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Kustova DD, Pochtovyi AA, Shpakova OG, Shtinova IA, Kuznetsova NA, Kleimenov DA, Komarov AG, Gushchin VA. [The Molecular and Biological Patterns Underlying Sustained SARS-CoV-2 Circulation in the Human Population]. Vopr Virusol 2024; 69:329-340. [PMID: 39361927 DOI: 10.36233/0507-4088-242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Indexed: 10/05/2024]
Abstract
INTRODUCTION For four years, SARS-CoV-2, the etiological agent of COVID-19, has been circulating among humans. By the end of the second year, an absence of immunologically naive individuals was observed, attributable to extensive immunization efforts and natural viral exposure. This study focuses on delineating the molecular and biological patterns that facilitate the persistence of SARS-CoV-2, thereby informing predictions on the epidemiological trajectory of COVID-19 toward refining pandemic countermeasures. The aim of this study was to describe the molecular biological patterns identified that contribute to the persistence of the virus in the human population. MATERIALS AND METHODS For over three years since the beginning of the COVID-19 pandemic, molecular genetic monitoring of SARS-CoV-2 has been conducted, which included the collection of nasopharyngeal swabs from infected individuals, assessment of viral load, and subsequent whole-genome sequencing. RESULTS We discerned dominant genetic lineages correlated with rising disease incidence. We scrutinized amino acid substitutions across SARS-CoV-2 proteins and quantified viral loads in swab samples from patients with emerging COVID-19 variants. Our findings suggest a model of viral persistence characterized by 1) periodic serotype shifts causing substantial diminutions in serum virus-neutralizing activity (> 10-fold), 2) serotype-specific accrual of point mutations in the receptor-binding domain (RBD) to modestly circumvent neutralizing antibodies and enhance receptor affinity, and 3) a gradually increasing amount of virus being shed in mucosal surfaces within a single serotype. CONCLUSION This model aptly accounts for the dynamics of COVID-19 incidence in Moscow. For a comprehensive understanding of these dynamics, acquiring population-level data on immune tension and antibody neutralization relative to genetic lineage compositions is essential.
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Affiliation(s)
- D D Kustova
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
- Federal State Budgetary Educational Institution of Higher Education Lomonosov Moscow State University
| | - A A Pochtovyi
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
- Federal State Budgetary Educational Institution of Higher Education Lomonosov Moscow State University
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University)
| | | | | | - N A Kuznetsova
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - D A Kleimenov
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | | | - V A Gushchin
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
- Federal State Budgetary Educational Institution of Higher Education Lomonosov Moscow State University
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University)
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Okaba K, Inokuchi G, Horioka K, Iwase H, Inoue H, Motomura A, Ishii N, Moue C, Shiomi T, Yajima D. Forensic application of three interstitial pneumonia markers: search for new pneumonia markers in dead bodies. Int J Legal Med 2024; 138:1583-1592. [PMID: 38379061 DOI: 10.1007/s00414-024-03187-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024]
Abstract
In forensic cases, detailed identification of pneumonia is important. Our objective was to statistically determine the applicability of three interstitial lung disease (ILD) markers for forensic diagnosis using serum collected from dead bodies with various postmortem intervals (PMIs). We retrospectively analyzed the levels of postmortem serum Krebs von den Lungen-6 (KL-6) and pulmonary surfactant-associated proteins A and D (SP-A and SP-D) using 221 samples obtained during forensic autopsy at our facility from 2019 to 2023. We evaluated the diagnostic efficacy of ILD markers for various pneumonias against the pathological diagnosis, and examined the assessment of the severity of ILD. When comparing the ILD group with bacterial pneumonia (BP) versus the control group, there was a significant increase in KL-6 in the ILD group. When comparing the severe ILD (SILD) group with the mild ILD (MILD) group, there was a significant increase in KL-6 and SP-D in the SILD group. The optimal cutoff values for differentiating SILD were 607.0 U/mL for KL-6, 55.5 ng/mL for SP-A, and 160.0 ng/mL for SP-D, and the sensitivity/specificity (%) of KL-6, SP-A, and SP-D for SILD were 84.1/95.2, 55.6/85.7, and 66.7/74.6, respectively. This is the first study to examine KL-6 in postmortem serum in forensic medicine. By analyzing dead bodies with various PMIs, our results confirmed statistically that postmortem serum KL-6 specifically detects ILD, postmortem serum SP-A has high sensitivity to lung injury, and postmortem serum SP-D is potentially useful in assessing the severity of ILD.
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Affiliation(s)
- Keisuke Okaba
- Department of Forensic Medicine, School of Medicine, International University of Health and Welfare, Narita, Japan.
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
| | - Go Inokuchi
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kie Horioka
- Department of Forensic Medicine, School of Medicine, International University of Health and Welfare, Narita, Japan
- Department of Forensic Medicine, Research Unit of Internal Medicine, Medical Research Center, University of Oulu, Oulu, Finland
| | - Hirotaro Iwase
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Inoue
- Department of Forensic Medicine, School of Medicine, International University of Health and Welfare, Narita, Japan
| | - Ayumi Motomura
- Department of Forensic Medicine, School of Medicine, International University of Health and Welfare, Narita, Japan
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Namiko Ishii
- Department of Forensic Medicine, School of Medicine, International University of Health and Welfare, Narita, Japan
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Chihiro Moue
- Department of Forensic Medicine, School of Medicine, International University of Health and Welfare, Narita, Japan
| | - Takayuki Shiomi
- Department of Pathology, School of Medicine, International University of Health and Welfare, Narita, Japan
| | - Daisuke Yajima
- Department of Forensic Medicine, School of Medicine, International University of Health and Welfare, Narita, Japan
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
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Shrestha S, Malla B, Angga MS, Sthapit N, Raya S, Hirai S, Rahmani AF, Thakali O, Haramoto E. Long-term SARS-CoV-2 surveillance in wastewater and estimation of COVID-19 cases: An application of wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165270. [PMID: 37400022 DOI: 10.1016/j.scitotenv.2023.165270] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
The role of wastewater-based epidemiology (WBE), a powerful tool to complement clinical surveillance, has increased as many grassroots-level facilities, such as municipalities and cities, are actively involved in wastewater monitoring, and the clinical testing of coronavirus disease 2019 (COVID-19) is downscaled widely. This study aimed to conduct long-term wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Yamanashi Prefecture, Japan, using one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay and estimate COVID-19 cases using a cubic regression model that is simple to implement. Influent wastewater samples (n = 132) from a wastewater treatment plant were collected normally once weekly between September 2020 and January 2022 and twice weekly between February and August 2022. Viruses in wastewater samples (40 mL) were concentrated by the polyethylene glycol precipitation method, followed by RNA extraction and RT-qPCR. The K-6-fold cross-validation method was used to select the appropriate data type (SARS-CoV-2 RNA concentration and COVID-19 cases) suitable for the final model run. SARS-CoV-2 RNA was successfully detected in 67 % (88 of 132) of the samples tested during the whole surveillance period, 37 % (24 of 65) and 96 % (64 of 67) of the samples collected before and during 2022, respectively, with concentrations ranging from 3.5 to 6.3 log10 copies/L. This study applied a nonnormalized SARS-CoV-2 RNA concentration and nonstandardized data for running the final 14-day (1 to 14 days) offset models to estimate weekly average COVID-19 cases. Comparing the parameters used for a model evaluation, the best model showed that COVID-19 cases lagged 3 days behind the SARS-CoV-2 RNA concentration in wastewater samples during the Omicron variant phase (year 2022). Finally, 3- and 7-day offset models successfully predicted the trend of COVID-19 cases from September 2022 until February 2023, indicating the applicability of WBE as an early warning tool.
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Affiliation(s)
- Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Made Sandhyana Angga
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Niva Sthapit
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sunayana Raya
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Soichiro Hirai
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Aulia Fajar Rahmani
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Ocean Thakali
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Kagami K, Oyamada R, Watanabe T, Nakakubo S, Hayashi T, Iwasaki S, Fukumoto T, Usami T, Hayasaka K, Fujisawa S, Watanabe C, Nishida M, Teshima T, Niinuma Y, Yokota I, Takekuma Y, Sugawara M, Ishiguro N. Factors associated with household transmission of SARS-CoV-2 omicron variant to health care workers: A retrospective cohort study. Int J Nurs Pract 2023; 29:e13195. [PMID: 37621085 DOI: 10.1111/ijn.13195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
AIM The aim of this study was to determine the risk factors for household transmission of the omicron variant of SARS-CoV-2. BACKGROUND The household infection rate has been reported to be higher for the omicron variant than for non-omicron variants of SARS-CoV-2. Determination of the risk factors for household transmission of the omicron variant is therefore important. DESIGN A Retrospective Cohort Study was conducted. METHODS When family members of health care workers (HCWs) were found to be infected with SARS-CoV-2, the HCWs had to receive two nucleic acid amplification tests for SARS-CoV-2: immediately after and 5 to 10 days after the onset of COVID-19 in the family members. Risk factors of household transmission were analysed by comparing cases (HCWs infected with SARS-CoV-2) and controls (HCWs not infected with SARS-CoV-2) using multivariable analysis. RESULTS Unvaccinated status (OR: 3.97), age of index cases (≤6 years) (OR: 1.94) and staying at home with index cases (OR: 10.18) were risk factors for household transmission. CONCLUSION If there is a strong desire to avoid household infection, family members infected with SARS-CoV-2 should live separately during the period of viral shedding.
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Affiliation(s)
- Keisuke Kagami
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Department of Pharmacy, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Reiko Oyamada
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Tsubasa Watanabe
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Sho Nakakubo
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Takahiro Hayashi
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Sumio Iwasaki
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Tatsuya Fukumoto
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Takayuki Usami
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Kasumi Hayasaka
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Shinichi Fujisawa
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Chiaki Watanabe
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Mutsumi Nishida
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Takanori Teshima
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido, Japan
| | - Yusuke Niinuma
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Department of Pharmacy, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Isao Yokota
- Department of Biostatistics, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, Japan
| | - Yoh Takekuma
- Department of Pharmacy, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Mitsuru Sugawara
- Department of Pharmacy, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Laboratory of Pharmacokinetics, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Nobuhisa Ishiguro
- Department of Infection Control and Prevention, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
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5
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Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B. Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Nat Struct Mol Biol 2023; 30:980-990. [PMID: 37430064 DOI: 10.1038/s41594-023-01023-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/17/2023] [Indexed: 07/12/2023]
Abstract
The Omicron subvariant BA.2 has become the dominant circulating strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in many countries. Here, we have characterized structural, functional and antigenic properties of the full-length BA.2 spike (S) protein and compared replication of the authentic virus in cell culture and an animal model with previously prevalent variants. BA.2 S can fuse membranes slightly more efficiently than Omicron BA.1, but still less efficiently than other previous variants. Both BA.1 and BA.2 viruses replicated substantially faster in animal lungs than the early G614 (B.1) strain in the absence of pre-existing immunity, possibly explaining the increased transmissibility despite their functionally compromised spikes. As in BA.1, mutations in the BA.2 S remodel its antigenic surfaces, leading to strong resistance to neutralizing antibodies. These results suggest that both immune evasion and replicative advantage may contribute to the heightened transmissibility of the Omicron subvariants.
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Affiliation(s)
- Jun Zhang
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Hailong Gao
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Christy L Lavine
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Wei Shi
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA, USA
| | - Krishna Anand
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA, USA
| | - Matina Kosikova
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Hyung Joon Kwon
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Pei Tong
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital; Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Avneesh Gautam
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital; Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | | | | | - Megan L Mayer
- The Harvard Cryo-EM Center for Structural Biology, Boston, MA, USA
| | - Duane R Wesemann
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital; Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jianming Lu
- Codex BioSolutions, Inc., Rockville, MD, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Tianshu Xiao
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA.
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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Morris CP, Eldesouki RE, Sachithanandham J, Fall A, Norton JM, Abdullah O, Gallagher N, Li M, Pekosz A, Klein EY, Mostafa HH. Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization. Clin Infect Dis 2023; 76:1276-1284. [PMID: 36366857 PMCID: PMC10069846 DOI: 10.1093/cid/ciac885] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The variant of concern Omicron has become the sole circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant for the past several months. Omicron subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 evolved over the time, with BA.1 causing the largest wave of infections globally in December 2021-January 2022. This study compared the clinical outcomes in patients infected with different Omicron subvariants and the relative viral loads and recovery of infectious virus from upper respiratory specimens. METHODS SARS-CoV-2-positive remnant clinical specimens, diagnosed at the Johns Hopkins Microbiology Laboratory between December 2021 and July 2022, were used for whole-genome sequencing. The clinical outcomes of infections with Omicron subvariants were compared with infections with BA.1. Cycle threshold (Ct) values and the recovery of infectious virus on the VeroTMPRSS2 cell line from clinical specimens were compared. RESULTS BA.1 was associated with the largest increase in SARS-CoV-2 positivity rate and coronavirus disease 2019 (COVID-19)-related hospitalizations at the Johns Hopkins system. After a peak in January, cases decreased in the spring, but the emergence of BA.2.12.1 followed by BA.5 in May 2022 led to an increase in case positivity and admissions. BA.1 infections had a lower mean Ct value when compared with other Omicron subvariants. BA.5 samples had a greater likelihood of having infectious virus at Ct values <20. CONCLUSIONS Omicron subvariants continue to be associated with a relatively high rate of polymerase chain reaction (PCR) positivity and hospital admissions. The BA.5 infections are more while BA.2 infections are less likely to have infectious virus, suggesting potential differences in infectibility during the Omicron waves.
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Affiliation(s)
- C Paul Morris
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, Maryland, USA
| | - Raghda E Eldesouki
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Histology, Genetics Unit, School of Medicine, Suez Canal University, Ismailia, Egypt
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amary Fall
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Julie M Norton
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Omar Abdullah
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, DC, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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7
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Hirotsu Y, Omata M. Genomic evidence for reinfection with different Omicron subvariants. J Infect 2023; 86:e61-e63. [PMID: 36642191 PMCID: PMC9834117 DOI: 10.1016/j.jinf.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023]
Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis 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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8
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Hirotsu Y, Kakizaki Y, Saito A, Tsutsui T, Hanawa S, Yamaki H, Ide S, Kawaguchi M, Kobayashi H, Miyashita Y, Omata M. Lung tropism in hospitalized patients following infection with SARS-CoV-2 variants from D614G to Omicron BA.2. COMMUNICATIONS MEDICINE 2023; 3:32. [PMID: 36841870 PMCID: PMC9959956 DOI: 10.1038/s43856-023-00261-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/10/2023] [Indexed: 02/27/2023] Open
Abstract
BACKGROUND The genetic and pathogenic characteristics of SARS-CoV-2 have evolved from the original isolated strains; however, the changes in viral virulence have not been fully defined. In this study, we analyzed the association between the severity of the pathogenesis of pneumonia in humans and SARS-CoV-2 variants that have been prevalent to date. METHODS We examined changes in the variants and tropism of SARS-CoV-2. A total of 514 patients admitted between February 2020 and August 2022 were included and evaluated for pneumonia by computed tomography (CT) as a surrogate of viral tropism. RESULTS The prevalence of pneumonia for each variant was as follows: D614G (57%, 65/114), Alpha (67%, 41/61), Delta (49%, 41/84), Omicron BA.1.1 (26%, 43/163), and Omicron BA.2 (11%, 10/92). The pneumonia prevalence in unvaccinated patients progressively declined from 70% to 11% as the variants changed: D614G (56%, 61/108), Alpha (70%, 26/37), Delta (60%, 38/63), BA.1.1 (52%, 15/29), and BA.2 (11%, 2/19). The presence of pneumonia in vaccinated patients was as follows: Delta (16%, 3/19), BA.1.1 (21%, 27/129), and BA.2 (11%, 8/73). Compared with D614G, the areas of lung involvement were also significantly reduced in BA.1.1 and BA.2 variants. CONCLUSIONS Compared with previous variants, there was a marked decrease in pneumonia prevalence and lung involvement in patients infected with Omicron owing to decreased tropism in the lungs that hindered viral proliferation in the alveolar epithelial tissue. Nevertheless, older, high-risk patients with comorbidities who are infected with an Omicron variant can still develop pneumonia and require early treatment.
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Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
| | - Yumiko Kakizaki
- grid.417333.10000 0004 0377 4044Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Akitoshi Saito
- Department of Radiology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Toshiharu Tsutsui
- grid.417333.10000 0004 0377 4044Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Syunya Hanawa
- grid.417333.10000 0004 0377 4044Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Haruna Yamaki
- grid.417333.10000 0004 0377 4044Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Syuichiro Ide
- grid.417333.10000 0004 0377 4044Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Makoto Kawaguchi
- grid.417333.10000 0004 0377 4044Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Hiroaki Kobayashi
- grid.417333.10000 0004 0377 4044Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yoshihiro Miyashita
- grid.417333.10000 0004 0377 4044Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Masao Omata
- grid.417333.10000 0004 0377 4044Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan ,grid.26999.3d0000 0001 2151 536XThe University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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9
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Teyssou E, Marot S, Cocherie T, Fauchois A, Abdi B, Todesco E, Akhavan S, Pourcher V, Calvez V, Marcelin AG, Soulie C. Prolonged replication of BA.1 and BA.2 Omicron lineages compared to Delta variant in nasopharyngeal samples from COVID-19 patients. Infect Dis Now 2023; 53:104629. [PMID: 36323397 PMCID: PMC9618294 DOI: 10.1016/j.idnow.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVES We aimed to characterize and compare the viral loads (VL) of the Omicron BA.1 and BA.2 lineages and the Delta variant in nasopharyngeal samples from newly diagnosed COVID-19 patients and their kinetics over time. PATIENTS AND METHODS The kinetics of the VL were measured on the CT data from 215 SARS-CoV-2 positive patients who presented at least two positive PCRs a day apart and were screened for SARS-CoV-2 viral lineages. RESULTS We observed no significant difference in median CT value during the first diagnostic test between the Delta variant and the two Omicron lineages. However, the kinetics of CT decreases for the BA.1 and BA.2 lineage were significantly lengthier in time than the kinetics for the Delta variant. The BA.2 lineage presented lower median CT value (-2 CT) (inversely proportional to the VL) than the BA.1 lineage. CONCLUSIONS BA.2 Omicron lineage presented higher VL than BA.1 Omicron lineage at diagnostic. Omicron BA.1 and BA.2 lineages have more prolonged replication than the Delta variant.
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Affiliation(s)
- Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France.
| | - Stéphane Marot
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Théophile Cocherie
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Antoine Fauchois
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Basma Abdi
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Eve Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Sepideh Akhavan
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Valérie Pourcher
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Service des maladies infectieuse, F-75013 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Cathia Soulie
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France.
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10
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Hirotsu Y, Omata M. Detection of the Omicron BA.2.75 subvariant in Japan. J Infect 2023; 86:e5-e7. [PMID: 36087746 PMCID: PMC9450472 DOI: 10.1016/j.jinf.2022.08.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/21/2022] [Accepted: 08/29/2022] [Indexed: 02/04/2023]
Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis 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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11
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Mimura W, Ishiguro C, Maeda M, Murata F, Fukuda H. Effectiveness of a Third Dose of COVID-19 mRNA Vaccine During the Omicron BA.1- and BA.2-Predominant Periods in Japan: The VENUS Study. Open Forum Infect Dis 2022; 9:ofac636. [PMID: 36589480 PMCID: PMC9792082 DOI: 10.1093/ofid/ofac636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background Vaccine effectiveness against the severe acute respiratory syndrome coronavirus 2 Omicron BA.2 sublineage in Japan is unknown. We assessed the effectiveness of a third dose of COVID-19 mRNA vaccine compared with that of 2 doses. Methods We performed a population-based cohort study using a municipality database located in the Chubu region of Japan during the Omicron BA.1- and BA.2-predominant periods (January 1-March 31, 2022 and April 1-27, 2022, respectively). We included residents aged ≥16 years who received a second vaccine dose at ≥14 days before the start of each period, regardless of the third dose. We compared the data at 14 days after the second and third dose and at 2-week intervals from 14 days to 10 weeks after the third dose using a Cox regression model. Vaccine effectiveness was defined as (1 - hazard ratio) × 100 (%). Results In total, 295 705 and 288 184 individuals were included in the BA.1- and BA.2-predominant periods, respectively. The effectiveness of a third dose against infection was 62.4% and 48.1% in the BA.1- and BA.2-predominant periods, respectively. Vaccine effectiveness at 2-3 weeks and ≥10 weeks after the third dose decreased from 63.6% (95% confidence interval [CI], 56.4-69.5%) to 52.9% (95% CI, 41.1-62.3%) and from 54.5% (95% CI, 3.0-78.7%) to 40.1% (95% CI, 15.1-57.7%) in the BA.1- and BA.2-predominant periods, respectively. Conclusions A third dose was moderately effective against BA.1 and BA.2 sublineages, but its effectiveness decreased by approximately 10% age points from 2-3 weeks to ≥10 weeks after the third vaccination.
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Affiliation(s)
- Wataru Mimura
- Section of Clinical Epidemiology, Department of Data Science, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Chieko Ishiguro
- Correspondence: Chieko Ishiguro, MPH, PhD, Section of Clinical Epidemiology, Department of Data Science, Center for Clinical Sciences, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan ()
| | - Megumi Maeda
- Department of Health Care Administration and Management, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Fumiko Murata
- Department of Health Care Administration and Management, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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12
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Samsunder N, de Vos M, Ngcapu S, Giandhari J, Lewis L, Kharsany ABM, Cawood C, de Oliveira T, Karim QA, Karim SA, Naidoo K, Escadafal C, Sivro A. Clinical Evaluation of Severe Acute Respiratory Syndrome Coronavirus 2 Rapid Antigen Tests During the Omicron Wave in South Africa. J Infect Dis 2022; 226:1412-1417. [PMID: 35921539 PMCID: PMC9384653 DOI: 10.1093/infdis/jiac333] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
We evaluated the performance of nasal and nasopharyngeal Standard Q COVID-19 [coronavirus disease 2019] Ag tests (SD Biosensor) and the Panbio COVID-19 Ag Rapid Test Device (nasal; Abbott) against the Abbott RealTime severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay during the Omicron (clades 21M, 21K, and 21L) wave in South Africa. Overall, all evaluated tests performed well, with high sensitivity (range, 77.78%-81.42%) and excellent specificity values (>99%). The sensitivity of rapid antigen tests increased above 90% in samples with cycle threshold <20, and all 3 tests performed best within the first week after symptom onset.
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Affiliation(s)
- Natasha Samsunder
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | | | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Ayesha B M Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
| | - Cherie Cawood
- Epicentre AIDS Risk Management, Durban, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, USA
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Epidemiology, Columbia University, New York City, USA
| | - Salim Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Epidemiology, Columbia University, New York City, USA
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- MRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | | | - Aida Sivro
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
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13
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Toya T, Atsuta Y, Sanada T, Honda T, Sadato D, Sekiya N, Kogure H, Takakuwa S, Onai D, Shingai N, Shimizu H, Najima Y, Kobayashi T, Ohashi K, Harada Y, Kohara M, Doki N. Attenuated humoral response against SARS-CoV-2 mRNA vaccination in allogeneic stem cell transplantation recipients. Cancer Sci 2022; 114:586-595. [PMID: 36161681 PMCID: PMC9538567 DOI: 10.1111/cas.15603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 02/07/2023] Open
Abstract
Antibody persistence several months after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccination in allogeneic stem cell transplantation recipients remains largely unknown. We sequentially evaluated the humoral response to two doses of mRNA vaccines in 128 adult recipients and identified the risk factors involved in a poor response. The median interval between stem cell transplantation and vaccination was 2.7 years. The SARS-CoV-2 S1 Ab became positive after the second vaccination dose in 87.6% of the recipients, and the median titer was 1235.4 arbitrary units (AU)/ml. In patients on corticosteroid treatment, the corticosteroid dose inversely correlated with Ab titer. Multivariate analysis identified risk factors for poor peak response such as an interval from stem cell transplantation ≤1 year, history of clinically significant CMV infection, and use of >5 mg/day prednisolone at vaccination. Six months after vaccination, the median titer decreased to 185.15 AU/ml, and use of >5 mg/day prednisolone at vaccination was significantly associated with a poor response. These results indicate that early vaccination after stem cell transplantation (<12 months) and CMV infection are risk factors for poor peak response, while steroid use is important for a peak as well as a persistent response. In conclusion, although humoral response is observed in many stem cell transplantation recipients after two doses of vaccination, Ab titers diminish with time, and factors associated with persistence and a peak immunity should be considered separately.
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Affiliation(s)
- Takashi Toya
- Hematology Division,Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Yuya Atsuta
- Hematology Division,Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Takahiro Sanada
- Department of Microbiology and Cell BiologyTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Tomoko Honda
- Department of Microbiology and Cell BiologyTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Daichi Sadato
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Noritaka Sekiya
- Department of Infection Prevention and Control, Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan,Department of Clinical Laboratory, Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Hiroko Kogure
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Sonomi Takakuwa
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Daishi Onai
- Hematology Division,Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Naoki Shingai
- Hematology Division,Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Hiroaki Shimizu
- Hematology Division,Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Yuho Najima
- Hematology Division,Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Takeshi Kobayashi
- Hematology Division,Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Kazuteru Ohashi
- Hematology Division,Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Yuka Harada
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
| | - Michinori Kohara
- Department of Microbiology and Cell BiologyTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Noriko Doki
- Hematology Division,Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan
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14
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Morris CP, Eldesouki RE, Sachithanandham J, Fall A, Norton JM, Abdullah O, Gallagher N, Li M, Pekosz A, Klein EY, Mostafa HH. Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.09.20.22280154. [PMID: 36172137 PMCID: PMC9516865 DOI: 10.1101/2022.09.20.22280154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background The variant of concern, Omicron, has become the sole circulating SARS-CoV-2 variant for the past several months. Omicron subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 evolved over the time, with BA.1 causing the largest wave of infections globally in December 2021- January 2022. In this study, we compare the clinical outcomes in patients infected with different Omicron subvariants and compare the relative viral loads, and recovery of infectious virus from upper respiratory specimens. Methods SARS-CoV-2 positive remnant clinical specimens, diagnosed at the Johns Hopkins Microbiology Laboratory between December 2021 and July 2022, were used for whole genome sequencing. The clinical outcomes of infections with Omicron subvariants were compared to infections with BA.1. Cycle threshold values (Ct) and the recovery of infectious virus on VeroTMPRSS2 cell line from clinical specimens were compared. Results The BA.1 was associated with the largest increase in SARS-CoV-2 positivity rate and COVID-19 related hospitalizations at the Johns Hopkins system. After a peak in January cases fell in the spring, but the emergence of BA.2.12.1 followed by BA.5 in May 2022 led to an increase in case positivity and admissions. BA.1 infections had a lower mean Ct when compared to other Omicron subvariants. BA.5 samples had a greater likelihood of having infectious virus at Ct values less than 20. Conclusions Omicron subvariants continue to associate with a relatively high positivity and admissions. The BA.5 infections are more while BA.2 infections are less likely to have infectious virus, suggesting potential differences in infectibility during the Omicron waves. Funding Centers for Disease Control and Prevention contract 75D30121C11061, NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, and The Modeling Infectious Diseases in Healthcare Network (MInD) under awards U01CK000589.
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Affiliation(s)
- C. Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
- National Institute of Allergy and Infectious Disease, National Institutes of Health
| | - Raghda E. Eldesouki
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
- Suez Canal University, School of Medicine, Department of Histology, Genetics unit, Egypt
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health
| | - Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Julie M. Norton
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Nicholas Gallagher
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health
- Department of Emergency Medicine, Johns Hopkins School of Medicine
| | - Eili Y. Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine
- Center for Disease Dynamics, Economics, and Policy, Washington DC
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
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15
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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] [Abstract] [Key Words] [MESH Headings] [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.
| | - 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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16
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Huang L. Adjusted control rate closely associated with the epidemiologic evolution of the recent COVID-19 wave in Shanghai, with 94.3% of all new cases being asymptomatic on first diagnosis. J Infect 2022; 85:e89-e91. [PMID: 35843384 PMCID: PMC9288239 DOI: 10.1016/j.jinf.2022.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/03/2022] [Accepted: 07/09/2022] [Indexed: 01/19/2023]
Affiliation(s)
- Lei Huang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Medical Center on Aging of Ruijin Hospital, MCARJH, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
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17
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Ortega MA, García-Montero C, Fraile-Martinez O, Colet P, Baizhaxynova A, Mukhtarova K, Alvarez-Mon M, Kanatova K, Asúnsolo A, Sarría-Santamera A. Recapping the Features of SARS-CoV-2 and Its Main Variants: Status and Future Paths. J Pers Med 2022; 12:995. [PMID: 35743779 PMCID: PMC9225183 DOI: 10.3390/jpm12060995] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/06/2022] [Accepted: 06/16/2022] [Indexed: 12/14/2022] Open
Abstract
Over the two years that we have been experiencing the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic, our challenges have been the race to develop vaccines and the difficulties in fighting against new variants due to the rapid ability of the virus to evolve. In this sense, different organizations have identified and classified the different variants that have been emerging, distinguishing between variants of concern (VOC), variants of interest (VOI), or variants under monitoring (VUM). The following review aims to describe the latest updates focusing on VOC and already de-escalated variants, as well as to describe the impact these have had on the global situation. Understanding the intrinsic properties of SARS-CoV-2 and its interaction with the immune system and vaccination is essential to make out the underlying mechanisms that have led to the appearance of these variants, helping to determine the next steps for better public management of this pandemic.
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Affiliation(s)
- Miguel A. Ortega
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (M.A.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Cielo García-Montero
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (M.A.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Oscar Fraile-Martinez
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (M.A.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Paolo Colet
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
| | - Ardak Baizhaxynova
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
| | - Kymbat Mukhtarova
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
| | - Melchor Alvarez-Mon
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (M.A.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Immune System Diseases-Rheumatology, Oncology Service an Internal Medicine (CIBEREHD), University Hospital Príncipe de Asturias, 28806 Alcala de Henares, Spain
| | - Kaznagul Kanatova
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
| | - Angel Asúnsolo
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
| | - Antonio Sarría-Santamera
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
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Nan BG, Zhang S, Li YC, Kang XP, Chen YH, Li L, Jiang T, Li J. Convolutional Neural Networks Based on Sequential Spike Predict the High Human Adaptation of SARS-CoV-2 Omicron Variants. Viruses 2022; 14:v14051072. [PMID: 35632811 PMCID: PMC9147419 DOI: 10.3390/v14051072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/04/2022] Open
Abstract
The COVID-19 pandemic has frequently produced more highly transmissible SARS-CoV-2 variants, such as Omicron, which has produced sublineages. It is a challenge to tell apart high-risk Omicron sublineages and other lineages of SARS-CoV-2 variants. We aimed to build a fine-grained deep learning (DL) model to assess SARS-CoV-2 transmissibility, updating our former coarse-grained model, with the training/validating data of early-stage SARS-CoV-2 variants and based on sequential Spike samples. Sequential amino acid (AA) frequency was decomposed into serially and slidingly windowed fragments in Spike. Unsupervised machine learning approaches were performed to observe the distribution in sequential AA frequency and then a supervised Convolutional Neural Network (CNN) was built with three adaptation labels to predict the human adaptation of Omicron variants in sublineages. Results indicated clear inter-lineage separation and intra-lineage clustering for SARS-CoV-2 variants in the decomposed sequential AAs. Accurate classification by the predictor was validated for the variants with different adaptations. Higher adaptation for the BA.2 sublineage and middle-level adaptation for the BA.1/BA.1.1 sublineages were predicted for Omicron variants. Summarily, the Omicron BA.2 sublineage is more adaptive than BA.1/BA.1.1 and has spread more rapidly, particularly in Europe. The fine-grained adaptation DL model works well for the timely assessment of the transmissibility of SARS-CoV-2 variants, facilitating the control of emerging SARS-CoV-2 variants.
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Affiliation(s)
| | | | | | | | | | | | | | - Jing Li
- Correspondence: (T.J.); (J.L.)
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