenza, 85100 Potenza, Italy
| | - Vittoria Letizia
- UOSD Genetics and Molecular Biology, AORN Sant’Anna e San Sebastiano di Caserta, 81100 Caserta, Italy
| | - Emilia Vaccaro
- Molecular Biology Units, AOU ‘S. Giovanni di Dio e Ruggi d’Aragona’ Università di Salerno, 84131 Salerno, Italy
| | | | | | - Sophie Testa
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Teresa Rocco
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | | | - Annamaria Cattelan
- Infectious Diseases Unit, Azienda Ospedale Università di Padova, 35128 Padova, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | - Loredana Sarmati
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Agostino Riva
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Spinello Antinori
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
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AlBahrani S, AlBarrak A, Al-Musawi T, AlGubaisi NA, Almalki M, Hakami FH, Alghamdi T, AlBeiuruti Z, Alkhrashi S, Almershad M, Alzahrani S, AlQuraiaan A, AlTourifi H, Jebakumar AZ, Al-Tawfiq JA. COVID-19 vaccine had a significant positive impact on patients with SARS-COV-2 during the third (Omicron) wave in Saudi Arabia. J Infect Public Health 2022; 15:1169-1174. [PMID: 36215800 PMCID: PMC9490953 DOI: 10.1016/j.jiph.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/31/2022] [Accepted: 09/18/2022] [Indexed: 12/05/2022] Open
Abstract
INTRODUCTION The third (Omicron) wave had caused significant increase in the number of COVID-19 cases around the globe. The severity of the disease dependeds on the extent of the vaccination status. METHODS This is a retrospective study of infected COVID-19 patients during the third (Omicron) wave in a hospital in Saudi Arabia. RESULTS A total of 400 patients were included with 220 (55 %) males and 180 (45 %) females, and a mean age (+/- SD) of 36.34 + 16.47 years. The most common presenting symptoms were: sore throat 159 (39.8 %), cough 158 (39.5 %), fever 132 (33 %), headache 122 (30.5 %), and muscle ache 124 (31%). There was no difference in underlying conditions, signs and symptoms between males and females apart from the occurrence of sore throat with an OR of 2.014 (95 % CI: 1.103-3.677, P = 0.023) and need of hospitalization OR 2.457 (95 % CI: 1.168-5.167, P value =.018) in a binary logistic regression comparison. The need for hospitalization was inversely related to the number of COVID-19 vaccination doses. The rate of admission was 8 (72.7 %), 34 (12 %), 4 (5.4 %) for one, two, and three doses of COVID-19 vaccine, respectively (P < 0.0001). Of all the patients, 14 (3.5 %) and 8 (2 %) required intensive care (ICU) admission and mechanical ventilation, respectively. The median Ct-value of SARS-CoV-2 was higher in those who had 2 or 3 doses compared to those who had one dose of the COVID-19 vaccine, but the difference did not reach statistical significance. None of the included patients died during the study period. CONCLUSION Omicron variant symptoms among infected patients are generally milder compared to other variants. Prior COVID-19 vaccination may limit disease severity and need for hospitalization.
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Affiliation(s)
- Salma AlBahrani
- Infectious Disease Unit, Specialty Internal Medicine, King Fahd Military Medical Complex, Dhahran, Saudi Arabia
| | - Ali AlBarrak
- Infectious Disease Division, Internal Medicine Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Tariq Al-Musawi
- Critical Care Department, Dr. Sulaiman Alhabib Hospital, Alkhobar, Saudi Arabia; Royal College of Surgeons in Ireland-Medical University of Bahrain, Bahrain
| | | | - Maram Almalki
- King Fahd Military Medical Complex, Dhahran, Saudi Arabia
| | | | - Turki Alghamdi
- King Fahd Military Medical Complex, Dhahran, Saudi Arabia
| | | | | | | | | | | | | | | | - Jaffar A Al-Tawfiq
- Infectious Disease Unit, Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Infectious Disease Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Infectious Disease Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Tuyji-Tok Y, Yücebağ E, Keleş AB, Kılınçarslan AC, Nohut OK, Salman-Yılmaz S, Kuşkucu MA, Midilli K. Novel SARS-CoV-2 Omicron variants in İstanbul; Rapid Preponderance of BA.2 and BA.5. INFECTIOUS DISEASES & CLINICAL MICROBIOLOGY 2022; 4:192-198. [PMID: 38633395 PMCID: PMC10985815 DOI: 10.36519/idcm.2022.143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/20/2022] [Indexed: 04/19/2024]
Abstract
Objective In Turkey, the fourth wave of SARS-CoV-2 started in December 2021 and peaked in mid-January 2022. Afterward, peaks were seen in the number of COVID-19 cases because of Omicron BA.2 and BA.5 variants. Our study aimed to observe the prevalence and viral load-related transmissibility rates of the Omicron BA.2 and BA.5 variant infections in our region between January 21 and July 01, 2022, using an easy and cost-effective PCR screening method. Methods The frequency of BA.2 and BA.5 were determined by the two-stage allele-specific and drop-out RT-PCR method targeting NSP6 105-107del, spike 69-70del, and spike L452R mutation-specific primers. Transmissibility of the Omicron variants was assessed using cycle threshold (Ct) values (a proxy for SARS-CoV-2 viral load and infectivity). Also, using the next generation sequencing (NGS) method, existing mutations were analyzed by generating full-length sequences of the representative, randomly selected samples from the Omicron variants determined by PCR screening test. Results We defined the first case of BA.2 on January 19, 2022, in İstanbul University-Cerrahpaşa School of Medicine COVID-19 Molecular Diagnosis Laboratory. Following this, it was observed that BA.1 lost its dominance due to the increased transmissibility of BA.2. On May 5, we defined the first case of BA.5, and as of July this Omicron variant rapidly became preponderant, with a frequency of more than 85%. Compared with BA.1, BA.2 and BA.5 were associated with 2.82 (95% CI: 2.33-4.12) and 2.49 (95% CI: 2.16-3.55) fewer cycles, respectively, meaning higher transmissibility. As confirmed by the NGS results, it was concluded that screening with NSP6 105-107del, spike 69-70del and spike L452R mutation targeted PCR method, which is used uniquely in our hospital in Turkey, can be an easy and cost-effective method in the follow-up of Omicron variants. Conclusion The higher viral load detection in infections with BA.2 and BA.5 reflects a prolonged disease period, and increased transmissibility, so rapid expansion of these Omicron variants in Turkey is inevitable. Even though the prevalence of the Omicron variants in the population can be monitored in near real-time by the PCR screening method, more sequencing studies are needed for the early identification of new mutations that will emerge.
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Affiliation(s)
- Yeşim Tuyji-Tok
- Department of Medical Microbiology, İstanbul
University-Cerrahpaşa School of Medicine, İstanbul, Turkey
| | - Ebru Yücebağ
- Department of Medical Microbiology, İstanbul
University-Cerrahpaşa School of Medicine, İstanbul, Turkey
| | - Ayşe Betül Keleş
- Department of Medical Microbiology, İstanbul
University-Cerrahpaşa School of Medicine, İstanbul, Turkey
| | - Ayşe Ceylan Kılınçarslan
- Department of Medical Microbiology, İstanbul
University-Cerrahpaşa School of Medicine, İstanbul, Turkey
| | - Okan Kadir Nohut
- Fikret Biyal Central Research Laboratory, İstanbul
University-Cerrahpaşa School of Medicine, İstanbul, Turkey
| | - Seda Salman-Yılmaz
- Department of Forensic Medicine and Forensic Sciences, İstanbul
University-Cerrahpaşa School of Medicine, Istanbul, Turkey
| | - Mert Ahmet Kuşkucu
- Department of Medical Microbiology, İstanbul
University-Cerrahpaşa School of Medicine, İstanbul, Turkey
| | - Kenan Midilli
- Department of Medical Microbiology, İstanbul
University-Cerrahpaşa School of Medicine, İstanbul, Turkey
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Sasanami M, Kayano T, Nishiura H. Monitoring the COVID-19 immune landscape in Japan. Int J Infect Dis 2022; 122:300-306. [PMID: 35688309 PMCID: PMC9173820 DOI: 10.1016/j.ijid.2022.06.005] [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: 04/22/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES COVID-19 vaccination in Japan started on February 17, 2021. Because the timing of vaccination and the risk of severe COVID-19 greatly varied with age, the present study aimed to monitor the age-specific fractions of the population who were immune to SARS-CoV-2 infection after vaccination. METHODS Natural infection remained extremely rare, accounting for less than 5% of the population by the end of 2021; thus, we ignored natural infection-induced immunity and focused on vaccine-induced immunity. We estimated the fraction of the population immune to infection by age group using vaccination registry data from February 17, 2021, to October 17, 2021. We accounted for two important sources of delay: (i) reporting delay and (ii) time from vaccination until immune protection develops. RESULTS At the end of the observation period, the proportion of individuals still susceptible to SARS-CoV-2 infection substantially varied by age and was estimated to be ≥90% among people aged 0-14 years, in contrast to approximately 20% among the population aged ≥65 years. We also estimated the effective reproduction number over time using a next-generation matrix while accounting for differences in the proportion immune to infection by age. CONCLUSION The COVID-19 immune landscape greatly varied by age, and a substantial proportion of young adults remained susceptible. Vaccination contributed to a marked decrease in the reproduction number.
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Affiliation(s)
| | | | - Hiroshi Nishiura
- Corresponding author: Hiroshi Nishiura, Kyoto University School of Public Health, Yoshida-Konoe, Sakyo, Kyoto 606-8601, Japan Tel: +81 75 753 4456; Fax: +81 75 753 4458
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Yu W, Guo Y, Zhang S, Kong Y, Shen Z, Zhang J. Proportion of asymptomatic infection and nonsevere disease caused by SARS-CoV-2 Omicron variant: A systematic review and analysis. J Med Virol 2022; 94:5790-5801. [PMID: 35961786 PMCID: PMC9538850 DOI: 10.1002/jmv.28066] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/21/2022] [Accepted: 08/09/2022] [Indexed: 01/06/2023]
Abstract
SARS-CoV-2 Omicron variant seemed to cause milder disease compared to previous predominated variants. We aimed to conduct a meta-analysis to assess the pooled proportion of nonsevere disease and asymptomatic infection among COVID-19 patients infected with Omicron and Delta. We searched PubMed, Embase, Web of Science, and China National Knowledge Infrastructure (CNKI) databases. We included studies of SARS-CoV-2 Omicron infection from November 1, 2021, to April 18, 2022, and studies of Delta infection from October 1, 2020, to June 30, 2022. Studies without corresponding data, with less than 50 patients, or obviously biased concerning main outcome were excluded. Meta-analysis was performed in R 4.2.0 with the "meta" package. Subgroup analyses were conducted by study group and vaccination status. The pooled proportion of asymptomatic infection and nonsevere disease with Omicron were 25.5% (95% confidence interval [CI] 17.0%-38.2%) and 97.9% (95% CI 97.1%-98.7%), significantly higher than those of Delta with 8.4% (95% CI 4.4%-16.2%) and 91.4% (95% CI 87.0%-96.0%). During Omicron wave, children and adolescents had higher proportion of asymptomatic infection, SOTR and the elderly had lower proportion of nonsevere disease, vaccination of a booster dose contributed to higher proportion of both asymptomatic infection and nonsevere disease. This study estimates the pooled proportion of asymptomatic infection and nonsevere disease caused by SARS-CoV-2 Omicron compared to other predominant variants. The result has important implications for future policy making.
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Affiliation(s)
- Weien Yu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan HospitalFudan UniversityShanghaiChina
| | - Yifei Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan HospitalFudan UniversityShanghaiChina
| | - Shenyan Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan HospitalFudan UniversityShanghaiChina
| | - Yide Kong
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan HospitalFudan UniversityShanghaiChina
| | - Zhongliang Shen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan HospitalFudan UniversityShanghaiChina,Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical CollegeFudan UniversityShanghaiChina,Department of Infectious Diseases, Jing' An Branch of Huashan HospitalFudan UniversityShanghaiChina
| | - Jiming Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan HospitalFudan UniversityShanghaiChina,Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical CollegeFudan UniversityShanghaiChina,Department of Infectious Diseases, Jing' An Branch of Huashan HospitalFudan UniversityShanghaiChina
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Colson P, Fournier P, Delerce J, Million M, Bedotto M, Houhamdi L, Yahi N, Bayette J, Levasseur A, Fantini J, Raoult D, La Scola B. Culture and identification of a "Deltamicron" SARS-CoV-2 in a three cases cluster in southern France. J Med Virol 2022; 94:3739-3749. [PMID: 35467028 PMCID: PMC9088576 DOI: 10.1002/jmv.27789] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022]
Abstract
Multiple SARS-CoV-2 variants have successively, or concomitantly spread worldwide since the summer of 2020. A few co-infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co-detection of signature mutations of different variants in a given genome. Here we report three infections in southern France with a Delta 21J_AY.4-Omicron 21K/BA.1 "Deltamicron" recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1163-1421 reads and a mean nucleotide diversity of 0.1%-0.6%. It is composed of the near full-length spike gene (from codons 156-179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening quantitative polymerase chain reaction (qPCR), we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
- Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | - Pierre‐Edouard Fournier
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)MarseilleFrance
| | | | - Matthieu Million
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
- Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | | | | | - Nouara Yahi
- Aix‐Marseille Université, INSERM UMR S 1072MarseilleFrance
| | | | - Anthony Levasseur
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
| | | | - Didier Raoult
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
| | - Bernard La Scola
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
- Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance
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Protective Effect of Inactivated COVID-19 Vaccines against Progression of SARS-CoV-2 Omicron and Delta Variant Infections to Pneumonia in Beijing, China, in 2022. Vaccines (Basel) 2022; 10:vaccines10081215. [PMID: 36016103 PMCID: PMC9413898 DOI: 10.3390/vaccines10081215] [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: 06/14/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 12/23/2022] Open
Abstract
This real-world study explores the effect of coronavirus disease 2019 (COVID-19) inactivated vaccines on the prevention of asymptomatic or mild Delta or Omicron variant infections progressing to pneumonia. Association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia cases and vaccination was measured with a multivariable logistic regression, stratified by genotype and age groups. We recruited 265 cases (111 (41.9%) infected with Delta and 154 (58.1%) with Omicron variants). There were 22 asymptomatic infected individuals, 156 mild cases without pneumonia, and 87 moderate cases with pneumonia. There was a markedly increased risk of progression to pneumonia in Delta infected cases, unvaccinated, or partially vaccinated COVID-19 patients with diabetes and those aged ≥60 years. Patients who had completed booster doses of inactivated vaccines had a reduced risk of 81.6% (95% CI: 55.6−92.4%) in progressing to pneumonia over those who were unvaccinated or partially vaccinated. The risk of progressing to pneumonia was less reduced by 88.7% (95% CI: 56.6−97%) and 73.9% (95% CI: 1.4−93.1%) among Delta and Omicron-infected patients, and was reduced by 78.5% (95% CI: 45.3−91.6%) and 94.1% (95% CI: 21.5−99.6%) among patients aged <60 and ≥60 years, respectively. Our data indicated that a complete vaccination with a booster reduced the risk of asymptomatic or mild Delta or Omicron variant COVID-19 progressing to pneumonia and, thus, reduced the pressure of severe illness on medical resources.
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Percentage of Asymptomatic Infections among SARS-CoV-2 Omicron Variant-Positive Individuals: A Systematic Review and Meta-Analysis. Vaccines (Basel) 2022; 10:vaccines10071049. [PMID: 35891214 PMCID: PMC9321237 DOI: 10.3390/vaccines10071049] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/19/2022] [Accepted: 06/28/2022] [Indexed: 02/06/2023] Open
Abstract
Background: Asymptomatic infections are potential sources of transmission for coronavirus disease 2019, especially during the epidemic of the SARS-CoV-2 Omicron variant. We aimed to assess the percentage of asymptomatic infections among SARS-CoV-2 Omicron variant-positive individuals detected by gene sequencing or specific polymerase chain reaction (PCR). Methods: We searched PubMed, EMBASE, and Web of Science from 26 November 2021 to 13 April 2022. This meta-analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and was registered with PROSPERO (CRD42022327894). Three researchers independently extracted data and two researchers assessed quality using pre-specified criteria. The pooled percentage with 95% confidence interval (CI) of asymptomatic infections of SARS-CoV-2 Omicron was estimated using random-effects models. Results: Our meta-analysis included eight eligible studies, covering 7640 Omicron variant-positive individuals with 2190 asymptomatic infections. The pooled percentage of asymptomatic infections was 32.40% (95% CI: 25.30−39.51%) among SARS-CoV-2 Omicron variant-positive individuals, which was higher in the population in developing countries (38.93%; 95% CI: 19.75−58.11%), with vaccine coverage ≥ 80% (35.93%; 95% CI: 25.36−46.51%), with a travel history (40.05%; 95% CI: 7.59−72.51%), community infection (37.97%; 95% CI: 10.07−65.87%), and with a median age < 20 years (43.75%; 95% CI: 38.45−49.05%). Conclusion: In this systematic review and meta-analysis, the pooled percentage of asymptomatic infections was 32.40% among SARS-CoV-2 Omicron variant-positive individuals. The people who were vaccinated, young (median age < 20 years), had a travel history, and were infected outside of a clinical setting (community infection) had higher percentages of asymptomatic infections. Screening is required to prevent clustered epidemics or sustained community transmission caused by asymptomatic infections of Omicron variants, especially for countries and regions that have successfully controlled SARS-CoV-2.
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Tso WWY, Kwan MYW, Wang YL, Leung LK, Leung D, Chua GT, Ip P, Fong DYT, Wong WHS, Chan SHS, Chan JFW, Peiris M, Lau YL, Rosa Duque JS. Severity of SARS-CoV-2 Omicron BA.2 infection in unvaccinated hospitalized children: Comparison to influenza and parainfluenza infections. Emerg Microbes Infect 2022; 11:1742-1750. [PMID: 35730665 PMCID: PMC9258055 DOI: 10.1080/22221751.2022.2093135] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There has been a rapid surge of hospitalization due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants globally. The severity of Omicron BA.2 in unexposed, unvaccinated, hospitalized children is unknown. We investigated the severity and clinical outcomes of COVID-19 infection during the Omicron wave in uninfected, unvaccinated hospitalized children and in comparison with influenza and parainfluenza viral infections. This population-based study retrieved data from the HK territory-wide CDARS database of hospitalisations in all public hospitals and compared severe outcomes for the Omicron BA.2-dominant fifth wave (5–28 February 2022, n = 1144), and influenza and parainfluenza viruses (1 January 2015–31 December 2019, n = 32212 and n = 16423, respectively) in children 0–11 years old. Two deaths (0.2%) out of 1144 cases during the initial Omicron wave were recorded. Twenty-one (1.8%) required PICU admission, and the relative risk was higher for Omicron than influenza virus (n = 254, 0.8%, adjusted RR = 2.1, 95%CI 1.3–3.3, p = 0.001). The proportion with neurological complications was 15.0% (n = 171) for Omicron, which was higher than influenza and parainfluenza viruses (n = 2707, 8.4%, adjusted RR = 1.6, 95%CI 1.4–1.9 and n = 1258, 7.7%, adjusted RR = 1.9, 95%CI 1.6–2.2, p < 0.001 for both, respectively). Croup occurred for Omicron (n = 61, 5.3%) more than influenza virus (n = 601, 1.9%, adjusted RR = 2.0, 95%CI 1.5–2.6, p < 0.001) but not parainfluenza virus (n = 889, 5.4%). Our findings showed that for hospitalized children who had no past COVID-19 or vaccination, Omicron BA.2 was not mild. Omicron BA.2 appeared to be more neuropathogenic than influenza and parainfluenza viruses. It targeted the upper airways more than influenza virus.
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Affiliation(s)
- Winnie W Y Tso
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, China
| | - Mike Y W Kwan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Yu Liang Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Lok Kan Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Daniel Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Gilbert T Chua
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Patrick Ip
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Daniel Y T Fong
- School of Nursing, The University of Hong Kong, Hong Kong, China
| | - Wilfred H S Wong
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Sophelia H S Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jasper F W Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jaime S Rosa Duque
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
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Guérin P, Yahi N, Azzaz F, Chahinian H, Sabatier JM, Fantini J. Structural Dynamics of the SARS-CoV-2 Spike Protein: A 2-Year Retrospective Analysis of SARS-CoV-2 Variants (from Alpha to Omicron) Reveals an Early Divergence between Conserved and Variable Epitopes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123851. [PMID: 35744971 PMCID: PMC9230616 DOI: 10.3390/molecules27123851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 12/17/2022]
Abstract
We analyzed the epitope evolution of the spike protein in 1,860,489 SARS-CoV-2 genomes. The structural dynamics of these epitopes was determined by molecular modeling approaches. The D614G mutation, selected in the first months of the pandemic, is still present in currently circulating SARS-CoV-2 strains. This mutation facilitates the conformational change leading to the demasking of the ACE2 binding domain. D614G also abrogated the binding of facilitating antibodies to a linear epitope common to SARS-CoV-1 and SARS-CoV-2. The main neutralizing epitope of the N-terminal domain (NTD) of the spike protein showed extensive structural variability in SARS-CoV-2 variants, especially Delta and Omicron. This epitope is located on the flat surface of the NTD, a large electropositive area which binds to electronegatively charged lipid rafts of host cells. A facilitating epitope located on the lower part of the NTD appeared to be highly conserved among most SARS-CoV-2 variants, which may represent a risk of antibody-dependent enhancement (ADE). Overall, this retrospective analysis revealed an early divergence between conserved (facilitating) and variable (neutralizing) epitopes of the spike protein. These data aid in the designing of new antiviral strategies that could help to control COVID-19 infection by mimicking neutralizing antibodies or by blocking facilitating antibodies.
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Affiliation(s)
| | - Nouara Yahi
- INSERM UMR_S 1072, Aix-Marseille University, CEDEX, 13015 Marseille, France; (N.Y.); (F.A.); (H.C.)
| | - Fodil Azzaz
- INSERM UMR_S 1072, Aix-Marseille University, CEDEX, 13015 Marseille, France; (N.Y.); (F.A.); (H.C.)
| | - Henri Chahinian
- INSERM UMR_S 1072, Aix-Marseille University, CEDEX, 13015 Marseille, France; (N.Y.); (F.A.); (H.C.)
| | - Jean-Marc Sabatier
- Inst Neurophysiopathol, Aix-Marseille University, CNRS, INP, CEDEX, 13005 Marseille, France;
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille University, CEDEX, 13015 Marseille, France; (N.Y.); (F.A.); (H.C.)
- Correspondence:
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Hoteit R, Yassine HM. Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences. Vaccines (Basel) 2022; 10:919. [PMID: 35746526 PMCID: PMC9230982 DOI: 10.3390/vaccines10060919] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.
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Affiliation(s)
- Reem Hoteit
- Clinical Research Institute, Faculty of Medicine, American University of Beirut, Beirut 110236, Lebanon;
| | - Hadi M. Yassine
- Biomedical Research Center and College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar
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Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients. Bull Exp Biol Med 2022; 173:229-234. [PMID: 35737161 PMCID: PMC9218049 DOI: 10.1007/s10517-022-05524-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 11/08/2022]
Abstract
We developed a new test system to detect the omicron variant of SARS-CoV-2 using allele-specific reverse transcription PCR and estimated the frequency of its detection in patients living in the Novosibirsk Region. Clinical samples were divided into 3 groups: samples collected from December 1 to December 30, 2021 (group 1; n=66), from December 30, 2021 to January 10, 2022 (group 2; n=20), and from January 11 to January 22, 2022 (group 3; n=101). Based on the identification of 5 mutations specific to SARS-CoV-2 (B.1.1.529), two systems of oligonucleotide primers and probes were developed for detecting this coronavirus genotype in clinical samples. Limit of detection (LOD95) was 4×103 genome equivalents per 1 ml of clinical sample for the first test system and 2×103 for the for the second test system. The omicron variant of SARS-CoV-2 was absent in group 1 of studied samples, but was detected in 20% (4/20) of group 2 samples and 88% of group 2 samples collected within less than 2 weeks of January 2022. Using developed test system, we showed that in less than 2 weeks the omicron variant has become dominant in patients, which confirms previously published data on its exceptional contagiousness.
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Zhang J, Chen N, Zhao D, Zhang J, Hu Z, Tao Z. Clinical Characteristics of COVID-19 Patients Infected by the Omicron Variant of SARS-CoV-2. Front Med (Lausanne) 2022; 9:912367. [PMID: 35615088 PMCID: PMC9125333 DOI: 10.3389/fmed.2022.912367] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 12/19/2022] Open
Abstract
Background Currently, as the omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surges amid the coronavirus disease 2019 (COVID-19) pandemic, its clinical characteristics with intrinsic severity and the protection from vaccination have been understudied. Methods We reported 169 COVID-19 patients that were infected with the omicron variant of SARS-CoV-2 and hospitalized in Suzhou, China, from February to March 2022, with their demographic information, medical/immunization history, clinical symptom, and hematological profile. At the same time, patients with none/partial (one-dose), full (two-dose) and three-dose vaccination were also compared to assess the vaccine effectiveness. Findings For the omicron COVID-19 patients included in this study, their median age was 33.0 [interquartile range (IQR): 24.0-45.5], 53.3% were male and the median duration from illness onset to hospitalization was 2 days. Hypertension, bronchitis, and diabetes were the leading comorbidities among patients. While the common clinical symptoms included cough, fever, expectoration, and fatigue, etc., asymptomatic patients took up a significant portion (46.7%). For hematological parameters, most values revealed the alleviated pathogenicity induced by the omicron variant infection. No critically ill or deceased patients due to COVID-19 infection were reported in this study. Interpretation Our results supported that the viremic effect of the omicron variant became milder than the previous circulating variants, while full vaccination or booster shot was greatly desired for an effective protection against clinical severity.
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Affiliation(s)
- Jianguo Zhang
- Department of Emergency Medicine, The Affiliated Hospital, Jiangsu University, Zhenjiang, China
| | - Nan Chen
- Jiangsu Province Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Daguo Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jinhui Zhang
- Department of Critical Care Medicine, The Affiliated Hospital, Jiangsu University, Zhenjiang, China
| | - Zhenkui Hu
- Department of Critical Care Medicine, The Affiliated Hospital, Jiangsu University, Zhenjiang, China
| | - Zhimin Tao
- Department of Emergency Medicine, The Affiliated Hospital, Jiangsu University, Zhenjiang, China
- Jiangsu Province Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
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40
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SARS-CoV-2 Omicron variant: recent progress and future perspectives. Signal Transduct Target Ther 2022; 7:141. [PMID: 35484110 PMCID: PMC9047469 DOI: 10.1038/s41392-022-00997-x] [Citation(s) in RCA: 278] [Impact Index Per Article: 139.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/27/2022] [Accepted: 04/13/2022] [Indexed: 02/06/2023] Open
Abstract
Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, there have been a few variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), one of which is the Omicron variant (B.1.1.529). The Omicron variant is the most mutated SARS-CoV-2 variant, and its high transmissibility and immune evasion ability have raised global concerns. Owing to its enhanced transmissibility, Omicron has rapidly replaced Delta as the dominant variant in several regions. However, recent studies have shown that the Omicron variant exhibits reduced pathogenicity due to altered cell tropism. In addition, Omicron exhibits significant resistance to the neutralizing activity of vaccines, convalescent serum, and most antibody therapies. In the present review, recent advances in the molecular and clinical characteristics of the infectivity, pathogenicity, and immune evasion of Omicron variant was summarized, and potential therapeutic applications in response to Omicron infection were discussed. Furthermore, we highlighted potential response to future waves and strategies to end the pandemic.
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41
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Menni C, Valdes AM, Polidori L, Antonelli M, Penamakuri S, Nogal A, Louca P, May A, Figueiredo JC, Hu C, Molteni E, Canas L, Österdahl MF, Modat M, Sudre CH, Fox B, Hammers A, Wolf J, Capdevila J, Chan AT, David SP, Steves CJ, Ourselin S, Spector TD. Symptom prevalence, duration, and risk of hospital admission in individuals infected with SARS-CoV-2 during periods of omicron and delta variant dominance: a prospective observational study from the ZOE COVID Study. Lancet 2022; 399:1618-1624. [PMID: 35397851 PMCID: PMC8989396 DOI: 10.1016/s0140-6736(22)00327-0] [Citation(s) in RCA: 468] [Impact Index Per Article: 234.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND The SARS-CoV-2 variant of concern, omicron, appears to be less severe than delta. We aim to quantify the differences in symptom prevalence, risk of hospital admission, and symptom duration among the vaccinated population. METHODS In this prospective longitudinal observational study, we collected data from participants who were self-reporting test results and symptoms in the ZOE COVID app (previously known as the COVID Symptoms Study App). Eligible participants were aged 16-99 years, based in the UK, with a body-mass index between 15 and 55 kg/m2, had received at least two doses of any SARS-CoV-2 vaccine, were symptomatic, and logged a positive symptomatic PCR or lateral flow result for SARS-CoV-2 during the study period. The primary outcome was the likelihood of developing a given symptom (of the 32 monitored in the app) or hospital admission within 7 days before or after the positive test in participants infected during omicron prevalence compared with those infected during delta prevalence. FINDINGS Between June 1, 2021, and Jan 17, 2022, we identified 63 002 participants who tested positive for SARS-CoV-2 and reported symptoms in the ZOE app. These patients were matched 1:1 for age, sex, and vaccination dose, across two periods (June 1 to Nov 27, 2021, delta prevalent at >70%; n=4990, and Dec 20, 2021, to Jan 17, 2022, omicron prevalent at >70%; n=4990). Loss of smell was less common in participants infected during omicron prevalence than during delta prevalence (16·7% vs 52·7%, odds ratio [OR] 0·17; 95% CI 0·16-0·19, p<0·001). Sore throat was more common during omicron prevalence than during delta prevalence (70·5% vs 60·8%, 1·55; 1·43-1·69, p<0·001). There was a lower rate of hospital admission during omicron prevalence than during delta prevalence (1·9% vs 2·6%, OR 0·75; 95% CI 0·57-0·98, p=0·03). INTERPRETATION The prevalence of symptoms that characterise an omicron infection differs from those of the delta SARS-CoV-2 variant, apparently with less involvement of the lower respiratory tract and reduced probability of hospital admission. Our data indicate a shorter period of illness and potentially of infectiousness which should impact work-health policies and public health advice. FUNDING Wellcome Trust, ZOE, National Institute for Health Research, Chronic Disease Research Foundation, National Institutes of Health, and Medical Research Council.
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Affiliation(s)
- Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Ana M Valdes
- Nottingham NIHR Biomedical Research Centre at the School of Medicine, University of Nottingham, Nottingham, UK
| | | | - Michela Antonelli
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | | | - Ana Nogal
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Panayiotis Louca
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles CA, USA
| | | | - Erika Molteni
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Liane Canas
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Marc F Österdahl
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Carole H Sudre
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; MRC Unit for Lifelong Health and Ageing, University College London, London, UK; Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
| | | | - Alexander Hammers
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; King's College London & Guy's and St Thomas' PET Centre, London, UK
| | | | | | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sean P David
- NorthShore University Health System & University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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Houhamdi L, Fournier PE. Smart apps for self-reporting clinical information. Lancet 2022; 399:1575-1576. [PMID: 35397852 PMCID: PMC8989392 DOI: 10.1016/s0140-6736(22)00453-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Linda Houhamdi
- IHU Méditerranée Infection, Marseille, France, 13005; Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Université, Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France, 13005.
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France, 13005; Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Université, Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France, 13005
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43
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Nguyen NN, Houhamdi L, Hoang VT, Stoupan D, Fournier PE, Raoult D, Colson P, Gautret P. High rate of reinfection with the SARS-CoV-2 Omicron variant. J Infect 2022; 85:174-211. [PMID: 35472367 PMCID: PMC9033627 DOI: 10.1016/j.jinf.2022.04.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Nhu Ngoc Nguyen
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Linda Houhamdi
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Van Thuan Hoang
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | | | - Pierre-Edouard Fournier
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Philippe Gautret
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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44
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Adamoski D, de Baura VA, Rodrigues AC, Royer CA, Aoki MN, Tschá MK, Bonatto AC, Wassem R, Nogueira MB, Raboni SM, de Almeida BMM, Trindade EDS, Gradia DF, Souza EM, Carvalho de Oliveira J. SARS-CoV-2 Delta and Omicron Variants Surge in Curitiba, Southern Brazil, and Its Impact on Overall COVID-19 Lethality. Viruses 2022; 14:v14040809. [PMID: 35458539 PMCID: PMC9027352 DOI: 10.3390/v14040809] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/04/2023] Open
Abstract
Screening efforts and genomic surveillance are essential tools to evaluate the course of the COVID-19 pandemic and assist the public healthcare system in dealing with an increasing number of infections. For the analysis of COVID-19 cases scenarios in Curitiba, Paraná, Brazil, we performed a diagnosis of positive cases, coupled with genotyping, for symptomatic and asymptomatic members of the Federal University of Paraná. We achieved over 1000 samples using RT-qPCR for diagnosis. The posterior genotyping allowed us to observe differences in the spread of strains in Curitiba, Brazil. The Delta variant was not associated with an infection wave, whereas the rapid Omicron variant spread became dominant in less than one month. We also evaluated the general vaccination coverage in the state, observing a striking reduction in lethality correlated to the vaccinated fraction of the population; although lower lethality rates were not much affected by the Omicron variant wave, the same effect was not translated in the number of infections. In summary, our results provide a general overview of the pandemic's course in Paraná State and how there was reduction in lethality after a combination of multiple infection waves and a large-scale vaccination program.
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Affiliation(s)
- Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, Brazil;
| | - Valter Antonio de Baura
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba 81530-000, Brazil;
| | - Ana Carolina Rodrigues
- Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Brazil; (A.C.R.); (C.A.R.); (A.C.B.); (R.W.); (D.F.G.)
| | - Carla Adriane Royer
- Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Brazil; (A.C.R.); (C.A.R.); (A.C.B.); (R.W.); (D.F.G.)
| | | | | | - Ana Claudia Bonatto
- Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Brazil; (A.C.R.); (C.A.R.); (A.C.B.); (R.W.); (D.F.G.)
| | - Roseli Wassem
- Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Brazil; (A.C.R.); (C.A.R.); (A.C.B.); (R.W.); (D.F.G.)
| | - Meri Bordignon Nogueira
- Virology Laboratory, Complexo Hospital de Clínicas, Universidade Federal do Paraná, Curitiba 80060-900, Brazil; (M.B.N.); (S.M.R.)
| | - Sonia Mara Raboni
- Virology Laboratory, Complexo Hospital de Clínicas, Universidade Federal do Paraná, Curitiba 80060-900, Brazil; (M.B.N.); (S.M.R.)
| | | | | | - Daniela Fiori Gradia
- Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Brazil; (A.C.R.); (C.A.R.); (A.C.B.); (R.W.); (D.F.G.)
| | - Emanuel Maltempi Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba 81530-000, Brazil;
- Correspondence: (E.M.S.); (J.C.d.O.)
| | - Jaqueline Carvalho de Oliveira
- Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Brazil; (A.C.R.); (C.A.R.); (A.C.B.); (R.W.); (D.F.G.)
- Correspondence: (E.M.S.); (J.C.d.O.)
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Gautret P, Hoang VT, Jimeno MT, Lagier JC, Rossi P, Fournier PE, Colson P, Raoult D. Severity of the first 207 infections with the SARS-CoV-2 Omicron BA.2 variant, in Marseille, France, December, 2021-February, 2022. J Med Virol 2022; 94:3494-3497. [PMID: 35365865 PMCID: PMC9088598 DOI: 10.1002/jmv.27760] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Philippe Gautret
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Van Thuan Hoang
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | | | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Pascal Rossi
- Assistance Publique - Hôpitaux de Marseille, Marseille, France
| | - Pierre Edouard Fournier
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
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46
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An evolutionary insight into Severe Acute Respiratory Syndrome Coronavirus 2 Omicron variant of concern. Virus Res 2022; 314:198753. [PMID: 35331836 PMCID: PMC8937608 DOI: 10.1016/j.virusres.2022.198753] [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: 01/05/2022] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 12/30/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel virus that belongs to the family Coronaviridae. This virus produces a respiratory illness known as coronavirus disease 2019 (COVID-19) and is to blame for the pandemic of COVID-19. Due to its massive circulation around the world and the capacity of mutation of this virus, genomic studies are much needed in to order to reveal new variants of concern (VOCs). On November 26th, 2021, the WHO announced that a new SARS-CoV-2 VOC, named Omicron, had emerged. In order to get insight into the emergence, spread and evolution of Omicron SARS-CoV-2 variants, a comprehensive phylogenetic study was performed. The results of these studies revealed significant differences in codon usage among the S genes of SARS-CoV-2 VOCs Alfa, Beta, Gamma, Delta and Omicron, which can be linked to SARS-CoV-2 genotypes. Omicron variant did not evolve out of one of the early VOCs, but instead it belongs to a complete different genetic lineage from previous ones. Strains classified as Omicron variants evolved from ancestors that existed around May 15th, 2020, suggesting that this VOC may have been circulating undetected for a period of time until its emergence was observed in South Africa. A rate of evolution of 5.61 × 10−4 substitutions/site/year was found for Omicron strains enrolled in these analyses. The results of these studies demonstrate that S genes have suitable genetic information for clear assignment of emerging VOCs to its specific genotypes.
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Colson P, Delerce J, Beye M, Levasseur A, Boschi C, Houhamdi L, Tissot-Dupont H, Yahi N, Million M, La Scola B, Fantini J, Raoult D, Fournier PE. First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France. J Med Virol 2022; 94:3421-3430. [PMID: 35243660 PMCID: PMC9088623 DOI: 10.1002/jmv.27695] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/22/2022]
Abstract
The SARS‐CoV‐2 21K/BA.1, 21L/BA.2, and BA.3 Omicron variants have recently emerged worldwide. To date, the 21L/BA.2 Omicron variant has remained very minority globally but became predominant in Denmark instead of the 21K/BA.1 variant. Here, we describe the first cases diagnosed with this variant in south‐eastern France. We identified 13 cases using variant‐specific qPCR and next‐generation sequencing between 28/11/2021 and 31/01/2022, the first two cases being diagnosed in travelers returning from Tanzania. Overall, viral genomes displayed a mean (±standard deviation) number of 65.9 ± 2.5 (range, 61–69) nucleotide substitutions and 31.0 ± 8.3 (27–50) nucleotide deletions, resulting in 49.6 ± 2.2 (45–52) amino acid substitutions (including 28 in the spike protein) and 12.4 ± 1.1 (12–15) amino acid deletions. Phylogeny showed the distribution in three different clusters of these genomes, which were most closely related to genomes from England and South Africa, from Singapore and Nepal, or from France and Denmark. Structural predictions highlighted a significant enlargement and flattening of the surface of the 21L/BA.2 N‐terminal domain of the spike protein compared to that of the 21K/BA.1 Omicron variant, which may facilitate initial viral interactions with lipid rafts. Close surveillance is needed at global, country, and center scales to monitor the incidence and clinical outcome of the 21L/BA.2 Omicron variant.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Mamadou Beye
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Linda Houhamdi
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Nouara Yahi
- Aix-Marseille Université, INSERM UMR S 1072, 51 boulevard Pierre Dramard, 13015, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Jacques Fantini
- Aix-Marseille Université, INSERM UMR S 1072, 51 boulevard Pierre Dramard, 13015, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France
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