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Singh UB, Deb S, Rani L, Gupta R, Verma S, Kumari L, Bhardwaj D, Bala K, Ahmed J, Gaurav S, Perumalla S, Nizam M, Mishra A, Stephenraj J, Shukla J, Nayer J, Aggarwal P, Kabra M, Ahuja V, Chaudhry R, Sinha S, Guleria R. Phylogeny and evolution of SARS-CoV-2 during Delta and Omicron variant waves in India. J Biomol Struct Dyn 2024; 42:4769-4781. [PMID: 37318006 DOI: 10.1080/07391102.2023.2222832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/02/2023] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was reported in patients without comorbidity (97%), while Omicron BA.2 was reported in patients with comorbidity (77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2. Higher propensity of Omicron variants to bronchial tissue, probably ensured increased transmission while Omicron BA.2 became the prevalent variant possibly due to evolutionary trade-off. Virus evolution continues to shape the epidemic and its culmination.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sushanta Deb
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Rani
- Central Core Research Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Sunita Verma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Kumari
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepika Bhardwaj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Kiran Bala
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jawed Ahmed
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sudesh Gaurav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sowjanya Perumalla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Md Nizam
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Anwita Mishra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - J Stephenraj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jyoti Shukla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jamshed Nayer
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care & Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
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Goller KV, Ziemann J, Kohler C, Becker K, Hübner NO. Clinical Manifestations of Infections with the Omicron Sub-Lineages BA.1, BA.2, and BA.5: A Retrospective Follow-Up Analysis of Public Health Data from Mecklenburg-Western Pomerania, Germany. Viruses 2024; 16:454. [PMID: 38543819 PMCID: PMC10974208 DOI: 10.3390/v16030454] [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: 01/09/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 05/23/2024] Open
Abstract
The Omicron variants BA.1, BA.2, and BA.5 caused several waves of SARS-CoV-2 in Germany in 2022. In this comparative study, public health data on SARS-CoV-2 infections from Mecklenburg-Western Pomerania, Germany, between January and October 2022 were examined retrospectively using Pearson's chi-squared tests and Fisher's exact tests for testing for statistical significance. Compared to BA.5 infections, BA.1 and BA.2 infections affected younger individuals aged up to 19 years significantly more often, whereas BA.5 infections occurred significantly more frequently in patients between 40 and 59 years of age when compared to BA.1 and BA.2. Infections with all three variants predominantly caused flu-like symptoms; nevertheless, there were significant differences between the reported symptoms of BA.1, BA.2, and BA.5 infections. Especially, the symptoms of 'fever', 'severe feeling of sickness', 'loss of taste', and 'loss of smell' were significantly more often present in patients with BA.5 infections compared to BA.1 and BA.2 cases. Additionally, BA.2 and BA.5 cases reported significantly more often the symptoms of 'runny nose' and 'cough' than BA.1-infected cases. Our findings indicate remarkable differences in the clinical presentations among the sub-lineages, especially in BA.5 infections. Furthermore, the study demonstrates a powerful tool to link epidemiological data with genetic data in order to investigate their potential impact on public health.
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Affiliation(s)
- Katja Verena Goller
- Central Unit for Infection Prevention and Control and Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Janine Ziemann
- Central Unit for Infection Prevention and Control and Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Christian Kohler
- Friedrich-Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany; (C.K.); (K.B.)
| | - Karsten Becker
- Friedrich-Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany; (C.K.); (K.B.)
| | - Nils-Olaf Hübner
- Central Unit for Infection Prevention and Control and Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, 17475 Greifswald, Germany;
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3
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Yin Z, Fang Q, Wen T, Zheng C, Fu C, Wang S, Li J, Gong X. Effectiveness of COVID-19 vaccines against SARS-CoV-2 Omicron variants during two outbreaks from March to May 2022 in Quzhou, China. Hum Vaccin Immunother 2023; 19:2163813. [PMID: 36704960 PMCID: PMC10012893 DOI: 10.1080/21645515.2022.2163813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Limited data are available on the effectiveness of COVID-19 vaccines used in China in real-world outbreaks - especially against Omicron variants in vaccinated individuals. Two outbreaks of SARS-CoV-2 Omicron variants - the first involving the sub-lineage BA.2 and the second the BA.1 variant - occurred in Quzhou. Infected people and their close contacts were divided according to vaccination status: unvaccinated, partially vaccinated, fully vaccinated, and boosted. The Cox proportional-hazard regression model was used to estimate the evolving hazard for vaccinated individuals after their first immunization. 138 people had been infected with the SARS-CoV-2 Omicron BA.2 variant and 13 with the BA.1 variant. Of the 151 infections, 99.34% (150/151) were mild or asymptomatic and 90.07% (136/151) were vaccine breakthrough cases. The total vaccine effectiveness (VE) of partial, full, and booster vaccinations during the two outbreaks was 47.4% (95%CI: 0-93.1%), 28.9% (95%CI: 0-60.2%), and 27.5% (95%CI: 0-58.3%). The VE of booster vaccination against the Omicron BA.1 variant was higher than that for the BA.2 variant. The cumulative hazard began to increase 220 days after the first immunization. The transmissibility of the Omicron BA.2 variant as for BA.1 did not increase in vaccinated individuals; booster vaccination after a primary course substantially increased protection. Our study found that the SARS-CoV-2 Omicron variant caused less severe illness and that the VE of boosters against the Omicron variant was less than 30%. Timely administration of the booster dose was important, especially for individuals aged over 80 years old.
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Affiliation(s)
- Zhiying Yin
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang Province, China.,School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
| | - Quanjun Fang
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang Province, China
| | - Tingcui Wen
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
| | - Canjie Zheng
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang Province, China
| | - Canya Fu
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
| | - Shuangqing Wang
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang Province, China
| | - Junji Li
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang Province, China
| | - Xiaoying Gong
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang Province, China
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4
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Luo M, Zhou B, Reddem ER, Tang B, Chen B, Zhou R, Liu H, Liu L, Katsamba PS, Au KK, Man HO, To KKW, Yuen KY, Shapiro L, Dang S, Ho DD, Chen Z. Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2. Emerg Microbes Infect 2023; 12:2146538. [PMID: 36354024 PMCID: PMC9817130 DOI: 10.1080/22221751.2022.2146538] [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: 09/30/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACTIncreasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis.
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Affiliation(s)
- Mengxiao Luo
- AIDS Institute, 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
| | - Biao Zhou
- AIDS Institute, 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
| | | | - Bingjie Tang
- Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China
| | - Bohao Chen
- AIDS Institute, 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
| | - Runhong Zhou
- AIDS Institute, 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
| | - Hang Liu
- Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Ka-Kit Au
- AIDS Institute, 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
| | - Hiu-On Man
- AIDS Institute, 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
| | - 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
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, 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, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - 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
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, 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, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behaviour Institute, New York, NY, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shangyu Dang
- Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People’s Republic of China
- HKUST-Shenzhen Research Institute, Nanshan, People’s Republic of China
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zhiwei Chen
- AIDS Institute, 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
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, 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, People’s Republic of China
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5
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Xia H, Yeung J, Kalveram B, Bills CJ, Chen JYC, Kurhade C, Zou J, Widen SG, Mann BR, Kondor R, Davis CT, Zhou B, Wentworth DE, Xie X, Shi PY. Cross-neutralization and viral fitness of SARS-CoV-2 Omicron sublineages. Emerg Microbes Infect 2023; 12:e2161422. [PMID: 36594261 PMCID: PMC9848280 DOI: 10.1080/22221751.2022.2161422] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The rapid evolution of SARS-CoV-2 Omicron sublineages mandates a better understanding of viral replication and cross-neutralization among these sublineages. Here we used K18-hACE2 mice and primary human airway cultures to examine the viral fitness and antigenic relationship among Omicron sublineages. In both K18-hACE2 mice and human airway cultures, Omicron sublineages exhibited a replication order of BA.5 ≥ BA.2 ≥ BA.2.12.1 > BA.1; no difference in body weight loss was observed among different sublineage-infected mice. The BA.1-, BA.2-, BA.2.12.1-, and BA.5-infected mice developed distinguishable cross-neutralizations against Omicron sublineages, but exhibited little neutralization against the index virus (i.e. USA-WA1/2020) or the Delta variant. Surprisingly, the BA.5-infected mice developed higher neutralization activity against heterologous BA.2 and BA.2.12.1 than that against homologous BA.5; serum neutralizing titres did not always correlate with viral replication levels in infected animals. Our results revealed a distinct antigenic cartography of Omicron sublineages and support the bivalent vaccine approach.
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Affiliation(s)
- Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jason Yeung
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Birte Kalveram
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Cody J. Bills
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - John Yun-Chung Chen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Steven G. Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Brian R. Mann
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rebecca Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - C. Todd Davis
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bin Zhou
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - David E. Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA, Xuping Xie ; Pei-Yong Shi
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA,Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA,Sealy, Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA,Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA,Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA,Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
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6
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Zhang Y, Zhao Y, Liang H, Xu Y, Zhou C, Yao Y, Wang H, Yang X. Innovation-driven trend shaping COVID-19 vaccine development in China. Front Med 2023; 17:1096-1116. [PMID: 38102402 DOI: 10.1007/s11684-023-1034-6] [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: 05/22/2023] [Accepted: 09/15/2023] [Indexed: 12/17/2023]
Abstract
Confronted with the Coronavirus disease 2019 (COVID-19) pandemic, China has become an asset in tackling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and mutation, with several innovative platforms, which provides various technical means in this persisting combat. Derived from collaborated researches, vaccines based on the spike protein of SARS-CoV-2 or inactivated whole virus are a cornerstone of the public health response to COVID-19. Herein, we outline representative vaccines in multiple routes, while the merits and plights of the existing vaccine strategies are also summarized. Likewise, new technologies may provide more potent or broader immunity and will contribute to fight against hypermutated SARS-CoV-2 variants. All in all, with the ultimate aim of delivering robust and durable protection that is resilient to emerging infectious disease, alongside the traditional routes, the discovery of innovative approach to developing effective vaccines based on virus properties remains our top priority.
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Affiliation(s)
- Yuntao Zhang
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Yuxiu Zhao
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Hongyang Liang
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Ying Xu
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Chuge Zhou
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Yuzhu Yao
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Hui Wang
- China National Biotec Group Company Limited, Beijing, 100029, China.
| | - Xiaoming Yang
- China National Biotec Group Company Limited, Beijing, 100029, China.
- National Engineering Technology Research Center of Combined Vaccines, Wuhan, 430207, China.
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7
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Ali KM, Rashid PMA, Ali AM, Tofiq AM, Salih GF, Dana OI, Rostam HM. Clinical outcomes and phylogenetic analysis in reflection with three predominant clades of SARS-CoV-2 variants. Eur J Clin Invest 2023; 53:e14004. [PMID: 37036255 DOI: 10.1111/eci.14004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/11/2023]
Abstract
BACKGROUND The pandemic of coronavirus disease 2019 (COVID-19) has a broad spectrum of clinical manifestations. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) undergoes continuous evolution, resulting in the emergence of several variants. Each variant has a different severity and mortality rate. MATERIALS AND METHODS In this study, 1174 COVID-19 patients were studied for mortality and severity over three SARS-CoV-2 predominating variant periods in 2021 and 2022 in Sulaimani Province, Iraq. In each period, a representative, variant virus was subjected to phylogenetic and molecular and clinical analysis. RESULTS Phylogenetic analysis revealed three SARS-CoV-2 variants, belonging to: Delta B.1.617.2, Omicron BA.1.17.2, and Omicron BA.5.6. The Delta variants showed more severe symptoms and a lower PCR-Ct value than Omicron variants regardless of gender, and only 4.3% of the cases were asymptomatic. The mortality rate was lower with Omicron (.5% for BA.5.2 and 1.3% for BA.1.17.2) compared with Delta variants (2.5%). The higher mortality rate with Delta variants was in males (2.84%), while that with Omicron BA1.17.2 and BA.5.2 was in females, 1.05% and .0%, respectively. Age group (≥70) years had the highest mortality rate; however, it was (.0%) in the age group (30-49) years with Omicron variants, compared with (.96%) in Delta variants. CONCLUSIONS There has been a surge in COVID-19 infection in the city due to the predominant lineages of SARS-CoV-2, B.1.617, Omicron BA.1.17.2 and Omicron BA.5.6, respectively. A higher PCR-Ct value and severity of the Delta variant over Omicron BA.1.17.2 and/or BA.5.2 variants were significantly correlated with a higher death rate in the same order.
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Affiliation(s)
- Kameran M Ali
- Medical Laboratory Technology Department, Kalar Technical College, Sulaimani Polytechnic University, Kalar, Iraq
| | - Peshnyar M A Rashid
- Medical Laboratory Science Department, Komar University of Science and Technology, Sulaimania, Iraq
| | - Ayad M Ali
- Department of Chemistry, University of Garmian, Kalar, Iraq
| | - Ahmed M Tofiq
- Department of Biology, College of Education, University of Garmian, Head of International Academic Relations (IRO), Kalar, Iraq
| | - Gaza F Salih
- Biology Department, College of Science, University of Sulaimani, Sulaimania, Iraq
| | - Omer I Dana
- College of Veterinary Medicine, University of Sulaimani, Sulaimani, Iraq
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8
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Girardi V, Gularte JS, Demoliner M, da Silva MS, Filippi M, de Abreu Góes Pereira VM, Hansen AW, Rosa RB, Fleck JD, Spilki FR. Reinfection by SARS-CoV-2 by divergent Omicron sublineages, 16 days apart. Braz J Microbiol 2023; 54:1847-1851. [PMID: 37269428 PMCID: PMC10239041 DOI: 10.1007/s42770-023-01018-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/09/2023] [Indexed: 06/05/2023] Open
Abstract
Since the beginning of the SARS-CoV-2 pandemic, studies on the variants and sublineages stand out, mainly in the cases of reinfection in a short period. In this study, we describe a case of infection by BA.1.1 sublineage in an individual from Southern Brazil. The same patient acquired reinfection with sublineage BA.2 within 16 days after the first detection. The viral extraction and RT-qPCR were performed on the samples LMM72045 (collected in May 2022) and LMM72044 (collected in June 2022). After the confirmation of SARS-CoV-2 infection, we conducted the sequencing and viral genome analysis. This case of reinfection affected a 52-year-old male patient, without comorbidities, with three doses of vaccines against COVID-19, showing symptoms on May 19. These symptoms lasted for approximately six days. The patient returned to work activities on May 30. However, on June 4, the patient felt a new round of clinical signs that lasted for approximately seven days. Analysis of the viral genomes recovered from patients' clinical samples revealed that the two COVID-19 episodes were related to two divergent VOC Omicron sublineages, namely, BA.1.1 for the first round of symptoms and BA.2 for the second infection. Based on our findings, we can say that the present case of reinfection is the shortest described so far.
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Affiliation(s)
- Viviane Girardi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil.
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Vyctoria Malayhka de Abreu Góes Pereira
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Raquel Borba Rosa
- Secretaria Municipal de Saúde, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
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9
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Montero S, Urrunaga-Pastor D, Soto-Becerra P, Cvetkovic-Vega A, Guillermo-Roman M, Figueroa-Montes L, Sagástegui AA, Alvizuri-Pastor S, Contreras-Macazana RM, Apolaya-Segura M, Díaz-Vélez C, Maguiña JL. Humoral response after a BNT162b2 heterologous third dose of COVID-19 vaccine following two doses of BBIBP-CorV among healthcare personnel in Peru. Vaccine X 2023; 14:100311. [PMID: 37207103 PMCID: PMC10162476 DOI: 10.1016/j.jvacx.2023.100311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/14/2023] [Accepted: 04/30/2023] [Indexed: 05/21/2023] Open
Abstract
Background The inactivated virus vaccine, BBIBP-CorV, was principally distributed across low- and middle-income countries as primary vaccination strategy to prevent poor COVID-19 outcomes. Limited information is available regarding its effect on heterologous boosting. We aim to evaluate the immunogenicity and reactogenicity of a third booster dose of BNT162b2 following a double BBIBP-CorV regime. Methods We conducted a cross-sectional study among healthcare providers from several healthcare facilities of the Seguro Social de Salud del Perú - ESSALUD. We included participants two-dose BBIBP-CorV vaccinated who presented a three-dose vaccination card at least 21 days passed since the vaccinees received their third dose and were willing to provide written informed consent. Antibodies were determined using LIAISON® SARS-CoV-2 TrimericS IgG (DiaSorin Inc., Stillwater, USA). Factors potentially associated with immunogenicity, and adverse events, were considered. We used a multivariable fractional polynomial modeling approach to estimate the association between anti-SARS-CoV-2 IgG antibodies' geometric mean (GM) ratios and related predictors. Results We included 595 subjects receiving a third dose with a median (IQR) age of 46 [37], [54], from which 40% reported previous SARS-CoV-2 infection. The overall geometric mean (IQR) of anti-SARS-CoV-2 IgG antibodies was 8,410 (5,115 - 13,000) BAU/mL. Prior SARS-CoV-2 history and full/part-time in-person working modality were significantly associated with greater GM. Conversely, time from boosting to IgG measure was associated with lower GM levels. We found 81% of reactogenicity in the study population; younger age and being a nurse were associated with a lower incidence of adverse events. Conclusions Among healthcare providers, a booster dose of BNT162b2 following a full BBIBP-CorV regime provided high humoral immune protection. Thus, SARS-CoV-2 previous exposure and working in person displayed as determinants that increase anti-SARS-CoV-2 IgG antibodies.
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Affiliation(s)
- Stephanie Montero
- Instituto de Evaluación de Tecnologías en Salud e Investigación - IETSI, ESSALUD, Lima, Peru
| | - Diego Urrunaga-Pastor
- Instituto de Evaluación de Tecnologías en Salud e Investigación - IETSI, ESSALUD, Lima, Peru
- Unidad para la Generación y Síntesis de Evidencias en Salud, Universidad San Ignacio de Loyola (USIL), Lima, Peru
| | - Percy Soto-Becerra
- Instituto de Evaluación de Tecnologías en Salud e Investigación - IETSI, ESSALUD, Lima, Peru
- Universidad Continental, Huancayo, Perú
| | - Aleksandar Cvetkovic-Vega
- Instituto de Evaluación de Tecnologías en Salud e Investigación - IETSI, ESSALUD, Lima, Peru
- Facultad de Medicina Humana, Universidad Privada Antenor Orrego, Trujillo, Peru
| | - Martina Guillermo-Roman
- Instituto de Evaluación de Tecnologías en Salud e Investigación - IETSI, ESSALUD, Lima, Peru
| | | | | | | | | | - Moisés Apolaya-Segura
- Instituto de Evaluación de Tecnologías en Salud e Investigación - IETSI, ESSALUD, Lima, Peru
- Facultad de Medicina Humana, Universidad Privada Antenor Orrego, Trujillo, Peru
| | - Cristian Díaz-Vélez
- Instituto de Evaluación de Tecnologías en Salud e Investigación - IETSI, ESSALUD, Lima, Peru
- Facultad de Medicina Humana, Universidad Privada Antenor Orrego, Trujillo, Peru
| | - Jorge L. Maguiña
- Instituto de Evaluación de Tecnologías en Salud e Investigación - IETSI, ESSALUD, Lima, Peru
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, Peru
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10
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Shipulin GA, Savochkina Y, Shuryaeva AK, Glushchenko EE, Luparev AR, Polyakova VA, Danilov DI, Davydova EE, Vinogradov KS, Stetsenko IF, Aiginin AA, Matsvay AD, Kolbutova KB, Bogdan SA, Vashukova MA, Yudin SM. Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2. Heliyon 2023; 9:e16917. [PMID: 37287602 PMCID: PMC10234363 DOI: 10.1016/j.heliyon.2023.e16917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/04/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023] Open
Abstract
The emergence of mutations in the coronavirus genome provides opportunities for occurrence new strains with higher transmissibility, severity and duration of the disease poses. In 2020, a new variant of the coronavirus SARS-COV-2 - Delta was identified in India. This genetic variant has spread rapidly and became dominant in many countries, including Russia. In November 2021, a new outbreak of COVID-19 occurred in Africa driven by a variant SARS-COV-2 named later Omicron. Both variants had increased transmissibility compared to previously encountered variants and quickly, replacing its around the world. To promptly monitor the epidemiological situation in the country, to assess the spread of dominant genetic variants of the virus and to take appropriate measures, we have developed an RT‒PCR reagent kit for the identification of Delta and Omicron by detecting a corresponding combination of major mutations. The minimum set of mutations was chosen which allows to differentiate Delta and Omicron variants, in order to increase the analysis productivity and reduce costs. Primers and LNA-modified probes were selected to detect mutations in the S gene, typical for the Delta and Omicron. Similar approach can be implemented for the rapid development of assays for differentiating important SARS-COV-2 variants or for other viruses genotyping for epidemiological surveillance or for diagnostic use in order to assist in making clinical decisions. It was demonstrated that the results of VOC Delta and Omicron detection and their typical mutations were concordant with genotyping based on WGS results for all 847 samples of SARS-CoV-2 RNA. The kit has high analytical sensitivity (1х103 copies/mL of SARS-CoV-2 RNA) for each of the detected genetic variants and possesses 100% analytic specificity for microorganism panel testing. The diagnostic sensitivity (95% confidence interval) obtained during pivotal trials was 91.1-100% for Omicron and 91.3-100% for Delta, while the diagnostic specificity with a 95% confidence interval was 92.2-100%. The use of a set of reagents in combination with sequencing of SARS-CoV-2 RNA as part of epidemiological monitoring made it possible to quickly track the dynamics of changes in Delta and Omicron prevalence in the Moscow region in the period from December 2021 to July 2022.
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Affiliation(s)
- G A Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - YuA Savochkina
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - A K Shuryaeva
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - E E Glushchenko
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - A R Luparev
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - V A Polyakova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - D I Danilov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - E E Davydova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - K S Vinogradov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - I F Stetsenko
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - A A Aiginin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - A D Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - K B Kolbutova
- Chief Federal State Budgetary Healthcare Institution "Centre of Hygiene and Epidemiology" of the Federal Medical Biological Agency, Moscow, Russia
| | - S A Bogdan
- Chief Federal State Budgetary Healthcare Institution "Centre of Hygiene and Epidemiology" of the Federal Medical Biological Agency, Moscow, Russia
| | - M A Vashukova
- Clinical Infectious Diseases Hospital Named After S.P. Botkin, St. Petersburg, Russia
| | - S M Yudin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
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11
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Russell TW, Townsley H, Abbott S, Hellewell J, Carr EJ, Chapman L, Pung R, Quilty BJ, Hodgson D, Fowler AS, Adams L, Bailey C, Mears HV, Harvey R, Clayton B, O’Reilly N, Ngai Y, Nicod J, Gamblin S, Williams B, Gandhi S, Swanton C, Beale R, Bauer DLV, Wall EC, Kucharski A. Within-host SARS-CoV-2 viral kinetics informed by complex life course exposures reveals different intrinsic properties of Omicron and Delta variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.17.23290105. [PMID: 37292842 PMCID: PMC10246130 DOI: 10.1101/2023.05.17.23290105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The emergence of successive SARS-CoV-2 variants of concern (VOC) during 2020-22, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics - such as varying levels of immunity - can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform COVID-19 planning and response, and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both inter-individual variation in Ct values and complex host characteristics - such as vaccination status, exposure history and age - we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least five prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs.
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Affiliation(s)
- Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Hermaleigh Townsley
- The Francis Crick Institute, 1 Midland Road, London, UK
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Joel Hellewell
- European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, UK
| | - Edward J Carr
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Lloyd Chapman
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Lancaster University, Bailrigg, Lancaster
| | - Rachael Pung
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Billy J. Quilty
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Lorin Adams
- The Francis Crick Institute, 1 Midland Road, London, UK
| | | | | | - Ruth Harvey
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Bobbi Clayton
- The Francis Crick Institute, 1 Midland Road, London, UK
| | | | - Yenting Ngai
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
| | - Jerome Nicod
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Steve Gamblin
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
- University College London, Gower Street, London
| | - Sonia Gandhi
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
| | - Charles Swanton
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
| | - Rupert Beale
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - David LV Bauer
- The Francis Crick Institute, 1 Midland Road, London, UK
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - Emma C Wall
- The Francis Crick Institute, 1 Midland Road, London, UK
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
- University College London, Gower Street, London
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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12
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Pradenas E, Marfil S, Urrea V, Trigueros M, Pidkova T, Pons-Grífols A, Ortiz R, Rovirosa C, Tarrés-Freixas F, Aguilar-Gurrieri C, Toledo R, Chamorro A, Noguera-Julian M, Mateu L, Blanco I, Grau E, Massanella M, Carrillo J, Clotet B, Trinité B, Blanco J. Impact of hybrid immunity booster vaccination and Omicron breakthrough infection on SARS-CoV-2 VOCs cross-neutralization. iScience 2023; 26:106457. [PMID: 36999095 PMCID: PMC10027310 DOI: 10.1016/j.isci.2023.106457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/02/2022] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
The elicitation of cross-variant neutralizing antibodies against SARS-CoV-2 represents a major goal for current COVID-19 vaccine strategies. Additionally, natural infection may also contribute to broaden neutralizing responses. To assess the contribution of vaccines and natural infection, we cross-sectionally analyzed plasma neutralization titers of six groups of individuals, organized according to the number of vaccines they received and their SARS-CoV-2 infection history. Two doses of vaccine had a limited capacity to generate cross-neutralizing antibodies against Omicron variants of concern (VOCs) in uninfected individuals, but efficiently synergized with previous natural immunization in convalescent individuals. In contrast, booster dose had a critical impact on broadening the cross-neutralizing response in uninfected individuals, to level similar to hybrid immunity, while still improving cross-neutralizing responses in convalescent individuals. Omicron breakthrough infection improved cross-neutralization of Omicron subvariants in non-previously infected vaccinated individuals. Therefore, ancestral Spike-based immunization, via infection or vaccination, contributes to broaden SARS-CoV-2 humoral immunity.
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Affiliation(s)
- Edwards Pradenas
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Silvia Marfil
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Víctor Urrea
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Macedonia Trigueros
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Tetyana Pidkova
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Anna Pons-Grífols
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Raquel Ortiz
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Carla Rovirosa
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Ferran Tarrés-Freixas
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Carmen Aguilar-Gurrieri
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Ruth Toledo
- Infectious Diseases Department, Fight AIDS and Infectious Diseases Foundation (FLS), Germans Trias i Pujol Hospital, 08916 Badalona, Catalonia, Spain
| | - Anna Chamorro
- Infectious Diseases Department, Fight AIDS and Infectious Diseases Foundation (FLS), Germans Trias i Pujol Hospital, 08916 Badalona, Catalonia, Spain
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Lourdes Mateu
- Infectious Diseases Department, Fight AIDS and Infectious Diseases Foundation (FLS), Germans Trias i Pujol Hospital, 08916 Badalona, Catalonia, Spain
| | - Ignacio Blanco
- Germans Trias i Pujol Hospital, 08916 Badalona, Catalonia, Spain
| | - Eulàlia Grau
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Marta Massanella
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
- University of Vic–Central University of Catalonia (UVic-UCC), 08500 Vic, Catalonia, Spain
- CIBER Infectious Diseases (CIBERINFEC), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
- Infectious Diseases Department, Fight AIDS and Infectious Diseases Foundation (FLS), Germans Trias i Pujol Hospital, 08916 Badalona, Catalonia, Spain
- University of Vic–Central University of Catalonia (UVic-UCC), 08500 Vic, Catalonia, Spain
| | - Benjamin Trinité
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Catalonia, Spain
- University of Vic–Central University of Catalonia (UVic-UCC), 08500 Vic, Catalonia, Spain
- CIBER Infectious Diseases (CIBERINFEC), Institute of Health Carlos III (ISCIII), Madrid, Spain
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13
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O’Keeffe JC, Constable M, Chiang J, Somerville M, Yerramilli A, Nolan R, Weeks G, O’Brien DP. Healthcare worker access to molnupiravir: A case series. PLoS One 2023; 18:e0282695. [PMID: 36917596 PMCID: PMC10013897 DOI: 10.1371/journal.pone.0282695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/19/2023] [Indexed: 03/16/2023] Open
Abstract
Molnupiravir, an oral antiviral shown to reduce COVID-19 severity, is available in Australia via the Pharmaceutical Benefits Scheme (PBS) for treatment of mild-moderate COVID-19. For people less than 70 years of age it is only available with risk factors for severe disease, hence the majority of healthcare workers do not qualify. Currently, Australian health services are under considerable strain due to COVID-related staff shortages. Thirty staff members of a tertiary hospital, not eligible under the PBS, were offered molnupiravir within the first five days of COVID-19 illness. Their median age was 43 years, and 73% were female. All completed treatment with rates of adverse events that were low and comparable with clinical trial data. The reported duration of illness ranged from 1-16 days with a median of four days. A negative rapid antigen test on the final day of treatment was reported in 81% of people, and 73% reported being well enough to return to work at the completion of mandatory isolation. Only 22% of people reported transmission in their household after they commenced treatment. The implementation of a policy allowing access to molnupiravir outside of PBS recommendations for healthcare workers with mild-moderate COVID-19 may have important individual benefits to workers health and wellbeing and help alleviate the acute staff shortages experienced currently by the Australian healthcare workforce.
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Affiliation(s)
- Jessica C. O’Keeffe
- Department of Infectious Diseases, Barwon Health, Geelong, Victoria, Australia
- Barwon South West Public Health Unit, Barwon Health, Geelong, Victoria, Australia
| | - Meg Constable
- StaffCare, Barwon Health, Geelong, Victoria, Australia
| | - Janice Chiang
- Pharmacy Department, Barwon Health, Geelong, Victoria, Australia
| | | | - Arvind Yerramilli
- Department of Infectious Diseases, Barwon Health, Geelong, Victoria, Australia
- Barwon South West Public Health Unit, Barwon Health, Geelong, Victoria, Australia
| | - Ross Nolan
- StaffCare, Barwon Health, Geelong, Victoria, Australia
| | - Greg Weeks
- Pharmacy Department, Barwon Health, Geelong, Victoria, Australia
| | - Daniel P. O’Brien
- Department of Infectious Diseases, Barwon Health, Geelong, Victoria, Australia
- Barwon South West Public Health Unit, Barwon Health, Geelong, Victoria, Australia
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14
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Sun Q, Zeng J, Tang K, Long H, Zhang C, Zhang J, Tang J, Xin Y, Zheng J, Sun L, Liu S, Du X. Variation in synonymous evolutionary rates in the SARS-CoV-2 genome. Front Microbiol 2023; 14:1136386. [PMID: 36970680 PMCID: PMC10034387 DOI: 10.3389/fmicb.2023.1136386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionCoronavirus disease 2019 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Influential variants and mutants of this virus continue to emerge, and more effective virus-related information is urgently required for identifying and predicting new mutants. According to earlier reports, synonymous substitutions were considered phenotypically silent; thus, such mutations were frequently ignored in studies of viral mutations because they did not directly cause amino acid changes. However, recent studies have shown that synonymous substitutions are not completely silent, and their patterns and potential functional correlations should thus be delineated for better control of the pandemic.MethodsIn this study, we estimated the synonymous evolutionary rate (SER) across the SARS-CoV-2 genome and used it to infer the relationship between the viral RNA and host protein. We also assessed the patterns of characteristic mutations found in different viral lineages.ResultsWe found that the SER varies across the genome and that the variation is primarily influenced by codon-related factors. Moreover, the conserved motifs identified based on the SER were found to be related to host RNA transport and regulation. Importantly, the majority of the existing fixed-characteristic mutations for five important virus lineages (Alpha, Beta, Gamma, Delta, and Omicron) were significantly enriched in partially constrained regions.DiscussionTaken together, our results provide unique information on the evolutionary and functional dynamics of SARS-CoV-2 based on synonymous mutations and offer potentially useful information for better control of the SARS-CoV-2 pandemic.
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Affiliation(s)
- Qianru Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jinfeng Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Kang Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Haoyu Long
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Chi Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jie Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jing Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Yuting Xin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jialu Zheng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Litao Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Siyang Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xiangjun Du
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15
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Lai J, Coleman KK, Tai SHS, German J, Hong F, Albert B, Esparza Y, Srikakulapu AK, Schanz M, Maldonado IS, Oertel M, Fadul N, Gold TL, Weston S, Mullins K, McPhaul KM, Frieman M, Milton DK. Exhaled Breath Aerosol Shedding of Highly Transmissible Versus Prior Severe Acute Respiratory Syndrome Coronavirus 2 Variants. Clin Infect Dis 2023; 76:786-794. [PMID: 36285523 PMCID: PMC9620356 DOI: 10.1093/cid/ciac846] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Aerosol inhalation is recognized as the dominant mode of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Three highly transmissible lineages evolved during the pandemic. One hypothesis to explain increased transmissibility is that natural selection favors variants with higher rates of viral aerosol shedding. However, the extent of aerosol shedding of successive SARS-CoV-2 variants is unknown. We aimed to measure the infectivity and rate of SARS-CoV-2 shedding into exhaled breath aerosol (EBA) by individuals during the Delta and Omicron waves and compared those rates with those of prior SARS-CoV-2 variants from our previously published work. METHODS Individuals with coronavirus disease 2019 (COVID-19) (n = 93; 32 vaccinated and 20 boosted) were recruited to give samples, including 30-minute breath samples into a Gesundheit-II EBA sampler. Samples were quantified for viral RNA using reverse-transcription polymerase chain reaction and cultured for virus. RESULTS Alpha (n = 4), Delta (n = 3), and Omicron (n = 29) cases shed significantly more viral RNA copies into EBAs than cases infected with ancestral strains and variants not associated with increased transmissibility (n = 57). All Delta and Omicron cases were fully vaccinated and most Omicron cases were boosted. We cultured virus from the EBA of 1 boosted and 3 fully vaccinated cases. CONCLUSIONS Alpha, Delta, and Omicron independently evolved high viral aerosol shedding phenotypes, demonstrating convergent evolution. Vaccinated and boosted cases can shed infectious SARS-CoV-2 via EBA. These findings support a dominant role of infectious aerosols in transmission of SARS-CoV-2. Monitoring aerosol shedding from new variants and emerging pathogens can be an important component of future threat assessments and guide interventions to prevent transmission.
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Affiliation(s)
- Jianyu Lai
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Kristen K Coleman
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - S H Sheldon Tai
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Jennifer German
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Filbert Hong
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Barbara Albert
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Yi Esparza
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Aditya K Srikakulapu
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Maria Schanz
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Isabel Sierra Maldonado
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Molly Oertel
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Naja Fadul
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - T Louie Gold
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kristin Mullins
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kathleen M McPhaul
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Donald K Milton
- Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
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16
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Gbaguidi GN, Aubert L, Schaeffer J, Fagour L, Dubremetz A, Enouf V, Glaudon-Louveau de la Guigneraye MH, Nestour F, Rosine J, Dos Santos G. Emergence and evolution of the Omicron SARS-CoV-2 variant in the island of Martinique. Infect Dis Now 2023; 53:104690. [PMID: 36868476 PMCID: PMC9977121 DOI: 10.1016/j.idnow.2023.104690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/24/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
INTRODUCTION We aimed to describe the epidemiological situation during the Omicron variant circulation in light of genomic surveillance data in Martinique, a territory with low vaccination rates. PATIENTS AND METHODS We exploited COVID-19 national databases of virological tests, for the collection of hospital data and for the sequencing data from December 13, 2021 to July 11, 2022. RESULTS Three prevailing sub-lineages of Omicron have been identified in Martinique (BA.1, BA.2, BA.5) during this period causing three distinct waves characterized by an increase in virological indicators compared to previous waves, with moderate severity in the first and last waves, caused by BA.1 and BA.5, respectively. CONCLUSION The SARS-CoV-2 outbreak is still progressing in Martinique. Genomic surveillance system in this overseas territory must be continued for rapid detection of emerging variants/sub-lineages.
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Affiliation(s)
- G N Gbaguidi
- French National Public Health Agency in the French West Indes, Fort-de-France, Martinique, France.
| | - L Aubert
- French National Public Health Agency in the French West Indes, Gourbeyre, Guadeloupe, France
| | - J Schaeffer
- French National Public Health Agency, Saint-Maurice, France
| | - L Fagour
- Department of Virology, University Hospital Center, Fort-de-France, Martinique, France
| | - A Dubremetz
- Department of Virology, University Hospital Center, Fort-de-France, Martinique, France
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, CNRS-UMR 3569, The Institut Pasteur, Paris, France; Mutualised Platform of Microbiology, Pasteur International Bioresources Network, The Institut Pasteur, Paris, France
| | | | - F Nestour
- BIOLAB Laboratory, Martinique, France
| | - J Rosine
- French National Public Health Agency in the French West Indes, Fort-de-France, Martinique, France
| | - G Dos Santos
- Department of Virology, University Hospital Center, Fort-de-France, Martinique, France; UMR 1058 - Pathogenesis & Control of Chronic & Emerging Infections, University of Montpellier, Montpellier, France
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17
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Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023; 21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 254] [Impact Index Per Article: 254.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
Abstract
In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed 'variants of concern' (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.
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Affiliation(s)
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Wendy S Barclay
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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18
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Teyssou E, Marot S, Cocherie T, Fauchois A, Abdi B, Todesco E, Akhavan S, Pourcher V, Calvez V, Marcelin AG, Soulie C. Prolonged replication of BA.1 and BA.2 Omicron lineages compared to Delta variant in nasopharyngeal samples from COVID-19 patients. Infect Dis Now 2023; 53:104629. [PMID: 36323397 PMCID: PMC9618294 DOI: 10.1016/j.idnow.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVES We aimed to characterize and compare the viral loads (VL) of the Omicron BA.1 and BA.2 lineages and the Delta variant in nasopharyngeal samples from newly diagnosed COVID-19 patients and their kinetics over time. PATIENTS AND METHODS The kinetics of the VL were measured on the CT data from 215 SARS-CoV-2 positive patients who presented at least two positive PCRs a day apart and were screened for SARS-CoV-2 viral lineages. RESULTS We observed no significant difference in median CT value during the first diagnostic test between the Delta variant and the two Omicron lineages. However, the kinetics of CT decreases for the BA.1 and BA.2 lineage were significantly lengthier in time than the kinetics for the Delta variant. The BA.2 lineage presented lower median CT value (-2 CT) (inversely proportional to the VL) than the BA.1 lineage. CONCLUSIONS BA.2 Omicron lineage presented higher VL than BA.1 Omicron lineage at diagnostic. Omicron BA.1 and BA.2 lineages have more prolonged replication than the Delta variant.
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Affiliation(s)
- Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France.
| | - Stéphane Marot
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Théophile Cocherie
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Antoine Fauchois
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Basma Abdi
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Eve Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Sepideh Akhavan
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Valérie Pourcher
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Service des maladies infectieuse, F-75013 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Cathia Soulie
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France.
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19
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Osterman A, Badell I, Dächert C, Schneider N, Kaufmann AY, Öztan GN, Huber M, Späth PM, Stern M, Autenrieth H, Muenchhoff M, Graf A, Krebs S, Blum H, Czibere L, Durner J, Kaderali L, Baldauf HM, Keppler OT. Variable detection of Omicron-BA.1 and -BA.2 by SARS-CoV-2 rapid antigen tests. Med Microbiol Immunol 2023; 212:13-23. [PMID: 36370197 PMCID: PMC9660148 DOI: 10.1007/s00430-022-00752-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/22/2022] [Indexed: 11/15/2022]
Abstract
During 2022, the COVID-19 pandemic has been dominated by the variant of concern (VoC) Omicron (B.1.1.529) and its rapidly emerging subvariants, including Omicron-BA.1 and -BA.2. Rapid antigen tests (RATs) are part of national testing strategies to identify SARS-CoV-2 infections on site in a community setting or to support layman's diagnostics at home. We and others have recently demonstrated an impaired RAT detection of infections caused by Omicron-BA.1 compared to Delta. Here, we evaluated the performance of five SARS-CoV-2 RATs in a single-centre laboratory study examining a total of 140 SARS-CoV-2 PCR-positive respiratory swab samples, 70 Omicron-BA.1 and 70 Omicron-BA.2, as well as 52 SARS-CoV-2 PCR-negative swabs collected from March 8th until April 10th, 2022. One test did not meet minimal criteria for specificity. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 4.2 × 104 to 9.2 × 105 RNA copies subjected to the RAT for Omicron-BA.1 compared to 1.3 × 105 to 1.5 × 106 for Omicron-BA.2. Overall, intra-assay differences for the detection of Omicron-BA.1-containing and Omicron-BA.2-containing samples were non-significant, while a marked overall heterogeneity among the five RATs was observed. To score positive in these point-of-care tests, up to 22-fold (LoD50) or 68-fold (LoD95) higher viral loads were required for the worst performing compared to the best performing RAT. The rates of true-positive test results for these Omicron subvariant-containing samples in the highest viral load category (Ct values < 25) ranged between 44.7 and 91.1%, while they dropped to 8.7 to 22.7% for samples with intermediate Ct values (25-30). In light of recent reports on the emergence of two novel Omicron-BA.2 subvariants, Omicron-BA.2.75 and BJ.1, awareness must be increased for the overall reduced detection rate and marked differences in RAT performance for these Omicron subvariants.
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Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Irina Badell
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Dächert
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Nikolas Schneider
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Anna-Yasemin Kaufmann
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gamze Naz Öztan
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Melanie Huber
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | | | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany.
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20
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Alidjinou EK, Demaret J, Corroyer-Simovic B, Vuotto F, Miczek S, Labreuche J, Goffard A, Trauet J, Lupau D, Dendooven A, Huvent-Grelle D, Podvin J, Dreuil D, Faure K, Deplanque D, Bocket L, Duhamel A, Sobaszek A, Hober D, Hisbergues M, Puisieux F, Autran B, Yazdanpanah Y, Labalette M, Lefèvre G. Serum neutralization of SARS coronavirus 2 Omicron sublineages BA.1 and BA.2 and cellular immune responses 3 months after booster vaccination. Clin Microbiol Infect 2023; 29:258.e1-258.e4. [PMID: 36257549 PMCID: PMC9576208 DOI: 10.1016/j.cmi.2022.10.014] [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: 06/26/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVES We investigated serum neutralizing activity against BA.1 and BA.2 Omicron sublineages and T cell response before and 3 months after administration of the booster vaccine in healthcare workers (HCWs). METHODS HCWs aged 18-65 years who were vaccinated and received booster doses of the BNT162b2 vaccine were included. Anti-SARS coronavirus 2 IgG levels and cellular response (through interferon γ ELISpot assay) were evaluated in all participants, and neutralizing antibodies against Delta, BA.1, and BA.2 were evaluated in participants with at least one follow-up visit 1 or 3 months after the administration of the booster dose. RESULTS Among 118 HCWs who received the booster dose, 102 and 84 participants attended the 1-month and 3-month visits, respectively. Before the booster vaccine dose, a low serum neutralizing activity against Delta, BA.1, and BA.2 was detectable in only 39/102 (38.2%), 8/102 (7.8%), and 12/102 (11.8%) participants, respectively. At 3 months, neutralizing antibodies against Delta, BA.1, and BA.2 were detected in 84/84 (100%), 79/84 (94%), and 77/84 (92%) participants, respectively. Geometric mean titres of neutralizing antibodies against BA.1 and BA.2 were 2.2-fold and 2.8-fold reduced compared with those for Delta. From 1 to 3 months after the administration of the booster dose, participants with a recent history of SARS coronavirus 2 infection (n = 21/84) had persistent levels of S1 reactive specific T cells and neutralizing antibodies against Delta and BA.2 and 2.2-fold increase in neutralizing antibodies against BA.1 (p 0.014). Conversely, neutralizing antibody titres against Delta (2.5-fold decrease, p < 0.0001), BA.1 (1.5-fold, p 0.02), and BA.2 (2-fold, p < 0.0001) declined from 1 to 3 months after the administration of the booster dose in individuals without any recent infection. DISCUSSION The booster vaccine dose provided significant and similar response against BA.1 and BA.2 Omicron sublineages; however, the immune response declined in the absence of recent infection.
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Affiliation(s)
| | - Julie Demaret
- CHU Lille, Institut d'Immunologie, INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, France
| | - Bénédicte Corroyer-Simovic
- CHU Lille, Pôle de Gériatrie, Hôpital gériatrique Les Bateliers, CHU de Lille, Université de Lille, Lille, France
| | - Fanny Vuotto
- CHU Lille, Département de Maladies Infectieuses, Lille, France
| | - Sophie Miczek
- CHU Lille, Médecine et santé-travail, CHU Lille, Lille, France
| | | | - Anne Goffard
- Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, CIIL U1019 - CIIL-Centre d'Infection et d'Immunité de Lille Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Jacques Trauet
- CHU Lille, Institut d'Immunologie, INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, France
| | - Daniela Lupau
- CHU Lille, Institut d'Immunologie, INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, France
| | - Arnaud Dendooven
- CHU Lille, Institut d'Immunologie, INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, France
| | - Dominique Huvent-Grelle
- CHU Lille, Pôle de Gériatrie, Hôpital gériatrique Les Bateliers, CHU de Lille, Université de Lille, Lille, France
| | - Juliette Podvin
- CHU Lille, Pôle de Gériatrie, Hôpital gériatrique Les Bateliers, CHU de Lille, Université de Lille, Lille, France
| | - Daniel Dreuil
- CHU Lille, Pôle de Gériatrie, Hôpital gériatrique Les Bateliers, CHU de Lille, Université de Lille, Lille, France
| | - Karine Faure
- CHU Lille, Département de Maladies Infectieuses, Lille, France
| | - Dominique Deplanque
- Université Lille, Inserm, CHU Lille, CIC 1403-Clinical Investigation Center, 59000 Lille, France
| | - Laurence Bocket
- Université Lille, CHU Lille, Laboratoire de Virologie, Lille, France
| | - Alain Duhamel
- Université Lille, CHU Lille, EA 2694 - Santé publique: épidémiologie et qualité des soins, Université de Lille, Lille, Hauts-de-France, France
| | - Annie Sobaszek
- CHU Lille, Médecine et santé-travail, Université Lille, CHU Lille, ULR 4483, Lille, France
| | - Didier Hober
- Université Lille, CHU Lille, Laboratoire de Virologie, Lille, France
| | - Michael Hisbergues
- CHU Lille, Université Lille, Centre de Ressources Biologiques, Lille, France
| | - Francois Puisieux
- CHU Lille, Pôle de Gériatrie, Hôpital gériatrique Les Bateliers, CHU de Lille, Université de Lille, Lille, France
| | - Brigitte Autran
- Sorbonne-Université, Paris, France; UMR-S Inserm/UPMC 1135, Centre de Recherches Immunité Maladies Infectieuses, Paris, France
| | - Yazdan Yazdanpanah
- INSERM, IAME, Hôpital Bichat - Claude-Bernard, Infectious Diseases Department, France
| | - Myriam Labalette
- CHU Lille, Institut d'Immunologie, INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, France
| | - Guillaume Lefèvre
- CHU Lille, Institut d'Immunologie, INFINITE - Institute for Translational Research in Inflammation Inserm Univ. Lille, France.
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21
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Mozaffer F, Cherian P, Krishna S, Wahl B, Menon GI. Effect of hybrid immunity, school reopening, and the Omicron variant on the trajectory of the COVID-19 epidemic in India: a modelling study. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 8:100095. [PMID: 36267800 PMCID: PMC9556909 DOI: 10.1016/j.lansea.2022.100095] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 01/11/2023]
Abstract
Background The course of the COVID-19 pandemic has been driven by several dynamic behavioral, immunological, and viral factors. We used mathematical modeling to explore how the concurrent reopening of schools, increasing levels of hybrid immunity, and the emergence of the Omicron variant affected the trajectory of the pandemic in India, using Andhra Pradesh (pop: 53 million) as an exemplar Indian state. Methods We constructed an age- and contact-structured compartmental model that allows for individuals to proceed through various states depending on whether they have received zero, one, or two doses of the COVID-19 vaccine. We calibrated our model using results from another model (i.e., INDSCI-SIM) as well as available context-specific serosurvey data. The introduction of the Omicron variant is modelled alongside protection gained from hybrid immunity. We predict disease dynamics in the background of hybrid immunity coming from infections and an ongoing vaccination program, given prior levels of seropositivity from earlier waves of infection. We describe the consequences of school reopening on cases across different age-bands, as well as the impact of the Omicron (BA.2) variant. Findings We show the existence of an epidemic peak in India that is strongly related to the value of background seroprevalence. As expected, because children were not vaccinated in India, re-opening schools increases the number of cases in children more than in adults, although in all scenarios, the peak number of active hospitalizations was never greater than 0.45 times the corresponding peak in the Delta wave before schools were reopened. We varied the level of infection induced seropositivity in our model and found the height of the peak associated with schools reopening reduced as background infection-induced seropositivity increased from 20% to 40%. At reported values of seropositivity of 64% from representative surveys done in India, no discernible peak was observed. We also explored counterfactual scenarios regarding the effect of vaccination on hybrid immunity. We found that in the absence of vaccination, even at high levels of seroprevalence (>60%), the emergence of the Omicron variant would have resulted in a large rise in cases across all age bands by as much as 1.8 times. We conclude that the presence of high levels of hybrid immunity resulted in fewer cases in the Omicron wave than in the Delta wave. Interpretation In India, decreasing prevalence of immunologically naïve individuals of all ages was associated with fewer cases reported once schools were reopened. In addition, hybrid immunity, together with the lower intrinsic severity of disease associated with the Omicron variant, contributed to low reported COVID-19 hospitalizations and deaths. Funding World Health Organization, Mphasis.
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Affiliation(s)
- Farhina Mozaffer
- The Institute of Mathematical Sciences, Chennai, India,Homi Bhabha National Institute, BARC Training School Complex, Mumbai, India
| | - Philip Cherian
- Department of Physics, Ashoka University, Sonepat, India
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Brian Wahl
- Johns Hopkins India, New Delhi, India,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA,International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA,Corresponding author at: Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Gautam I. Menon
- The Institute of Mathematical Sciences, Chennai, India,Homi Bhabha National Institute, BARC Training School Complex, Mumbai, India,Department of Physics, Ashoka University, Sonepat, India,Department of Biology, Ashoka University, Sonepat, India,Corresponding author at: Ashoka University, Sonepat, India
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22
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Dhama K, Nainu F, Frediansyah A, Yatoo MI, Mohapatra RK, Chakraborty S, Zhou H, Islam MR, Mamada SS, Kusuma HI, Rabaan AA, Alhumaid S, Mutair AA, Iqhrammullah M, Al-Tawfiq JA, Mohaini MA, Alsalman AJ, Tuli HS, Chakraborty C, Harapan H. Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies. J Infect Public Health 2023; 16:4-14. [PMID: 36446204 PMCID: PMC9675435 DOI: 10.1016/j.jiph.2022.11.024] [Citation(s) in RCA: 99] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/06/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022] Open
Abstract
Newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuously posing high global public health concerns and panic resulting in waves of coronavirus disease 2019 (COVID-19) pandemic. Depending on the extent of genomic variations, mutations and adaptation, few of the variants gain the ability to spread quickly across many countries, acquire higher virulency and ability to cause severe disease, morbidity and mortality. These variants have been implicated in lessening the efficacy of the current COVID-19 vaccines and immunotherapies resulting in break-through viral infections in vaccinated individuals and recovered patients. Altogether, these could hinder the protective herd immunity to be achieved through the ongoing progressive COVID-19 vaccination. Currently, the only variant of interest of SARS-CoV-2 is Omicron that was first identified in South Africa. In this review, we present the overview on the emerging SARS-CoV-2 variants with a special focus on the Omicron variant, its lineages and hybrid variants. We discuss the hypotheses of the origin, genetic change and underlying molecular mechanism behind higher transmissibility and immune escape of Omicron variant. Major concerns related to Omicron including the efficacy of the current available immunotherapeutics and vaccines, transmissibility, disease severity, and mortality are discussed. In the last part, challenges and strategies to counter Omicron variant, its lineages and hybrid variants amid the ongoing COVID-19 pandemic are presented.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India.
| | - Firzan Nainu
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Andri Frediansyah
- Research Division for Natural Product Technology (BPTBA), National Research and Innovation Agency (BRIN), Gunungkidul, Yogyakarta 55861, Indonesia
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir 190006, India
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, Odisha, India
| | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences and Animal Husbandry, R.K. Nagar, West Tripura, Tripura, India
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Microbiology, NYU Grossman School of Medicine, New York 10016, USA
| | - Md Rabiul Islam
- Department of Pharmacy, University of Asia Pacific, 74/A Green Road, Farmgate, Dhaka 1205, Bangladesh
| | - Sukamto S Mamada
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Hendrix Indra Kusuma
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia; Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia; Biology Education Department, Faculty of Tarbiyah and Teacher Training, Universitas Islam Negeri Ar-Raniry, Jl. Syeikh Abdur Rauf, Kopelma Darussalaml, Banda Aceh 23111, Indonesia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia; College of Nursing, Prince Nora University, Riyadh 11564, Saudi Arabia; School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia; Nursing Department, Prince Sultan Military College of Health Sciences, Dhahran 33048, Saudi Arabia
| | - Muhammad Iqhrammullah
- Graduate School of Mathematics and Applied Sciences, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine and Quality Department, 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
| | - Mohammed Al Mohaini
- Basic Sciences Department, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Al-Ahsa 31982, Saudi Arabia; King Abdullah International Medical Research Center, Al-Ahsa 31982, Saudi Arabia
| | - Abdulkhaliq J Alsalman
- Department of Clinical Pharmacy, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar University, Mullana, Ambala 133207, Haryana, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126, India
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia; Tropical Diseases Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia; Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh 23111, Indonesia.
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23
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Migueres M, Mansuy JM, Vasseur S, Claverie N, Lougarre C, Soulier F, Trémeaux P, Izopet J. Omicron Wave SARS-CoV-2 Diagnosis: Evaluation of Saliva, Anterior Nasal, and Nasopharyngeal Swab Samples. Microbiol Spectr 2022; 10:e0252122. [PMID: 36318040 PMCID: PMC9769796 DOI: 10.1128/spectrum.02521-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The Omicron variant differs from earlier strains of SARS-CoV-2 in the way it enters host cells and grows in vitro. We therefore reevaluated its diagnosis using saliva, nasopharyngeal swab (NPs), and anterior nasal swab (ANs) specimens from 202 individuals (64.9% symptomatic) tested at the Toulouse University Hospital SARS-CoV-2 drive-through testing center. All tests were done with the Thermo Fisher TaqPath COVID-19 reverse transcription-PCR (RT-PCR) kit. Overall, 92 subjects (45.5%) had one or more positive specimens. Global sensitivities of saliva, NPs, and ANs were 94.6%, 90.2%, and 82.6%, respectively. Saliva provided significantly greater sensitivity among symptomatic patients tested within 5 days of symptom onset (100%) than did ANs (83.1%) or NPs (89.8%). We obtained follow-up samples for 7/20 individuals with discordant results. Among them, 5 symptomatic patients were diagnosed positive on saliva sample only, soon after symptom onset; NPs and ANs became positive only later. Thus, saliva samples are effective tools for the detection of the Omicron variant. In addition to its many advantages, such as improved patient acceptance and reduced cost, saliva sampling could help limit viral spread through earlier viral detection. IMPORTANCE Diagnostic testing for SARS-CoV-2 is an essential component of the global strategy for the prevention and control of COVID-19. Since the beginning of the pandemic, numerous studies have evaluated the diagnostic sensitivity of different respiratory and oral specimens for SARS-CoV-2 detection. The pandemic has been since dominated by the emergence of new variants, the latest being the Omicron variant characterized by numerous mutations and changes in host tropism in vitro that might affect the diagnostic performance of tests depending on the sampling location. In this prospective study, we evaluated the clinical performance of NPs, ANs, and saliva for SARS-CoV-2 diagnosis during the Omicron wave. Our results highlight the effectiveness of saliva-based RT-PCR for the early detection of the Omicron variant. These findings may help to refine guidelines and support the use of a highly sensitive diagnostic method that allows earlier diagnosis, when transmission is the most critical.
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Affiliation(s)
- Marion Migueres
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jean-Michel Mansuy
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
| | - Sandrine Vasseur
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Nicolas Claverie
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Catherine Lougarre
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Françoise Soulier
- CHU Toulouse, Hôpital Purpan, Centre de prélèvement COVID, Toulouse, France
| | - Pauline Trémeaux
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
| | - Jacques Izopet
- CHU Toulouse, Hôpital Purpan, Institut fédératif de Biologie, Laboratoire de virologie, Toulouse, France
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
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24
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Hegazy N, Cowan A, D'Aoust PM, Mercier É, Towhid ST, Jia JJ, Wan S, Zhang Z, Kabir MP, Fang W, Graber TE, MacKenzie AE, Guilherme S, Delatolla R. Understanding the dynamic relation between wastewater SARS-CoV-2 signal and clinical metrics throughout the pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158458. [PMID: 36075428 PMCID: PMC9444583 DOI: 10.1016/j.scitotenv.2022.158458] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 05/27/2023]
Abstract
Wastewater surveillance (WWS) of SARS-CoV-2 was proven to be a reliable and complementary tool for population-wide monitoring of COVID-19 disease incidence but was not as rigorously explored as an indicator for disease burden throughout the pandemic. Prior to global mass immunization campaigns and during the spread of the wildtype COVID-19 and the Alpha variant of concern (VOC), viral measurement of SARS-CoV-2 in wastewater was a leading indicator for both COVID-19 incidence and disease burden in communities. As the two-dose vaccination rates escalated during the spread of the Delta VOC in Jul. 2021 through Dec. 2021, relations weakened between wastewater signal and community COVID-19 disease incidence and maintained a strong relationship with clinical metrics indicative of disease burden (new hospital admissions, ICU admissions, and deaths). Further, with the onset of the vaccine-resistant Omicron BA.1 VOC in Dec. 2021 through Mar. 2022, wastewater again became a strong indicator of both disease incidence and burden during a period of limited natural immunization (no recent infection), vaccine escape, and waned vaccine effectiveness. Lastly, with the populations regaining enhanced natural and vaccination immunization shortly prior to the onset of the Omicron BA.2 VOC in mid-Mar 2022, wastewater is shown to be a strong indicator for both disease incidence and burden. Hospitalization-to-wastewater ratio is further shown to be a good indicator of VOC virulence when widespread clinical testing is limited. In the future, WWS is expected to show moderate indication of incidence and strong indication of disease burden in the community during future potential seasonal vaccination campaigns.
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Affiliation(s)
- Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Aaron Cowan
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Md Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Stéphanie Guilherme
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada.
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25
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Tsang NNY, So HC, Cowling BJ, Leung GM, Ip DKM. Effectiveness of BNT162b2 and CoronaVac COVID-19 vaccination against asymptomatic and symptomatic infection of SARS-CoV-2 omicron BA.2 in Hong Kong: a prospective cohort study. THE LANCET. INFECTIOUS DISEASES 2022; 23:421-434. [PMID: 36521506 PMCID: PMC9744442 DOI: 10.1016/s1473-3099(22)00732-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND COVID-19 vaccines provide protection against symptomatic infection that might require medical attention and against severe outcomes; however, there is a paucity of evidence regarding the effectiveness of the BNT162b2 and CoronaVac vaccines and their booster regimens against asymptomatic or mild omicron infections in the community. We aimed to measure the effectiveness of BNT162b2 and CoronaVac vaccines against asymptomatic and symptomatic SARS-CoV-2 omicron infections, during a period of omicron BA.2 predominance in Hong Kong. METHODS In this prospective cohort study in a population that was generally infection-naive before the large omicron BA.2 wave between January and late May, 2022, we established a public health surveillance platform to monitor the evolving activity of SARS-CoV-2 infections in the community. We recruited a cohort of individuals aged 5 years and older between March 1 and March 7, 2022, from the general population. Individuals were enrolled from all 18 districts of Hong Kong, according to a predefined age-stratified quota, primarily by random digit dialing (generating suitable eight-digit local telephone numbers by randomly picking sets of the first four digits from a sampling frame, and randomly generating the last four digits), and supplemented by our existing cohorts (which included cohorts for studying influenza vaccination from school-based vaccination programmes and cohorts for SARS-CoV-2 seroprevalence from the community), to ensure representativeness of the population in Hong Kong. Participants did weekly rapid antigen testing with a self-collected pooled nasal and throat swab, regardless of symptom and exposure status, from March 1 to April 15, 2022. Individuals reporting a history of SARS-CoV-2 infection confirmed by laboratory PCR testing before enrolment were excluded from the vaccine effectiveness analysis to avoid potential bias due to infection-induced immunity. The primary outcomes of the study were the incidence of SARS-CoV-2 infection, including asymptomatic and symptomatic infections, and the vaccine effectiveness of BNT162b2 and CoronaVac vaccines. The effectiveness of one, two, and three doses of vaccination was estimated with a Cox proportional hazards regression model with time-dependent covariates, allowing for changes in vaccination status over time, after adjustment for demographic factors and pre-existing medical conditions. FINDINGS Of the 8636 individuals included in the analysis, 7233 (84%) received at least two doses of vaccine, 3993 (46%) received booster doses, and 903 (10%) reported SARS-CoV-2 infection. Among these infections 589 (65·2%) were symptomatic and 314 (34·8%) were asymptomatic at the time of testing. Statistically significant protection against asymptomatic and symptomatic SARS-CoV-2 omicron infection was found only for those who received a BNT162b2 or CoronaVac booster dose, with a vaccine effectiveness of 41·4% (23·2 to 55·2; p=0·0001) and 32·4% (9·0 to 49·8; p=0·0098), respectively. The vaccine effectiveness of BNT162b2 and CoronaVac boosters was further increased to 50·9% (95% CI 31·0-65·0; p<0·0001) and 41·6% (15·0-59·8; p=0·0049), respectively, for symptomatic omicron infections. A similar pattern of vaccine effectiveness (55·8%, 22·9-74·6; p=0·0040) was also conferred after receipt of a BNT162b2 booster by individuals who received a CoronaVac primary vaccination series. INTERPRETATION Two doses of either vaccine did not provide significant protection against COVID-19 infection. However, receipt of a BNT162b2 booster or CoronaVac booster was associated with a significantly lower risk of omicron BA.2 infection and symptomatic infection. Our findings confirm the effectiveness of booster doses to protect against mild and asymptomatic infection. FUNDING Henry Fok Foundation and Hong Kong Health Bureau.
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Affiliation(s)
- Nicole Ngai Yung Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hau Chi So
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dennis Kai Ming Ip
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
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26
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Hansen C, Perofsky AC, Burstein R, Famulare M, Boyle S, Prentice R, Marshall C, McCormick BJJ, Reinhart D, Capodanno B, Truong M, Schwabe-Fry K, Kuchta K, Pfau B, Acker Z, Lee J, Sibley TR, McDermot E, Rodriguez-Salas L, Stone J, Gamboa L, Han PD, Duchin JS, Waghmare A, Englund JA, Shendure J, Bedford T, Chu HY, Starita LM, Viboud C. Trends in Risk Factors and Symptoms Associated With SARS-CoV-2 and Rhinovirus Test Positivity in King County, Washington, June 2020 to July 2022. JAMA Netw Open 2022; 5:e2245861. [PMID: 36484987 PMCID: PMC9856230 DOI: 10.1001/jamanetworkopen.2022.45861] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
IMPORTANCE Few US studies have reexamined risk factors for SARS-CoV-2 positivity in the context of widespread vaccination and new variants or considered risk factors for cocirculating endemic viruses, such as rhinovirus. OBJECTIVES To evaluate how risk factors and symptoms associated with SARS-CoV-2 test positivity changed over the course of the pandemic and to compare these with the risk factors associated with rhinovirus test positivity. DESIGN, SETTING, AND PARTICIPANTS This case-control study used a test-negative design with multivariable logistic regression to assess associations between SARS-CoV-2 and rhinovirus test positivity and self-reported demographic and symptom variables over a 25-month period. The study was conducted among symptomatic individuals of all ages enrolled in a cross-sectional community surveillance study in King County, Washington, from June 2020 to July 2022. EXPOSURES Self-reported data for 15 demographic and health behavior variables and 16 symptoms. MAIN OUTCOMES AND MEASURES Reverse transcription-polymerase chain reaction-confirmed SARS-CoV-2 or rhinovirus infection. RESULTS Analyses included data from 23 498 individuals. The median (IQR) age of participants was 34.33 (22.42-45.08) years, 13 878 (59.06%) were female, 4018 (17.10%) identified as Asian, 654 (2.78%) identified as Black, and 2193 (9.33%) identified as Hispanic. Close contact with an individual with SARS-CoV-2 (adjusted odds ratio [aOR], 3.89; 95% CI, 3.34-4.57) and loss of smell or taste (aOR, 3.49; 95% CI, 2.77-4.41) were the variables most associated with SARS-CoV-2 test positivity, but both attenuated during the Omicron period. Contact with a vaccinated individual with SARS-CoV-2 (aOR, 2.03; 95% CI, 1.56-2.79) was associated with lower odds of testing positive than contact with an unvaccinated individual with SARS-CoV-2 (aOR, 4.04; 95% CI, 2.39-7.23). Sore throat was associated with Omicron infection (aOR, 2.27; 95% CI, 1.68-3.20) but not Delta infection. Vaccine effectiveness for participants fully vaccinated with a booster dose was 93% (95% CI, 73%-100%) for Delta, but not significant for Omicron. Variables associated with rhinovirus test positivity included being younger than 12 years (aOR, 3.92; 95% CI, 3.42-4.51) and experiencing a runny or stuffy nose (aOR, 4.58; 95% CI, 4.07-5.21). Black race, residing in south King County, and households with 5 or more people were significantly associated with both SARS-CoV-2 and rhinovirus test positivity. CONCLUSIONS AND RELEVANCE In this case-control study of 23 498 symptomatic individuals, estimated risk factors and symptoms associated with SARS-CoV-2 infection changed over time. There was a shift in reported symptoms between the Delta and Omicron variants as well as reductions in the protection provided by vaccines. Racial and sociodemographic disparities persisted in the third year of SARS-CoV-2 circulation and were also present in rhinovirus infection. Trends in testing behavior and availability may influence these results.
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Affiliation(s)
- Chelsea Hansen
- Brotman Baty Institute, University of Washington, Seattle
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Amanda C. Perofsky
- Brotman Baty Institute, University of Washington, Seattle
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Roy Burstein
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, Washington
| | - Michael Famulare
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shanda Boyle
- Brotman Baty Institute, University of Washington, Seattle
| | - Robin Prentice
- Brotman Baty Institute, University of Washington, Seattle
| | | | | | - David Reinhart
- Brotman Baty Institute, University of Washington, Seattle
| | - Ben Capodanno
- Brotman Baty Institute, University of Washington, Seattle
| | - Melissa Truong
- Brotman Baty Institute, University of Washington, Seattle
| | | | - Kayla Kuchta
- Brotman Baty Institute, University of Washington, Seattle
| | - Brian Pfau
- Brotman Baty Institute, University of Washington, Seattle
| | - Zack Acker
- Brotman Baty Institute, University of Washington, Seattle
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Evan McDermot
- Brotman Baty Institute, University of Washington, Seattle
| | | | - Jeremy Stone
- Brotman Baty Institute, University of Washington, Seattle
| | - Luis Gamboa
- Brotman Baty Institute, University of Washington, Seattle
| | - Peter D. Han
- Brotman Baty Institute, University of Washington, Seattle
- Department of Genome Sciences, University of Washington, Seattle
| | - Jeffery S. Duchin
- Public Health Seattle and King County, Seattle, Washington
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- School of Public Health, University of Washington, Seattle
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Seattle Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle
| | - Janet A. Englund
- Brotman Baty Institute, University of Washington, Seattle
- Seattle Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle
| | - Jay Shendure
- Brotman Baty Institute, University of Washington, Seattle
- Department of Genome Sciences, University of Washington, Seattle
- Howard Hughes Medical Institute, Seattle, Washington
| | - Trevor Bedford
- Brotman Baty Institute, University of Washington, Seattle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
- Howard Hughes Medical Institute, Seattle, Washington
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Lea M. Starita
- Brotman Baty Institute, University of Washington, Seattle
- Department of Genome Sciences, University of Washington, Seattle
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
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27
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Kandel C, Lee Y, Taylor M, Llanes A, McCready J, Crowl G, Powis J, Li AX, Shigayeva A, Yip L, Katz K, Kozak R, Mubareka S, McGeer A. Viral dynamics of the SARS-CoV-2 Omicron Variant among household contacts with 2 or 3 COVID-19 vaccine doses. J Infect 2022; 85:666-670. [PMID: 36283495 PMCID: PMC9595488 DOI: 10.1016/j.jinf.2022.10.027] [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: 05/31/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVES SARS-CoV-2 shedding has changed as new variants have emerged. It is important to understand the trajectory of PCR positivity due to Omicron in vaccinated populations. METHODS Double- or triple-vaccinated adult household contacts of individuals with COVID-19 self-collected oral-nasal swabs for 14 days. A hierarchical linear model estimated viral load trajectories and an exploratory logistic regression model assessed for factors associated with viral detection before symptom onset. RESULTS Forty-one participants developed COVID-19 with 37 (90%) symptomatic. Viral load peaked 3 days after symptom onset at a median concentration of 8.83 log10 copies/milliliter (range 5.95-10.32) and the mean difference between participants with two or three COVID-19 vaccine doses was 0.02 log10 copies/milliliter (95% CI -0.13 to 0.16). PCR positivity began with a range of 4 days prior to 3 days after symptom onset and was positive on the day of symptom onset in 76% (28/37). SARS-CoV-2 detection on the day of symptom onset was less likely among those with 2 vaccine doses (OR 0.13, 95%CI 0.02-0.79). 68% (25/37) of infected participants had detectable SARS-CoV-2 with Ct<30 at 7 days after symptom onset. CONCLUSIONS Peak viral load and duration of PCR positivity were similar in participants with COVID-19 after two versus three COVID-19 vaccine doses. Onset of viral detection relative to symptom onset was variable.
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Affiliation(s)
- Christopher Kandel
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada.
| | - Yaejin Lee
- Sunnybrook Health Sciences Centre, 2075 Bayview Ave, Toronto, Ontario M4N 3M5, Canada,Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Maureen Taylor
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Andrea Llanes
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Janine McCready
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Gloria Crowl
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Jeff Powis
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Angel Xinliu Li
- Sinai Health System, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Altynay Shigayeva
- Sinai Health System, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Lily Yip
- Sunnybrook Health Sciences Centre, 2075 Bayview Ave, Toronto, Ontario M4N 3M5, Canada
| | - Kevin Katz
- Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada,North York General Hospital, 4001 Leslie St, North York, Ontario M2K 1E1, Canada,Shared Hospital Laboratory, 555 Finch Ave W, Toronto, Ontario M2R 1N5, Canada
| | - Robert Kozak
- Sunnybrook Health Sciences Centre, 2075 Bayview Ave, Toronto, Ontario M4N 3M5, Canada,Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Samira Mubareka
- Sunnybrook Health Sciences Centre, 2075 Bayview Ave, Toronto, Ontario M4N 3M5, Canada,Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Allison McGeer
- Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Sinai Health System, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.
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28
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SARS-CoV-2 nasopharyngeal viral load in individuals infected with BA.2, compared to Alpha, Gamma, Delta and BA.1 variants: A single-center comparative analysis. J Clin Virol 2022; 157:105299. [PMID: 36183546 PMCID: PMC9511897 DOI: 10.1016/j.jcv.2022.105299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/18/2022] [Accepted: 09/24/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND SARS-CoV-2 has evolved, leading to the emergence of new Variants Of Concern (VOCs) with significant impact on transmissibility. Although the transmission process is complex, higher nasopharyngeal viral load (NP-VL) can be considered as a proxy for greater transmissibility. OBJECTIVES The aim of this analysis was to compare NP-VL across a set of representative VOCs observed in mildly symptomatic patients. STUDY DESIGN Observational single-center comparative analysis of patients with early mild-to-moderate COVID-19, enrolled within the early treatment access program of Lazzaro Spallanzani Institute (March 2021-March 2022). NP-VL before drug administration was estimated through RT-PCR, based on cycle threshold values (CTs); VOCs were identified by Sanger sequencing. VOCs' average treatment effect (ATE) was estimated on the CTs fitted in the log2 scale, controlling for potential confounders. RESULTS A total of 707 patients were included. VOCs were: 10% Alpha, 3% Gamma, 34% Delta, 34% BA.1, 19% BA.2. Mean CTs for BA.1 and BA.2 were lower than Delta and BA.1, respectively. After adjusting for calendar time, age, immunodeficiency and vaccination, CTs for Gamma were lower than those seen for Alpha and higher than Delta, for Delta were similar to BA.1, for BA.2 were lower than Delta and BA.1. CONCLUSIONS Our analysis shows higher NP-VL of BA.2 compared to previously circulating VOCs, even after controlling for factors potentially contributing to the amount of nasopharyngeal viral RNA, included vaccination, supporting the increased transmissibility of BA.2. Further studies are necessary to clarify this mechanism and to provide guidance for public health measures.
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Roohani J, Keikha M. Global challenge with the SARS-CoV-2 omicron BA.2 (B.1.1.529.2) subvariant: Should we be concerned? World J Virol 2022; 11:496-501. [PMID: 36483099 PMCID: PMC9724199 DOI: 10.5501/wjv.v11.i6.496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/23/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
BA.2 is a novel omicron offshoot of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has gone viral. There is limited knowledge regarding this variant of concern. Current evidence suggests that this variant is more contagious but less severe than previous SARS-CoV-2 variants. However, there is concern regarding the virus mutations that could influence pathogenicity, transmissibility, and immune evasion.
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Affiliation(s)
- Jalil Roohani
- Department of Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 13131-99137, Iran
| | - Masoud Keikha
- Department of Medical Microbiology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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Valenzuela-Fernández A, Cabrera-Rodriguez R, Ciuffreda L, Perez-Yanes S, Estevez-Herrera J, González-Montelongo R, Alcoba-Florez J, Trujillo-González R, García-Martínez de Artola D, Gil-Campesino H, Díez-Gil O, Lorenzo-Salazar JM, Flores C, Garcia-Luis J. Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19. Front Bioeng Biotechnol 2022; 10:1052436. [PMID: 36507266 PMCID: PMC9732709 DOI: 10.3389/fbioe.2022.1052436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/26/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.
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Affiliation(s)
- Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Romina Cabrera-Rodriguez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Laura Ciuffreda
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Silvia Perez-Yanes
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Judith Estevez-Herrera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Julia Alcoba-Florez
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Rodrigo Trujillo-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- Departamento de Análisis Matemático, Facultad de Ciencias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Helena Gil-Campesino
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Oscar Díez-Gil
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Jonay Garcia-Luis
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
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Zhang L, Narayanan KK, Cooper L, Chan KK, Skeeters SS, Devlin CA, Aguhob A, Shirley K, Rong L, Rehman J, Malik AB, Procko E. An ACE2 decoy can be administered by inhalation and potently targets omicron variants of SARS-CoV-2. EMBO Mol Med 2022. [PMID: 36094679 DOI: 10.1101/2022.03.28.486075v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Monoclonal antibodies targeting the SARS-CoV-2 spike (S) neutralize infection and are efficacious for the treatment of COVID-19. However, SARS-CoV-2 variants, notably sublineages of B.1.1.529/omicron, have emerged that escape antibodies in clinical use. As an alternative, soluble decoy receptors based on the host entry receptor ACE2 broadly bind and block S from SARS-CoV-2 variants and related betacoronaviruses. The high-affinity and catalytically active decoy sACE22 .v2.4-IgG1 was previously shown to be effective against SARS-CoV-2 variants when administered intravenously. Here, inhalation of aerosolized sACE22 .v2.4-IgG1 increased survival and ameliorated lung injury in K18-hACE2 mice inoculated with P.1/gamma virus. Loss of catalytic activity reduced the decoy's therapeutic efficacy, which was further confirmed by intravenous administration, supporting dual mechanisms of action: direct blocking of S and turnover of ACE2 substrates associated with lung injury and inflammation. Furthermore, sACE22 .v2.4-IgG1 tightly binds and neutralizes BA.1, BA.2, and BA.4/BA.5 omicron and protects K18-hACE2 mice inoculated with a high dose of BA.1 omicron virus. Overall, the therapeutic potential of sACE22 .v2.4-IgG1 is demonstrated by the inhalation route and broad neutralization potency persists against highly divergent SARS-CoV-2 variants.
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Affiliation(s)
- Lianghui Zhang
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL, USA
| | | | - Laura Cooper
- Department of Microbiology and Immunology, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Kui K Chan
- Cyrus Biotechnology, Inc., Seattle, WA, USA
| | | | | | | | | | - Lijun Rong
- Department of Microbiology and Immunology, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Asrar B Malik
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, IL, USA
- Cyrus Biotechnology, Inc., Seattle, WA, USA
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32
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Zhang L, Narayanan KK, Cooper L, Chan KK, Skeeters SS, Devlin CA, Aguhob A, Shirley K, Rong L, Rehman J, Malik AB, Procko E. An ACE2 decoy can be administered by inhalation and potently targets omicron variants of SARS-CoV-2. EMBO Mol Med 2022; 14:e16109. [PMID: 36094679 PMCID: PMC9539395 DOI: 10.15252/emmm.202216109] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Monoclonal antibodies targeting the SARS-CoV-2 spike (S) neutralize infection and are efficacious for the treatment of COVID-19. However, SARS-CoV-2 variants, notably sublineages of B.1.1.529/omicron, have emerged that escape antibodies in clinical use. As an alternative, soluble decoy receptors based on the host entry receptor ACE2 broadly bind and block S from SARS-CoV-2 variants and related betacoronaviruses. The high-affinity and catalytically active decoy sACE22 .v2.4-IgG1 was previously shown to be effective against SARS-CoV-2 variants when administered intravenously. Here, inhalation of aerosolized sACE22 .v2.4-IgG1 increased survival and ameliorated lung injury in K18-hACE2 mice inoculated with P.1/gamma virus. Loss of catalytic activity reduced the decoy's therapeutic efficacy, which was further confirmed by intravenous administration, supporting dual mechanisms of action: direct blocking of S and turnover of ACE2 substrates associated with lung injury and inflammation. Furthermore, sACE22 .v2.4-IgG1 tightly binds and neutralizes BA.1, BA.2, and BA.4/BA.5 omicron and protects K18-hACE2 mice inoculated with a high dose of BA.1 omicron virus. Overall, the therapeutic potential of sACE22 .v2.4-IgG1 is demonstrated by the inhalation route and broad neutralization potency persists against highly divergent SARS-CoV-2 variants.
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Affiliation(s)
- Lianghui Zhang
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular BiologyThe University of Illinois College of MedicineChicagoILUSA
- Present address:
Division of Pulmonary, Allergy and Critical Care Medicine, Department of MedicineUniversity of Pittsburgh Medical CenterPittsburghPAUSA
| | | | - Laura Cooper
- Department of Microbiology and ImmunologyThe University of Illinois College of MedicineChicagoILUSA
| | | | | | | | | | | | - Lijun Rong
- Department of Microbiology and ImmunologyThe University of Illinois College of MedicineChicagoILUSA
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular BiologyThe University of Illinois College of MedicineChicagoILUSA
- Department of Biochemistry and Molecular GeneticsThe University of Illinois College of MedicineChicagoILUSA
| | - Asrar B Malik
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular BiologyThe University of Illinois College of MedicineChicagoILUSA
| | - Erik Procko
- Department of BiochemistryUniversity of IllinoisUrbanaILUSA
- Cyrus Biotechnology, Inc.SeattleWAUSA
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33
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Genomic and epidemiologic surveillance of SARS-CoV-2 in Southern Brazil and identification of a new Omicron-L452R sublineage. Virus Res 2022; 321:198907. [PMID: 36055471 PMCID: PMC9425700 DOI: 10.1016/j.virusres.2022.198907] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/04/2022] [Accepted: 08/29/2022] [Indexed: 12/24/2022]
Abstract
Recently, SARS-CoV-2 Omicron variant (B.1.1.529) was first identified in Botswana in November 2021. In a short period of time, this highly mutated variant replaced the previous dominant Delta variant, causing an exponential increase in the number of COVID-19 cases, resulting in a new wave of pandemic. This current research article aims to analyze and summarize information about the genetic characteristics, amino acid mutations and epidemiological data providing scientific findings to enrich the SARS-CoV-2 knowledge. More importantly, we describe here, for the first time, the identification of a new Omicron variant of concern: Omicron-L452R in Brazil.
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34
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Qu P, Evans JP, Faraone J, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Lozanski G, Panchal A, Saif LJ, Oltz EM, Xu K, Gumina RJ, Liu SL. Distinct Neutralizing Antibody Escape of SARS-CoV-2 Omicron Subvariants BQ.1, BQ.1.1, BA.4.6, BF.7 and BA.2.75.2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.19.512891. [PMID: 36299423 PMCID: PMC9603827 DOI: 10.1101/2022.10.19.512891] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Continued evolution of SARS-CoV-2 has led to the emergence of several new Omicron subvariants, including BQ.1, BQ. 1.1, BA.4.6, BF.7 and BA.2.75.2. Here we examine the neutralization resistance of these subvariants, as well as their ancestral BA.4/5, BA.2.75 and D614G variants, against sera from 3-dose vaccinated health care workers, hospitalized BA.1-wave patients, and BA.5-wave patients. We found enhanced neutralization resistance in all new subvariants, especially the BQ.1 and BQ.1.1 subvariants driven by a key N460K mutation, and to a lesser extent, R346T and K444T mutations, as well as the BA.2.75.2 subvariant driven largely by its F486S mutation. The BQ.1 and BQ.1.1 subvariants also exhibited enhanced fusogenicity and S processing dictated by the N460K mutation. Interestingly, the BA.2.75.2 subvariant saw an enhancement by the F486S mutation and a reduction by the D1199N mutation to its fusogenicity and S processing, resulting in minimal overall change. Molecular modelling revealed the mechanisms of receptor-binding and non-receptor binding monoclonal antibody-mediated immune evasion by R346T, K444T, F486S and D1199N mutations. Altogether, these findings shed light on the concerning evolution of newly emerging SARS-CoV-2 Omicron subvariants.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - John P. Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Julia Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mirela Anghelina
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick Stevens
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Soledad Fernandez
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ashish Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, USA
| | - Linda J. Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J. Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
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35
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Kumar A, Sharma A, Vijay Tirpude N, Padwad Y, Sharma S, Kumar S. Perspective Chapter: Emerging SARS-CoV-2 Variants of Concern (VOCs) and Their Impact on Transmission Rate, Disease Severity and Breakthrough Infections. Infect Dis (Lond) 2022. [DOI: 10.5772/intechopen.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SARS-CoV-2, like all RNA viruses, evolves over time, and genetic mutations have been linked to increased replication fitness and evolvability. SARS-CoV-2 spreads quickly between countries, resulting in new mutations. SARS-CoV-2 genome sequencing reveals that variants emerge through point mutations, insertions, and deletions. Concerns have been raised about the ability of currently approved vaccines to protect against emerging variants. Viral spike protein is a component of many approved vaccine candidates, and mutations in the S-protein may affect transmission dynamics and the risk of immune escape, resulting this pandemic last-longer in populations. Understanding the evolution of the SARS-CoV-2 virus, as well as its potential relationship with transmissibility, infectivity, and disease severity, may help us predict the consequences of future pandemics. SARS-CoV-2 genome studies have identified a few mutations that could potentially alter the transmissibility and pathogenicity of the SARS-CoV-2 virus. At the moment, it is worth mentioning that a few variants have increased the transmissibility of SARS-CoV-2. The Alpha, Beta, Gamma, Delta, Delta+, and omicron variants are designated as variants of concern (VOCs) by the World Health Organisation and have been linked with an increased risk to the community in terms of transmission, hospitalisation, and mortality. This chapter thoroughly discusses the impact of SARS-CoV-2 mutations, mainly VOCs, on public health by mining many published articles.
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Alba JMG, Pérez-Martínez Z, Boga JA, Rojo-Alba S, de Oña JG, Alvarez-Argüelles ME, Rodríguez GM, Gonzalez IC, González IH, Coto E, García SM. Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy. Microorganisms 2022; 10:1954. [PMID: 36296230 PMCID: PMC9610377 DOI: 10.3390/microorganisms10101954] [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: 08/19/2022] [Revised: 09/07/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants. METHODS From January to June 2022, 34,591 variants were determined by the SNP method. From them, 445 were characterized by the WGS method and classified following pangolin program and phylogenic analysis. RESULTS The Omicron variant went from being detected in 2438 (78%) samples in the first week of January 2021 to 4074 (98%) in the third week, according to the SNP method. Using the WGS method, 159 BA.1 (35.7%), 256 BA.2 (57.6%), 1 BA.4 (0.2%) and 10 BA.5 (2.2%) Omicron variants were found. Phylogenetic analysis detected that three new sub-clades, BA.2,3.5, BA.2.56 and BF1, were circulating. CONCLUSIONS The increase in the incidence of SARS-CoV2 caused the circulation of new emerging variants. Viral evolution calls for continuous genomic surveillance.
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Affiliation(s)
- José María González Alba
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Zulema Pérez-Martínez
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - José A. Boga
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Susana Rojo-Alba
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Juan Gómez de Oña
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Genetic Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Marta E. Alvarez-Argüelles
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Garbriel Martín Rodríguez
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Isabel Costales Gonzalez
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | | | - Eliecer Coto
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Genetic Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Santiago Melón García
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Increased household transmission and immune escape of the SARS-CoV-2 Omicron compared to Delta variants. Nat Commun 2022; 13:5706. [PMID: 36175424 PMCID: PMC9520116 DOI: 10.1038/s41467-022-33233-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Understanding the epidemic growth of the novel SARS-CoV-2 Omicron variant is critical for public health. We compared the ten-day secondary attack rate (SAR) of the Omicron and Delta variants in households using Norwegian contact tracing data, December 2021 - January 2022. Omicron SAR was higher than Delta, with a relative risk (RR) of 1.41 (95% CI 1.27-1.56). We observed increased susceptibility to Omicron infection in household contacts compared to Delta, independent of contacts’ vaccination status. Among three-dose vaccinated contacts, the mean SAR was lower for both variants. We found increased Omicron transmissibility from primary cases to contacts in all vaccination groups, except 1-dose vaccinated, compared to Delta. Omicron SAR of three-dose vaccinated primary cases was high, 46% vs 11 % for Delta. In conclusion, three-dose vaccinated primary cases with Omicron infection can efficiently spread in households, while three-dose vaccinated contacts have a lower risk of being infected by Delta and Omicron. In this study the authors investigate household transmission of SARS-CoV-2 in Norway. They find that the secondary attack rate was higher for Omicron than Delta, but that among three-dose vaccinated contacts the secondary attack rate was lower for both variants compared to contacts with two doses.
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Yu CY, Wong SY, Liew NWC, Joseph N, Zakaria Z, Nurulfiza I, Soe HJ, Kairon R, Amin-Nordin S, Chee HY. Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: From alpha to Omicron. Front Med (Lausanne) 2022; 9:1001022. [PMID: 36213636 PMCID: PMC9537942 DOI: 10.3389/fmed.2022.1001022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Countries around the world are gearing for the transition of the coronavirus disease 2019 (COVID-19) from pandemic to endemic phase but the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants could lead to a prolonged pandemic. SARS-CoV-2 has continued to evolve as it optimizes its adaptation to the human host and the successive waves of COVID-19 have been linked to the explosion of particular variant of concern. As the genetic diversity and epidemiological landscape of SARS-CoV-2 differ from country to country, this study aims to provide insights into the variants that are circulating in Malaysia. Whole genome sequencing was performed for 204 SARS-CoV-2 from COVID-19 cases and an additional 18,667 SARS-CoV-2 genome sequences were retrieved from the GISAID EpiCoV database for clade, lineage and genetic variation analyses. Complete genome sequences with high coverage were then used for phylogeny investigation and the resulting phylogenetic tree was constructed from 8,716 sequences. We found that the different waves of COVID-19 in Malaysia were dominated by different clades with the L and O clade for first and second wave, respectively, whereas the progressive replacement by G, GH, and GK of the GRA clade were observed in the subsequence waves. Continuous monitoring of the genetic diversity of SARS-CoV-2 is important to identify the emergence and dominance of new variant in different locality so that the appropriate countermeasures can be taken to effectively contain the spread of SARS-CoV-2.
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Affiliation(s)
- Choo Yee Yu
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Sie Yeng Wong
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nancy Woan Charn Liew
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Narcisse Joseph
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Zunita Zakaria
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Isa Nurulfiza
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | | | | | - Syafinaz Amin-Nordin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hui Yee Chee
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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Qassim SH, Chemaitelly H, Ayoub HH, AlMukdad S, Tang P, Hasan MR, Yassine HM, Al-Khatib HA, Smatti MK, Abdul-Rahim HF, Nasrallah GK, Al-Kuwari MG, Al-Khal A, Coyle P, Kaleeckal AH, Shaik RM, Latif AN, Al-Kuwari E, Jeremijenko A, Butt AA, Bertollini R, Al-Romaihi HE, Al-Thani MH, Abu-Raddad LJ. Effects of BA.1/BA.2 subvariant, vaccination and prior infection on infectiousness of SARS-CoV-2 omicron infections. J Travel Med 2022; 29:taac068. [PMID: 35639932 PMCID: PMC9213851 DOI: 10.1093/jtm/taac068] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/20/2022] [Indexed: 11/24/2022]
Affiliation(s)
- Suelen H Qassim
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
- World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine–Qatar, Cornell University, Qatar Foundation – Education City, Doha, Qatar
- Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Hiam Chemaitelly
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
- World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine–Qatar, Cornell University, Qatar Foundation – Education City, Doha, Qatar
- Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Houssein H Ayoub
- Mathematics Program, Department of Mathematics, Statistics, and Physics, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Sawsan AlMukdad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
- World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine–Qatar, Cornell University, Qatar Foundation – Education City, Doha, Qatar
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | | | - Hadi M Yassine
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Hebah A Al-Khatib
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Maria K Smatti
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Hanan F Abdul-Rahim
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Gheyath K Nasrallah
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | | | | | - Peter Coyle
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar
- Hamad Medical Corporation, Doha, Qatar
- Wellcome-Wolfson Institute for Experimental Medicine, Queens University, Belfast, UK
| | | | | | | | | | | | - Adeel A Butt
- Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Hamad Medical Corporation, Doha, Qatar
- Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | | | | | - Laith J Abu-Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
- World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine–Qatar, Cornell University, Qatar Foundation – Education City, Doha, Qatar
- Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
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40
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Ke H, Chang MR, Marasco WA. Immune Evasion of SARS-CoV-2 Omicron Subvariants. Vaccines (Basel) 2022; 10:1545. [PMID: 36146623 PMCID: PMC9501521 DOI: 10.3390/vaccines10091545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Since the SARS-CoV-2 Omicron variant (B.1.1.529) was declared a variant of concern (VOC) by the WHO on 24 November 2021, it has caused another global surge of cases. With extensive mutations in its spike glycoprotein, Omicron gained substantial capabilities to evade the antiviral immunity provided by vaccination, hybrid immunity, or monoclonal antibodies. The Omicron subvariants BA.1, BA.2, BA.2.12.1, BA.4 and BA.5 extended this immune evasion capability by having additional unique mutations in their respective spike proteins. The ongoing Omicron wave and emergence of new Omicron subvariants leads to additional concerns regarding the efficacy of the current antiviral measurements. To have a better understanding of the Omicron subvariants, this review summarizes reports of the immune evasion of subvariants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5 as well as the molecular basis of immune evasion.
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Affiliation(s)
- Hanzhong Ke
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Matthew R. Chang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Wayne A. Marasco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
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41
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Barroso da Silva FL, Giron CC, Laaksonen A. Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule. J Phys Chem B 2022; 126:6835-6852. [PMID: 36066414 DOI: 10.1021/acs.jpcb.2c04225] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein-protein systems under different physical-chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This "RBD charge rule" should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.
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Affiliation(s)
- Fernando L Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no-campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil.,Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no-campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil.,Hospital de Clínicas, Universidade Federal do Triângulo Mineiro, Av. Getúlio Guaritá, 38025-440 Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.,State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, 210009, P. R. China.,Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda, 41A, 700487 Iasi, Romania.,Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden.,Department of Chemical and Geological Sciences, Campus Monserrato, University of Cagliari, SS 554 bivio per Sestu, 09042 Monserrato, Italy
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Konyak BM, Sharma M, Kharia S, Pandey RP, Chang CM. A Systematic Review on the Emergence of Omicron Variant and Recent Advancement in Therapies. Vaccines (Basel) 2022; 10:1468. [PMID: 36146546 PMCID: PMC9503441 DOI: 10.3390/vaccines10091468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 01/18/2023] Open
Abstract
With the ongoing COVID-19 pandemic, the emergence of the novel Omicron variant in November 2021 has created chaos around the world. Despite mass vaccination, Omicron has spread rapidly, raising concerns around the globe. The Omicron variant has a vast array of mutations, as compared to another variant of concern, with a total of 50 mutations, 30 of which are present on its spike protein alone. These mutations have led to immune escape and more transmissibility compared to other variants, including the Delta variant. A cluster of mutations (H655Y, N679K, and P681H) present in the Omicron spike protein could aid in transmission. Currently, no virus-specific data are available to predict the efficacy of the anti-viral and mAbs drugs. However, two monoclonal antibody drugs, Sotrovimab and Evusheld, are authorized for emergency use in COVID-19 patients. This virus is not fading away soon. The easiest solution and least expensive measure to fight against this pandemic are to follow the appropriate COVID-19 protocols. There is a need to strengthen the level of research for the development of potential vaccines and anti-viral drugs. It is also important to monitor and expand the genomic surveillance to keep track of the emergence of new variants, thus avoiding the spread of new diseases worldwide. This article highlights the emergence of the new SARS-CoV-2 variant of concern, Omicron (B.1.1.529), and the vast number of mutations in its protein. In addition, recent advancements in drugs approved by FDA to treat COVID patients have been listed and focused in this paper.
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Affiliation(s)
- Beyau M. Konyak
- Integrated Molecular Diagnostic and Research Laboratory (BSL-2), District Hospital Tuensang, Tuensang 798612, Nagaland, India
| | - Mohan Sharma
- Integrated Molecular Diagnostic and Research Laboratory (BSL-2), District Hospital Tuensang, Tuensang 798612, Nagaland, India
| | - Shabnam Kharia
- Department of Life Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), Department of Biotechnology & Microbiology SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India
| | - Chung-Ming Chang
- Master & Ph.D. Program in Biotechnology Industry, Division of Biotechnology, Chang Gung University, No. 259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan
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Ching WY, Adhikari P, Jawad B, Podgornik R. Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex. Int J Mol Sci 2022; 23:10091. [PMID: 36077490 PMCID: PMC9456519 DOI: 10.3390/ijms231710091] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.
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Affiliation(s)
- Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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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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de Michelena P, Olea B, Torres I, González‐Candelas F, Navarro D. SARS-CoV-2 RNA load in nasopharyngeal specimens from outpatients with breakthrough COVID-19 due to Omicron BA.1 and BA.2. J Med Virol 2022; 94:5836-5840. [PMID: 35986484 PMCID: PMC9537928 DOI: 10.1002/jmv.28079] [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: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 01/06/2023]
Abstract
This retrospective observational study compared severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA load in nasopharyngeal specimens (NPs) from patients with breakthrough coronavirus disease 2019 (COVID-19) caused by the Omicron BA.1 or BA.2 sublineages. The convenience sample was composed of 277 outpatients (176 female/112 male; median age, 48 years; range, 12-97) with breakthrough COVID-19 (n = 130 due to BA.1 and n = 147 due to BA.2). All participants had completed a full vaccination schedule and 56% had received a booster vaccine dose at the time of COVID-19 breakthrough microbiological diagnosis. NPs were collected within 7 days (median 2 days) after symptom onset. The TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific) was used to estimate viral loads in NPs. Overall, viral RNA loads in NPs were comparable (p = 0.31) for BA.1 (median, 7.1 log10 copies/ml; range, 2.7-10.6) and BA.2 (median, 7.5 log10 copies/ml; range, 2.7-10.6), yet peak viral load appeared to be reached sooner for BA.2 than for BA.1 (Day 1 vs. Days 3-5; p = 0.002). Time elapsed since last vaccine dose had no significant impact on SARS-CoV-2 RNA loads in the upper respiratory tract (URT) for either BA.1 or BA.2. The data presented do not support that the transmissibility advantage of BA.2 over BA.1 is related to generation of higher viral loads in the URT early after infection.
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Affiliation(s)
- Paula de Michelena
- Microbiology Service, Clinic University HospitalINCLIVA Health Research InstituteValenciaSpain
| | - Beatriz Olea
- Microbiology Service, Clinic University HospitalINCLIVA Health Research InstituteValenciaSpain
| | - Ignacio Torres
- Microbiology Service, Clinic University HospitalINCLIVA Health Research InstituteValenciaSpain
| | - Fernando González‐Candelas
- Joint Research Unit Infection and Public Health FISABIO‐University of ValenciaInstitute for Integrative Systems Biology (I2SysBio, UV‐CSIC) and CIBER in Epidemiology and Public HealthValenciaSpain
| | - David Navarro
- Microbiology Service, Clinic University HospitalINCLIVA Health Research InstituteValenciaSpain,Department of Microbiology, School of MedicineUniversity of ValenciaValenciaSpain
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Gladkikh A, Dedkov V, Sharova A, Klyuchnikova E, Sbarzaglia V, Arbuzova T, Forghani M, Ramsay E, Dolgova A, Shabalina A, Tsyganova N, Totolian A. Uninvited Guest: Arrival and Dissemination of Omicron Lineage SARS-CoV-2 in St. Petersburg, Russia. Microorganisms 2022; 10:1676. [PMID: 36014093 PMCID: PMC9414241 DOI: 10.3390/microorganisms10081676] [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: 07/19/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze the dissemination dynamics of Omicron strains in Saint Petersburg, Russia's second largest city. The first case of Omicron lineage BA.1 was registered in St. Petersburg on 10 December 2021. Rapid expansion of the variant and increased incidence followed. The peak incidence was reached in February 2022, followed by an observed decline coinciding with the beginning of spread of the BA.2 variant. SARS-CoV-2 lineage change dynamics were shown in three categories: airport arrivals; clinical outpatients; and clinical inpatients. It is shown that the distribution of lineage BA.1 occurred as a result of multiple imports. Variability within the BA.1 and BA.2 lineages in St. Petersburg was also revealed. On the basis of phylogenetic analysis, an attempt was made to trace the origin of the first imported strain, and an assessment was made of the quarantine measures used to prevent the spread of this kind of infection.
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Affiliation(s)
- Anna Gladkikh
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | - Vladimir Dedkov
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow 119435, Russia
| | - Alena Sharova
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | | | | | - Tatiana Arbuzova
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | - Majid Forghani
- Krasovskii Institute of Mathematics and Mechanics, Yekaterinburg 620108, Russia
| | - Edward Ramsay
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | - Anna Dolgova
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | - Anna Shabalina
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | | | - Areg Totolian
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
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47
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Barnard RC, Davies NG, Jit M, Edmunds WJ, Leclerc QJ, Tully DC, Hodgson D, Pung R, Hellewell J, Koltai M, Simons D, Abbas K, Kucharski AJ, Procter SR, Sandmann FG, Pearson CAB, Prem K, Showering A, Meakin SR, O’Reilly K, McCarthy CV, Quaife M, Wong KLM, Jafari Y, Deol AK, Houben RMGJ, Diamond C, Jombart T, Villabona-Arenas CJ, Waites W, Eggo RM, Endo A, Gibbs HP, Klepac P, Williams J, Quilty BJ, Brady O, Emery JC, Atkins KE, Chapman LAC, Sherratt K, Abbott S, Bosse NI, Mee P, Funk S, Lei J, Liu Y, Flasche S, Rudge JW, Sun FY, Medley G, Russell TW, Gimma A, Hué S, Jarvis CI, Finch E, Clifford S, Jit M, Edmunds WJ. Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era. Nat Commun 2022; 13:4879. [PMID: 35986002 PMCID: PMC9389516 DOI: 10.1038/s41467-022-32404-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
England has experienced a heavy burden of COVID-19, with multiple waves of SARS-CoV-2 transmission since early 2020 and high infection levels following the emergence and spread of Omicron variants since late 2021. In response to rising Omicron cases, booster vaccinations were accelerated and offered to all adults in England. Using a model fitted to more than 2 years of epidemiological data, we project potential dynamics of SARS-CoV-2 infections, hospital admissions and deaths in England to December 2022. We consider key uncertainties including future behavioural change and waning immunity and assess the effectiveness of booster vaccinations in mitigating SARS-CoV-2 disease burden between October 2021 and December 2022. If no new variants emerge, SARS-CoV-2 transmission is expected to decline, with low levels remaining in the coming months. The extent to which projected SARS-CoV-2 transmission resurges later in 2022 depends largely on assumptions around waning immunity and to some extent, behaviour, and seasonality.
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Affiliation(s)
- Rosanna C. Barnard
- grid.8991.90000 0004 0425 469XCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK ,grid.8991.90000 0004 0425 469XDepartment of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Nicholas G. Davies
- grid.8991.90000 0004 0425 469XCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK ,grid.8991.90000 0004 0425 469XDepartment of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | | | - Mark Jit
- grid.8991.90000 0004 0425 469XCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK ,grid.8991.90000 0004 0425 469XDepartment of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - W. John Edmunds
- grid.8991.90000 0004 0425 469XCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK ,grid.8991.90000 0004 0425 469XDepartment of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
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48
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Patel RS, Agrawal B. Heterologous immunity induced by 1 st generation COVID-19 vaccines and its role in developing a pan-coronavirus vaccine. Front Immunol 2022; 13:952229. [PMID: 36045689 PMCID: PMC9420909 DOI: 10.3389/fimmu.2022.952229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome virus-2 (SARS-CoV-2), the causative infectious agent of the COVID-19 pandemic, has led to multiple (4-6) waves of infections worldwide during the past two years. The development of vaccines against SARS-CoV-2 has led to successful mass immunizations worldwide, mitigating the worldwide mortality due the pandemic to a great extent. Yet the evolution of new variants highlights a need to develop a universal vaccine which can prevent infections from all virulent SARS-CoV-2. Most of the current first generation COVID-19 vaccines are based on the Spike protein from the original Wuhan-hu-1 virus strain. It is encouraging that they still protect from serious illnesses, hospitalizations and mortality against a number of mutated viral strains, to varying degrees. Understanding the mechanisms by which these vaccines provide heterologous protection against multiple highly mutated variants can reveal strategies to develop a universal vaccine. In addition, many unexposed individuals have been found to harbor T cells that are cross-reactive against SARS-CoV-2 antigens, with a possible protective role. In this review, we will discuss various aspects of natural or vaccine-induced heterologous (cross-reactive) adaptive immunity against SARS-CoV-2 and other coronaviruses, and their role in achieving the concept of a pan-coronavirus vaccine.
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Affiliation(s)
| | - Babita Agrawal
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
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Risk Factors for Slow Viral Decline in COVID-19 Patients during the 2022 Omicron Wave. Viruses 2022; 14:v14081714. [PMID: 36016336 PMCID: PMC9412339 DOI: 10.3390/v14081714] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023] Open
Abstract
Formulating termination of isolation (de-isolation) policies requires up-to-date knowledge about viral shedding dynamics. However, current de-isolation policies are largely based on viral load data obtained before the emergence of Omicron variant. In this retrospective cohort study involving adult patients hospitalised for COVID-19 between January and February 2022, we sought to determine SARS-CoV-2 viral shedding kinetics and to investigate the risk factors associated with slow viral decline during the 2022 Omicron wave. A total of 104 patients were included. The viral load was highest (Ct value was lowest) on days 1 post-symptom-onset (PSO) and gradually declined. Older age, hypertension, hyperlipidaemia and chronic kidney disease were associated with slow viral decline in the univariate analysis on both day 7 and day 10 PSO, while incomplete or no vaccination was associated with slow viral decline on day 7 PSO only. However, older age was the only risk factor that remained statistically significant in the multivariate analysis. In conclusion, older age is an independent risk factor associated with slow viral decline in this study conducted during the Omicron-dominant 2022 COVID-19 wave. Transmission-based precaution guidelines should take age into consideration when determining the timing of de-isolation.
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50
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Niemann CU, da Cunha-Bang C, Helleberg M, Ostrowski SR, Brieghel C. Patients with CLL have a lower risk of death from COVID-19 in the Omicron era. Blood 2022; 140:445-450. [PMID: 35588468 PMCID: PMC9122776 DOI: 10.1182/blood.2022016147] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/12/2022] [Indexed: 12/15/2022] Open
Abstract
Previous studies have shown that patients with chronic lymphocytic leukemia (CLL) and coronavirus disease 2019 (COVID-19) have high mortality rates. Infection with the Omicron variant has been described as a milder disease course in the general population. However, the outcome for immunocompromised patients has not previously been reported. In a cohort of patients with CLL tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at hospital test sites in the time periods before and after dominance of the Omicron variant, rates of hospitalizations and intensive care unit admissions declined significantly, whereas 30-day mortality remained as high as 23% in the period with dominance of the Omicron sublineage BA.2 variant. However, for a larger population-based cohort of patients with CLL (including the hospital cohort), 30-day mortality was 2%. Thus, patients with CLL with close hospital contacts and, in particular, those >70 years of age with 1 or more comorbidities should be considered for closer monitoring and preemptive antiviral therapy upon a positive SARS-CoV-2 test.
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Affiliation(s)
- Carsten U Niemann
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Marie Helleberg
- Department of Infectious Diseases
- Center of Excellence for Health, Immunity and Infections, and
| | - Sisse R Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark; and
| | - Christian Brieghel
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
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