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Li Y, Jiang X, Qiu Y, Gao F, Xin H, Li D, Qin Y, Li Z. Latent and incubation periods of Delta, BA.1, and BA.2 variant cases and associated factors: a cross-sectional study in China. BMC Infect Dis 2024; 24:294. [PMID: 38448822 PMCID: PMC10916204 DOI: 10.1186/s12879-024-09158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The latent and incubation periods characterize the transmission of infectious viruses and are the basis for the development of outbreak prevention and control strategies. However, systematic studies on the latent period and associated factors with the incubation period for SAS-CoV-2 variants are still lacking. We inferred the two durations of Delta, BA.1, and BA.2 cases and analyzed the associated factors. METHODS The Delta, BA.1, and BA.2 (and its lineages BA.2.2 and BA.2.76) cases with clear transmission chains and infectors from 10 local SAS-CoV-2 epidemics in China were enrolled. The latent and incubation periods were fitted by the Gamma distribution, and associated factors were analyzed using the accelerated failure time model. RESULTS The mean latent period for 672 Delta, 208 BA.1, and 677 BA.2 cases was 4.40 (95%CI: 4.24 ~ 4.63), 2.50 (95%CI: 2.27 ~ 2.76), and 2.58 (95%CI: 2.48 ~ 2.69) days, respectively, with 85.65% (95%CI: 83.40 ~ 87.77%), 97.80% (95%CI: 96.35 ~ 98.89%), and 98.87% (95%CI: 98.40 ~ 99.27%) of them starting to shed viruses within 7 days after exposure. In 405 Delta, 75 BA.1, and 345 BA.2 symptomatic cases, the mean latent period was 0.76, 1.07, and 0.79 days shorter than the mean incubation period [5.04 (95%CI: 4.83 ~ 5.33), 3.42 (95%CI: 3.00 ~ 3.89), and 3.39 (95%CI: 3.24 ~ 3.55) days], respectively. No significant difference was observed in the two durations between BA.1 and BA.2 cases. After controlling for the sex, clinical severity, vaccination history, number of infectors, the length of exposure window and shedding window, the latent period [Delta: exp(β) = 0.81, 95%CI: 0.66 ~ 0.98, p = 0.034; Omicron: exp(β) = 0.82, 95%CI: 0.71 ~ 0.94, p = 0.004] and incubation period [Delta: exp(β) = 0.69, 95%CI: 0.55 ~ 0.86, p < 0.001; Omicron: exp(β) = 0.83, 95%CI: 0.72 ~ 0.96, p = 0.013] were significantly shorter in 18 ~ 49 years but did not change significantly in ≥ 50 years compared with 0 ~ 17 years. CONCLUSION Pre-symptomatic transmission can occur in Delta, BA.1, and BA.2 cases. The latent and incubation periods between BA.1 and BA.2 were similar but shorter compared with Delta. Age may be associated with the latent and incubation periods of SARS-CoV-2.
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Affiliation(s)
- Yu Li
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xinli Jiang
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yan Qiu
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Feng Gao
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hualei Xin
- 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, Hong Kong, China
- School of Population Medicine and Public Health, Chinese Academy of Medical Science (CAMS), Peking Union Medical College (PUMC), No. 9, Dongdan Santiao, Dongcheng District, Beijing, 100730, China
| | - Dan Li
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ying Qin
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhongjie Li
- Division of Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- School of Population Medicine and Public Health, Chinese Academy of Medical Science (CAMS), Peking Union Medical College (PUMC), No. 9, Dongdan Santiao, Dongcheng District, Beijing, 100730, China.
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Lanièce Delaunay C, Martínez-Baz I, Sève N, Domegan L, Mazagatos C, Buda S, Meijer A, Kislaya I, Pascu C, Carnahan A, Oroszi B, Ilić M, Maurel M, Melo A, Sandonis Martín V, Trobajo-Sanmartín C, Enouf V, McKenna A, Pérez-Gimeno G, Goerlitz L, de Lange M, Rodrigues AP, Lazar M, Latorre-Margalef N, Túri G, Castilla J, Falchi A, Bennett C, Gallardo V, Dürrwald R, Eggink D, Guiomar R, Popescu R, Riess M, Horváth JK, Casado I, García MDC, Hooiveld M, Machado A, Bacci S, Kaczmarek M, Kissling E. COVID-19 vaccine effectiveness against symptomatic infection with SARS-CoV-2 BA.1/ BA.2 lineages among adults and adolescents in a multicentre primary care study, Europe, December 2021 to June 2022. Euro Surveill 2024; 29:2300403. [PMID: 38551095 PMCID: PMC10979526 DOI: 10.2807/1560-7917.es.2024.29.13.2300403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/14/2023] [Indexed: 04/01/2024] Open
Abstract
BackgroundScarce European data in early 2021 suggested lower vaccine effectiveness (VE) against SARS-CoV-2 Omicron lineages than previous variants.AimWe aimed to estimate primary series (PS) and first booster VE against symptomatic BA.1/BA.2 infection and investigate potential biases.MethodsThis European test-negative multicentre study tested primary care patients with acute respiratory symptoms for SARS-CoV-2 in the BA.1/BA.2-dominant period. We estimated PS and booster VE among adults and adolescents (PS only) for all products combined and for Comirnaty alone, by time since vaccination, age and chronic condition. We investigated potential bias due to correlation between COVID-19 and influenza vaccination and explored effect modification and confounding by prior SARS-CoV-2 infection.ResultsAmong adults, PS VE was 37% (95% CI: 24-47%) overall and 60% (95% CI: 44-72%), 43% (95% CI: 26-55%) and 29% (95% CI: 13-43%) < 90, 90-179 and ≥ 180 days post vaccination, respectively. Booster VE was 42% (95% CI: 32-51%) overall and 56% (95% CI: 47-64%), 22% (95% CI: 2-38%) and 3% (95% CI: -78% to 48%), respectively. Primary series VE was similar among adolescents. Restricting analyses to Comirnaty had little impact. Vaccine effectiveness was higher among older adults. There was no signal of bias due to correlation between COVID-19 and influenza vaccination. Confounding by previous infection was low, but sample size precluded definite assessment of effect modification.ConclusionPrimary series and booster VE against symptomatic infection with BA.1/BA.2 ranged from 37% to 42%, with similar waning post vaccination. Comprehensive data on previous SARS-CoV-2 infection would help disentangle vaccine- and infection-induced immunity.
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Affiliation(s)
| | - Iván Martínez-Baz
- Instituto de Salud Pública de Navarra - IdiSNA, Pamplona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Noémie Sève
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Lisa Domegan
- Health Protection Surveillance Centre, Dublin, Ireland
| | - Clara Mazagatos
- National Centre of Epidemiology, CIBERESP, Carlos III Health Institute, Madrid, Spain
| | - Silke Buda
- Department for Infectious Disease Epidemiology, Respiratory Infections Unit, Robert Koch Institute, Berlin, Germany
| | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Irina Kislaya
- Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Catalina Pascu
- Cantacuzino National Military Medical Institute for Research and Development, Bucharest, Romania
| | | | - Beatrix Oroszi
- National Laboratory for Health Security, Epidemiology and Surveillance Centre, Semmelweis University, Budapest, Hungary
| | - Maja Ilić
- Croatian Institute of Public Health (CIPH), Zagreb, Croatia
| | | | - Aryse Melo
- Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | | | - Camino Trobajo-Sanmartín
- Instituto de Salud Pública de Navarra - IdiSNA, Pamplona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Vincent Enouf
- Institut Pasteur, Pasteur International Bioresources network (PIBnet), Plateforme de Microbiologie Mutualisée (P2M), Paris, France
- Institut Pasteur, Centre National de Référence Virus des Infections Respiratoires (CNR VIR), Paris, France
| | - Adele McKenna
- Health Protection Surveillance Centre, Dublin, Ireland
| | - Gloria Pérez-Gimeno
- National Centre of Epidemiology, CIBERESP, Carlos III Health Institute, Madrid, Spain
| | - Luise Goerlitz
- Department for Infectious Disease Epidemiology, Respiratory Infections Unit, Robert Koch Institute, Berlin, Germany
| | - Marit de Lange
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Mihaela Lazar
- Cantacuzino National Military Medical Institute for Research and Development, Bucharest, Romania
| | | | - Gergő Túri
- National Laboratory for Health Security, Epidemiology and Surveillance Centre, Semmelweis University, Budapest, Hungary
| | - Jesús Castilla
- Instituto de Salud Pública de Navarra - IdiSNA, Pamplona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | | | - Charlene Bennett
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Virtudes Gallardo
- Dirección General de Salud Pública y Ordenación Farmacéutica, Junta de Andalucía, Sevilla, Spain
| | - Ralf Dürrwald
- National Reference Centre for Influenza, Robert Koch Institute, Berlin, Germany
| | - Dirk Eggink
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Raquel Guiomar
- Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | | | | | - Judit Krisztina Horváth
- National Laboratory for Health Security, Epidemiology and Surveillance Centre, Semmelweis University, Budapest, Hungary
| | - Itziar Casado
- Instituto de Salud Pública de Navarra - IdiSNA, Pamplona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Mª Del Carmen García
- Subdirección de Epidemiología, Dirección General de Salud Pública, Servicio Extremeño de Salud, Mérida, Spain
| | | | - Ausenda Machado
- Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Sabrina Bacci
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Marlena Kaczmarek
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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Sarkar A, Omar S, Alshareef A, Fanous K, Sarker S, Alroobi H, Zamir F, Yousef M, Zakaria D. The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review. Hum Vaccin Immunother 2023; 19:2212568. [PMID: 37254497 DOI: 10.1080/21645515.2023.2212568] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
The Omicron variant of SARS-CoV-2 was detected in October 2021 and exhibited high transmissibility, immune evasion, and reduced severity when compared to the earlier variants. The lesser vaccine effectiveness against Omicron and its reduced severity created vaccination hesitancy among the public. This review compiled data reporting the relative prevalence of Omicron as compared to the early variants to give an insight into the existing variants, which may shape the decisions regarding the targets of the newly developed vaccines. Complied data revealed more than 90% prevalence within the infected cohorts in some countries. The BA.1 subvariant predominated over the BA.2 during the early stages of the Omicron wave. Moreover, BA.4/BA.5 subvariants were detected in South Africa, USA and Italy between October 2021 and April 2022. It is therefore important to develop vaccines that protect against Omicron as well as the early variants, which are known to cause more severe complications.
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Affiliation(s)
| | - Sara Omar
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Aya Alshareef
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Kareem Fanous
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Shaunak Sarker
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Hasan Alroobi
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Fahad Zamir
- Premedical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Mahmoud Yousef
- Premedical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Dalia Zakaria
- Premedical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
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4
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Zeng Y, Xia F, Guo C, Hu C, Li Y, Wang X, Wu Q, Chen Z, Lu J, Wang Z. Virological Characteristics of Five SARS-CoV-2 Variants, Including Beta, Delta and Omicron BA.1, BA.2, BA.5. Viruses 2023; 15:2394. [PMID: 38140635 PMCID: PMC10747097 DOI: 10.3390/v15122394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) show increasing transmissibility and infectivity and induce substantial injuries to human health and the ecology. Therefore, it is vital to understand the related features for controlling infection. In this study, SARS-CoV-2 WIV04 (prototype) and five VOCs (Beta, Delta, Omicron BA.1, BA.2 and BA.5 variants) were inoculated in Vero cells to observe their growth activities. Apart from evaluating the environmental stability at different temperatures, residual virus titers and infectivity at different temperatures (4 °C, room temperature (RT) and 37 °C) were measured over 7 days. The experiment also assessed the infectivity for different incubation durations. The growth capacity assay suggested that the WIV04, Beta and Delta variants replicated efficiently in Vero cells compared with Omicron Variants, and BA.2 replicated more efficiently in Vero cells than BA.1 and BA.5. In addition, all variants exhibited longer survivals at 4 °C and could remain infectious after 7 days, compared to RT' survival after 5 days and at 37 °C after 1 day. The virus infection assay indicated that the Omicron variant had a weaker ability to infect cells compared to the WIV04, Beta and Delta strains, and a longer infection time was required for these strains, except for BA.2.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jia Lu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (Y.Z.); (F.X.); (C.G.); (C.H.); (Y.L.); (X.W.); (Q.W.); (Z.C.)
| | - Zejun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (Y.Z.); (F.X.); (C.G.); (C.H.); (Y.L.); (X.W.); (Q.W.); (Z.C.)
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5
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de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron ( BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023; 37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
Abstract
Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
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Kimura I, Yamasoba D, Nasser H, Ito H, Zahradnik J, Wu J, Fujita S, Uriu K, Sasaki J, Tamura T, Suzuki R, Deguchi S, Plianchaisuk A, Yoshimatsu K, Kazuma Y, Mitoma S, Schreiber G, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Takaori-Kondo A, Ito J, Shirakawa K, Takayama K, Irie T, Hashiguchi T, Nakagawa S, Fukuhara T, Saito A, Ikeda T, Sato K. Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics. J Virol 2023; 97:e0101123. [PMID: 37796123 PMCID: PMC10781145 DOI: 10.1128/jvi.01011-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/16/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Most studies investigating the characteristics of emerging SARS-CoV-2 variants have been focusing on mutations in the spike proteins that affect viral infectivity, fusogenicity, and pathogenicity. However, few studies have addressed how naturally occurring mutations in the non-spike regions of the SARS-CoV-2 genome impact virological properties. In this study, we proved that multiple SARS-CoV-2 Omicron BA.2 mutations, one in the spike protein and another downstream of the spike gene, orchestrally characterize this variant, shedding light on the importance of Omicron BA.2 mutations out of the spike protein.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daichi Yamasoba
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Faculty of Medicine, Kobe University, Kobe, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuya Mitoma
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - The Genotype to Phenotype Japan (G2P-Japan) Consortium
MisawaNaoko1KosugiYusuke1PanLin1SuganamiMai1ChibaMika1YoshimuraRyo1YasudaKyoko1IidaKeiko1OhsumiNaomi1StrangeAdam P.1KakuYu1PlianchaisukArnon1GuoZiyi1HinayAlfredo Jr. Amolong1Mendoza TolentinoJarel Elgin1ChenLuo1ShimizuRyo2Monira BegumM. S. T.2TakahashiOtowa2IchiharaKimiko2JonathanMichael2MugitaYuka2SuzukiSaori3SuzukiTateki4KimuraKanako4NakajimaYukari4YajimaHisano4HashimotoRina4WatanabeYukio4SakamotoAyaka4YasuharaNaoko4NagataKayoko4NomuraRyosuke4HorisawaYoshihito4TashiroYusuke4KawaiYugo4ShibataniYuki5NishiuchiTomoko5YoshidaIsao6KawabataRyoko7MatsunoKeita8NaoNaganori9SawaHirofumi9TanakaShinya10TsudaMasumi10WangLei10OdaYoshikata10FerdousZannatul10ShishidoKenji10MotozonoChihiro11ToyodaMako11UenoTakamasa11TabataKaori12Institute of Medical Science, University of Tokyo, Tokyo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, JapanHokkaido University, Sapporo, JapanKyoto University, Kyoto, JapanUniversity of Miyazaki, Miyazaki, JapanTokyo Metropolitan Institute of Public Health, Tokyo, JapanHiroshima University, Hiroshima, JapanOne Health Research Center, Hokkaido University, Sapporo, JapanInternational Institute for Zoonosis Control, Hokkaido University, Sapporo, JapanHokkaido University, Sapporo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto, JapanKyushu University, Fukuoka, Japan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Faculty of Medicine, Kobe University, Kobe, Japan
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
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7
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Osterman A, Krenn F, Iglhaut M, Badell I, Lehner A, Späth PM, Stern M, Both H, Bender S, Muenchhoff M, Graf A, Krebs S, Blum H, Grimmer T, Durner J, Czibere L, Dächert C, Grzimek-Koschewa N, Protzer U, Kaderali L, Baldauf HM, Keppler OT. Automated antigen assays display a high heterogeneity for the detection of SARS-CoV-2 variants of concern, including several Omicron sublineages. Med Microbiol Immunol 2023; 212:307-322. [PMID: 37561226 PMCID: PMC10501957 DOI: 10.1007/s00430-023-00774-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Diagnostic tests for direct pathogen detection have been instrumental to contain the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Automated, quantitative, laboratory-based nucleocapsid antigen (Ag) tests for SARS-CoV-2 have been launched alongside nucleic acid-based test systems and point-of-care (POC) lateral-flow Ag tests. Here, we evaluated four commercial Ag tests on automated platforms for the detection of different sublineages of the SARS-CoV-2 Omicron variant of concern (VoC) (B.1.1.529) in comparison with "non-Omicron" VoCs. A total of 203 Omicron PCR-positive respiratory swabs (53 BA.1, 48 BA.2, 23 BQ.1, 39 XBB.1.5 and 40 other subvariants) from the period February to March 2022 and from March 2023 were examined. In addition, tissue culture-expanded clinical isolates of Delta (B.1.617.2), Omicron-BA.1, -BF.7, -BN.1 and -BQ.1 were studied. These results were compared to previously reported data from 107 clinical "non-Omicron" samples from the end of the second pandemic wave (February to March 2021) as well as cell culture-derived samples of wildtype (wt) EU-1 (B.1.177), Alpha VoC (B.1.1.7) and Beta VoC (B.1.351)). All four commercial Ag tests were able to detect at least 90.9% of Omicron-containing samples with high viral loads (Ct < 25). The rates of true-positive test results for BA.1/BA.2-positive samples with intermediate viral loads (Ct 25-30) ranged between 6.7% and 100.0%, while they dropped to 0 to 15.4% for samples with low Ct values (> 30). This heterogeneity was reflected also by the tests' 50%-limit of detection (LoD50) values ranging from 44,444 to 1,866,900 Geq/ml. Respiratory samples containing Omicron-BQ.1/XBB.1.5 or other Omicron subvariants that emerged in 2023 were detected with enormous heterogeneity (0 to 100%) for the intermediate and low viral load ranges with LoD50 values between 23,019 and 1,152,048 Geq/ml. In contrast, detection of "non-Omicron" samples was more sensitive, scoring positive in 35 to 100% for the intermediate and 1.3 to 32.9% of cases for the low viral loads, respectively, corresponding to LoD50 values ranging from 6181 to 749,792 Geq/ml. All four assays detected cell culture-expanded VoCs Alpha, Beta, Delta and Omicron subvariants carrying up to six amino acid mutations in the nucleocapsid protein with sensitivities comparable to the non-VoC EU-1. Overall, automated quantitative SARS-CoV-2 Ag assays are not more sensitive than standard rapid antigen tests used in POC settings and show a high heterogeneity in performance for VoC recognition. The best of these automated Ag tests may have the potential to complement nucleic acid-based assays for SARS-CoV-2 diagnostics in settings not primarily focused on the protection of vulnerable groups. In light of the constant emergence of new Omicron subvariants and recombinants, most recently the XBB lineage, these tests' performance must be regularly re-evaluated, especially when new VoCs carry mutations in the nucleocapsid protein or immunological and clinical parameters change.
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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
| | - Franziska Krenn
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Iglhaut
- 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
| | - Andreas Lehner
- 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 Both
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sabine Bender
- 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, 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
| | - Timo Grimmer
- Department of Psychiatry and Psychotherapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Munich, Germany
| | | | - Christopher Dächert
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Natascha Grzimek-Koschewa
- 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, Germany
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum 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, Germany.
- COVID‑19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Reddy KRC, Sahni C, Singh R, Chandana H, Sharma R. Ayurvedic medicines in alleviating the symptoms of SARS-CoV-2 omicron variant in North Indian population: a regional genomic study. Drug Metab Pers Ther 2023; 38:289-291. [PMID: 37062805 DOI: 10.1515/dmpt-2023-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/27/2023] [Indexed: 04/18/2023]
Affiliation(s)
- Konduru Rama Chandra Reddy
- Department of Rasa shastra & Bhaishajya kalpana, Faculty of Ayurveda, Institute of Medical sciences, Banaras Hindu university, Varanasi, Uttar Pradesh, India
| | - Chetan Sahni
- Department of Anatomy, Institute of Medical sciences,Banaras Hindu university, Varanasi, Uttar Pradesh, India
| | - Royana Singh
- Department of Anatomy, Institute of Medical sciences,Banaras Hindu university, Varanasi, Uttar Pradesh, India
| | - Hari Chandana
- Vydehi Institute of Medical Sciences and Research Centre is in Whitefield, Bangalore, India
| | - Rohit Sharma
- Department of Rasa shastra & Bhaishajya kalpana, Faculty of Ayurveda, Institute of Medical sciences, Banaras Hindu university, Varanasi, Uttar Pradesh, India
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10
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Andrade-Molina DA, Morey-León GA, Muñoz-Mawyin KE, Cruz-Fatuly FF, Fernández-Cadena JC, Cárdenas P. First sequenced cases of Omicron BA.2 sublineage in Ecuador. Virus Res 2023; 334:199169. [PMID: 37406934 PMCID: PMC10410591 DOI: 10.1016/j.virusres.2023.199169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
The largest wave of infection with SARS-CoV-2 virus in Ecuador was observed in mid-December 2021 and early January 2022, driven by B.1.1.529/BA (Omicron) variant. During the second half of March, an increase in the number of daily cases was observed and coincided with the emergence of the BA.2 variant, which we describe in the present study. The first sequenced five cases of SARS-CoV-2 21L/BA.2 in Ecuador were identified using variant specific genotyping by qPCR and confirmed by whole genome sequencing (WGS). The first sequenced Ecuadorian BA.2 isolate was obtained from a person with international travel history who became symptomatic 3 days after travelling, whereas in the other cases no travel history was recorded.
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Affiliation(s)
- D A Andrade-Molina
- Omics Sciences Laboratory, Faculty of Health Sciences, Universidad Espíritu Santo, Samborondón, Ecuador.
| | - G A Morey-León
- Faculty of Health Sciences, Universidad de Guayaquil, Guayaquil, Ecuador
| | - K E Muñoz-Mawyin
- Omics Sciences Laboratory, Faculty of Health Sciences, Universidad Espíritu Santo, Samborondón, Ecuador
| | - F F Cruz-Fatuly
- Omics Sciences Laboratory, Faculty of Health Sciences, Universidad Espíritu Santo, Samborondón, Ecuador
| | | | - P Cárdenas
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
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11
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Alexiev I, Ivanov I, Giovanetti M, Cella E, Stoikov I, Donchev D, Grigorova L, Gancheva A, Dimitrova R, Scarpa F, Korsun N, Trifonova I, Dobrinov V, Kantardjiev T, Christova I, Ciccozzi M. Early Detection of the Recombinant SARS-CoV-2 XAN Variant in Bulgaria: Initial Genomic Insights into Yet Another Piece of the Growing Puzzle of Recombinant Clades. Microorganisms 2023; 11:2041. [PMID: 37630601 PMCID: PMC10457977 DOI: 10.3390/microorganisms11082041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/29/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The first recombinant SARS-CoV-2 variants were identified in 2022, causing public health concerns. The importance of recombinant variants has increased especially since the WHO designated the recombinant variant XBB and its lineages as subvariants that require monitoring on 20 November 2022. In this study, we provide the first insights into the new SARS-CoV-2 variant named XAN, a recombinant composed of Omicron sub-lineages BA.2 and BA.5. To our knowledge, this is the first report on the recombinant SARS-CoV-2 XAN variant identified in Bulgaria.
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Affiliation(s)
- Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Ivan Ivanov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Marta Giovanetti
- Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil;
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA;
| | - Ivan Stoikov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Deyan Donchev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Lyubomira Grigorova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Anna Gancheva
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Reneta Dimitrova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Neli Korsun
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Ivelina Trifonova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Veselin Dobrinov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Todor Kantardjiev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Iva Christova
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (I.S.); (D.D.); (L.G.); (A.G.); (R.D.); (N.K.); (I.T.); (V.D.); (T.K.); (I.C.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
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12
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Bozidis P, Petridi E, Gartzonika K. An ARMS-Multiplex PCR Targeting SARS-CoV-2 Omicron Sub-Variants. Pathogens 2023; 12:1017. [PMID: 37623977 PMCID: PMC10459702 DOI: 10.3390/pathogens12081017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
As of November 2021, the SARS-CoV-2 Omicron variant had made its appearance, gradually replacing the predominant Delta variant. Since its emergence, the Omicron variant has been continuously evolving through more than 500 strains, most of which belong to five sub-variants known as BA.1, BA.2, BA.3, BA.4, and BA.5. The aim of this study was to develop a multiplex polymerase chain reaction (PCR) that will be able to distinguish the basic sub-variants of Omicron in a rapid and specific way. Full genome sequences of Omicron strains with high frequency and wide geographical distribution were retrieved by the NCBI Virus and ENA databases. These sequences were compared to each other in order to locate single nucleotide polymorphisms common to all strains of the same sub-variant. These polymorphisms should also be capable of distinguishing Omicron sub-variants not only from each other but from previously circulating variants of SARS-CoV-2 as well. Thus, specific primers targeting characteristic polymorphisms of the four Omicron main branches BA.1, BA.2, BA.4, and BA.5 were designed according to the principles of the amplification refractory mutation system (ARMS) and with the ability to react under multiplex PCR conditions. According to our results, the ARMS-multiplex PCR could successfully distinguish all Omicron sub-variants that carry the corresponding mutations.
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Affiliation(s)
- Petros Bozidis
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.P.); (K.G.)
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13
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Chung HY, Jian MJ, Chang CK, Lin JC, Yeh KM, Chen CW, Hsieh SS, Hung KS, Chen CS, Tang SH, Perng CL, Chang FY, Wang CH, Hung YJ, Shang HS. Accelerating pandemic response with the emergency Omicron RT-PCR test: A comprehensive solution for COVID-19 diagnosis and tracking. J Med Virol 2023; 95:e28914. [PMID: 37394776 DOI: 10.1002/jmv.28914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 07/04/2023]
Abstract
The Omicron variant of concern (VOC) has surged in many countries and replaced the previously reported VOC. To identify different Omicron strains/sublineages on a rapid, convenient, and precise platform, we report a novel multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) method in one tube based on the Omicron lineage sequence variants' information. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) subvariants were used in a PCR-based assay for rapid identification of Omicron sublineage genotyping in 1000 clinical samples. Several characteristic mutations were analyzed using specific primers and probes for the spike gene, del69-70, and F486V. To distinguish Omicron sublineages (BA.2, BA.4, and BA.5), the NSP1:141-143del in the ORF1a region and D3N mutation in membrane protein occurring outside the spike protein region were analyzed. Results from the real-time PCR assay for one-tube accuracy were compared to those of whole genome sequencing. The developed PCR assay was used to analyze 400 SARS-CoV-2 positive samples. Ten samples determined as BA.4 were positive for NSP1:141-143del, del69-70, and F486V mutations; 160 BA.5 samples were positive for D3N, del69-70, and F486V mutations, and 230 BA.2 samples were without del69-70. Screening these samples allowed the identification of epidemic trends at different time intervals. Our novel one-tube multiplex PCR assay was effective in identifying Omicron sublineages.
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Affiliation(s)
- Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chi-Sheng Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Hung Wang
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yi-Jen Hung
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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14
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Shahab M, Akter S, Sarkar MMH, Banu TA, Goswami B, Chowdhury SF, Naser SR, Habib MA, Shaikh AA, Saki M, Zheng G, Khan MS. Computational design of medicinal compounds to inhibit RBD-hACE2 interaction in the Omicron variant: unveiling a vulnerable target site. Inform Med Unlocked 2023; 40:101281. [PMID: 37265644 PMCID: PMC10210851 DOI: 10.1016/j.imu.2023.101281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/03/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has globally affected both human health and economy. Several variants with a high potential for reinfection and the ability to evade immunity were detected shortly after the initial reported case of COVID-19. A total of 30 mutations in the spike protein (S) have been reported in the SARS-CoV-2 (BA.2) variant in India and South Africa, while half of these mutations are in the receptor-binding domain and have spread rapidly throughout the world. Drug repurposing offers potential advantages over the discovery of novel drugs, and one is that it can be delivered quickly without lengthy assessments and time-consuming clinical trials. In this study, computational drug design, such as pharmacophore-based virtual screening and MD simulation has been concentrated, in order to find a novel small molecular inhibitor that prevents hACE2 from binding to the receptor binding domain (RBD). three medicinal compound databases: North-East African, North African, and East African were screened and carried out a multi-step screening approach that identified three compounds, which are thymoquinol 2-O-beta-glucopyranoside (C1), lanneaflavonol (C2), and naringenin-4'-methoxy-7-O-Alpha-L-rhamnoside (C3), with excellent anti-viral properties against the RBD of the omicron variant. Furthermore, PAIN assay interference, computation bioactivity prediction, binding free energy, and dissociation constant were used to validate the top hits, which indicated good antiviral activity. The three compounds that were found may be useful against COVID-19, though more research is required. These findings could aid the development of novel therapeutic drugs against the emerging Omicron variant of SARS-CoV-2.
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Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Showti Raheel Naser
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Aftab Ali Shaikh
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Md Salim Khan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
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15
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Nair MS, Huang Y, Wang M, Weathers PJ. SARS-CoV-2 omicron variants are susceptible in vitro to Artemisia annua hot water extracts. J Ethnopharmacol 2023; 308:116291. [PMID: 36804200 PMCID: PMC9937997 DOI: 10.1016/j.jep.2023.116291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 06/05/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Artemisia annua L. has >2000 yr of history in treating fever a symptom common to many infectious diseases including viruses. The plant is widely used as a tea infusion in many areas of the globe to thwart many infectious diseases. AIM OF THE STUDY The SARS-CoV-2 (COVID-19) virus continues to infect millions while rapidly evolving new variants that are more transmissible and evade vaccine-elicited antibodies, e.g., omicron and its subvariants. Having shown potency against all previously tested variants, A. annua L. extracts were further tested against highly infectious omicron and its recent subvariants. MATERIALS AND METHODS Using Vero E6 cells, we measured the in vitro efficacy (IC50) of stored (frozen) dried-leaf hot-water A. annua L. extracts of four cultivars (A3, BUR, MED, and SAM) against SARS-CoV-2 variants: original WA1 (WT), BA.1 (omicron), BA.2, BA.2.12.1, and BA.4. End point virus titers of infectivity in cv. BUR-treated human lung A459 cells overexpressing hu-ACE2 were determined for both WA1 and BA.4 viruses. RESULTS When normalized to the artemisinin (ART) or leaf dry weight (DW) equivalent of the extract, the IC50 values ranged from 0.5 to 16.5 μM ART and from 20 to 106 μg DW. IC50 values were within limits of assay variation of our earlier studies. End-point titers confirmed a dose-response inhibition in ACE2 overexpressing human lung cells to the BUR cultivar. Cell viability losses were not measurable at leaf dry weights ≤50 μg for any cultivar extract. CONCLUSIONS A. annua hot-water extracts (tea infusions) continue to show efficacy against SARS-CoV-2 and its rapidly evolving variants and deserve greater attention as a possible cost-effective therapeutic.
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Affiliation(s)
- M S Nair
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, USA.
| | - Y Huang
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, USA.
| | - M Wang
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, USA.
| | - P J Weathers
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.
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16
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Ulhuq FR, Barge M, Falconer K, Wild J, Fernandes G, Gallagher A, McGinley S, Sugadol A, Tariq M, Maloney D, Kenicer J, Dewar R, Templeton K, McHugh MP. Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations. Microb Genom 2023; 9:mgen000991. [PMID: 37083576 PMCID: PMC10210939 DOI: 10.1099/mgen.0.000991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/22/2023] [Indexed: 04/22/2023] Open
Abstract
The ARTIC protocol uses a multiplexed PCR approach with two primer pools tiling the entire SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genome. Primer pool updates are necessary for accurate amplicon sequencing of evolving SARS-CoV-2 variants with novel mutations. The suitability of the ARTIC V4 and updated V4.1 primer scheme was assessed using whole genome sequencing of Omicron from clinical samples using Oxford Nanopore Technology. Analysis of Omicron BA.1 genomes revealed that 93.22 % of clinical samples generated improved genome coverage at 50× read depth with V4.1 primers when compared to V4 primers. Additionally, the V4.1 primers improved coverage of BA.1 across amplicons 76 and 88, which resulted in the detection of the variant-defining mutations G22898A, A26530G and C26577G. The Omicron BA.2 sub-variant (VUI-22JAN-01) replaced BA.1 as the dominant variant by March 2022, and analysis of 168 clinical samples showed reduced coverage across amplicons 15 and 75. Upon further interrogation of primer binding sites, a mutation at C4321T [present in 163/168 (97 %) of samples] was identified as a possible cause of complete dropout of amplicon 15. Furthermore, two mutations were identified within the primer binding regions for amplicon 75: A22786C (present in 90 % of samples) and C22792T (present in 12.5 % of samples). Together, these mutations may result in reduced coverage of amplicon 75, and further primer updates would allow the identification of the two BA.2-defining mutations present in amplicon 75: A22688G and T22679C. This work highlights the need for ongoing surveillance of primer matches as circulating variants evolve and change.
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Affiliation(s)
- Fatima R. Ulhuq
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Madhuri Barge
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Kerry Falconer
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Goncalo Fernandes
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Abbie Gallagher
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Suzie McGinley
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Ahmad Sugadol
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Muhammad Tariq
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Daniel Maloney
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Juliet Kenicer
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Rebecca Dewar
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Kate Templeton
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
| | - Martin P. McHugh
- Viral Genotyping Reference Laboratory, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, EH16 4SA, UK
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK
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17
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Alcantara MC, Higuchi Y, Kirita Y, Matoba S, Hoshino A. Deep Mutational Scanning to Predict Escape from Bebtelovimab in SARS-CoV-2 Omicron Subvariants. Vaccines (Basel) 2023; 11:vaccines11030711. [PMID: 36992294 DOI: 10.3390/vaccines11030711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
The major concern with COVID-19 therapeutic monoclonal antibodies is the loss of efficacy against continuously emerging variants of SARS-CoV-2. To predict antibody efficacy against future Omicron subvariants, we conducted deep mutational scanning (DMS) encompassing all single mutations of the receptor-binding domain of the BA.2 strain utilizing an inverted infection assay with an ACE2-harboring virus and library spike-expressing cells. In the case of bebtelovimab, which preserves neutralization activity against BA.2 and BA.5, a broad range of amino acid substitutions at K444, V445, and G446, and some substitutions at P499 and T500, were indicated to achieve the antibody escape. Among subvariants with current rises in case numbers, BA2.75 with G446S partially evaded neutralization by bebtelovimab, while complete evasion was observed in XBB with V445P and BQ.1 with K444T. This is consistent with the DMS results against BA.2, highlighting the potential of DMS as a predictive tool for antibody escape.
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Affiliation(s)
- Mellissa C Alcantara
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Yusuke Higuchi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
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18
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Scutari R, Fox V, De Ioris MA, Fini V, Granaglia A, Costabile V, Colagrossi L, Russo C, Mastronuzzi A, Locatelli F, Perno CF, Alteri C. A case of SARS-CoV-2 Omicron reinfection resulting in a significant immunity boost in a paediatric patient affected by B-cell acute lymphoblastic leukemia. BMC Infect Dis 2023; 23:133. [PMID: 36882724 PMCID: PMC9990052 DOI: 10.1186/s12879-023-08111-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/21/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Since its emergence in November 2021, SARS-CoV-2 Omicron clade has quickly become dominant, due to its increased transmissibility and immune evasion. Different sublineages are currently circulating, which differ in mutations and deletions in regions of the SARS-CoV-2 genome implicated in the immune response. In May 2022, BA.1 and BA.2 were the most prevalent sublineages in Europe, both characterized by ability of evading natural acquired and vaccine-induced immunity and of escaping monoclonal antibodies neutralization. CASE PRESENTATION A 5-years old male affected by B-cell acute lymphoblastic leukemia in reinduction was tested positive for SARS-CoV-2 by RT-PCR at the Bambino Gesù Children Hospital in Rome in December 2021. He experienced a mild COVID-19 manifestation, and a peak of nasopharyngeal viral load corresponding to 15.5 Ct. Whole genome sequencing identified the clade 21 K (Omicron), sublineage BA.1.1. The patient was monitored over time and tested negative for SARS-CoV-2 after 30 days. Anti-S antibodies were detected positive with modest titre (3.86 BAU/mL), while anti-N antibodies were negative. 74 days after the onset of the first infection and 23 days after the last negative test, the patient was readmitted to hospital with fever, and tested positive for SARS-CoV-2 by RT-PCR (peak of viral load corresponding to 23.3 Ct). Again, he experienced a mild COVID-19. Whole genome sequencing revealed an infection with the Omicron lineage BA.2 (21L clade). Sotrovimab administration was started at the fifth day of positivity, and RT-PCR negativity occurred 10 days later. Surveillance SARS-CoV-2 RT-PCR were persistently negative, and in May 2022, anti-N antibodies were found positive and anti-S antibodies reached titres > 5000 BAU/mL. CONCLUSIONS By this clinical case, we showed that SARS-CoV-2 reinfection within the Omicron clade can occur and can be correlated to inadequate immune responses to primary infection. We also showed that the infection's length was shorter in the second respect to first episode, suggesting that pre-existing T cell-mediated immunity, though not preventing re-infection, might have limited the SARS-CoV-2 replication capacity. Lastly, Sotrovimab treatment retained activity against BA.2, probably accelerating the viral clearance in the second infectious episode, after which seroconversion and increase of anti-S antibodies titres were observed.
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Affiliation(s)
- Rossana Scutari
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Fox
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Antonietta De Ioris
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Vanessa Fini
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Annarita Granaglia
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valentino Costabile
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Luna Colagrossi
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristina Russo
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Carlo Federico Perno
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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19
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Jäger M, Diem G, Sahanic S, Fux V, Griesmacher A, Lass-Flörl C, Wilflingseder D, Tancevski I, Posch W. Immunity of heterologous and homologous boosted or convalescent individuals against Omicron BA.1, BA.2 and BA.4/5 variants. J Infect Dis 2023:7069351. [PMID: 36869832 DOI: 10.1093/infdis/jiad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND The emerged SARS-CoV-2 Omicron variants BA.1, BA.2 and BA.4/5 demonstrate higher transmission and infection compared to previous variants of concern. To evaluate effectiveness of heterologous and homologous booster vaccination, we directly compared cellular and humoral immune responses as well as neutralizing capacity against replication-competent SARS-CoV-2 wild type, Delta and Omicron variants BA.1, BA.2, BA.4/5. METHODS For this, peripheral blood mononuclear cells (PBMCs) and serum samples of 137 participants divided into three major groups were investigated. Individuals of the first group were twice ChAdOx1 vaccinated and mRNA (BNT162b2 or mRNA-1273)-boosted, the second group included triple mRNA vaccinated participants and the third group consisted of twice vaccinated and convalescent individuals. RESULTS Vaccination and convalescence resulted in the highest levels of SARS-CoV-2-specific antibodies, stronger T cell responses and best neutralization against WT, Delta Omicron BA.2 and BA.4/5, while a combination of twice ChAdOx1 and BNT162b2-vaccinated regimen displayed elevated neutralizing capacity against Omicron BA.1. In addition, heterologous boosted individuals showed higher efficacy against Omicron BA.2 as well as BA.4/5 compared to homologous booster regimens. CONCLUSIONS We here showed that twice vaccinated and convalescent individuals demonstrated the strongest immunity against Omicron BA.2 and BA.4/5 variant followed by heterologous and homologous booster vaccine regimens.
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Affiliation(s)
- Michael Jäger
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriel Diem
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sabina Sahanic
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Vilmos Fux
- Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria
| | - Andrea Griesmacher
- Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ivan Tancevski
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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20
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Kislaya I, Casaca P, Borges V, Sousa C, Ferreira BI, Fonte A, Fernandes E, Dias CM, Duarte S, Almeida JP, Grenho I, Coelho L, Ferreira R, Ferreira PP, Borges CM, Isidro J, Pinto M, Menezes L, Sobral D, Nunes A, Santos D, Gonçalves AM, Vieira L, Gomes JP, Leite PP, Nunes B, Machado A, Peralta-Santos A. Comparative Effectiveness of COVID-19 Vaccines in Preventing Infections and Disease Progression from SARS-CoV-2 Omicron BA.5 and BA.2, Portugal. Emerg Infect Dis 2023; 29:569-575. [PMID: 36737101 PMCID: PMC9973705 DOI: 10.3201/eid2903.221367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We estimated comparative primary and booster vaccine effectiveness (VE) of SARS-CoV-2 Omicron BA.5 and BA.2 lineages against infection and disease progression. During April-June 2022, we implemented a case-case and cohort study and classified lineages using whole-genome sequencing or spike gene target failure. For the case-case study, we estimated the adjusted odds ratios (aORs) of vaccination using a logistic regression. For the cohort study, we estimated VE against disease progression using a penalized logistic regression. We observed no reduced VE for primary (aOR 1.07 [95% CI 0.93-1.23]) or booster (aOR 0.96 [95% CI 0.84-1.09]) vaccination against BA.5 infection. Among BA.5 case-patients, booster VE against progression to hospitalization was lower than that among BA.2 case-patients (VE 77% [95% CI 49%-90%] vs. VE 93% [95% CI 86%-97%]). Although booster vaccination is less effective against BA.5 than against BA.2, it offers substantial protection against progression from BA.5 infection to severe disease.
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Affiliation(s)
| | | | - Vítor Borges
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Carlos Sousa
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Bibiana I. Ferreira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Ana Fonte
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Eugénia Fernandes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Carlos Matias Dias
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Sílvia Duarte
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - José Pedro Almeida
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Inês Grenho
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Luís Coelho
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Rita Ferreira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Patrícia Pita Ferreira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Cláudia Medeiros Borges
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Joana Isidro
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Miguel Pinto
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Luís Menezes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Daniel Sobral
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Alexandra Nunes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Daniela Santos
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - António Maia Gonçalves
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Luís Vieira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - João Paulo Gomes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Pedro Pinto Leite
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
| | - Baltazar Nunes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, C. Matias Dias, S. Duarte, L. Coelho, R. Ferreira, J. Isidro, M. Pinto, D. Sobral, A. Nunes, D. Santos, L. Vieira, J.P. Gomes, B. Nunes, A. Machado)
- Comprehensive Health Research Centre, Lisbon (I. Kislaya, C. Matias Dias, B. Nunes, A. Machado, A. Peralta-Santos)
- Direção-Geral da Saúde, Lisbon (P. Casaca, E. Fernandes, P. Pita Ferreira, P. Pinto Leite, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida, L. Menezes, A. Maia Gonçalves)
- Algarve Biomedical Center Research Institute, Faro, Portugal (B.I. Ferreira, I. Grenho)
- Administração Central do Sistema de Saúde, Lisbon (A. Fonte, C.M. Borges)
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Zhou R, Liu N, Li X, Peng Q, Yiu CK, Huang H, Yang D, Du Z, Kwok HY, Au KK, Cai JP, Fan-Ngai Hung I, Kai-Wang To K, Xu X, Yuen KY, Chen Z. Three-dose vaccination-induced immune responses protect against SARS-CoV-2 Omicron BA.2: a population-based study in Hong Kong. Lancet Reg Health West Pac 2023; 32:100660. [PMID: 36591327 PMCID: PMC9786166 DOI: 10.1016/j.lanwpc.2022.100660] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
Abstract
Background The ongoing outbreak of SARS-CoV-2 Omicron BA.2 infections in Hong Kong, the model city of universal masking of the world, has resulted in a major public health crisis. Although the third vaccination resulted in strong boosting of neutralization antibody, vaccine efficacy and correlate of immune protection against the major circulating Omicron BA.2 remain to be investigated. Methods We investigated the vaccine efficacy against the Omicron BA.2 breakthrough infection among 470 public servants who had received different SARS-CoV-2 vaccine regimens including two-dose BNT162b2 (2 × BNT, n = 169), three-dose BNT162b2 (3 × BNT, n = 168), two-dose CoronaVac (2 × CorV, n = 34), three-dose CoronaVac (3 × CorV, n = 67) and third-dose BNT162b2 following 2 × CorV (2 × CorV+1BNT, n = 32). Humoral and cellular immune responses after three-dose vaccination were further characterized and correlated with clinical characteristics of BA.2 infection. Findings During the BA.2 outbreak, 27.7% vaccinees were infected. The timely third-dose vaccination provided significant protection with lower incidence rates of breakthrough infections (2 × BNT 46.2% vs 3 × BNT 13.1%, p < 0.0001; 2 × CorV 44.1% vs 3 × CorV 19.4%, p = 0.003). Investigation of immune responses on blood samples derived from 90 subjects in three-dose vaccination cohorts collected before the BA.2 outbreak revealed that the third-dose vaccination activated spike (S)-specific memory B cells and Omicron cross-reactive T cell responses, which correlated with reduced frequencies of breakthrough infections and disease severity rather than with types of vaccines. Moreover, the frequency of S-specific activated memory B cells was significantly lower in infected vaccinees than uninfected vaccinees before vaccine-breakthrough infection whereas IFN-γ+ CD4 T cells were negatively associated with age and viral clearance time. Critically, BA.2 breakthrough infection boosted cross-reactive memory B cells with enhanced cross-neutralizing antibodies to Omicron sublineages, including BA.2.12.1 and BA.4/5, in all vaccinees tested. Interpretation Our results imply that the timely third vaccination and immune responses are likely required for vaccine-mediated protection against Omicron BA.2 pandemic. Although BA.2 conferred the highest neutralization resistance compared with variants of concern tested before the emergence of BA.2.12.1 and BA.4/5, the third dose vaccination-activated S-specific memory B cells and Omicron cross-reactive T cell responses contributed to reduced frequencies of breakthrough infection and disease severity. Neutralizing antibody potency enhanced by BA.2 breakthrough infection in vaccinees with prior 3 doses of CoronaVac or BNT162b2 may reduce the risk of infection against ongoing BA.2.12.1 and BA.4/5. Funding Hong Kong Research Grants Council Collaborative Research Fund, Health and Medical Research Fund, Wellcome Trust, Shenzhen Science and Technology Program, the Health@InnoHK, Innovation and Technology Commission of Hong Kong, China, National Program on Key Research Project, Emergency Key Program of Guangzhou Laboratory, donations from the Friends of Hope Education Fund and the Hong Kong Theme-Based Research Scheme.
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Affiliation(s)
- Runhong Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Na Liu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Xin Li
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of a China
| | - Qiaoli Peng
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Cheuk-Kwan Yiu
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Haode Huang
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Dawei Yang
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Zhenglong Du
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hau-Yee Kwok
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ka-Kit Au
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Jian-Piao Cai
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of a China
| | - Xiaoning Xu
- Centre for Immunology & Vaccinology, Chelsea and Westminster Hospital, Department of Medicine, Imperial College London, London, United Kingdom
| | - Kwok-Yung Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of a China
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Zhiwei Chen
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
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22
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Scarpa F, Sanna D, Azzena I, Casu M, Cossu P, Fiori PL, Benvenuto D, Imperia E, Giovanetti M, Ceccarelli G, Cauda R, Cassone A, Pascarella S, Ciccozzi M. Genome-based comparison between the recombinant SARS-CoV-2 XBB and its parental lineages. J Med Virol 2023; 95:e28625. [PMID: 36852665 DOI: 10.1002/jmv.28625] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/01/2023] [Accepted: 02/19/2023] [Indexed: 03/01/2023]
Abstract
Recombination is the main contributor to RNA virus evolution, and SARS-CoV-2 during the pandemic produced several recombinants. The most recent SARS-CoV-2 recombinant is the lineage labeled XBB, also known as Gryphon, which arose from BJ.1 and BM.1.1.1. Here we performed a genome-based survey aimed to compare the new recombinant with its parental lineages that never became dominant. Genetic analyses indicated that the recombinant XBB and its first descendant XBB.1 show an evolutionary condition typical of an evolutionary blind background with no further epidemiologically relevant descendant. Genetic variability and expansion capabilities are slightly higher than parental lineages. Bayesian Skyline Plot indicates that XBB reached its plateau around October 6, 2022 and after an initial rapid growth the viral population size did not further expand, and around November 10, 2022 its levels of genetic variability decreased. Simultaneously with the reduction of the XBB population size, an increase of the genetic variability of its first sub-lineage XBB.1 occurred, that in turn reached the plateau around November 9, 2022 showing a kind of vicariance with its direct progenitors. Structure analysis indicates that the affinity for ACE2 surface in XBB/XBB.1 RBDs is weaker than for BA.2 RBD. In conclusion, at present XBB and XBB.1 do not show evidence about a particular danger or high expansion capability. Genome-based monitoring must continue uninterrupted in order to individuate if further mutations can make XBB more dangerous or generate new subvariants with different expansion capability. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Piero Cossu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Azienza Ospedaliera Universitaria (AOU) Sassari, Sassari, Italy
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy.,Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico of Rome, 00128, Rome, Italy
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Roberto Cauda
- UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168, Rome, Italy
| | | | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Jørgensen TS, Pedersen MS, Blin K, Kuntke F, Salling HK, Marvig RL, Michaelsen TY, Albertsen M, Larsen H. SpikeSeq: A rapid, cost efficient and simple method to identify SARS-CoV-2 variants of concern by Sanger sequencing part of the spike protein gene. J Virol Methods 2023; 312:114648. [PMID: 36368344 DOI: 10.1016/j.jviromet.2022.114648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
In 2020, the novel coronavirus, SARS-CoV-2, caused a pandemic, which is still raging at the time of writing this. Here, we present results from SpikeSeq, the first published Sanger sequencing-based method for the detection of Variants of Concern (VOC) and key mutations, using a 1 kb amplicon from the recognized ARTIC Network primers. The proposed setup relies entirely on materials and methods already in use in diagnostic RT-qPCR labs and on existing commercial infrastructure offering sequencing services. For data analysis, we provide an automated, open source, and browser-based mutation calling software (https://github.com/kblin/covid-spike-classification, https://ssi.biolib.com/covid-spike-classification). We validated the setup on 195 SARS-CoV-2 positive samples, and we were able to profile 85% of RT-qPCR positive samples, where the last 15% largely stemmed from samples with low viral count. We compared the SpikeSeq results to WGS results. SpikeSeq has been used as the primary variant identification tool on > 10.000 SARS-CoV-2 positive clinical samples during 2021. At approximately 4€ per sample in material cost, minimal hands-on time, little data handling, and a short turnaround time, the setup is simple enough to be implemented in any SARS-CoV-2 RT-qPCR diagnostic lab. Our protocol provides results that can be used to choose antibodies in a clinical setting and for the tracking and surveillance of all positive samples for new variants and known ones such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) Delta (B.1.617.2), Omicron BA.1(B.1.1.529), BA.2, BA.4/5, BA.2.75.x, and many more, as of October 2022.
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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26
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Chen CS, Jian MJ, Chang CK, Chung HY, Li SY, Lin JC, Yeh KM, Yang YS, Chen CW, Hsieh SS, Tang SH, Perng CL, Chang FY, Shang HS. Monitoring algorithm of hospitalized patients in a medical center with SARS-CoV-2 (Omicron variant) infection: clinical epidemiological surveillance and immunological assessment. PeerJ 2023; 11:e14666. [PMID: 36710871 PMCID: PMC9879147 DOI: 10.7717/peerj.14666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/09/2022] [Indexed: 01/24/2023] Open
Abstract
Purpose Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major healthcare threat worldwide. Since it was first identified in November 2021, the Omicron (B.1.1.529) variant of SARS-CoV-2 has evolved into several lineages, including BA.1, BA.2-BA.4, and BA.5. SARS-CoV-2 variants might increase transmissibility, pathogenicity, and resistance to vaccine-induced immunity. Thus, the epidemiological surveillance of circulating lineages using variant phenotyping is essential. The aim of the current study was to characterize the clinical outcome of Omicron BA.2 infections among hospitalized COVID-19 patients and to perform an immunological assessment of such cases against SARS-CoV-2. Patients and Methods We evaluated the analytical and clinical performance of the BioIC SARS-CoV-2 immunoglobulin (Ig)M/IgG detection kit, which was used for detecting antibodies against SARS-CoV-2 in 257 patients infected with the Omicron variant. Results Poor prognosis was noted in 38 patients, including eight deaths in patients characterized by comorbidities predisposing them to severe COVID-19. The variant-of-concern (VOC) typing and serological analysis identified time-dependent epidemic trends of BA.2 variants emerging in the outbreak of the fourth wave in Taiwan. Of the 257 specimens analyzed, 108 (42%) and 24 (9.3%) were positive for anti-N IgM and IgG respectively. Conclusion The VOC typing of these samples allowed for the identification of epidemic trends by time intervals, including the B.1.1.529 variant replacing the B.1.617.2 variant. Moreover, antibody testing might serve as a complementary method for COVID-19 diagnosis. The combination of serological testing results with the reverse transcription-polymerase chain reaction cycle threshold value has potential value in disease prognosis, thereby aiding in epidemic investigations conducted by clinicians or the healthcare department.
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Affiliation(s)
- Chi-Sheng Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Shih-Yi Li
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, Taipei, Taiwan
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, Taipei, Taiwan
| | - Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, Taipei, Taiwan
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, Taipei, Taiwan
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, Taipei, Taiwan
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
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27
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Torres C, Nabaes Jodar M, Acuña D, Montaño RMZ, Culasso ACA, Amadio AF, Aulicino P, Ceballos S, Cacciabue M, Debat H, Dus Santos MJ, Eberhardt MF, Espul C, Fay F, Fernández MA, Fernández F, Muñoz JMF, Ferrini F, Gallego F, Giri AA, Cerri A, Bolatti E, Gismondi MI, Goya S, Gramundi I, Irazoqui JM, König GA, Leiva V, Lucero H, Marquez N, Nardi C, Ortiz B, Pianciola L, Pintos CB, Puebla AF, Rastellini CV, Rojas AE, Sfalcin J, Suárez A, Tittarelli E, Toro R, Villanova GV, Ziehm MC, Zimmermann MC, Zunino S, Proyecto Pais Working Group, Valinotto L, Viegas M. Omicron Waves in Argentina: Dynamics of SARS-CoV-2 Lineages BA.1, BA.2 and the Emerging BA.2.12.1 and BA.4/BA.5. Viruses 2023; 15. [PMID: 36851525 DOI: 10.3390/v15020312] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.
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28
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Foulkes S, Monk EJM, Sparkes D, Hettiarachchi N, Milligan ID, Munro K, Taylor-Kerr A, Platt N, Howells A, Kyaw JYA, Adaji E, Gallagher E, Khawam J, Wellington E, Price L, Crossman D, Norman C, de Lacy E, Cromey L, Corrigan D, Lackenby A, Barbero P, Elegunde B, Zambon M, Chand MA, Brown CS, Islam J, Atti A, Hopkins S, Hall VJ, Cole MJ. Early Warning Surveillance for SARS-CoV-2 Omicron Variants, United Kingdom, November 2021-September 2022. Emerg Infect Dis 2023; 29:184-188. [PMID: 36454718 PMCID: PMC9796219 DOI: 10.3201/eid2901.221293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Since June 2020, the SARS-CoV-2 Immunity and Reinfection Evaluation (SIREN) study has conducted routine PCR testing in UK healthcare workers and sequenced PCR-positive samples. SIREN detected increases in infections and reinfections and delected Omicron subvariant waves emergence contemporaneous with national surveillance. SIREN's sentinel surveillance methods can be used for variant surveillance.
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29
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Maeda H, Saito N, Igarashi A, Ishida M, Terada M, Ito T, Ikeda H, Kamura H, Motohashi I, Kimura Y, Komino M, Arai H, Kuwamitsu O, Akuzawa N, Sando E, Morikawa T, Imura H, Inoue H, Hayakawa T, Teshigahara O, Ohara Y, Suzuki M, Morimoto K. Effectiveness of mRNA COVID-19 vaccines against symptomatic SARS-CoV-2 infections during the SARS-CoV-2 Omicron BA.1 and BA.2 epidemic in Japan: vaccine effectiveness real-time surveillance for SARS-CoV-2 (VERSUS). Expert Rev Vaccines 2023; 22:288-298. [PMID: 36883371 DOI: 10.1080/14760584.2023.2188950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
BACKGROUND Evaluating COVID-19 vaccine effectiveness (VE) domestically is crucial for assessing and determining national vaccination policy. This study aimed to evaluate VE of mRNA COVID-19 vaccines in Japan. METHODS We conducted a multicenter test-negative case-control study. The study comprised individuals aged ≥16 visiting medical facilities with COVID-19-related signs or symptoms from 1 January to 26 June 2022, when Omicron BA.1 and BA.2 were dominant nationwide. We evaluated VE of primary and booster vaccination against symptomatic SARS-CoV-2 infections and relative VE of booster compared with primary. RESULTS We enrolled 7,931 episodes, including 3,055 test positive. The median age was 39, 48.0% were male, and 20.5% had underlying medical conditions. In individuals aged 16 to 64, VE of primary vaccination within 90 days was 35.6% (95% CI, 19.0-48.8%). After booster, VE increased to 68.7% (60.6-75.1%). In individuals aged ≥65, VE of primary and booster was 31.2% (-44.0-67.1%) and 76.5% (46.7-89.7%), respectively. Relative VE of booster compared with primary vaccination was 52.9% (41.0-62.5%) in individuals aged 16 to 64 and 65.9% (35.7-81.9%) in individuals aged ≥65. CONCLUSIONS During BA.1 and BA.2 epidemic in Japan, mRNA COVID-19 primary vaccination provided modest protection. Booster vaccination was necessary to protect against symptomatic infections.
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Affiliation(s)
- Haruka Maeda
- Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Department of Clinical Tropical Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Nobuo Saito
- Department of Microbiology, Faculty of Medicine, Oita University, Oita, Japan
| | - Ataru Igarashi
- Department of Public Health, Yokohama City University School of Medicine, Kanagawa, Japan
- Department of Health Economics and Outcomes Research, Graduate School of Pharmaceutical Sciences, the University of Tokyo, Tokyo, Japan
| | - Masayuki Ishida
- Department of Infectious Disease Medicine, Chikamori Hospital, Kochi, Japan
| | - Mayumi Terada
- Department of Internal Medicine, Nijigaoka Hospital, Nagasaki, Japan
| | - Takayasu Ito
- Department of Emergency Medicine, Toyota Kosei Hospital, Aichi, Japan
- Department of Clinical Training and Career Development, Gifu University, Gifu, Japan
| | - Hideko Ikeda
- Department of Nursing, Toyota Kosei Hospital, Aichi, Japan
| | | | - Iori Motohashi
- Department of General Internal Medicine, Kawasaki Municipal Tama Hospital, Kanagawa, Japan
| | - Yuya Kimura
- Department of Cardiology, Saiseikai Kazo Hospital, Saitama, Japan
| | - Masaru Komino
- Department of Nursing, Saiseikai Kazo Hospital, Saitama, Japan
| | - Hiromi Arai
- Department of Nursing, Saiseikai Kazo Hospital, Saitama, Japan
| | | | - Nobuhiro Akuzawa
- Department of Internal Medicine, Gunma Chuo Hospital, Gunma, Japan
| | - Eiichiro Sando
- Department of General Internal Medicine and Clinical Infectious Diseases, Kita-Fukushima Medical Center, Fukushima, Japan
- Department of General Internal Medicine and Clinical Infectious Diseases, Fukushima Medical University, Fukushima, Japan
| | - Toru Morikawa
- Department of General Medicine, Nara City Hospital, Nara, Japan
| | - Haruki Imura
- Department of Infectious Disease Medicine, Rakuwakai Otowa Hospital, Kyoto, Japan
| | - Hiroki Inoue
- Department of Infectious Disease Medicine, Rakuwakai Otowa Hospital, Kyoto, Japan
| | | | | | - Yasuji Ohara
- Department of Internal Medicine, Takagi Hospital, Aichi, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Konosuke Morimoto
- Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
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Zhou Y, Zhi H, Teng Y. The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity. J Med Virol 2023; 95:e28138. [PMID: 36097349 PMCID: PMC9538491 DOI: 10.1002/jmv.28138] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron defined by the World Health Organization during the COVID-19 pandemic. As of August 2022, Omicron is classified into five main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to the previous VOCs (Alpha, Beta, Gamma, and Delta), all the Omicron lineages have the most highly mutations in the spike protein, and with 50 mutations accumulated throughout the genome. Early data indicated that Omicron BA.2 sublineage had higher infectivity and more immune escape than the early wild-type (WT) strain, the previous VOCs, and BA.1. Recently, global surveillance data suggest a higher transmissibility of BA.4/BA.5 than BA.1, BA.1.1 and BA.2, and BA.4/BA.5 is becoming dominant strain in many countries globally.
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Affiliation(s)
- Yongbing Zhou
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huilin Zhi
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Teng
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Singh JK, Dubey S, Srivastava G, Siddiqi MI, Srivastava SK. Neohesperidin and spike RBD interaction in omicron and its sub-variants: In silico, structural and simulation studies. Comput Biol Med 2023; 152:106392. [PMID: 36502697 DOI: 10.1016/j.compbiomed.2022.106392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged first around December 2019 in the city of Wuhan, China. Since then, several variants of the virus have emerged with different biological properties. This pandemic has so far led to widespread infection cycles with millions of fatalities and infections globally. In the recent cycle, a new variant omicron and its three sub-variants BA.1, BA.2 and BA.3 have emerged which seems to evade host immune defences and have brisk infection rate. Particularly, BA.2 variant has shown high transmission rate over BA.1 strain in different countries including India. In the present study, we have evaluated a set of eighty drugs/compounds using in silico docking calculations in omicron and its variants. These molecules were reported previously against SARS-CoV-2. Our docking and simulation analyses suggest differences in affinity of these compounds in omicron and BA.2 compared to SARS-CoV-2. These studies show that neohesperidin, a natural flavonoid found in Citrus aurantium makes a stable interaction with spike receptor domain of omicron and BA.2 compared to other variants. Free energy binding analyses further validates that neohesperidin forms a stable complex with spike RBD in omicron and BA.2 with a binding energy of -237.9 ± 18.7 kJ/mol and -164.1 ± 17.5 kJ/mol respectively. Key residual differences in the RBD interface of these variants form the basis for differential interaction affinities with neohesperidin as drug binding site overlaps with RBD-human ACE2 interface. These data might be useful for the design and development of novel scaffolds and pharmacophores to develop specific therapeutic strategies against these novel variants.
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Focosi D, McConnell S, Casadevall A. The Omicron variant of concern: Diversification and convergent evolution in spike protein, and escape from anti-Spike monoclonal antibodies. Drug Resist Updat 2022; 65:100882. [PMID: 36260961 PMCID: PMC9528072 DOI: 10.1016/j.drup.2022.100882] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 01/17/2023]
Abstract
WHO-defined SARS-CoV-2 variants of concern (VOC) drive therapeutics and vaccine development. The Omicron VOC is dominating the arena since November 2021, but the number of its sublineages is growing in complexity. Omicron represent a galaxy with a myriad of stars that suddenly rise and expand before collapsing into apparent extinction when a more fit sublineage appears. This has already happened with BA.1, BA.2, and BA.4/5 and is happening with BA.2.75. We review here the current PANGO phylogeny, focusing on sublineages with Spike mutations, and show how frequently xxxxxxxx convergent evolution has occurred in these sublineages. We finally summarize how Omicron evolution has progressively defeated the anti-Spike monoclonal antibodies authorized so far, leaving clinicians to again fall back on COVID19 convalescent plasma from vaccinated donors as the only antibody-based therapy available.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy.
| | - Scott McConnell
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [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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Rosati M, Terpos E, Bear J, Burns R, Devasundaram S, Ntanasis-Stathopoulos I, Gavriatopoulou M, Kastritis E, Dimopoulos MA, Pavlakis GN, Felber BK. Low Spike Antibody Levels and Impaired BA.4/5 Neutralization in Patients with Multiple Myeloma or Waldenstrom's Macroglobulinemia after BNT162b2 Booster Vaccination. Cancers (Basel) 2022; 14. [PMID: 36497296 DOI: 10.3390/cancers14235816] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Patients with symptomatic monoclonal gammopathies have impaired humoral responses to COVID-19 vaccination. Their ability to recognize SARS-CoV-2 Omicron variants is of concern. We compared the response to BNT162b2 mRNA vaccinations of patients with multiple myeloma (MM, n = 60) or Waldenstrom's macroglobulinemia (WM, n = 20) with healthy vaccine recipients (n = 37). Patient cohorts on active therapy affecting B cell development had impaired binding and neutralizing antibody (NAb) response rate and magnitude, including several patients lacking responses, even after a 3rd vaccine dose, whereas non-B cell depleting therapies had a lesser effect. In contrast, MM and WM cohorts off-therapy showed increased NAb with a broad response range. ELISA Spike-Receptor Binding Domain (RBD) Ab titers in healthy vaccine recipients and patient cohorts were good predictors of the ability to neutralize not only the original WA1 but also the most divergent Omicron variants BA.4/5. Compared to WA1, significantly lower NAb responses to BA.4/5 were found in all patient cohorts on-therapy. In contrast, the MM and WM cohorts off-therapy showed a higher probability to neutralize BA.4/5 after the 3rd vaccination. Overall, the boost in NAb after the 3rd dose suggests that repeat vaccination of MM and WM patients is beneficial even under active therapy.
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Kimura I, Yamasoba D, Tamura T, Nao N, Suzuki T, Oda Y, Mitoma S, Ito J, Nasser H, Zahradnik J, Uriu K, Fujita S, Kosugi Y, Wang L, Tsuda M, Kishimoto M, Ito H, Suzuki R, Shimizu R, Begum MM, Yoshimatsu K, Kimura KT, Sasaki J, Sasaki-Tabata K, Yamamoto Y, Nagamoto T, Kanamune J, Kobiyama K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Shirakawa K, Takaori-Kondo A, Kuramochi J, Schreiber G, Ishii KJ, Hashiguchi T, Ikeda T, Saito A, Fukuhara T, Tanaka S, Matsuno K, Sato K. Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5. Cell 2022; 185:3992-4007.e16. [PMID: 36198317 PMCID: PMC9472642 DOI: 10.1016/j.cell.2022.09.018] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/20/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4, and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. We further provided the structure of the BA.4/5 spike receptor-binding domain that binds to human ACE2 and considered how the substitutions in the BA.4/5 spike play roles in ACE2 binding and immune evasion. Moreover, experiments using hamsters suggested that BA.4/5 is more pathogenic than BA.2. Our multiscale investigations suggest that the risk of BA.2 subvariants, particularly BA.4/5, to global health is greater than that of original BA.2.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daichi Yamasoba
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Faculty of Medicine, Kobe University, Kobe, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Shuya Mitoma
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hayato Ito
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | | | - Kanako Terakado Kimura
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | | | | | | | - Kouji Kobiyama
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jin Kuramochi
- Interpark Kuramochi Clinic, Utsunomiya, Japan; Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Keita Matsuno
- One Health Research Center, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan; Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
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Valentina M, Alessandro CL, Francesca C, Silvia R, Eleonora L, Claudia C, Jessica P, Ilaria M, Serena V, Lavinia F, Alessandra V, Gaetano M, Fabrizio C, Simone L, Emanuela C, Eugenia M, Raffaella L, Pierluca P, Enrico G, AnnaRosa G, Francesco V, Fabrizio M, Emanuele N, Andrea A. Viral load decrease in SARS-CoV-2 BA.1 and BA.2 Omicron sublineages infection after treatment with monoclonal antibodies and direct antiviral agents. J Med Virol 2022; 95:e28186. [PMID: 36184918 PMCID: PMC9539310 DOI: 10.1002/jmv.28186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 01/11/2023]
Abstract
The efficacy on the Omicron variant of the approved early coronavirus disease-2019 (COVID-19) therapies, especially monoclonal antibodies, has been challenged by in vitro neutralization data, while data on in vivo antiviral activity are lacking. We assessed potential decrease from Day 1 to Day 7 viral load (VL) in nasopharyngeal swabs of outpatients receiving Sotrovimab, Molnupiravir, Remdesivir, or Nirmatrelvir/ritonavir for mild-to-moderate COVID-19 due to sublineages BA.1 or BA.2, and average treatment effect by weighted marginal linear regression models. A total of 521 patients (378 BA.1 [73%], 143 [27%] BA.2) received treatments (Sotrovimab 202, Molnupiravir 117, Nirmatrelvir/ritonavir 84, and Remdesivir 118): median age 66 years, 90% vaccinated, median time from symptoms onset 3 days. Day 1 mean VL was 4.12 log2 (4.16 for BA.1 and 4.01 for BA.2). The adjusted analysis showed that Nirmatrelvir/ritonavir significantly reduced VL compared to all the other drugs, except versus Molnupiravir in BA.2. Molnupiravir was superior to Remdesivir in both BA.1 and BA.2, and to Sotrovimab in BA.2. Sotrovimab had better activity than Remdesivir only against BA.1. Nirmatrelvir/ritonavir showed the greatest antiviral activity against Omicron variant, comparable to Molnupiravir only in the BA.2 subgroup. VL decrease could be a valuable surrogate of drug activity in the context of the high prevalence of vaccinated people and low probability of hospital admission.
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Affiliation(s)
- Mazzotta Valentina
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly,PhD course in Microbiology, Immunology, Infectious Diseases, and Transplants (MIMIT)University of Rome Tor VergataRomeItaly
| | - Cozzi Lepri Alessandro
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME)Institute for Global HealthUCLLondonUK
| | - Colavita Francesca
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Rosati Silvia
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Lalle Eleonora
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Cimaglia Claudia
- Clinical Epidemiology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Paulicelli Jessica
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Mastrorosa Ilaria
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Vita Serena
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Fabeni Lavinia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Vergori Alessandra
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Maffongelli Gaetano
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Carletti Fabrizio
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Lanini Simone
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Caraffa Emanuela
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Milozzi Eugenia
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Libertone Raffaella
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Piselli Pierluca
- Clinical Epidemiology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Girardi Enrico
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Garbuglia AnnaRosa
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Vaia Francesco
- General Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Maggi Fabrizio
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Nicastri Emanuele
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Antinori Andrea
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
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Kumar S, Karuppanan K, Subramaniam G. Omicron (BA.1) and sub-variants (BA.1.1, BA.2, and BA.3) of SARS-CoV-2 spike infectivity and pathogenicity: A comparative sequence and structural-based computational assessment. J Med Virol 2022; 94:4780-4791. [PMID: 35680610 PMCID: PMC9347785 DOI: 10.1002/jmv.27927] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/28/2022] [Accepted: 06/05/2022] [Indexed: 12/16/2022]
Abstract
The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread throughout the world. We used computational tools to assess the spike infectivity, transmission, and pathogenicity of Omicron (BA.1) and sub-variants (BA.1.1, BA.2, and BA.3) in this study. BA.1 has 39 mutations, BA.1.1 has 40 mutations, BA.2 has 31 mutations, and BA.3 has 34 mutations, with 21 shared mutations between all. We observed 11 common mutations in Omicron's receptor-binding domain (RBD) and sub-variants. In pathogenicity analysis, the Y505H, N786K, T95I, N211I, N856K, and V213R mutations in omicron and sub-variants are predicted to be deleterious. Due to the major effect of the mutations characterizing in the RBD, we found that Omicron and sub-variants had a higher positive electrostatic surface potential. This could increase interaction between RBD and negative electrostatic surface potential human angiotensin-converting enzyme 2 (hACE2). Omicron and sub-variants had a higher affinity for hACE2 and the potential for increased transmission when compared to the wild-type (WT). Negative electrostatic potential of N-terminal domain (NTD) of the spike protein value indicates that the Omicron variant binds receptors less efficiently than the WT. Given that at least one receptor is highly expressed in lung and bronchial cells, the electrostatic potential of NTD negative value could be one of the factors contributing to why the Omicron variant is thought to be less harmful to the lower respiratory tract. Among Omicron sub-lineages, BA.2 and BA.3 have a higher transmission potential than BA.1 and BA.1.1. We predicted that mutated residues in BA.1.1 (K478), BA.2 (R400, R490, and R495), and BA.3 (R397 and H499) formation of new salt bridges and hydrogen bonds. Omicron and sub-variant mutations at Receptor-binding Motif (RBM) residues such as Q493R, N501Y, Q498, T478K, and Y505H all contribute significantly to binding affinity with human ACE2. Interactions with Omicron variant mutations at residues 493, 496, 498, and 501 seem to restore ACE2 binding effectiveness lost due to other mutations like K417N.
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Affiliation(s)
- Suresh Kumar
- Department of Diagnostic & Allied Health Science, Faculty of Health and Life SciencesManagement and Science UniversityShah AlamSelangorMalaysia
| | - Kalimuthu Karuppanan
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
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38
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Oloye FF, Xie Y, Asadi M, Cantin J, Challis JK, Brinkmann M, McPhedran KN, Kristian K, Keller M, Sadowski M, Jones PD, Landgraff C, Mangat C, Fuzzen M, Servos MR, Giesy JP. Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities. Sci Total Environ 2022; 841:156741. [PMID: 35716745 PMCID: PMC9212401 DOI: 10.1016/j.scitotenv.2022.156741] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 05/21/2023]
Abstract
Monitoring the communal incidence of COVID-19 is important for both government and residents of an area to make informed decisions. However, continuous reliance on one means of monitoring might not be accurate because of biases introduced by government policies or behaviours of residents. Wastewater surveillance was employed to monitor concentrations of SARS-CoV-2 RNA in raw influent wastewater from wastewater treatment plants serving three Canadian Prairie cities with different population sizes. Data obtained from wastewater are not directly influenced by government regulations or behaviours of individuals. The means of three weekly samples collected using 24 h composite auto-samplers were determined. Viral loads were determined by RT-qPCR, and whole-genome sequencing was used to charaterize variants of concern (VOC). The dominant VOCs in the three cities were the same but with different proportions of sub-lineages. Sub-lineages of Delta were AY.12, AY.25, AY.27 and AY.93 in 2021, while the major sub-lineage of Omicron was BA.1 in January 2022, and BA.2 subsequently became a trace-level sub-variant then the predominant VOC. When each VOC was first detected varied among cities; However, Saskatoon, with the largest population, was always the first to present new VOCs. Viral loads varied among cities, but there was no direct correlation with population size, possibly because of differences in flow regimes. Population is one of the factors that affects trends in onset and development of local outbreaks during the pandemic. This might be due to demography or the fact that larger populations had greater potential for inter- and intra-country migration. Hence, wastewater surveillance data from larger cities can typically be used to indicate what to expect in smaller communities.
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Affiliation(s)
- Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jonathan K Challis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kevin Kristian
- Wastewater Treatment Plant, Public Work Department, City of Prince Albert, Prince Albert, SK, Canada
| | - Mark Keller
- Wastewater Treatment Plant, City Operations, City of North Battleford, North Battleford, SK, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department, City of Saskatoon, Saskatoon, SK, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chand Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory Winnipeg, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
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39
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Aggarwal A, Akerman A, Milogiannakis V, Silva MR, Walker G, Stella AO, Kindinger A, Angelovich T, Waring E, Amatayakul-Chantler S, Roth N, Manni S, Hauser T, Barnes T, Condylios A, Yeang M, Wong M, Jean T, Foster CSP, Christ D, Hoppe AC, Munier ML, Darley D, Churchill M, Stark DJ, Matthews G, Rawlinson WD, Kelleher AD, Turville SG. SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. EBioMedicine 2022; 84:104270. [PMID: 36130476 PMCID: PMC9482529 DOI: 10.1016/j.ebiom.2022.104270] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/09/2022] [Accepted: 09/02/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Genetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. The introduction of global vaccine programs has contributed to lower COVID-19 hospitalisation and mortality rates, particularly in developed countries. In late 2021, Omicron BA.1 emerged, with substantially altered genetic differences and clinical effects from other variants of concern. Shortly after dominating global spread in early 2022, BA.1 was supplanted by the genetically distinct Omicron lineage BA.2. A sub-lineage of BA.2, designated BA.5, presently has an outgrowth advantage over BA.2 and other BA.2 sub-lineages. Here we study the neutralisation of Omicron BA.1, BA.2 and BA.5 and pre-Omicron variants using a range of vaccine and convalescent sera and therapeutic monoclonal antibodies using a live virus neutralisation assay. Using primary nasopharyngeal swabs, we also tested the relative fitness of BA.5 compared to pre-Omicron and Omicron viral lineages in their ability to use the ACE2-TMPRSS2 pathway. METHODS Using low passage clinical isolates of Clade A.2.2, Beta, Delta, BA.1, BA.2 and BA.5, we determined humoral neutralisation in vitro in vaccinated and convalescent cohorts, using concentrated human IgG pooled from thousands of plasma donors, and licensed monoclonal antibody therapies. We then determined infectivity to particle ratios in primary nasopharyngeal samples and expanded low passage isolates in a genetically engineered ACE2/TMPRSS2 cell line in the presence and absence of the TMPRSS2 inhibitor Nafamostat. FINDINGS Peak responses to 3 doses of BNT162b2 vaccine were associated with a 9-fold reduction in neutralisation for Omicron lineages BA.1, BA.2 and BA.5. Concentrated pooled human IgG from convalescent and vaccinated donors and BNT162b2 vaccination with BA.1 breakthrough infections were associated with greater breadth of neutralisation, although the potency was still reduced 7-fold across all Omicron lineages. Testing of clinical grade antibodies revealed a 14.3-fold reduction using Evusheld and 16.8-fold reduction using Sotrovimab for the BA.5. Whilst the infectivity of BA.1 and BA.2 was attenuated in ACE2/TMPRSS2 entry, BA.5 was observed to be equivalent to that of an early 2020 circulating clade and had greater sensitivity to the TMPRSS2 inhibitor Nafamostat. INTERPRETATION Observations support all Omicron variants to significantly escape neutralising antibodies across a range of vaccination and/or convalescent responses. Potency of therapeutic monoclonal antibodies is also reduced and differs across Omicron lineages. The key difference of BA.5 from other Omicron sub-variants is the reversion in tropism back to using the well-known ACE2-TMPRSS2 pathway, utilised efficiently by pre-Omicron lineages. Monitoring if these changes influence transmission and/or disease severity will be key for ongoing tracking and management of Omicron waves globally. FUNDING This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (ST, GM & WDR), MRF2001684 (ADK and ST) and Medical Research Future Fund Antiviral Development Call grant (WDR), Medical Research Future Fund COVID-19 grant (MRFF2001684, ADK & SGT) and the New South Wales Health COVID-19 Research Grants Round 2 (SGT).
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Affiliation(s)
- Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Anouschka Akerman
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | | | - Mariana Ruiz Silva
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Gregory Walker
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | | | - Andrea Kindinger
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Thomas Angelovich
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Emily Waring
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | | | - Nathan Roth
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Sandro Manni
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Hauser
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Barnes
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Anna Condylios
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Malinna Yeang
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Maureen Wong
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Tyra Jean
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Charles S P Foster
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Mee Ling Munier
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - David Darley
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Melissa Churchill
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Damien J Stark
- Molecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Gail Matthews
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - William D Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, New South Wales, Australia.
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40
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Oloye FF, Xie Y, Asadi M, Cantin J, Challis JK, Brinkmann M, McPhedran KN, Kristian K, Keller M, Sadowski M, Jones PD, Landgraff C, Mangat C, Fuzzen M, Servos MR, Giesy JP. Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities. Sci Total Environ 2022. [PMID: 35716745 PMCID: PMC8887651 DOI: 10.1021/acsestwater.1c00349&ref=pdf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Monitoring the communal incidence of COVID-19 is important for both government and residents of an area to make informed decisions. However, continuous reliance on one means of monitoring might not be accurate because of biases introduced by government policies or behaviours of residents. Wastewater surveillance was employed to monitor concentrations of SARS-CoV-2 RNA in raw influent wastewater from wastewater treatment plants serving three Canadian Prairie cities with different population sizes. Data obtained from wastewater are not directly influenced by government regulations or behaviours of individuals. The means of three weekly samples collected using 24 h composite auto-samplers were determined. Viral loads were determined by RT-qPCR, and whole-genome sequencing was used to charaterize variants of concern (VOC). The dominant VOCs in the three cities were the same but with different proportions of sub-lineages. Sub-lineages of Delta were AY.12, AY.25, AY.27 and AY.93 in 2021, while the major sub-lineage of Omicron was BA.1 in January 2022, and BA.2 subsequently became a trace-level sub-variant then the predominant VOC. When each VOC was first detected varied among cities; However, Saskatoon, with the largest population, was always the first to present new VOCs. Viral loads varied among cities, but there was no direct correlation with population size, possibly because of differences in flow regimes. Population is one of the factors that affects trends in onset and development of local outbreaks during the pandemic. This might be due to demography or the fact that larger populations had greater potential for inter- and intra-country migration. Hence, wastewater surveillance data from larger cities can typically be used to indicate what to expect in smaller communities.
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Affiliation(s)
- Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jonathan K Challis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kevin Kristian
- Wastewater Treatment Plant, Public Work Department, City of Prince Albert, Prince Albert, SK, Canada
| | - Mark Keller
- Wastewater Treatment Plant, City Operations, City of North Battleford, North Battleford, SK, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department, City of Saskatoon, Saskatoon, SK, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chand Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory Winnipeg, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
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41
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Aggarwal A, Akerman A, Milogiannakis V, Silva MR, Walker G, Stella AO, Kindinger A, Angelovich T, Waring E, Amatayakul-Chantler S, Roth N, Manni S, Hauser T, Barnes T, Condylios A, Yeang M, Wong M, Jean T, Foster CSP, Christ D, Hoppe AC, Munier ML, Darley D, Churchill M, Stark DJ, Matthews G, Rawlinson WD, Kelleher AD, Turville SG. SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. EBioMedicine 2022; 84:104270. [PMID: 36130476 DOI: 10.1101/2021.12.14.21267772] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/09/2022] [Accepted: 09/02/2022] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Genetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. The introduction of global vaccine programs has contributed to lower COVID-19 hospitalisation and mortality rates, particularly in developed countries. In late 2021, Omicron BA.1 emerged, with substantially altered genetic differences and clinical effects from other variants of concern. Shortly after dominating global spread in early 2022, BA.1 was supplanted by the genetically distinct Omicron lineage BA.2. A sub-lineage of BA.2, designated BA.5, presently has an outgrowth advantage over BA.2 and other BA.2 sub-lineages. Here we study the neutralisation of Omicron BA.1, BA.2 and BA.5 and pre-Omicron variants using a range of vaccine and convalescent sera and therapeutic monoclonal antibodies using a live virus neutralisation assay. Using primary nasopharyngeal swabs, we also tested the relative fitness of BA.5 compared to pre-Omicron and Omicron viral lineages in their ability to use the ACE2-TMPRSS2 pathway. METHODS Using low passage clinical isolates of Clade A.2.2, Beta, Delta, BA.1, BA.2 and BA.5, we determined humoral neutralisation in vitro in vaccinated and convalescent cohorts, using concentrated human IgG pooled from thousands of plasma donors, and licensed monoclonal antibody therapies. We then determined infectivity to particle ratios in primary nasopharyngeal samples and expanded low passage isolates in a genetically engineered ACE2/TMPRSS2 cell line in the presence and absence of the TMPRSS2 inhibitor Nafamostat. FINDINGS Peak responses to 3 doses of BNT162b2 vaccine were associated with a 9-fold reduction in neutralisation for Omicron lineages BA.1, BA.2 and BA.5. Concentrated pooled human IgG from convalescent and vaccinated donors and BNT162b2 vaccination with BA.1 breakthrough infections were associated with greater breadth of neutralisation, although the potency was still reduced 7-fold across all Omicron lineages. Testing of clinical grade antibodies revealed a 14.3-fold reduction using Evusheld and 16.8-fold reduction using Sotrovimab for the BA.5. Whilst the infectivity of BA.1 and BA.2 was attenuated in ACE2/TMPRSS2 entry, BA.5 was observed to be equivalent to that of an early 2020 circulating clade and had greater sensitivity to the TMPRSS2 inhibitor Nafamostat. INTERPRETATION Observations support all Omicron variants to significantly escape neutralising antibodies across a range of vaccination and/or convalescent responses. Potency of therapeutic monoclonal antibodies is also reduced and differs across Omicron lineages. The key difference of BA.5 from other Omicron sub-variants is the reversion in tropism back to using the well-known ACE2-TMPRSS2 pathway, utilised efficiently by pre-Omicron lineages. Monitoring if these changes influence transmission and/or disease severity will be key for ongoing tracking and management of Omicron waves globally. FUNDING This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (ST, GM & WDR), MRF2001684 (ADK and ST) and Medical Research Future Fund Antiviral Development Call grant (WDR), Medical Research Future Fund COVID-19 grant (MRFF2001684, ADK & SGT) and the New South Wales Health COVID-19 Research Grants Round 2 (SGT).
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Affiliation(s)
- Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Anouschka Akerman
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | | | - Mariana Ruiz Silva
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Gregory Walker
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | | | - Andrea Kindinger
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Thomas Angelovich
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Emily Waring
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | | | - Nathan Roth
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Sandro Manni
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Hauser
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Barnes
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Anna Condylios
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Malinna Yeang
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Maureen Wong
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Tyra Jean
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Charles S P Foster
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Mee Ling Munier
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - David Darley
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Melissa Churchill
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Damien J Stark
- Molecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Gail Matthews
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - William D Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, New South Wales, Australia.
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Le TTB, Vasanthakumaran T, Thi Hien HN, Hung I, Luu MN, Khan ZA, An NT, Tran VP, Lee WJ, Abdul Aziz JM, Ali T, Dumre SP, Huy NT. SARS-CoV-2 Omicron and its current known unknowns: A narrative review. Rev Med Virol 2022; 33:e2398. [PMID: 36150052 PMCID: PMC9538895 DOI: 10.1002/rmv.2398] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 02/06/2023]
Abstract
The emergence of the SARS-CoV-2 Omicron variant (B.1.1.529) has created great global distress. This variant of concern shows multiple sublineages, importantly B.1.1.529.1 (BA.1), BA.1 + R346K (BA.1.1), and B.1.1.529.2 (BA.2), each with unique properties. However, little is known about this new variant, specifically its sub-variants. A narrative review was conducted to summarise the latest findings on transmissibility, clinical manifestations, diagnosis, and efficacy of current vaccines and treatments. Omicron has shown two times higher transmission rates than Delta and above ten times more infectious than other variants over a similar period. With more than 30 mutations in the spike protein's receptor-binding domain, there is reduced detection by conventional RT-PCR and rapid antigen tests. Moreover, the two-dose vaccine effectiveness against Delta and Omicron variants was found to be approximately 21%, suggesting an urgent need for a booster dose to prevent the possibility of breakthrough infections. However, the current vaccines remain highly efficacious against severe disease, hospitalisation, and mortality. Japanese preliminary lab data elucidated that the Omicron sublineage BA.2 shows a higher illness severity than BA.1. To date, the clinical management of Omicron remains unchanged, except for monoclonal antibodies. Thus far, only Bebtelovimab could sufficiently treat all three sub-variants of Omicron. Further studies are warranted to understand the complexity of Omicron and its sub-variants. Such research is necessary to improve the management and prevention of Omicron infection.
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Affiliation(s)
- Trang Thi Bich Le
- Online Research ClubNagasakiJapan,University of Medicine and Pharmacy at Ho Chi Minh CityHo Chi Minh CityVietnam
| | - Tamilarasy Vasanthakumaran
- Online Research ClubNagasakiJapan,Global Clinical Scholars Research Training ProgramHarvard Medical SchoolBostonMassachusettsUSA
| | - Hau Nguyen Thi Hien
- Online Research ClubNagasakiJapan,Faculty of MedicineCollege of Medicine and PharmacyDuy Tan UniversityDa NangVietnam,Institue for Research and Training in MedicineBiology and Pharmacy, Duy Tan UniversityDa NangVietnam
| | | | - Mai Ngoc Luu
- Online Research ClubNagasakiJapan,Department of Internal MedicineUniversity of Medicine and Pharmacy at Ho Chi Minh CityHo Chi Minh CityVietnam
| | - Zeeshan Ali Khan
- Online Research ClubNagasakiJapan,Shadan Institute of Medical SciencesHyderabadTelanganaIndia
| | - Nguyen Thanh An
- Online Research ClubNagasakiJapan,Faculty of MedicineCollege of Medicine and PharmacyDuy Tan UniversityDa NangVietnam,Institue for Research and Training in MedicineBiology and Pharmacy, Duy Tan UniversityDa NangVietnam
| | - Van Phu Tran
- Online Research ClubNagasakiJapan,Tra Vinh UniversityTra VinhVietnam
| | - Wei Jun Lee
- Online Research ClubNagasakiJapan,School of MedicineInternational Medical UniversityKuala LumpurMalaysia
| | - Jeza Muhamad Abdul Aziz
- Online Research ClubNagasakiJapan,Medical Laboratory SciencesCollege of Health SciencesUniversity of Human DevelopmentSulaimaniKurdistan RegionIraq,Baxshin Research CenterBaxshin HospitalSulaimaniKurdistan RegionIraq
| | - Tasnim Ali
- Online Research ClubNagasakiJapan,Faculty of MedicineUniversity of KhartoumKhartoumSudan
| | | | - Nguyen Tien Huy
- Online Research ClubNagasakiJapan,School of Tropical Medicine and Global HealthNagasaki UniversityNagasakiJapan
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Chan JFW, Hu B, Chai Y, Shuai H, Liu H, Shi J, Liu Y, Yoon C, Zhang J, Hu JC, Hou Y, Huang X, Yuen TTT, Zhu T, Li W, Cai JP, Luo C, Yip CCY, Zhang AJ, Zhou J, Yuan S, Zhang BZ, Huang JD, To KKW, Yuen KY, Chu H. Virological features and pathogenicity of SARS-CoV-2 Omicron BA.2. Cell Rep Med 2022; 3:100743. [PMID: 36084644 PMCID: PMC9420712 DOI: 10.1016/j.xcrm.2022.100743] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/27/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 was a dominant circulating SARS-CoV-2 variant worldwide. Recent reports hint that BA.2 is similarly potent regarding antibody evasion but may be more transmissible than BA.1. The pathogenicity of BA.2 remains unclear and is of critical public health significance. Here we investigated the virological features and pathogenicity of BA.2 with in vitro and in vivo models. We show that BA.2 is less dependent on transmembrane protease serine 2 (TMPRSS2) for virus entry in comparison with BA.1 in vitro. In K18-hACE2 mice, BA.2 replicates more efficiently than BA.1 in the nasal turbinates and replicates marginally less efficiently in the lungs, leading to decreased body weight loss and improved survival. Our study indicates that BA.2 is similarly attenuated in lungs compared with BA.1 but is potentially more transmissible because of its better replication at the nasal turbinates.
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Affiliation(s)
- Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Bingjie Hu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yue Chai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Huiping Shuai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Huan Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jialu Shi
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yuanchen Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Chaemin Yoon
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jinjin Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jing-Chu Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Yuxin Hou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Terrence Tsz-Tai Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Tianrenzheng Zhu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wenjun Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Anna Jinxia Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Bao-Zhong Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Jian-Dong Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Guangzhou Laboratory, Guangdong Province, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
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Pastorio C, Zech F, Noettger S, Jung C, Jacob T, Sanderson T, Sparrer KMJ, Kirchhoff F. Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2. Cell Host Microbe 2022; 30:1255-1268.e5. [PMID: 35931073 PMCID: PMC9289044 DOI: 10.1016/j.chom.2022.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 12/02/2022]
Abstract
SARS-CoV-2 Omicron rapidly outcompeted other variants and currently dominates the COVID-19 pandemic. Its enhanced transmission and immune evasion are thought to be driven by numerous mutations in the Omicron Spike protein. Here, we systematically introduced BA.1 and/or BA.2 Omicron Spike mutations into the ancestral Spike protein and examined the impacts on Spike function, processing, and susceptibility to neutralization. Individual mutations of S371F/L, S375F, and T376A in the ACE2-receptor-binding domain as well as Q954H and N969K in the hinge region 1 impaired infectivity, while changes to G339D, D614G, N764K, and L981F moderately enhanced it. Most mutations in the N-terminal region and receptor-binding domain reduced the sensitivity of the Spike protein to neutralization by sera from individuals vaccinated with the BNT162b2 vaccine and by therapeutic antibodies. Our results represent a systematic functional analysis of Omicron Spike adaptations that have allowed this SARS-CoV-2 variant to dominate the current pandemic.
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Affiliation(s)
- Chiara Pastorio
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Sabrina Noettger
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; Electrochemical Energy Storage, Helmholtz-Institute-Ulm (HIU), 89081 Ulm, Germany; Karlsruhe Institute of Technology (KIT), 76344 Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany
| | | | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Centre, 89081 Ulm, Germany.
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Anichini G, Terrosi C, Gori Savellini G, Gandolfo C, Barbagli F, Carta GA, Fabrizi S, Miceli GB, Cusi MG. Antibody Response against Circulating Omicron Variants 8 Months after the Third Dose of mRNA Vaccine. Vaccines (Basel) 2022; 10:vaccines10091512. [PMID: 36146590 PMCID: PMC9501623 DOI: 10.3390/vaccines10091512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 02/05/2023] Open
Abstract
The COVID-19 wave is being recently propelled by BA.2 and, particularly, BA.5 lineages, showing clear transmission advantages over the previously circulating strains. In this study, neutralizing antibody responses against SARS-CoV-2 Wild-Type, BA.2 and BA.5 Omicron sublineages were evaluated among vaccinees, uninfected or infected with Omicron BA.1 strain, 8 months after the third dose of SARS-CoV-2 vaccine. The aim of this study was to compare the cross-protective humoral response to the currently circulating variant strains induced by vaccination, followed by Omicron infection in some subjects. Results showed a low antibody titer against all three variants in uninfected vaccinated subjects. On the other hand, vaccinated subjects, infected with BA.1 variant after receiving the third dose (about 40 days later), showed a strong response against both BA.2 and BA.5 strains, albeit with lower titers. This reinforces the concept that vaccination is fundamental to induce an adequate and protective immune response against SARS-CoV-2, but needs to be updated, in order to also widen the range of action towards emerging variants, phylogenetically distant from the Wuhan strain, against which the current formulation is targeted.
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Affiliation(s)
- Gabriele Anichini
- Virology Unit, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Chiara Terrosi
- Virology Unit, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Gianni Gori Savellini
- Virology Unit, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Claudia Gandolfo
- Virology Unit, Santa Maria AlleScotte University Hospital, V.le Bracci 1, 53100 Siena, Italy
| | - Francesca Barbagli
- Preventive Medicine and Health Surveillance Unit, Santa Maria AlleScotte University Hospital, V.le Bracci 1, 53100 Siena, Italy
| | - Giulio Alberto Carta
- Preventive Medicine and Health Surveillance Unit, Santa Maria AlleScotte University Hospital, V.le Bracci 1, 53100 Siena, Italy
| | - Simonetta Fabrizi
- Preventive Medicine and Health Surveillance Unit, Santa Maria AlleScotte University Hospital, V.le Bracci 1, 53100 Siena, Italy
| | - Giovanni Battista Miceli
- Preventive Medicine and Health Surveillance Unit, Santa Maria AlleScotte University Hospital, V.le Bracci 1, 53100 Siena, Italy
| | - Maria Grazia Cusi
- Virology Unit, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Virology Unit, Santa Maria AlleScotte University Hospital, V.le Bracci 1, 53100 Siena, Italy
- Correspondence:
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46
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Lentini A, Pereira A, Winqvist O, Reinius B. Monitoring of the SARS-CoV-2 Omicron BA.1/ BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases. Med (N Y) 2022; 3:636-643.e4. [PMID: 35981541 PMCID: PMC9359497 DOI: 10.1016/j.medj.2022.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/31/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022]
Abstract
Background Throughout the SARS-CoV-2 pandemic, multiple waves of variants of concern have swept across populations, leading to a chain of new and yet more contagious variants dominating COVID-19 cases. Here, we tracked the remarkably rapid shift from Omicron BA.1 to BA.2 sublineage dominance in the Swedish population in early 2022 at a day-by-day basis. Methods Using a custom SARS-CoV-2 Omicron BA.1 lineage-typing RT-PCR assay, we analyzed 174,933 clinical upper airway samples collected during January to March 2022. Findings Our study demonstrates the feasibility and reliability of parallel lineage assignment of select variants at population scale, tracking the dominant sublineage transition from BA.1 to BA.2 at day-to-day resolution and uncovering nearly 2-fold higher levels of viral RNA in cases infected with Omicron BA.2 relative to BA.1. Conclusions Our data provide unique insights into the Omicron BA.1 to BA.2 transition that occurred in Sweden during early 2022, and later, across the world. This may help to understand the increased transmissibility of the BA.2 variant. Early population tracking is critical for informed decision-making and handling of the SARS-CoV-2 pandemic during outbreaks of variant strains of concern. Omicron variant infections emerged during late 2021, but at the time, lineage assignment relied on sequencing or separate genotyping assays in addition to the clinical SARS-CoV-2 RT-PCR, burdening laboratories and restricting the scope of lineage monitoring. Here, researchers at the Karolinska Institute and ABC Labs developed a single RT-PCR assay to simultaneously classify COVID-19 and Omicron BA.1 lineage status and demonstrated the feasibility of parallel lineage assignment of select variants at population scale. The authors show, at day-to-day resolution, the rapid transition from Omicron BA.1 to BA.2 sublineage dominance in the Swedish population, exposing factors that could influence this transition.
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Affiliation(s)
- Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Solna, Sweden
| | | | | | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Solna, Sweden.
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47
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Hirotsu Y, Maejima M, Shibusawa M, Natori Y, Nagakubo Y, Hosaka K, Sueki H, Mochizuki H, Tsutsui T, Kakizaki Y, Miyashita Y, Omata M. Classification of Omicron BA.1, BA.1.1, and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data. Int J Infect Dis 2022; 122:486-491. [PMID: 35760380 PMCID: PMC9233878 DOI: 10.1016/j.ijid.2022.06.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/01/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES Recently, the Omicron strain of SARS-CoV-2 has spread and replaced the previously dominant Delta strain. Several Omicron sublineages (BA.1, BA.1.1, and BA.2) have been identified, with in vitro and preclinical reports showing that the pathogenicity and therapeutic efficacy differs between BA.1 and BA.2. We sought to develop a TaqMan assay to identify these subvariants. METHODS A TaqMan assay was constructed for rapid identification and genotyping of Omicron sublineages with 171 samples. We analyzed three characteristic mutations of the spike gene, Δ69-70, G339D, and Q493R, by TaqMan assay. The accuracy of the TaqMan assay was examined by comparing its results with the results of whole genome sequencing (WGS) analysis. RESULTS A total of 171 SARS-CoV-2 positive samples were analyzed by WGS and TaqMan assay. The 127 samples determined as BA.1/BA.1.1 by WGS were all positive for Δ69-70, G339D and Q493R by TaqMan assay. A total of 42 samples, determined as BA.2 by WGS, were negative for Δ69-70 but positive for G339D and Q493R by TaqMan. Two samples with G339N were determined to be inconclusive by the TaqMan method. Except for these two samples, the concordance rate between WGS and the TaqMan assay was 100% (169/169). CONCLUSION TaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages.
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Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan,Corresponding author: Yosuke Hirotsu, Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan, Post code: 400-8506, Tel: +81-55-253-7111; fax: +81-55-253-8011, ORCID ID: 0000-0002-8002-834X
| | - Makoto Maejima
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Masahiro Shibusawa
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yume Natori
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yuki Nagakubo
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan,Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Kazuhiro Hosaka
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Hitomi Sueki
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan,Central Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan,Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Toshiharu Tsutsui
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yumiko Kakizaki
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan,The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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Mefsin YM, Chen D, Bond HS, Lin Y, Cheung JK, Wong JY, Ali ST, Lau EHY, Wu P, Leung GM, Cowling BJ. Epidemiology of Infections with SARS-CoV-2 Omicron BA.2 Variant, Hong Kong, January-March 2022. Emerg Infect Dis 2022; 28:1856-1858. [PMID: 35914518 PMCID: PMC9423929 DOI: 10.3201/eid2809.220613] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Our analysis of data collected from multiple epidemics in Hong Kong indicated a shorter serial interval and generation time of infections with the SARS-CoV-2 Omicron variant. The age-specific case-fatality risk for Omicron BA.2.2 case-patients without complete primary vaccination was comparable to that of persons infected with ancestral strains in earlier waves.
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49
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Leuzinger K, Roloff T, Egli A, Hirsch HH. Impact of SARS-CoV-2 Omicron on Rapid Antigen Testing Developed for Early-Pandemic SARS-CoV-2 Variants. Microbiol Spectr 2022; 10:e0200622. [PMID: 35943268 PMCID: PMC9431421 DOI: 10.1128/spectrum.02006-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/02/2022] Open
Abstract
Rapid antigen tests (RATs) are widely used for point-of-care or self-testing to identify SARS-CoV-2 (SCoV2), but currently circulating Omicron variants may impair detection. In this study, we prospectively evaluated the Roche-SARS-CoV-2-Antigen and Acon-FlowFlex-SARS-CoV-2-Antigen in 150 consecutively collected nasopharyngeal patient swabs (50 SCoV2 RNA undetectable; 100 SCoV2 Omicron BA.1). Omicron BA.1 results were compared to 92 Ct-matched early-pandemic SCoV2 variants (B.1.160 and B.1.177), to 100 Omicron BA.2 positive and to 100 Omicron BA.5 positive samples. For Omicron BA.1, Roche-SARS-CoV-2-Antigen detected 87% of samples having Ct-values <29 reflecting 3.6% lower rates compared to B.1.160 and B.1.177. Acon-FlowFlex-SARS-CoV-2-Antigen was less affected and detected 90% of Omicron BA.1 with Ct-values <29. Omicron BA.2 and BA.5 detection rates were significantly reduced by 20% and 10%, respectively, for the Roche-SARS-CoV-2-Antigen in samples with Ct-values <29 but remained similar for Acon-FlowFlex-SARS-CoV-2-Antigen. RATs need to be continuously evaluated as new SCoV2-variants emerge. Spreading of Omicron-BA.2, and the recently emerged Omicron BA.5 variant, may not only result from escape from postvaccine or postinfection immunity, but also from false-negative RATs misguiding point-of-care and self-testing decisions at times of restricted molecular testing. IMPORTANCE Antigen tests are widely used for rapid identification of SCoV2-positive cases and their increased risk of transmission. At present, there are several FDA- and CE-cleared tests available in North America and Europe. However, their diagnostic performance has been evaluated with early-pandemic variants. This study provides evidence that variation within the nucleocapsid protein as seen in recently emerged and now globally spreading Omicron BA.2 and BA.5 variants significantly impairs detection rates of widely used antigen tests. Consequently, antigen tests need to be reevaluated when new pandemic SCoV2 variants emerge and start to predominate globally.
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Affiliation(s)
- Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Laboratory Medicine, Department Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Laboratory Medicine, Department Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Hans H. Hirsch
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland
- Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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