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Singh G, Warang P, García-Bernalt Diego J, Chang L, Bykov Y, Singh S, Pache L, Cuadrado-Castano S, Webb B, Garcia-Sastre A, Schotsaert M. Host immune responses associated with SARS-CoV-2 Omicron infection result in protection or pathology during reinfection depending on mouse genetic background. RESEARCH SQUARE 2023:rs.3.rs-3637405. [PMID: 38077015 PMCID: PMC10705603 DOI: 10.21203/rs.3.rs-3637405/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Rapid emergence of antigenic distinct SARS-CoV-2 variants implies a greater risk of reinfection as viruses can escape neutralizing antibodies induced by vaccination or previous viral exposure. Disease severity during COVID-19 depends on many variables such as age-related comorbidities, host immune status and genetic variation. The host immune response during infection with SARS-CoV-2 may contribute to disease severity, which can range from asymptomatic to severe with fatal outcome. Furthermore, the extent of host immune response activation may rely on underlying genetic predisposition for disease or protection. To address these questions, we performed immune profiling studies in mice with different genetic backgrounds - transgenic K18-hACE2 and wild-type 129S1 mice - subjected to reinfection with the severe disease-causing SARS-CoV-2 B.1.351 variant, 30 days after experimental milder BA.1 infection. BA.1 preinfection conferred protection against B.1.351-induced morbidity in K18-hACE2 mice but aggravated disease in 129S1 mice. We found that he cytokine/chemokine profile in B.1.351 re-infected 129S1mice is similar to that during severe SARS-CoV-2 infection in humans and is characterized by a much higher level of IL-10, IL-1β, IL-18 and IFN-γ, whereas in B.1.351 re-infected K18-hACE2 mice, the cytokine profile echoes the signature of naïve mice undergoing viral infection for the first time. Interestingly, the enhanced pathology observed in 129S1 mice upon reinfection cannot be attributed to a less efficient induction of adaptive immune responses to the initial BA.1 infection, as both K18-hACE2 and 129S1 mice exhibited similar B and T cell responses at 30 DPI against BA.1, with similar anti-BA.1 or B.1.351 spike-specific ELISA binding titers, levels of germinal center B-cells, and SARS-CoV-2-Spike specific tissue-resident T-cells. Long-term effects of BA.1 infection are associated with differential transcriptional changes in bronchoalveolar lavage-derived CD11c + immune cells from K18-hACE2 and 129S1, with K18-hACE2 CD11c + cells showing a strong antiviral defense gene expression profile whereas 129S1 CD11c + cells showed a more pro-inflammatory response. In conclusion, initial infection with BA.1 induces cross-reactive adaptive immune responses in both K18-hACE2 and 129S1 mice, however the different disease outcome of reinfection seems to be driven by differential responses of CD11c + cells in the alveolar space.
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Affiliation(s)
| | | | | | | | | | - Sarabjot Singh
- RT-PCR COVID-19 Laboratory, Civil Hospital, Moga, Punjab, India
| | - Lars Pache
- Sanford Burnham Prebys Medical Discovery Institute
| | | | - Brett Webb
- Department of Veterinary Sciences, University of Wyoming
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102
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Nan X, Hardinge P, Hoehn S, Dighe SN, Ukeri J, Pease DF, Griffin J, Warrington JI, Saud Z, Hottinger E, Webster G, Jones D, Kille P, Weightman A, Stanton R, Castell OK, Murray JAH, Jurkowski TP. VarLOCK: sequencing-independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance. Sci Rep 2023; 13:20832. [PMID: 38012215 PMCID: PMC10681975 DOI: 10.1038/s41598-023-47289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023] Open
Abstract
The COVID-19 pandemic demonstrated the need for rapid molecular diagnostics. Vaccination programs can provide protection and facilitate the opening of society, but newly emergent and existing viral variants capable of evading the immune system endanger their efficacy. Effective surveillance for Variants of Concern (VOC) is therefore important. Rapid and specific molecular diagnostics can provide speed and coverage advantages compared to genomic sequencing alone, benefitting the public health response and facilitating VOC containment. Here we expand the recently developed SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) to provide rapid and sensitive discrimination of SARS-CoV-2 VOCs that can be used at point of care, implemented in the pipelines of small or large testing facilities, and even determine the proportion of VOCs in pooled population-level wastewater samples. This technology complements sequencing efforts to allow facile and rapid identification of individuals infected with VOCs to help break infection chains. We show the optimisation of our VarLOCK assays (Variant-specific SHERLOCK) for multiple specific mutations in the S gene of SARS-CoV-2 and validation with samples from the Cardiff University Testing Service. We also show the applicability of VarLOCK to national wastewater surveillance of SARS-CoV-2 variants and the rapid adaptability of the technique for new and emerging VOCs.
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Affiliation(s)
- Xinsheng Nan
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Patrick Hardinge
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - Sven Hoehn
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Shrinivas Nivrutti Dighe
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - John Ukeri
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Darius F Pease
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Joshua Griffin
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Jessica I Warrington
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- Biodexa Pharmaceuticals (Wales) Ltd, 1 Caspian Point, Caspian Way, Cardiff, CF10 4DQ, UK
| | - Zack Saud
- Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Emma Hottinger
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Gordon Webster
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Davey Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Peter Kille
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Andrew Weightman
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Richard Stanton
- Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Oliver K Castell
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Tomasz P Jurkowski
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
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103
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Maniscalco L, Genovese D, Ravazzolo B, Vella G, Sparacia B, Vitale F, Matranga D, Amodio E. Low Risk of SARS-CoV-2 Reinfection for Fully or Boosted mRNA Vaccinated Subjects in Sicily: A Population-Based Study Using Real-World Data. Vaccines (Basel) 2023; 11:1757. [PMID: 38140163 PMCID: PMC10748171 DOI: 10.3390/vaccines11121757] [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: 10/20/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Background: Reinfections occur as a response to natural infections wanes and novel strains of SARS-CoV-2 emerge. The present research explored the correlation between sex, age, COVID-19 vaccination, prior infection hospitalization, and SARS-CoV-2 reinfection in Sicily, Italy. Materials and Methods: A population-based retrospective cohort study was articulated using the vaccination flux from a regional registry and the Sicilian COVID-19 monitoring system of the Italian Institute of Health. Only adult Sicilians were included in the study, and hazard ratios were calculated using Cox regression. Results: Partial vaccination provided some protection (adj-HR: 0.92), when compared to unvaccinated individuals; furthermore, reinfection risk was reduced by full vaccination (adj-HR: 0.43), and the booster dose (adj-HR: 0.41). Males had a lower risk than females of reinfection with SARS-CoV-2 (adj-HR: 0.75). Reinfection with SARS-CoV-2 was diminished by hospitalization during the first infection (adj-HR: 0.78). Reinfection risk was higher among those aged 30-39 and 40-49 compared to those aged 18-29, whereas those aged 60-69, 70-79, and 80+ were statistically protected. Reinfection was significantly more frequent during the wild-type-Alpha, Delta, Delta-Omicron, and Omicron dominance/codominance waves compared to the wild type. Conclusions: This study establishes a solid base for comprehending the reinfection phenomenon in Sicily by pinpointing the most urgent policy hurdles and identifying some of the major factors. COVID-19 vaccination, one of the most effective public health tools, protects against reinfection, mostly caused by the Omicron strain. Elderly and hospitalized people's lower risk suggests stricter PPE use.
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Affiliation(s)
- Laura Maniscalco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro” (PROMISE), University of Palermo, Via del Vespro 133, 90127 Palermo, Italy; (L.M.); (G.V.); (B.S.); (F.V.); (D.M.); (E.A.)
| | - Dario Genovese
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro” (PROMISE), University of Palermo, Via del Vespro 133, 90127 Palermo, Italy; (L.M.); (G.V.); (B.S.); (F.V.); (D.M.); (E.A.)
| | - Barbara Ravazzolo
- Unità Operativa Complessa di Epidemiologia Clinica con Registro Tumori, Azienda Ospedaliera Universitaria Policlinico “Paolo Giaccone”, 90127 Palermo, Italy;
| | - Giuseppe Vella
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro” (PROMISE), University of Palermo, Via del Vespro 133, 90127 Palermo, Italy; (L.M.); (G.V.); (B.S.); (F.V.); (D.M.); (E.A.)
| | - Benedetta Sparacia
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro” (PROMISE), University of Palermo, Via del Vespro 133, 90127 Palermo, Italy; (L.M.); (G.V.); (B.S.); (F.V.); (D.M.); (E.A.)
| | - Francesco Vitale
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro” (PROMISE), University of Palermo, Via del Vespro 133, 90127 Palermo, Italy; (L.M.); (G.V.); (B.S.); (F.V.); (D.M.); (E.A.)
- Unità Operativa Complessa di Epidemiologia Clinica con Registro Tumori, Azienda Ospedaliera Universitaria Policlinico “Paolo Giaccone”, 90127 Palermo, Italy;
| | - Domenica Matranga
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro” (PROMISE), University of Palermo, Via del Vespro 133, 90127 Palermo, Italy; (L.M.); (G.V.); (B.S.); (F.V.); (D.M.); (E.A.)
| | - Emanuele Amodio
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro” (PROMISE), University of Palermo, Via del Vespro 133, 90127 Palermo, Italy; (L.M.); (G.V.); (B.S.); (F.V.); (D.M.); (E.A.)
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104
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Ismail NF, Rahman AE, Kulkarni D, Zhu F, Wang X, del Carmen Morales G, Srivastava A, Allen KE, Spinardi J, Kyaw MH, Nair H. Incidence and outcome of SARS-CoV-2 reinfection in the pre-Omicron era: A global systematic review and meta-analysis. J Glob Health 2023; 13:06051. [PMID: 37994839 PMCID: PMC10667793 DOI: 10.7189/jogh.13.06051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
Background With the emergence of new variants and sub-lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reinfections can significantly impact herd immunity, vaccination policies, and decisions on other public health measures. We conducted a systematic review and meta-analysis to synthesise the global evidence on SARS-CoV-2 reinfections in the pre-Omicron era. Methods We searched five global databases (MEDLINE, Embase, CINAHL Plus, Global Health, WHO COVID-19) on 12 May 2022 and 28 July 2023 and three Chinese databases (CNKI, Wanfang, CQvip) on 16 October 2022 for articles reporting incidence and outcomes of SARS-CoV-2 reinfection before the period of Omicron (B.1.1.529) predominance. We assessed risk of bias using Joanna Briggs Institute critical appraisal tools and conducted meta-analyses with random effects models to estimate the proportion of SARS-CoV-2 reinfection among initially infected cases and hospitalisation and mortality proportions among reinfected ones. Results We identified 7593 studies and extracted data from 64 included ones representing 21 countries. The proportion of SARS-CoV-2 reinfection was 1.16% (95% confidence interval (CI) = 1.01-1.33) based on 11 639 247 initially infected cases, with ≥45 days between the two infections. Healthcare providers (2.28%; 95% CI = 1.37-3.40) had a significantly higher risk of reinfection than the general population (1.00%; 95% CI = 0.81-1.20), while young adults aged 18 to 35 years (1.01%; 95% CI = 0.8-1.25) had a higher reinfection burden than other age groups (children <18 years old: 0.57%; 95% CI = 0.39-0.79, older adults aged 36-65 years old: 0.53%; 95% CI = 0.41-0.65, elderly >65 years old: 0.37%; 95% CI = 0.15-0.66). Among the reinfected cases, 8.12% (95% CI = 5.30-11.39) were hospitalised, 1.31% (95% CI = 0.29-2.83) were admitted to the intensive care unit, and 0.71% (95% CI = 0.02-2.01) died. Conclusions Our data suggest a relatively low risk of SARS-CoV-2 reinfection in the pre-Omicron era, but the risk of hospitalisation was relatively high among the reinfected cases. Considering the possibility of underdiagnosis, the reinfection burden may be underestimated. Registration PROSPERO: CRD42023449712.
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Affiliation(s)
- Nabihah Farhana Ismail
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- Communicable Disease Control Unit, Public Health Department, Johor State, Malaysia
| | - Ahmed Ehsanur Rahman
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- International Centre for Diarrhoeal Diseases Research, Bangladesh
| | - Durga Kulkarni
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
| | - Fuyu Zhu
- School of Public Health, Nanjing Medical University, Jiangsu, China
| | - Xin Wang
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- School of Public Health, Nanjing Medical University, Jiangsu, China
| | | | - Amit Srivastava
- Pfizer, Vaccines, Emerging Markets
- Orbital Therapeutics, United States of America
| | | | | | | | - Harish Nair
- Centre for Global Health, University of Edinburgh, Edinburgh, United Kingdom
- School of Public Health, Nanjing Medical University, Jiangsu, China
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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105
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Lorenzo-Redondo R, de Sant’Anna Carvalho AM, Hultquist JF, Ozer EA. SARS-CoV-2 genomics and impact on clinical care for COVID-19. J Antimicrob Chemother 2023; 78:ii25-ii36. [PMID: 37995357 PMCID: PMC10667012 DOI: 10.1093/jac/dkad309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/02/2023] [Indexed: 11/25/2023] Open
Abstract
The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that had been previously applied on a more limited basis to other viral pathogens, such as HIV and influenza viruses. The need for WGS was driven in part by the low mutation rate of SARS-CoV-2, which necessitated measuring variation along the entire genome sequence to effectively differentiate lineages and characterize viral evolution. Several WGS approaches designed to maximize throughput and accuracy were quickly adopted by surveillance labs around the world. These broad-based SARS-CoV-2 genomic sequencing efforts revealed ongoing evolution of the virus, highlighted by the successive emergence of new viral variants throughout the course of the pandemic. These genomic insights were instrumental in characterizing the effects of viral mutations on transmissibility, immune escape and viral tropism, which in turn helped guide public health policy, the use of monoclonal antibody therapeutics and vaccine development strategies. As the use of direct-acting antivirals for the treatment of COVID-19 became more widespread, the potential for emergence of antiviral resistance has driven ongoing efforts to delineate resistance mutations and to monitor global sequence databases for their emergence. Given the critical role of viral genomics in the international effort to combat the COVID-19 pandemic, coordinated efforts should be made to expand global genomic surveillance capacity and infrastructure towards the anticipation and prevention of future pandemics.
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Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Alexandre Machado de Sant’Anna Carvalho
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
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106
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Wang L, Nicols A, Turtle L, Richter A, Duncan CJA, Dunachie SJ, Klenerman P, Payne RP. T cell immune memory after covid-19 and vaccination. BMJ MEDICINE 2023; 2:e000468. [PMID: 38027416 PMCID: PMC10668147 DOI: 10.1136/bmjmed-2022-000468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The T cell memory response is a crucial component of adaptive immunity responsible for limiting or preventing viral reinfection. T cell memory after infection with the SARS-CoV-2 virus or vaccination is broad, and spans multiple viral proteins and epitopes, about 20 in each individual. So far the T cell memory response is long lasting and provides a high level of cross reactivity and hence resistance to viral escape by variants of the SARS-CoV-2 virus, such as the omicron variant. All current vaccine regimens tested produce robust T cell memory responses, and heterologous regimens will probably enhance protective responses through increased breadth. T cell memory could have a major role in protecting against severe covid-19 disease through rapid viral clearance and early presentation of epitopes, and the presence of cross reactive T cells might enhance this protection. T cell memory is likely to provide ongoing protection against admission to hospital and death, and the development of a pan-coronovirus vaccine might future proof against new pandemic strains.
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Affiliation(s)
- Lulu Wang
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Alex Nicols
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Christopher JA Duncan
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Susanna J Dunachie
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University Faculty of Science, Bangkok, Thailand
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
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107
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Howerton E, Contamin L, Mullany LC, Qin M, Reich NG, Bents S, Borchering RK, Jung SM, Loo SL, Smith CP, Levander J, Kerr J, Espino J, van Panhuis WG, Hochheiser H, Galanti M, Yamana T, Pei S, Shaman J, Rainwater-Lovett K, Kinsey M, Tallaksen K, Wilson S, Shin L, Lemaitre JC, Kaminsky J, Hulse JD, Lee EC, McKee CD, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Pastore Y Piontti A, Vespignani A, Rosenstrom ET, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore S, Perkins A, Hladish T, Pillai A, Ben Toh K, Longini I, Chen S, Paul R, Janies D, Thill JC, Bouchnita A, Bi K, Lachmann M, Fox SJ, Meyers LA, Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Hurt B, Chen J, Mortveit H, Wilson A, Marathe M, Hoops S, Bhattacharya P, Machi D, Cadwell BL, Healy JM, Slayton RB, Johansson MA, Biggerstaff M, Truelove S, Runge MC, Shea K, Viboud C, Lessler J. Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty. Nat Commun 2023; 14:7260. [PMID: 37985664 PMCID: PMC10661184 DOI: 10.1038/s41467-023-42680-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023] Open
Abstract
Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections.
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Affiliation(s)
- Emily Howerton
- The Pennsylvania State University, University Park, PA, USA.
| | | | - Luke C Mullany
- Johns Hopkins University Applied Physics Lab, Laurel, MD, USA
| | | | | | - Samantha Bents
- National Institutes of Health Fogarty International Center, Bethesda, MD, USA
| | - Rebecca K Borchering
- The Pennsylvania State University, University Park, PA, USA
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sung-Mok Jung
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sara L Loo
- Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | - J Espino
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | | | - Sen Pei
- Columbia University, New York, NY, USA
| | | | | | - Matt Kinsey
- Johns Hopkins University Applied Physics Lab, Laurel, MD, USA
| | - Kate Tallaksen
- Johns Hopkins University Applied Physics Lab, Laurel, MD, USA
| | - Shelby Wilson
- Johns Hopkins University Applied Physics Lab, Laurel, MD, USA
| | - Lauren Shin
- Johns Hopkins University Applied Physics Lab, Laurel, MD, USA
| | | | | | | | | | | | - Alison Hill
- Johns Hopkins University, Baltimore, MD, USA
| | - Dean Karlen
- University of Victoria, Victoria, BC, Canada
| | | | | | - Kunpeng Mu
- Northeastern University, Boston, MA, USA
| | | | | | | | | | - Julie S Ivy
- North Carolina State University, Raleigh, NC, USA
| | | | | | | | - Sean Cavany
- University of Notre Dame, Notre Dame, IN, USA
| | - Sean Moore
- University of Notre Dame, Notre Dame, IN, USA
| | | | | | | | | | | | - Shi Chen
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Rajib Paul
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Daniel Janies
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Kaiming Bi
- University of Texas at Austin, Austin, TX, USA
| | | | | | | | | | | | | | | | - Bryan Lewis
- University of Virginia, Charlottesville, VA, USA
| | - Brian Klahn
- University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | | | | | - Stefan Hoops
- University of Virginia, Charlottesville, VA, USA
| | | | - Dustin Machi
- University of Virginia, Charlottesville, VA, USA
| | - Betsy L Cadwell
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica M Healy
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | | | - Michael C Runge
- U.S. Geological Survey Eastern Ecological Science Center, Laurel, MD, USA
| | - Katriona Shea
- The Pennsylvania State University, University Park, PA, USA
| | - Cécile Viboud
- National Institutes of Health Fogarty International Center, Bethesda, MD, USA.
| | - Justin Lessler
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Johns Hopkins University, Baltimore, MD, USA.
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Kanokudom S, Chansaenroj J, Assawakosri S, Suntronwong N, Yorsaeng R, Wongsrisang L, Aeemjinda R, Vichaiwattana P, Klinfueng S, Thatsanathorn T, Honsawek S, Poovorawan Y. Real-World Study: Hybrid Immunity against SARS-CoV-2 Influences the Antibody Levels and Persistency Lasting More than One Year. Vaccines (Basel) 2023; 11:1693. [PMID: 38006025 PMCID: PMC10674428 DOI: 10.3390/vaccines11111693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/31/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
This study investigated the impact of hybrid immunity on antibody responses in the participants who received two to seven doses of the COVID-19 vaccine. The study was conducted between April and June 2023. Out of 771 serum samples analyzed, 71.7% exhibited hybrid immunity (positive for total anti-N Ig), while 28.3% showed vaccine-induced immunity (negative for total anti-N Ig). Participants were categorized based on the number of vaccine doses: 2, 3, 4, and ≥5. The findings highlight a trend where a higher number of vaccine doses received was associated with a lower infection rate. There was no significant difference in total RBD Ig levels between those who received 3, 4, or ≥5 doses in both the hybrid immunity and vaccination alone groups across all observed durations as follows: <6 months, 6 to <9 months, 9 to <12 months, and ≥12 months. Hybrid immunity consistently maintained higher total RBD Ig levels and durability compared to vaccination alone, with estimated half-lives (T1/2) of 189.5 days versus 106.8 days for vaccine alone. This investigation underscored the potential benefit of hybrid immunity and raised questions about the optimal strategies for further vaccine dosing.
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Affiliation(s)
- Sitthichai Kanokudom
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
- Center of Excellence in Osteoarthritis and Musculoskeleton, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Jira Chansaenroj
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
| | - Suvichada Assawakosri
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
- Center of Excellence in Osteoarthritis and Musculoskeleton, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Nungruthai Suntronwong
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
| | - Ritthideach Yorsaeng
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
| | - Lakkhana Wongsrisang
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
| | - Ratchadawan Aeemjinda
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
| | - Preeyaporn Vichaiwattana
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
| | - Sirapa Klinfueng
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
| | - Thaksaporn Thatsanathorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
| | - Sittisak Honsawek
- Center of Excellence in Osteoarthritis and Musculoskeleton, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (J.C.); (S.A.); (N.S.); (R.Y.); (L.W.); (R.A.); (P.V.); (S.K.); (T.T.)
- Fellow of the Royal Society of Thailand (FRS [T]), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok 10300, Thailand
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Brainard J, Lake IR, Morbey RA, Jones NR, Elliot AJ, Hunter PR. Comparison of surveillance systems for monitoring COVID-19 in England: a retrospective observational study. Lancet Public Health 2023; 8:e850-e858. [PMID: 37832574 DOI: 10.1016/s2468-2667(23)00219-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND During the COVID-19 pandemic, cases were tracked using multiple surveillance systems. Some systems were completely novel, and others incorporated multiple data streams to estimate case incidence and prevalence. How well these different surveillance systems worked as epidemic indicators is unclear, which has implications for future disease surveillance and outbreak management. The aim of this study was to compare case counts, prevalence and incidence, timeliness, and comprehensiveness of different COVID-19 surveillance systems in England. METHODS For this retrospective observational study of COVID-19 surveillance systems in England, data from 12 surveillance systems were extracted from publicly available sources (Jan 1, 2020-Nov 30, 2021). The main outcomes were correlations between different indicators of COVID-19 incidence or prevalence. These data were integrated as daily time-series and comparisons undertaken using Spearman correlation between candidate alternatives and the most timely (updated daily, clinical case register) and the least biased (from comprehensive household sampling) COVID-19 epidemic indicators, with comparisons focused on the period of Sept 1, 2020-Nov 30, 2021. FINDINGS Spearman statistic correlations during the full focus period between the least biased indicator (from household surveys) and other epidemic indicator time-series were 0·94 (95% CI 0·92 to 0·95; clinical cases, the most timely indicator), 0·92 (0·90 to 0·94; estimates of incidence generated after incorporating information about self-reported case status on the ZoeApp, which is a digital app), 0·67 (95% CI 0·60 to 0·73, emergency department attendances), 0·64 (95% CI 0·60 to 0·68, NHS 111 website visits), 0·63 (95% CI 0·56 to 0·69, wastewater viral genome concentrations), 0·60 (95% CI 0·52 to 0·66, admissions to hospital with positive COVID-19 status), 0·45 (95% CI 0·36 to 0·52, NHS 111 calls), 0·08 (95% CI -0·03 to 0·18, Google search rank for "covid"), -0·04 (95% CI -0·12 to 0·05, in-hours consultations with general practitioners), and -0·37 (95% CI -0·46 to -0·28, Google search rank for "coronavirus"). Time lags (-14 to +14 days) did not markedly improve these rho statistics. Clinical cases (the most timely indicator) captured a more consistent proportion of cases than the self-report digital app did. INTERPRETATION A suite of monitoring systems is useful. The household survey system was the most comprehensive and least biased epidemic monitor, but not very timely. Data from laboratory testing, the self-reporting digital app, and attendances to emergency departments were comparatively useful, fairly accurate, and timely epidemic trackers. FUNDING National Institute for Health and Care Research Health Protection Research Unit in Emergency Preparedness and Response, a partnership between the UK Health Security Agency, King's College London, and the University of East Anglia.
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Affiliation(s)
- Julii Brainard
- Norwich Medical School, University of East Anglia, Norwich, UK.
| | - Iain R Lake
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Roger A Morbey
- Real-time Syndromic Surveillance Team, Field Services, Health Protection Operations, UK Health Security Agency, Birmingham, UK
| | - Natalia R Jones
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Alex J Elliot
- Real-time Syndromic Surveillance Team, Field Services, Health Protection Operations, UK Health Security Agency, Birmingham, UK
| | - Paul R Hunter
- Norwich Medical School, University of East Anglia, Norwich, UK
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Diexer S, Klee B, Gottschick C, Xu C, Broda A, Purschke O, Binder M, Frese T, Girndt M, Hoell JI, Moor I, Gekle M, Mikolajczyk R. Association between virus variants, vaccination, previous infections, and post-COVID-19 risk. Int J Infect Dis 2023; 136:14-21. [PMID: 37634619 DOI: 10.1016/j.ijid.2023.08.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/19/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023] Open
Abstract
OBJECTIVES The SARS-CoV-2 Omicron variant has spread rapidly and has been the dominant variant since 2022. The course of acute infection, in a vaccinated population, with Omicron is milder compared with earlier variants. However, little is known about how the occurrence of long-term symptoms after Omicron infection compared with other variants is modulated by previous infections and/or vaccinations. METHODS Participants of the DigiHero study provided information about their SARS-CoV-2 infections, vaccinations, and symptoms 12 or more weeks after infection (post-COVID-19 condition - PCC). RESULTS Participants infected with wildtype SARS-CoV-2 had the highest PCC risk (adjusted odds ratio [aOR] 6.44, 95% confidence interval (CI): 5.49; 7.56), followed by participants infected with Alpha and Delta compared with the reference group (individuals infected with Omicron having received three or more vaccinations). Among those infected with a specific variant, the number of preceding vaccinations was not associated with a risk reduction for PCC, whereas previous infection was strongly associated with a lower PCC risk (aOR 0.14, 95% CI 0.07; 0.25). CONCLUSIONS While infection with Omicron is less likely to result in PCC compared with previous variants, lack of protection by vaccination suggests a substantial challenge for the healthcare system during the early endemic period. In the midterm, the protective effects of previous infections can reduce the burden of PCC.
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Affiliation(s)
- Sophie Diexer
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Bianca Klee
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Cornelia Gottschick
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Chao Xu
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Anja Broda
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Oliver Purschke
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Haematology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Thomas Frese
- Institute of General Practice and Family Medicine, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Matthias Girndt
- Department of Internal Medicine II, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jessica I Hoell
- Paediatric Haematology and Oncology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Irene Moor
- Institute for Medical Sociology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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Khan MS, Kim E, Le Hingrat Q, Kleinman A, Ferrari A, Sammartino JC, Percivalle E, Xu C, Huang S, Kenniston TW, Cassaniti I, Baldanti F, Pandrea I, Gambotto A, Apetrei C. Tetravalent SARS-CoV-2 S1 subunit protein vaccination elicits robust humoral and cellular immune responses in SIV-infected rhesus macaque controllers. mBio 2023; 14:e0207023. [PMID: 37830800 PMCID: PMC10653869 DOI: 10.1128/mbio.02070-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/30/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE The study provides important insights into the immunogenicity and efficacy of a tetravalent protein subunit vaccine candidate against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The vaccine induced both humoral and cellular immune responses in nonhuman primates with controlled SIVagm infection and was able to generate Omicron variant-specific antibodies without specifically vaccinating with Omicron. These findings suggest that the tetravalent composition of the vaccine candidate could provide broad protection against multiple SARS-CoV-2 variants while minimizing the risk of immune escape and the emergence of new variants. Additionally, the use of rhesus macaques with controlled SIVsab infection may better represent vaccine immunogenicity in humans with chronic viral diseases, highlighting the importance of preclinical animal models in vaccine development. Overall, the study provides valuable information for the development and implementation of coronavirus disease 2019 vaccines, particularly for achieving global vaccine equity and addressing emerging variants.
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Affiliation(s)
- Muhammad S. Khan
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Eun Kim
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Quentin Le Hingrat
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Adam Kleinman
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alessandro Ferrari
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Pavia, Italy
| | - Jose C. Sammartino
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elena Percivalle
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Pavia, Italy
| | - Cuiling Xu
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Shaohua Huang
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas W. Kenniston
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Irene Cassaniti
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Ivona Pandrea
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Andrea Gambotto
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Cristian Apetrei
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Port JR, Yinda CK, Riopelle JC, Weishampel ZA, Saturday TA, Avanzato VA, Schulz JE, Holbrook MG, Barbian K, Perry-Gottschalk R, Haddock E, Martens C, Shaia CI, Lambe T, Gilbert SC, van Doremalen N, Munster VJ. Infection- or AZD1222 vaccine-mediated immunity reduces SARS-CoV-2 transmission but increases Omicron competitiveness in hamsters. Nat Commun 2023; 14:6592. [PMID: 37852960 PMCID: PMC10584863 DOI: 10.1038/s41467-023-42346-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Limited data is available on the effect of vaccination and previous virus exposure on the nature of SARS-CoV-2 transmission and immune-pressure on variants. To understand the impact of pre-existing immunity on SARS-CoV-2 airborne transmission efficiency, we perform a transmission chain experiment using naïve, intranasally or intramuscularly AZD1222 vaccinated, and previously infected hamsters. A clear gradient in transmission efficacy is observed: Transmission in hamsters vaccinated via the intramuscular route was reduced over three airborne chains (approx. 60%) compared to naïve animals, whereas transmission in previously infected hamsters and those vaccinated via the intranasal route was reduced by 80%. We also find that the Delta B.1.617.2 variant outcompeted Omicron B.1.1.529 after dual infection within and between hosts in naïve, vaccinated, and previously infected transmission chains, yet an increase in Omicron B.1.1.529 competitiveness is observed in groups with pre-existing immunity against Delta B.1.617.2. This correlates with an increase in the strength of the humoral response against Delta B.1.617.2, with the strongest response seen in previously infected animals. These data highlight the continuous need to improve vaccination strategies and address the additional evolutionary pressure pre-existing immunity may exert on SARS-CoV-2.
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Affiliation(s)
- Julia R Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jade C Riopelle
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Zachary A Weishampel
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Taylor A Saturday
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Victoria A Avanzato
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jonathan E Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Myndi G Holbrook
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kent Barbian
- Genomics Research Section, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Rose Perry-Gottschalk
- Rocky Mountain Visual and Medical Arts Unit, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Elaine Haddock
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Genomics Research Section, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Carl I Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sarah C Gilbert
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Neeltje van Doremalen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
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Rivers P, Jovel K, Ramadan F, Barnett JJA, Ellingson KD, Burgess JL, Lutrick K. Disease and social factors associated with healthcare utilization for the treatment of SARS-CoV-2 infections in a longitudinal cohort of essential workers in Arizona. BMC Health Serv Res 2023; 23:1118. [PMID: 37853403 PMCID: PMC10585717 DOI: 10.1186/s12913-023-10064-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Demands on health systems due to COVID-19 are substantial, but drivers of healthcare utilization are not well defined in non-severe SARS-CoV-2 infections. Among a prospective cohort of frontline workers from July 2020 to February 2023, we assessed predictors of healthcare utilization during SARS-CoV-2 infection. METHODS Weekly specimens tested via real-time reverse transcriptase polymerase chain reaction analysis. Participants reported sociodemographic, health status information, and illness experience information. Primary outcome was healthcare utilization during SARS-CoV-2 infection. Predictors included sociodemographic characteristics, baseline health status, and measures of illness severity. Multivariable logistic regression was utilized to generate odds ratios for predictors of healthcare utilization. RESULTS 1,923 SARS-CoV-2 infections (1,276 first infections and 647 reinfections from 4,208 participants): 1221 (63.5%) individuals were between 40 and 65 years old; 1115 (58.0%) were female; 449 (23.3%) were Hispanic and 1305 (67.9%) non-Hispanic White. 294 (15.3%) individuals sought medical care during first infection, 106 (5.5%) during reinfection. Sociodemographic and baseline health characteristics were not associated with healthcare utilization during infections from any variant for first infections, while age (OR 1.04, 95%CI 1.01-1.07) was during Omicron reinfection. In first infection, number of symptoms (OR 1.16, 95%CI 1.00-1.36 in Origin/Alpha, OR 1.12, 95%CI 1.00-1.49 in Delta, OR 1.09, 95%CI 1.01-1.16 in Omicron), number of days spent in bed (OR 1.13, 95%CI 1.02-1.33 in Origin/Alpha, OR 1.23, 95%CI 1.00-1.59 in Delta, OR 1.12, 95%CI 1.03-1.22 in Omicron), and illness duration (OR 1.01, 95%CI 1.00-1.04 in Origin/Alpha, OR 1.01, 95%CI 1.00-1.03 in Delta, OR 1.01, 95%CI 1.00-1.02 in Omicron) were related to healthcare utilization for all variants. Number of days in bed (OR 1.12, 95%CI 1.01-1.27), illness duration (OR 1.01, 95%CI 1.00-1.02), and hours of work missed (OR 2.24, 95%CI 1.11-4.74) were positively associated with healthcare utilization during Omicron reinfection. CONCLUSION The main factors associated with healthcare utilization for SARS-CoV-2 infection were symptom severity and duration. Practices and therapeutics aimed at decreasing these factors would be most helpful in easing the burden on health systems.
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Affiliation(s)
- Patrick Rivers
- College of Medicine, University of Arizona, Tucson, USA.
- Department of Family and Community Medicine, University of Arizona, 655 N. Alvernon Way, Tucson, AZ, 85712, USA.
| | - Krystal Jovel
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, USA
| | - Ferris Ramadan
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, USA
| | | | | | - Jefferey L Burgess
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, USA
| | - Karen Lutrick
- College of Medicine, University of Arizona, Tucson, USA
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Shi G, Li T, Lai KK, Johnson RF, Yewdell JW, Compton AA. Omicron Spike confers enhanced infectivity and interferon resistance to SARS-CoV-2 in human nasal tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.539698. [PMID: 37425811 PMCID: PMC10327209 DOI: 10.1101/2023.05.06.539698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Omicron emerged following COVID-19 vaccination campaigns, displaced previous SARS-CoV-2 variants of concern worldwide, and gave rise to lineages that continue to spread. Here, we show that Omicron exhibits increased infectivity in primary adult upper airway tissue relative to Delta. Using recombinant forms of SARS-CoV-2 and nasal epithelial cells cultured at the liquid-air interface, enhanced infectivity maps to the step of cellular entry and evolved recently through mutations unique to Omicron Spike. Unlike earlier variants of SARS-CoV-2, Omicron enters nasal cells independently of serine transmembrane proteases and instead relies upon metalloproteinases to catalyze membrane fusion. This entry pathway unlocked by Omicron Spike enables evasion of constitutive and interferon-induced antiviral factors that restrict SARS-CoV-2 entry following attachment. Therefore, the increased transmissibility exhibited by Omicron in humans may be attributed not only to its evasion of vaccine-elicited adaptive immunity, but also to its superior invasion of nasal epithelia and resistance to the cell-intrinsic barriers present therein.
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Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD
| | - Tiansheng Li
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD
| | - Reed F. Johnson
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Alex A Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD
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Munywoki PK, Bigogo G, Nasimiyu C, Ouma A, Aol G, Oduor CO, Rono S, Auko J, Agogo GO, Njoroge R, Oketch D, Odhiambo D, Odeyo VW, Kikwai G, Onyango C, Juma B, Hunsperger E, Lidechi S, Ochieng CA, Lo TQ, Munyua P, Herman-Roloff A. Heterogenous transmission and seroprevalence of SARS-CoV-2 in two demographically diverse populations with low vaccination uptake in Kenya, March and June 2021. Gates Open Res 2023; 7:101. [PMID: 37990692 PMCID: PMC10661969 DOI: 10.12688/gatesopenres.14684.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2023] [Indexed: 11/23/2023] Open
Abstract
Background SARS-CoV-2 has extensively spread in cities and rural communities, and studies are needed to quantify exposure in the population. We report seroprevalence of SARS-CoV-2 in two well-characterized populations in Kenya at two time points. These data inform the design and delivery of public health mitigation measures. Methods Leveraging on existing population based infectious disease surveillance (PBIDS) in two demographically diverse settings, a rural site in western Kenya in Asembo, Siaya County, and an urban informal settlement in Kibera, Nairobi County, we set up a longitudinal cohort of randomly selected households with serial sampling of all consenting household members in March and June/July 2021. Both sites included 1,794 and 1,638 participants in the March and June/July 2021, respectively. Individual seroprevalence of SARS-CoV-2 antibodies was expressed as a percentage of the seropositive among the individuals tested, accounting for household clustering and weighted by the PBIDS age and sex distribution. Results Overall weighted individual seroprevalence increased from 56.2% (95%CI: 52.1, 60.2%) in March 2021 to 63.9% (95%CI: 59.5, 68.0%) in June 2021 in Kibera. For Asembo, the seroprevalence almost doubled from 26.0% (95%CI: 22.4, 30.0%) in March 2021 to 48.7% (95%CI: 44.3, 53.2%) in July 2021. Seroprevalence was highly heterogeneous by age and geography in these populations-higher seroprevalence was observed in the urban informal settlement (compared to the rural setting), and children aged <10 years had the lowest seroprevalence in both sites. Only 1.2% and 1.6% of the study participants reported receipt of at least one dose of the COVID-19 vaccine by the second round of serosurvey-none by the first round. Conclusions In these two populations, SARS-CoV-2 seroprevalence increased in the first 16 months of the COVID-19 pandemic in Kenya. It is important to prioritize additional mitigation measures, such as vaccine distribution, in crowded and low socioeconomic settings.
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Affiliation(s)
- Patrick K. Munywoki
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Godfrey Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Carolyne Nasimiyu
- Global Health Program, Washington State University – Global Health Kenya (WSU-GH Kenya), Nairobi, Kenya
- Paul G. Allen School of Global Health, Washington State University, Pullman, Washington, USA
| | - Alice Ouma
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - George Aol
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Clifford O. Oduor
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Samuel Rono
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Joshua Auko
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - George O. Agogo
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Ruth Njoroge
- Global Health Program, Washington State University – Global Health Kenya (WSU-GH Kenya), Nairobi, Kenya
| | - Dismas Oketch
- Global Health Program, Washington State University – Global Health Kenya (WSU-GH Kenya), Nairobi, Kenya
| | - Dennis Odhiambo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Victor W. Odeyo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Gilbert Kikwai
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Clayton Onyango
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Bonventure Juma
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Elizabeth Hunsperger
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Shirley Lidechi
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | | | - Terrence Q. Lo
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Peninah Munyua
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Amy Herman-Roloff
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
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Santos da Silva E, Servais JY, Kohnen M, Arendt V, Staub T, Krüger R, Fagherazzi G, Wilmes P, Hübschen JM, Ollert M, Perez-Bercoff D, Seguin-Devaux C. Validation of a SARS-CoV-2 Surrogate Neutralization Test Detecting Neutralizing Antibodies against the Major Variants of Concern. Int J Mol Sci 2023; 24:14965. [PMID: 37834413 PMCID: PMC10573711 DOI: 10.3390/ijms241914965] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
SARS-CoV-2 infection and/or vaccination elicit a broad range of neutralizing antibody responses against the different variants of concern (VOC). We established a new variant-adapted surrogate virus neutralization test (sVNT) and assessed the neutralization activity against the ancestral B.1 (WT) and VOC Delta, Omicron BA.1, BA.2, and BA.5. Analytical performances were compared against the respective VOC to the reference virus neutralization test (VNT) and two CE-IVD labeled kits using three different cohorts collected during the COVID-19 waves. Correlation analyses showed moderate to strong correlation for Omicron sub-variants (Spearman's r = 0.7081 for BA.1, r = 0.7205 for BA.2, and r = 0.6042 for BA.5), and for WT (r = 0.8458) and Delta-sVNT (r = 0.8158), respectively. Comparison of the WT-sVNT performance with two CE-IVD kits, the "Icosagen SARS-CoV-2 Neutralizing Antibody ELISA kit" and the "Genscript cPass, kit" revealed an overall good correlation ranging from 0.8673 to -0.8773 and a midway profile between both commercial kits with 87.76% sensitivity and 90.48% clinical specificity. The BA.2-sVNT performance was similar to the BA.2 Genscript test. Finally, a correlation analysis revealed a strong association (r = 0.8583) between BA.5-sVNT and VNT sVNT using a double-vaccinated cohort (n = 100) and an Omicron-breakthrough infection cohort (n = 91). In conclusion, the sVNT allows for the efficient prediction of immune protection against the various VOCs.
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Affiliation(s)
- Eveline Santos da Silva
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Jean-Yves Servais
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Michel Kohnen
- National Service of Infectious Diseases, Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (V.A.); (T.S.)
| | - Vic Arendt
- National Service of Infectious Diseases, Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (V.A.); (T.S.)
| | - Therese Staub
- National Service of Infectious Diseases, Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (V.A.); (T.S.)
| | | | | | - Rejko Krüger
- Transversal Translational Medicine, Luxembourg Institute of Health; Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg;
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Guy Fagherazzi
- Department of Precision Health, Luxembourg Institute of Health, 1AB Rue Thomas Edison, L-1445 Strassen, Luxembourg;
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, 7 Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg;
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Judith M. Hübschen
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Danielle Perez-Bercoff
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
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Allué-Guardia A, Torrelles JB, Sigal A. Tuberculosis and COVID-19 in the elderly: factors driving a higher burden of disease. Front Immunol 2023; 14:1250198. [PMID: 37841265 PMCID: PMC10569613 DOI: 10.3389/fimmu.2023.1250198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Mycobacterium tuberculosis (M.tb) and SARS-CoV-2 are both infections that can lead to severe disease in the lower lung. However, these two infections are caused by very different pathogens (Mycobacterium vs. virus), they have different mechanisms of pathogenesis and immune response, and differ in how long the infection lasts. Despite the differences, SARS-CoV-2 and M.tb share a common feature, which is also frequently observed in other respiratory infections: the burden of disease in the elderly is greater. Here, we discuss possible reasons for the higher burden in older adults, including the effect of co-morbidities, deterioration of the lung environment, auto-immunity, and a reduced antibody response. While the answer is likely to be multifactorial, understanding the main drivers across different infections may allow us to design broader interventions that increase the health-span of older people.
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Affiliation(s)
- Anna Allué-Guardia
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Jordi B. Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- International Center for the Advancement of Research and Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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118
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Demirev AV, Lee K, Bae JY, Park H, Park S, Kim H, Lee J, Cho J, Yang JS, Kim KC, Lee JY, Kim K, Lemey P, Park MS, Kim JI. Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea. iScience 2023; 26:107689. [PMID: 37680469 PMCID: PMC10481354 DOI: 10.1016/j.isci.2023.107689] [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: 05/15/2023] [Revised: 07/28/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
SARS-CoV-2 variants have continuously emerged globally, including in South Korea. To characterize the molecular evolution of SARS-CoV-2 in South Korea, we performed phylogenetic and genomic recombination analyses using more than 12,000 complete genome sequences collected until October 2022. The variants in South Korea originated from globally identified variants of concern and harbored genetic clade-common and clade-specific amino acid mutations mainly around the N-terminal domain (NTD) or receptor binding domain (RBD) in the spike protein. Several point mutation residues in key antigenic sites were under positive selection persistently with changing genetic clades of SARS-CoV-2. Furthermore, we detected 17 potential genomic recombinants and 76.4% (13/17) retained the mosaic NTD or RBD genome. Our results suggest that point mutations and genomic recombination in the spike contributed to the molecular evolution of SARS-CoV-2 in South Korea, which will form an integral part of global prevention and control measures against SARS-CoV-2.
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Affiliation(s)
- Atanas V. Demirev
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyuyoung Lee
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sejik Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyunbeen Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jungmin Lee
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Junhyung Cho
- Division of Emerging Viral Diseases and Vector Research, Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea
| | - Jeong-Sun Yang
- Division of Emerging Viral Diseases and Vector Research, Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea
| | - Kyung-Chang Kim
- Division of Emerging Viral Diseases and Vector Research, Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea
| | - Joo-Yeon Lee
- Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea
| | - Kisoon Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Philippe Lemey
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
- Biosafety Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Il Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
- Biosafety Center, Korea University College of Medicine, Seoul, Republic of Korea
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119
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Rizvi ZA, Dandotiya J, Sadhu S, Khatri R, Singh J, Singh V, Adhikari N, Sharma K, Das V, Pandey AK, Das B, Medigeshi G, Mani S, Bhatnagar S, Samal S, Pandey AK, Garg PK, Awasthi A. Omicron sub-lineage BA.5 infection results in attenuated pathology in hACE2 transgenic mice. Commun Biol 2023; 6:935. [PMID: 37704701 PMCID: PMC10499788 DOI: 10.1038/s42003-023-05263-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 08/20/2023] [Indexed: 09/15/2023] Open
Abstract
A recently emerged sub-lineage of Omicron, BA.5, together with BA.4, caused a fifth wave of coronavirus disease (COVID-19) in South Africa and subsequently emerged as a predominant strain globally due to its high transmissibility. The lethality of BA.5 infection has not been studied in an acute hACE2 transgenic (hACE2.Tg) mouse model. Here, we investigated tissue-tropism and immuno-pathology induced by BA.5 infection in hACE2.Tg mice. Our data show that intranasal infection of BA.5 in hACE2.Tg mice resulted in attenuated pulmonary infection and pathology with diminished COVID-19-induced clinical and pathological manifestations. BA.5, similar to Omicron (B.1.1.529), infection led to attenuated production of inflammatory cytokines, anti-viral response and effector T cell response as compared to the ancestral strain of SARS-CoV-2, Wuhan-Hu-1. We show that mice recovered from B.1.1.529 infection showed robust protection against BA.5 infection associated with reduced lung viral load and pathology. Together, our data provide insights as to why BA.5 infection escapes previous SARS-CoV-2 exposure induced-T cell immunity but may result in milder immuno-pathology and alleviated chances of re-infectivity in Omicron-recovered individuals.
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Affiliation(s)
- Zaigham Abbas Rizvi
- Centre for Immuno-biology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
| | - Jyotsna Dandotiya
- Centre for Immuno-biology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Srikanth Sadhu
- Centre for Immuno-biology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Ritika Khatri
- Centre for Viral Therapeutics and Vaccines, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Janmejay Singh
- Bioassay Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Virendra Singh
- Centre for Immuno-biology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Neeta Adhikari
- Centre for Immuno-biology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Kritika Sharma
- Centre for Immuno-biology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Vinayake Das
- Centre for Immuno-biology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Amit Kumar Pandey
- Centre for Tuberculosis and Bacterial Diseases Research, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Bhabatosh Das
- Centre for Microbiome and Anti-Microbial Resistance, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Guruprasad Medigeshi
- Bioassay Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Shalendra Mani
- Centre for Viral Therapeutics and Vaccines, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Shinjini Bhatnagar
- Centre for Maternal and Child Health, Translational Health Science and Technology NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Sweety Samal
- Centre for Viral Therapeutics and Vaccines, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Anil Kumar Pandey
- Department of Physiology, ESIC Medical College & Hospital, Faridabad, 121001, India
| | - Pramod Kumar Garg
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Amit Awasthi
- Centre for Immuno-biology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
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120
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Zhao Y, Wong SWK. A comparative study of compartmental models for COVID-19 transmission in Ontario, Canada. Sci Rep 2023; 13:15050. [PMID: 37700081 PMCID: PMC10497623 DOI: 10.1038/s41598-023-42043-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 09/04/2023] [Indexed: 09/14/2023] Open
Abstract
The number of confirmed COVID-19 cases reached over 1.3 million in Ontario, Canada by June 4, 2022. The continued spread of the virus underlying COVID-19 has been spurred by the emergence of variants since the initial outbreak in December, 2019. Much attention has thus been devoted to tracking and modelling the transmission of COVID-19. Compartmental models are commonly used to mimic epidemic transmission mechanisms and are easy to understand. Their performance in real-world settings, however, needs to be more thoroughly assessed. In this comparative study, we examine five compartmental models-four existing ones and an extended model that we propose-and analyze their ability to describe COVID-19 transmission in Ontario from January 2022 to June 2022.
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Affiliation(s)
- Yuxuan Zhao
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Samuel W K Wong
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, N2L 3G1, Canada.
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Perrotta C, Fenizia C, Carnovale C, Pozzi M, Trabattoni D, Cervia D, Clementi E. Updated Considerations for the Immunopharmacological Aspects of the "Talented mRNA Vaccines". Vaccines (Basel) 2023; 11:1481. [PMID: 37766157 PMCID: PMC10534931 DOI: 10.3390/vaccines11091481] [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: 08/21/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Messenger RNA (mRNA) vaccines belong to a new class of medications, RNA therapeutics, including both coding and non-coding RNAs. The use of mRNA as a therapy is based on the biological role of mRNA itself, namely its translation into a functional protein. The goal of mRNA vaccines is to produce a specific antigen in cells to elicit an immune response that might be prophylactic or therapeutic. The potential of mRNA as vaccine has been envisaged for years but its efficacy has been clearly demonstrated with the approval of COVID-19 vaccines in 2021. Since then, mRNA vaccines have been in the pipeline for diseases that are still untreatable. There are many advantages of mRNA vaccines over traditional vaccines, including easy and cost-effective production, high safety, and high-level antigen expression. However, the nature of mRNA itself and some technical issues pose challenges associated with the vaccines' development and use. Here we review the immunological and pharmacological features of mRNA vaccines by discussing their pharmacokinetics, mechanisms of action, and safety, with a particular attention on the advantages and challenges related to their administration. Furthermore, we present an overview of the areas of application and the clinical trials that utilize a mRNA vaccine as a treatment.
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Affiliation(s)
- Cristiana Perrotta
- Department of Biomedical and Clinical Sciences (DIBIC), Università degli Studi di Milano, 20157 Milano, Italy; (C.C.); (D.T.)
| | - Claudio Fenizia
- Department of Pathophysiology and Transplantation (DEPT), Università degli Studi di Milano, 20122 Milano, Italy;
| | - Carla Carnovale
- Department of Biomedical and Clinical Sciences (DIBIC), Università degli Studi di Milano, 20157 Milano, Italy; (C.C.); (D.T.)
| | - Marco Pozzi
- Scientific Institute IRCCS Eugenio Medea, 23842 Bosisio Parini, Italy;
| | - Daria Trabattoni
- Department of Biomedical and Clinical Sciences (DIBIC), Università degli Studi di Milano, 20157 Milano, Italy; (C.C.); (D.T.)
| | - Davide Cervia
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), Università degli Studi della Tuscia, 01100 Viterbo, Italy;
| | - Emilio Clementi
- Department of Biomedical and Clinical Sciences (DIBIC), Università degli Studi di Milano, 20157 Milano, Italy; (C.C.); (D.T.)
- Scientific Institute IRCCS Eugenio Medea, 23842 Bosisio Parini, Italy;
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Girardi V, Gularte JS, Demoliner M, da Silva MS, Filippi M, de Abreu Góes Pereira VM, Hansen AW, Rosa RB, Fleck JD, Spilki FR. Reinfection by SARS-CoV-2 by divergent Omicron sublineages, 16 days apart. Braz J Microbiol 2023; 54:1847-1851. [PMID: 37269428 PMCID: PMC10239041 DOI: 10.1007/s42770-023-01018-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/09/2023] [Indexed: 06/05/2023] Open
Abstract
Since the beginning of the SARS-CoV-2 pandemic, studies on the variants and sublineages stand out, mainly in the cases of reinfection in a short period. In this study, we describe a case of infection by BA.1.1 sublineage in an individual from Southern Brazil. The same patient acquired reinfection with sublineage BA.2 within 16 days after the first detection. The viral extraction and RT-qPCR were performed on the samples LMM72045 (collected in May 2022) and LMM72044 (collected in June 2022). After the confirmation of SARS-CoV-2 infection, we conducted the sequencing and viral genome analysis. This case of reinfection affected a 52-year-old male patient, without comorbidities, with three doses of vaccines against COVID-19, showing symptoms on May 19. These symptoms lasted for approximately six days. The patient returned to work activities on May 30. However, on June 4, the patient felt a new round of clinical signs that lasted for approximately seven days. Analysis of the viral genomes recovered from patients' clinical samples revealed that the two COVID-19 episodes were related to two divergent VOC Omicron sublineages, namely, BA.1.1 for the first round of symptoms and BA.2 for the second infection. Based on our findings, we can say that the present case of reinfection is the shortest described so far.
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Affiliation(s)
- Viviane Girardi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil.
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Vyctoria Malayhka de Abreu Góes Pereira
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Raquel Borba Rosa
- Secretaria Municipal de Saúde, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
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Reimann H, Moosmann C, Schober K, Lang V, Verhagen J, Zeun J, Mackensen A, Kremer AN, Völkl S, Aigner M. Identification and characterization of T-cell receptors with therapeutic potential showing conserved specificity against all SARS-CoV 2 strains. Immunobiology 2023; 228:152720. [PMID: 37541134 DOI: 10.1016/j.imbio.2023.152720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 08/06/2023]
Abstract
INTRODUCTION Treatment of severe COVID-19 disease can be challenging in immunocompromized patients due to newly emerging virus variants of concern (VOC) escaping the humoral response. Thus, T cells recognizing to date unmutated epitopes are not only relevant for patients' immune responses against VOC, but might also serve as a therapeutic option for patients with severe COVID-19 disease in the future, e.g. following allogenic stem cell transplantation. METHODS To this purpose, the activation, cytokine profile and specificity of T-cell clones against unmutated and omicron Spike (S)-protein was analyzed, HLA restriction was determined and most promising T-cell receptor (TCR) was introduced into allogeneic T cells via CRISPR/Cas9-mediated orthotopic TCR replacement. Finally, T-cell responses of engineered T cells was determined and durability of the TCR replacement measured. PERSPECTIVE SARS-CoV-2 specific engineered T cells recognizing a genomically stable region of the S-protein of all SARS-CoV 2 variants were successfully generated. Such transgenic T cells exhibit favorable effector functions and provide a treatment option of immunocompromised COVID-19 patients.
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Affiliation(s)
- Hannah Reimann
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany.
| | - Carolin Moosmann
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Kilian Schober
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Vanessa Lang
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Johan Verhagen
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Department of Internal Medicine 3, Rheumatology and Immunology, University Hospital Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Medizinische Klinik mit Schwerpunkt Rheumatologie und Klinische Immunologie, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Zeun
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Andreas Mackensen
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Anita N Kremer
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Simon Völkl
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Michael Aigner
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
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Kovanen PT, Vuorio A. SARS-CoV-2 reinfection: Adding insult to dysfunctional endothelium in patients with atherosclerotic cardiovascular disease. ATHEROSCLEROSIS PLUS 2023; 53:1-5. [PMID: 37293388 PMCID: PMC10238112 DOI: 10.1016/j.athplu.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
In this short narrative review, we aim at defining the pathophysiological role endothelial dysfunction in the observed COVID-19-associated rise in risk of cardiovascular disease. Variants of the SARS-CoV-2 virus have caused several epidemic waves of COVID-19, and the emergence and rapid spread of new variants and subvariants are likely. Based on a large cohort study, the incidence rate of SARS-CoV-2 reinfection is about 0.66 per 10 000 person-weeks. Both the first infection and reinfection with SARS-CoV-2 increase cardiac event risk, particularly in vulnerable patients with cardiovascular risk factors and the accompanying systemic endothelial dysfunction. By worsening pre-existing endothelial dysfunction, both the first infection and reinfection with ensuing COVID-19 may turn the endothelium procoagulative and prothrombotic, and ultimately lead to local thrombus formation. When occurring in an epicardial coronary artery, the risk of an acute coronary syndrome increases, and when occurring in intramyocardial microvessels, scattered myocardial injuries will ensue, both predisposing the COVID-19 patients to adverse cardiovascular outcomes. In conclusion, considering weakened protection against the cardiovascular risk-enhancing reinfections with emerging new subvariants of SARS-CoV-2, treatment of COVID-19 patients with statins during the illness and thereafter is recommended, partly because the statins tend to reduce endothelial dysfunction.
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Affiliation(s)
| | - Alpo Vuorio
- Mehiläinen, Airport Health Center, Vantaa, Finland
- University of Helsinki, Department of Forensic Medicine, Helsinki, Finland
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Ko L, Malet G, Chang LL, Nguyen H, Mayes R. COVID-19 Infection Rates in Vaccinated and Unvaccinated Inmates: A Retrospective Cohort Study. Cureus 2023; 15:e44684. [PMID: 37680261 PMCID: PMC10482361 DOI: 10.7759/cureus.44684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2023] [Indexed: 09/09/2023] Open
Abstract
Background In 2023, breakthrough COVID-19 infections among vaccinated individuals and reinfections in previously infected people have become common. Additionally, infections are due to Omicron subvariants of the virus that behave differently from those at the onset of the pandemic. Understanding how vaccination and natural immunity influence COVID-19 infection rates is crucial, especially in high-density congregate settings such as prisons, to inform public health strategies. Methods We analyzed COVID-19 surveillance data from January to July 2023 across 33 California state prisons, primarily a male population of 96,201 individuals. We computed the incidence rate of new COVID-19 infections among COVID-bivalent-vaccinated and entirely unvaccinated groups (those not having received either the bivalent or monovalent vaccine). Results Our results indicate that the infection rates in the bivalent-vaccinated and entirely unvaccinated groups are 3.24% (95% confidence interval (CI): 3.06-3.42%) and 2.72% (CI: 2.50-2.94%), respectively, with an absolute risk difference of only 0.52%. When the data were filtered for those aged 50 and above, the infection rates were 4.07% (CI: 3.77-4.37%) and 3.1% (CI: 2.46-3.74%), respectively, revealing a mere 0.97% absolute risk difference. Among those aged 65 and above, the infection rates were 6.45% (CI: 5.74-7.16%) and 4.5% (CI: 2.57-6.43%), respectively, with an absolute risk difference of 1.95%. Conclusion We note low infection rates in both the vaccinated and unvaccinated groups, with a small absolute difference between the two across age groups. A combination of monovalent and bivalent vaccines and natural infections likely contributed to immunity and a lower level of infection rates compared to the height of the pandemic. It is possible that a degree of 'herd immunity' has been achieved. Yet, using p<0.05 as the threshold for statistical significance, the bivalent-vaccinated group had a slightly but statistically significantly higher infection rate than the unvaccinated group in the statewide category and the age ≥50 years category. However, in the older age category (≥65 years), there was no significant difference in infection rates between the two groups. This suggests that while the bivalent vaccine might offer protection against severe outcomes, it may not significantly reduce the risk of infections entirely. Further research is needed to understand the reasons behind these findings and to consider other factors, such as underlying health conditions. This study underscores the importance of developing vaccines that target residual COVID-19 infections, especially in regard to evolving COVID-19 variants.
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Affiliation(s)
- Luke Ko
- Biomedical Sciences Pathway Program, California High School, San Ramon, USA
| | - Gary Malet
- Internal Medicine, California Correctional Healthcare Services, Stockton, USA
| | - Lisa L Chang
- College of Education, Governors State University, University Park, USA
| | - Huu Nguyen
- Internal Medicine, California Correctional Healthcare Services, Stockton, USA
| | - Robert Mayes
- Internal Medicine, California Correctional Healthcare Services, Stockton, USA
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Kanokudom S, Suntronwong N, Duangchinda T, Wanlapakorn N, Poovorawan Y. Dynamic Antibody Response and Hybrid Immunity Following Multiple COVID-19 Vaccine Doses and Infection: A Case Study. Cureus 2023; 15:e45531. [PMID: 37731681 PMCID: PMC10507991 DOI: 10.7759/cureus.45531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 09/22/2023] Open
Abstract
This case study highlights the dynamic nature of the antibody response to SARS-CoV-2 in a vulnerable subject aged 70 years between 2021 and 2023. This individual had been vaccinated with six doses of the ancestral (Wuhan-Hu-1) COVID-19 vaccine and had a breakthrough infection 126 days after receiving Covovax™- (CO) as the sixth dose. The serostatus for total immunoglobulin specific to the receptor binding domain (total RBD Ig) changed from negative to positive following a two-dose CoronaVac (CV) vaccination, indicating a successful immune response. Booster doses, including AZD1222 (AZ), half-dose BNT162b2 (PF), and CO, increased the total RBD Ig levels, except for CV. The individual experienced a breakthrough infection by the Omicron BA.5 variant, leading to a substantial surge in total RBD Ig to over 105 U/mL. This generated sustained and extended antibody persistence, with the half-life of total RBD Ig lasting approximately 103.6 days. Furthermore, it has been observed that this breakthrough infection generated the highest neutralizing antibodies against BA.5, followed by XBB.1.5, BQ.1.1, and BA.2.75, respectively.
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Affiliation(s)
- Sitthichai Kanokudom
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, THA
| | - Nungruthai Suntronwong
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, THA
| | - Thaneeya Duangchinda
- Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency, Pathum Thani, THA
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, THA
| | - Yong Poovorawan
- Center of Excellence In Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, THA
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Djorwé S, Bousfiha A, Nzoyikorera N, Nyandwi J, Kawthar B, Malki A. Evaluation of SARS-CoV-2 infection risks after primary vaccination with BNT162b2, BBIBP-CorV, or ChAdOx1-nCOV-19 and after homologous and heterologous booster vaccinations with these vaccines and evaluation of SARS-CoV-2 reinfection profiles. Biomedicine (Taipei) 2023; 13:31-48. [PMID: 37937059 PMCID: PMC10627210 DOI: 10.37796/2211-8039.1412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/01/2023] [Indexed: 11/09/2023] Open
Abstract
Background The emergence of SARS-CoV-2 variants has significantly increased the number of cases of COVID-19 among vaccinated individuals, raising concerns about the effectiveness of current vaccines. The aim of this study was to analyze the SARS-CoV-2 infection risks after primary vaccination with BNT162b2, BBIBP-CorV, or ChAdOx1-nCOV-19 and after homologues and heterologous booster vaccinations with these vaccines, as well as the profiles of reinfected patients. Methods We analyzed retrospectively 1082 patients vaccinated or unvaccinated with BNT162b2, BBIBP-CorV, and/or ChAdOx1nCoV-19 vaccines to determine their SARS-CoV2 infection statuses using the reverse transcription-polymerase chain reaction (RT-PCR) in addition to their clinical features. The infection risks of patients receiving the different vaccine regimens were compared using multivariate logistic regression analysis, comparing the adjusted OR of a positive COVID-19 test result. Results Among 596 vaccinated patients, 53%(n = 286) tested positive for SARS-CoV-2 and 57%(n = 310) tested negative. Among positive cases, 10 were reinfection cases. The risk of SARS-CoV-2 infection was 1.6 (adj. OR) for patients who received one dose compared with those who received two doses (95% CI = 1.3-1.8; p < 0.01).The risk was 2.6 (adj. OR) for patients who received one dose compared with those who received three doses (95%CI = 2.1-3.3; p < 0.01), and 1.6 (adj. OR) for patients who received two doses compared with those who received three doses (95% CI = 1.3-2; p < 0.01). The patients who received two doses that were heterologous to that of the primary vaccine had the lowest risk of infection. Booster vaccinations (third dose) significantly reduced the number of positive cases with an acceptable safety profile. Higher cycle-threshold (Ct) values (indicative of viral load) were observed in vaccinated patients, whereas low Ct values were observed in unvaccinated patients. Conclusion A complete cycle of vaccination with homologous vaccines or heterologous vaccines resulted in an acceptable reduction in SARS-CoV-2 infection. Further, vaccination was associated with a reduction in viral load.
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Affiliation(s)
- Soulandi Djorwé
- Laboratory of Physiopathology and Molecular Genetics, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca (Morocco), Avenue Cdt Driss El Harti, Sidi Othman, PB 7955, Casablanca,
Morocco
- Bourgogne Laboratory of Medical and Scientific Analysis, 136, Residence Belhcen, Bd Bourgogne, Casablanca,
Morocco
| | - Amale Bousfiha
- Laboratory of Physiopathology and Molecular Genetics, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca (Morocco), Avenue Cdt Driss El Harti, Sidi Othman, PB 7955, Casablanca,
Morocco
| | - Néhémie Nzoyikorera
- National Reference Laboratory, National Institute of Public Health,
Burundi
- Higher Institute of Biosciences and Biotechnology, Mohammed VI University of Health Sciences (UM6SS), Casablanca,
Morocco
- Laboratory of Microbial Biotechnology and Infectiology Research, Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Rabat,
Morocco
| | - Joseph Nyandwi
- Département de Médecine, Faculté de Médecine, Université du Burundi,
Burundi
- Ministére de la Santé Publique et de la Lutte Contre le Sida, Institut National de Santé Publique de Bujumbura,
Burundi
| | - Bellamine Kawthar
- Bourgogne Laboratory of Medical and Scientific Analysis, 136, Residence Belhcen, Bd Bourgogne, Casablanca,
Morocco
| | - Abderrahim Malki
- Laboratory of Physiopathology and Molecular Genetics, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca (Morocco), Avenue Cdt Driss El Harti, Sidi Othman, PB 7955, Casablanca,
Morocco
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Liu C, Lu J, Li P, Feng S, Guo Y, Li K, Zhao B, Su Y, Chen T, Zou X. A comparative study on epidemiological characteristics, transmissibility, and pathogenicity of three COVID-19 outbreaks caused by different variants. Int J Infect Dis 2023; 134:78-87. [PMID: 36736993 PMCID: PMC9890806 DOI: 10.1016/j.ijid.2023.01.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES The Omicron BA.2 variant is probably the main epidemic strain worldwide at present. Comparing the epidemiological characteristics, transmissibility, and influencing factors of SARS-CoV-2, the results obtained in this paper will help to provide theoretical support for disease control. METHODS This study was a historical information analysis, using the R programming language and SPSS 24.0 for statistical analysis. The Geoda and Arc GIS were used for spatial autocorrelation analysis. RESULTS Local spatial autocorrelations of the incidence rate were observed in Delta and Omicron BA.1 outbreaks, whereas Omicron BA.2 outbreaks showed a random distribution in incidence rate. The time-dependent reproduction number of Delta, Omicron BA.1, and Omicron BA.2 were 3.21, 4.29, and 2.96, respectively, and correspondingly, the mean serial interval were 4.29 days (95% confidence interval [CI]: 0.37-8.21), 3.84 days (95% CI: 0-8.37), and 2.77 days (95% CI: 0-5.83). The asymptomatic infection rate of cases in Delta, Omicron BA.1, and Omicron BA.2 outbreaks were 21.71%, 6.25%, and 4.35%, respectively. CONCLUSION The Omicron BA.2 variant had the greatest serial interval, transmissibility, and transmission speed, followed by BA.1, and then Delta. Compared with Delta and Omicron BA.1 variants, the Omicron BA.2 variant may be less pathogenic and more difficult to control than Omicron BA.1 and Delta.
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Affiliation(s)
- Chan Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China.
| | - Jianhua Lu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China.
| | - Peihua Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China.
| | - Siyang Feng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China.
| | - Yichao Guo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China.
| | - Kangguo Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China.
| | - Benhua Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China.
| | - Yanhua Su
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China.
| | - Tianmu Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, People's Republic of China.
| | - Xuan Zou
- Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China.
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Xie G, Wang L, Zhang J. How are countries responding differently to COVID-19: a systematic review of guidelines on isolation measures. Front Public Health 2023; 11:1190519. [PMID: 37719732 PMCID: PMC10502310 DOI: 10.3389/fpubh.2023.1190519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction Isolation strategies have been implemented in numerous countries worldwide during the ongoing community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, various countries and organizations have implemented their isolation measures at varying intensities, even during the same period. Therefore, we systematically reviewed the key information contained in currently available guidelines regarding the isolation of the general population, aiming to better identify the heterogeneity of the current isolation strategies. Methods We conducted searches in four evidence-based medicine (EBM) databases and five guideline websites to identify guidelines, guidance, protocols, and policy documents published by authoritative advisory bodies or healthcare organizations, which provided information on the implementation of isolation for general populations with COVID-19. One author extracted data using a standardized data extraction checklist, and a second author double-checked all extractions for completeness and correctness. Discrepancies were resolved through discussion. The information extracted from the included articles was summarized both narratively and using tables. Results We included 15 articles that provided information on isolation measures recommended by nine different countries and organizations. The included articles consistently recommended isolating individuals with a positive COVID-19 test, regardless of the presence of symptoms. However, there were variations in the duration of isolation, and substantial differences also existed in the criteria for ending the isolation of COVID-19 patients. Conclusion Different countries and organizations have substantial differences in their isolation policies. This reminds us that scientifically sound guidelines on isolation that balance the risk of prematurely ending isolation with the burden of prolonged isolation are a crucial topic of discussion when faced with a pandemic.
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Affiliation(s)
- Guangmei Xie
- Reproductive Medicine Center, Gansu Maternal and Child Health Care Hospital, Lanzhou, Gansu, China
- Reproductive Medicine Center, Gansu Provincial Central Hospital, Lanzhou, Gansu, China
| | - Li Wang
- Reproductive Medicine Center, Gansu Maternal and Child Health Care Hospital, Lanzhou, Gansu, China
- Reproductive Medicine Center, Gansu Provincial Central Hospital, Lanzhou, Gansu, China
| | - Jun Zhang
- School of Nursing, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
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Bourdas DI, Bakirtzoglou P, Travlos AK, Andrianopoulos V, Zacharakis E. Exploring the Impact of COVID-19 on Physical Activity One Month after Infection and Its Potential Determinants: Re-Infections, Pre-Illness Vaccination Profiles/Types, and Beyond. Vaccines (Basel) 2023; 11:1431. [PMID: 37766108 PMCID: PMC10538036 DOI: 10.3390/vaccines11091431] [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: 07/25/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023] Open
Abstract
This study investigated changes in physical activity (PA) after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection while considering age, PA level, underlying medical conditions (UMCs), vaccination profiles/types, re-infections, disease severity, and treatment. Data were collected from 5829 respondents by using a validated web-based questionnaire. The findings showed that there was a significant overall decrease in PA (-16.2%), including in daily occupation (-11.9%), transportation (-13.5%), leisure-time (-16.4%), and sporting (-27.6%) activities. Age, PA level, UMCs, vaccination profiles/types, disease severity, and treatment played a role in determining PA in individuals' post-acute SARS-CoV-2 infections. Re-infections did not impact the decline in PA. Unvaccinated individuals experienced a significant decline in PA (-13.7%). Younger (-22.4%) and older adults (-22.5%), those with higher PA levels (-20.6%), those with 2-5 UMCs (-23.1%), those who were vaccinated (-16.9%) or partially vaccinated (-19.1%), those with mRNA-type vaccines only (-17.1%), those with recurrent (-19.4%)-to-persistent (-54.2%) symptoms, and those that required hospital (-51.8%) or intensive care unit (-67.0%) admission during their infections had more pronounced declines in PA. These findings emphasize the complex relationship between post-acute SARS-CoV-2 infection and PA and highlight the need for targeted interventions, further research, and multidisciplinary care to promote PA resumption and mitigate long-term effects on global public health.
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Affiliation(s)
- Dimitrios I. Bourdas
- Section of Sport Medicine & Biology of Exercise, School of Physical Education and Sports Science, National and Kapodistrian University of Athens, 41 Ethnikis Antistasis, 17237 Daphne, Greece; (D.I.B.); (V.A.); (E.Z.)
| | - Panteleimon Bakirtzoglou
- School of Physical Education and Sport Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonios K. Travlos
- Department of Sports Organization and Management, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese, Efstathiou and Stamatikis Valioti & Plataion Avenue, 23100 Sparta, Greece;
| | - Vasileios Andrianopoulos
- Section of Sport Medicine & Biology of Exercise, School of Physical Education and Sports Science, National and Kapodistrian University of Athens, 41 Ethnikis Antistasis, 17237 Daphne, Greece; (D.I.B.); (V.A.); (E.Z.)
| | - Emmanouil Zacharakis
- Section of Sport Medicine & Biology of Exercise, School of Physical Education and Sports Science, National and Kapodistrian University of Athens, 41 Ethnikis Antistasis, 17237 Daphne, Greece; (D.I.B.); (V.A.); (E.Z.)
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131
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Lee JH, Hwang JH, Jang EJ, Kim RK, Lee KH, Park SK, Gwack J, Park YJ. Risk Factors Related to COVID-19 Reinfection and Fatality During the Omicron (BA.1/BA.2) Period in Korea. J Korean Med Sci 2023; 38:e269. [PMID: 37644683 PMCID: PMC10462479 DOI: 10.3346/jkms.2023.38.e269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/20/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND This study aimed to investigate the deaths due to coronavirus disease 2019 (COVID-19) reinfection and related risk factors. METHODS National cohort data were collected for a six-month period when omicron BA.1/BA.2 variant was dominant in South Korea. RESULTS The long-term care facility residents (adjusted odds ratio, 3.11; 95% confidence interval [CI], 2.98-3.25) had significantly higher risk of reinfection than the general population. The risk of reinfection was significantly lower for persons with 2 or more vaccine doses compared to the unvaccinated. The risk of death was significantly higher in the reinfection group than in the primary infection group for persons in the 60-74 years age group (adjusted relative risk [aRR], 1.62; 95% CI, 1.19-2.20), and immunocompromised group (aRR, 4.56; 95% CI, 2.34-8.90). CONCLUSION In these data, vaccination history was significantly related to reduced COVID-19 reinfection and severe progression, and scheduled vaccinations were important even with a history of infection.
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Affiliation(s)
- Ju Hee Lee
- Division of Epidemiological Investigation Analysis, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Ji Hae Hwang
- Division of Epidemiological Investigation Analysis, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Eun Jung Jang
- Division of Epidemiological Investigation Analysis, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Ryu Kyung Kim
- Division of Epidemiological Investigation Analysis, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Kil Hun Lee
- Division of Epidemiological Investigation Analysis, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Seon Kyeong Park
- Division of Epidemiological Investigation Analysis, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Jin Gwack
- Division of Infectious Disease Control, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - Young Joon Park
- Division of Epidemiological Investigation Analysis, Korea Disease Control and Prevention Agency, Cheongju, Korea.
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Choi G, Rejinold NS, Piao H, Ryu YB, Kwon HJ, Lee IC, Seo JI, Yoo HH, Jin GW, Choy JH. The Next Generation COVID-19 Antiviral; Niclosamide-Based Inorganic Nanohybrid System Kills SARS-CoV-2. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2305148. [PMID: 37635100 DOI: 10.1002/smll.202305148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/31/2023] [Indexed: 08/29/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is a serious global threat with surging new variants of concern. Although global vaccinations have slowed the pandemic, their longevity is still unknown. Therefore, new orally administrable antiviral agents are highly demanded. Among various repurposed drugs, niclosamide (NIC) is the most potential one for various viral diseases such as COVID-19, SARS (severe acute respiratory syndrome), MERS (middle east respiratory syndrome), influenza, RSV (respiratory syncytial virus), etc. Since NIC cannot be effectively absorbed, a required plasma concentration for antiviral potency is hard to maintain, thereby restricting its entry into the infected cells. Such a 60-year-old bioavailability challenging issue has been overcome by engineering with MgO and hydroxypropyl methylcellulose (HPMC), forming hydrophilic NIC-MgO-HPMC, with improved intestinal permeability without altering NIC metabolism as confirmed by parallel artificial membrane permeability assay. The inhibitory effect on SARS-CoV-2 replication is confirmed in the Syrian hamster model to reduce lung injury. Clinical studies reveal that the bioavailability of NIC hybrid drug can go 4 times higher than the intact NIC. The phase II clinical trial shows a dose-dependent bioavailability of NIC from hybrid drug suggesting its potential applicability as a game changer in achieving the much-anticipated endemic phase.
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Affiliation(s)
- Goeun Choi
- Intelligent Nanohybrid Materials Laboratory (INML), Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, 31116, Republic of Korea
- College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - N Sanoj Rejinold
- Intelligent Nanohybrid Materials Laboratory (INML), Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, 31116, Republic of Korea
| | - Huiyan Piao
- Intelligent Nanohybrid Materials Laboratory (INML), Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, 31116, Republic of Korea
| | - Young Bae Ryu
- Functional Biomaterials Research Center, Korea Research Institute of Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 34141, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterials Research Center, Korea Research Institute of Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 34141, Republic of Korea
| | - In Chul Lee
- Functional Biomaterials Research Center, Korea Research Institute of Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 34141, Republic of Korea
| | - Jeong In Seo
- Institute of Pharmaceutical Science and Technology, College of Pharmacy, Hanyang University, Ansan, 15588, Republic of Korea
| | - Hye Hyun Yoo
- Institute of Pharmaceutical Science and Technology, College of Pharmacy, Hanyang University, Ansan, 15588, Republic of Korea
| | - Geun-Woo Jin
- R&D Center, CnPharm Co. LTD., Seoul, 03759, Republic of Korea
| | - Jin-Ho Choy
- Intelligent Nanohybrid Materials Laboratory (INML), Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, 31116, Republic of Korea
- Department of Pre-Medical Course, College of Medicine, Dankook University, Cheonan, 31116, Republic of Korea
- International Research Frontier Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
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Flisiak R, Zarębska-Michaluk D, Dobrowolska K, Rorat M, Rogalska M, Kryńska JA, Moniuszko-Malinowska A, Czupryna P, Kozielewicz D, Jaroszewicz J, Sikorska K, Bednarska A, Piekarska A, Rzymski P. Change in the Clinical Picture of Hospitalized Patients with COVID-19 between the Early and Late Period of Dominance of the Omicron SARS-CoV-2 Variant. J Clin Med 2023; 12:5572. [PMID: 37685639 PMCID: PMC10488127 DOI: 10.3390/jcm12175572] [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: 07/22/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
This study aimed to compare the clinical picture of COVID-19 in the initial and later period of Omicron dominance and to identify populations still at risk. A retrospective comparison of the clinical data of 965 patients hospitalized during the early period of Omicron's dominance (EO, January-June 2022) with 897 patients from a later period (LO, July 2022-April 2023) from the SARSTer database was performed. Patients hospitalized during LO, compared to EO, were older, had a better clinical condition on admission, had a lower need for oxygen and mechanical ventilation, had less frequent lung involvement in imaging, and showed much faster clinical improvement. Moreover, the overall mortality during EO was 14%, higher than that in LO-9%. Despite the milder course of the disease, mortality exceeding 15% was similar in both groups among patients with lung involvement. The accumulation of risk factors such as an age of 60+, comorbidities, lung involvement, and oxygen saturation <90% resulted in a constant need for oxygen in 98% of patients, an 8% risk of mechanical ventilation, and a 30% mortality rate in the LO period. Multiple logistic regression revealed lower odds of death during the LO phase. Despite the milder course of infections caused by the currently dominant subvariants, COVID-19 prophylaxis is necessary in people over 60 years of age, especially those with comorbidities, and in the case of pneumonia and respiratory failure.
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Affiliation(s)
- Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland; (R.F.); (M.R.); (J.A.K.)
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases and Allergology, Jan Kochanowski University, 25-317 Kielce, Poland;
| | | | - Marta Rorat
- Department of Infectious Diseases and Hepatology, Wrocław Medical University, 51-149 Wrocław, Poland;
- Department of Forensic Medicine, Wrocław Medical University, 50-367 Wrocław, Poland
| | - Magdalena Rogalska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland; (R.F.); (M.R.); (J.A.K.)
| | - Justyna Anna Kryńska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland; (R.F.); (M.R.); (J.A.K.)
| | - Anna Moniuszko-Malinowska
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-809 Białystok, Poland; (A.M.-M.); (P.C.)
| | - Piotr Czupryna
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-809 Białystok, Poland; (A.M.-M.); (P.C.)
| | - Dorota Kozielewicz
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Toruń, Poland;
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia in Katowice, 41-902 Bytom, Poland;
| | - Katarzyna Sikorska
- Division of Tropical and Parasitic Diseases, Faculty of Health Sciences, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Agnieszka Bednarska
- Department of Adult’s Infectious Diseases, Medical University of Warsaw, Hospital for Infectious Diseases, 02-091 Warsaw, Poland;
| | - Anna Piekarska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, 90-419 Łódź, Poland;
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznań University of Medical Sciences, 60-806 Poznań, Poland;
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134
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Zhou Y, Zhao X, Jiang Y, Lin DJ, Lu C, Wang Y, Le S, Li R, Yan J. A Mechanical Assay for the Quantification of Anti-RBD IgG Levels in Finger-Prick Whole Blood. ACS Sens 2023; 8:2986-2995. [PMID: 37582229 PMCID: PMC10464602 DOI: 10.1021/acssensors.3c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/01/2023] [Indexed: 08/17/2023]
Abstract
A large portion of the global population has been vaccinated with various vaccines or infected with SARS-CoV-2, the virus that causes COVID-19. The resulting IgG antibodies that target the receptor binding domain (RBD) of SARS-CoV-2 play a vital role in reducing infection rates and severe disease outcomes. Different immune histories result in the production of anti-RBD IgG antibodies with different binding affinities to RBDs of different variants, and the levels of these antibodies decrease over time. Therefore, it is important to have a low-cost, rapid method for quantifying the levels of anti-RBD IgG in decentralized testing for large populations. In this study, we describe a 30 min assay that allows for the quantification of anti-RBD IgG levels in a single drop of finger-prick whole blood. This assay uses force-dependent dissociation of nonspecifically absorbed RBD-coated superparamagnetic microbeads to determine the density of specifically linked microbeads to a protein A-coated transparent surface through anti-RBD IgGs, which can be measured using a simple light microscope and a low-magnification lens. The titer of serially diluted anti-RBD IgGs can be determined without any additional sample processing steps. The limit of detection for this assay is 0.7 ± 0.1 ng/mL referenced to the CR3022 anti-RBD IgG. The limits of the technology and its potential to be further developed to meet the need for point-of-care monitoring of immune protection status are discussed.
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Affiliation(s)
- Yu Zhou
- Mechanobiology
Institute, National University of Singapore, 117411, Singapore
| | - Xiaodan Zhao
- Department
of Physics, National University of Singapore, 117542, Singapore
- Centre
for Bioimaging Sciences, National University
of Singapore, 117557, Singapore
| | - Yanqige Jiang
- Mechanobiology
Institute, National University of Singapore, 117411, Singapore
| | | | - Chen Lu
- Department
of Physics, National University of Singapore, 117542, Singapore
| | - Yinan Wang
- Department
of Physics, National University of Singapore, 117542, Singapore
| | - Shimin Le
- Department
of Physics, Xiamen University, Xiamen361005, P. R. China
| | - Rong Li
- Mechanobiology
Institute, National University of Singapore, 117411, Singapore
| | - Jie Yan
- Mechanobiology
Institute, National University of Singapore, 117411, Singapore
- Department
of Physics, National University of Singapore, 117542, Singapore
- Centre
for Bioimaging Sciences, National University
of Singapore, 117557, Singapore
- Joint
School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, China
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135
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Rosa RG, Falavigna M, Manfio JL, de Araujo CLP, Cohen M, do Valle Barbosa GRG, de Souza AP, Romeiro Silva FK, Sganzerla D, da Silva MMD, Ferreira D, de Oliveira Rodrigues C, de Souza EM, de Oliveira JC, Gradia DF, Brandalize APC, Royer CA, Luiz RM, Kucharski GA, Pedrotti F, Valluri SR, Srivastava A, Julião VW, Melone OC, Allen KE, Kyaw MH, Spinardi J, Del Carmen Morales Castillo G, McLaughlin JM. BNT162b2 mRNA COVID-19 against symptomatic Omicron infection following a mass vaccination campaign in southern Brazil: A prospective test-negative design study. Vaccine 2023; 41:5461-5468. [PMID: 37507274 DOI: 10.1016/j.vaccine.2023.07.038] [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: 04/23/2023] [Revised: 07/01/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND Evidence regarding effectiveness of BNT162b2 mRNA COVID-19 vaccine against Omicron in Latin America is limited. We estimated BNT162b2 effectiveness against symptomatic COVID-19 in Brazil when Omicron was predominant. METHODS This prospective test-negative, case-control study was conducted in Toledo, Brazil, following a mass COVID-19 vaccination with BNT162b2. Patients were included if they were aged ≥12 years, sought care for acute respiratory symptoms in the public health system between November 3, 2021 and June 20, 2022, and were tested for SARS-CoV-2 using RT-PCR. In the primary analysis, we determined the effectiveness of two doses of BNT162b2 against symptomatic COVID-19. RESULTS A total of 4,574 were enrolled; of these, 1,758 patients (586 cases and 1,172 controls) were included in the primary analysis. Mean age was 27.7 years, 53.8 % were women, and 90.1 % had a Charlson comorbidity index of zero. Omicron accounted for >97 % of all identified SARS-CoV-2 variants, with BA.1 and BA.2 accounting for 84.3 % and 12.6 %, respectively. Overall adjusted estimate of two-dose vaccine effectiveness against symptomatic COVID-19 was 46.7 % (95 %CI, 19.9 %-64.6 %) after a median time between the second dose and the beginning of COVID-19 symptoms of 94 days (IQR, 60-139 days). Effectiveness waned from 77.7 % at 7-29 days after receipt of a second dose to <30 % (non-significant) after ≥120 days. CONCLUSION In a relatively young and healthy Brazilian population, two doses of BNT162b2 provided protection against symptomatic Omicron infection. However, this protection waned significantly over time, underscoring the need for boosting with variant-adapted vaccines in this population prior to waves of disease activity. TRIAL REGISTRATION NUMBER ClinicalTrials.gov number, NCT05052307 (https://clinicaltrials.gov/ct2/show/NCT05052307).
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Affiliation(s)
- Regis Goulart Rosa
- Internal Medicine Department, Hospital Moinhos de Vento (HMV), Porto Alegre, RS, Brazil; Research Unit, Inova Medical, Porto Alegre, RS, Brazil; Research Institute, HMV, Porto Alegre, RS, Brazil.
| | - Maicon Falavigna
- Research Unit, Inova Medical, Porto Alegre, RS, Brazil; Research Institute, HMV, Porto Alegre, RS, Brazil; Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | | | | | - Mírian Cohen
- Research Institute, HMV, Porto Alegre, RS, Brazil; Federal University of Rio Grande do Sul (UFRGS), Brazil
| | | | | | | | | | | | | | | | | | | | - Daniela Fiori Gradia
- Department of Biochemistry and Molecular Biology, Department of Genetics - UFPR, Brazil
| | | | - Carla Adriane Royer
- Department of Biochemistry and Molecular Biology, Department of Genetics - UFPR, Brazil
| | - Rafael Messias Luiz
- Faculty of Medicine - Campus Toledo - Federal University of Paraná (UFPR), Brazil
| | | | | | - Srinivas Rao Valluri
- Pfizer, Vaccines Medical and Scientific Affairs - Emerging Markets, Collegeville, PA, USA
| | - Amit Srivastava
- Pfizer, Vaccines Medical and Scientific Affairs - Emerging Markets, Collegeville, PA, USA; Orbital Therapeutics, Cambridge, MA, USA
| | - Viviane Wal Julião
- Pfizer, Vaccines Medical and Scientific Affairs - Emerging Markets, Collegeville, PA, USA
| | - Olga Chameh Melone
- Pfizer, Vaccines Medical and Scientific Affairs - Emerging Markets, Collegeville, PA, USA
| | - Kristen E Allen
- Pfizer, Vaccines Medical and Scientific Affairs - Emerging Markets, Collegeville, PA, USA
| | - Moe H Kyaw
- Pfizer, Vaccines Medical and Scientific Affairs - Emerging Markets, Collegeville, PA, USA
| | - Julia Spinardi
- Pfizer, Vaccines Medical and Scientific Affairs - Emerging Markets, Collegeville, PA, USA
| | | | - John M McLaughlin
- Pfizer, Vaccines Medical and Scientific Affairs - Emerging Markets, Collegeville, PA, USA
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Zhang S, Dong C, Zhen Q, Shi C, Tian H, Li C, Kong X, Dai Q, Huang H, Simayi A, Zhu F, Xu Y, Hu J, Xu K, Chen L, Bao C, Jin H, Zhu L. Unveiling a New Perspective on Distinguishing Omicron Breakthrough Cases and Postimmune COVID-19-Naive Individuals: Insights from Antibody Profiles. Microbiol Spectr 2023; 11:e0180823. [PMID: 37432106 PMCID: PMC10433813 DOI: 10.1128/spectrum.01808-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/24/2023] [Indexed: 07/12/2023] Open
Abstract
In the situation of mass vaccination against COVID-19, few studies have reported on the early kinetics of specific antibodies (IgG/IgM/IgA) of vaccine breakthrough cases. There is still a lack of epidemiological evidence about the value of serological indicators in the auxiliary diagnosis of COVID-19 infection, especially when the nucleic acid results were undetectable. Omicron breakthrough cases post-inactivated vaccination (n = 456) and COVID-19-naive individuals with two doses of inactivated vaccination (n = 693) were enrolled. Blood samples were collected and tested for SARS-CoV-2 antibody levels based on the magnetic chemiluminescence enzyme immunoassay. Among Omicron breakthrough cases, the serum IgG antibody level was 36.34 Sample/CutOff (S/CO) (95% confidence interval [CI], 31.89 to 40.79) in the acute phase and 88.45 S/CO (95% CI, 82.79 to 94.12) in the recovery phase. Serum IgA can be detected in the first week post-symptom onset (PSO) and showed an almost linear increase within 5 weeks PSO. Compared with those of breakthrough cases, IgG and IgA titers of the postimmune group were much lower (4.70 S/CO and 0.46 S/CO, respectively). Multivariate regression showed that serum IgG and IgA levels in Omicron breakthrough cases were mainly affected by the weeks PSO (P < 0.001). Receiver operating characteristic ROC0 curve analysis showed that the area under the curve (AUC) was 0.744 and 0.806 when the cutoff values of IgA and IgG were 1 S/CO and 15 S/CO, respectively. Omicron breakthrough infection can lead to a further increase in IgG and IgA levels relative to those of the immunized population. When nucleic acid real-time PCR was negative, we would use the kinetics of IgG and IgA levels to distinguish the breakthrough cases from the immunized population. IMPORTANCE This study fills a gap in the epidemiological evidence by investigating the value of serological indicators, particularly IgG and IgA levels, in the auxiliary diagnosis of COVID-19 infections when nucleic acid results are undetectable. The findings reveal that among Omicron breakthrough cases, both IgG and IgA antibody levels exhibit significant changes. Serum IgG levels increase during the acute phase and rise further in the recovery phase. Serum IgA can be detected as early as the first week post-symptom onset (PSO), showing a consistent linear increase within 5 weeks PSO. Furthermore, receiver operating characteristic (ROC) curve analysis demonstrates the potential of IgG and IgA cutoff values as diagnostic markers. The study's conclusion underscores the importance of monitoring IgG and IgA kinetics in distinguishing Omicron breakthrough cases from vaccinated individuals. These findings contribute to the development of more accurate diagnostic approaches and help inform public health strategies during the ongoing COVID-19 pandemic.
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Affiliation(s)
- Shihan Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Chen Dong
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Qian Zhen
- Department of Acute Infectious Disease Control and Prevention, Changzhou Center for Disease Control and Prevention, Changzhou, China
| | - Chao Shi
- Department of Acute Infectious Disease Control and Prevention, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Hua Tian
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Chuchu Li
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiaoxiao Kong
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Qigang Dai
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Haodi Huang
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Aidibai Simayi
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Fengcai Zhu
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yawen Xu
- Yangzhou Center for Disease Control and Prevention, Yangzhou, China
| | - Jianli Hu
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Ke Xu
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Liling Chen
- Suzhou Center for Disease Control and Prevention, Suzhou, China
| | - Changjun Bao
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- Jiangsu Province Engineering Research Center of Health Emergency, Nanjing, China
| | - Hui Jin
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Liguo Zhu
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
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Mayor E, Miani A. A topic models analysis of the news coverage of the Omicron variant in the United Kingdom press. BMC Public Health 2023; 23:1509. [PMID: 37559013 PMCID: PMC10410915 DOI: 10.1186/s12889-023-16444-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic has caused numerous casualties, overloaded hospitals, reduced the wellbeing of many and had a substantial negative economic impact globally. As the population of the United Kingdom was preparing for recovery, the uncertainty relating to the discovery of the new Omicron variant on November 24 2021 threatened those plans. There was thus an important need for sensemaking, which could be provided, partly, through diffusion of information in the press, which we here examine. METHOD We used topic modeling, to extract 50 topics from close to 1,500 UK press articles published during a period of approximately one month from the appearance of Omicron. We performed ANOVAs in order to compare topics between full weeks, starting on week 48 of 2021. RESULTS The three topics documenting the new variant (Omicron origins, Virus mutations, News of a new variant) as well as mentions of vaccination excluding booster, Scotlands First minister statement (Communications) travel bans and mask wearing (Restrictions) and the impact of market and investing (Domains and events) decreased through time (all ps < .01). Some topics featured lower representation at week two or three with higher values before and after: Government's Scientific Advisory Group for Emergencies recommendations (Communications), Situation in the US, Situation in Europe (Other countries and regions), all ps < .01. Several topics referring to symptoms and cases-e.g., rises of infections, hospitalisations, the pandemic the holidays, mild symptoms and care; restrictions and measures-e.g., financial help, Christmas and Plan B, restrictions and New Year; and domains of consequences and events-e.g., such as politics, NHS and patients, retail sales and airlines, featured increasing representation, (all ps < .01). Other topics featured less regular or non-significant patterns. CONCLUSION Changes in sensemaking in the press closely matched the changes in the official discourse relating to Omicron and reflects the trajectory of the infection and its local consequences.
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Affiliation(s)
- Eric Mayor
- Department of Psychology, University of Basel, Missionsstrasse 62a, 4055, Basel, Switzerland.
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Adrawa N, Ongiro S, Lotee K, Seret J, Adeke M, Izudi J. Use of a context-specific package to increase sputum smear monitoring among people with pulmonary tuberculosis in Uganda: a quality improvement study. BMJ Open Qual 2023; 12:e002314. [PMID: 37558284 PMCID: PMC10414073 DOI: 10.1136/bmjoq-2023-002314] [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: 02/09/2023] [Accepted: 07/30/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND People with bacteriologically confirmed pulmonary tuberculosis (BC-PTB) require sputum smear monitoring (SSM) to ascertain response to anti-TB treatment and cure from TB disease. We aimed to increase SSM at 2, 5 and 6 months among people with BC-PTB from the baseline (March to July 2021) of 68%, 37% and 39%, respectively, to 90% in February 2022 by implementing a context-specific improvement package at a rural health facility in northeastern Uganda. METHODS We designed a continuous quality improvement (CQI) study for people with BC-PTB, developed and tested an improvement package that consisted of the following context-specific measures: (1) line listing of all eligible persons for SSM; (2) use of reminder stickers to identify eligible persons for SSM; (3) use of community health workers to conduct home visits for people with missed clinic visits; and (4) integration of SSM into community-based ART points for distant persons. We implemented the measures using the plan-do-study-act cycle and tracked the progress in SSM through monthly data reviews and analyses. RESULTS SSM at 2 months improved from 68% (17/25) at the baseline to 74% (32/43) during phase I (p=0.818) and then to 94% (17/18) during phase II (p=0.562). SSM at 5 months improved from 37% (11/29) at the baseline to 82% (41/50) during phase I (p=0.094) and then to 100% (10/10) during phase II (p=0.688). SSM at 6 months improved from 39% (9/23) at the baseline to 59% (28/39) during phase I (p=0.189) and then to 100% (12/12) during phase II (p=0.487). CONCLUSION The use of a context-relevant CQI package was accompanied by improved SSM at 2, 5 and 6 months among people with BC-PTB. Trends are encouraging but this should be considered as preliminary report because of limited numbers. These data can inform the design of a fully powered randomised controlled trial.
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Affiliation(s)
- Norbert Adrawa
- The AIDS Support Organization (TASO) Soroti Region Project, Soroti, Uganda
| | - Simon Ongiro
- Tokora Health Centre IV, Nakapiripirit District, Uganda
| | - Kizito Lotee
- Tokora Health Centre IV, Nakapiripirit District, Uganda
| | - Jacob Seret
- Tokora Health Centre IV, Nakapiripirit District, Uganda
| | - Mary Adeke
- Tokora Health Centre IV, Nakapiripirit District, Uganda
| | - Jonathan Izudi
- Department of Community Health, Mbarara University of Science and Technology, Mbarara, Uganda
- Infectious Diseases Institute (IDI), Makerere University, Kampala, Uganda
- The African Population and Health Research Center (APHRC), Nairobi, Kenya
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Wang K, Pan Y, Wang D, Yuan Y, Li M, Chen Y, Bi L, Zhang XE. Altered hACE2 binding affinity and S1/S2 cleavage efficiency of SARS-CoV-2 spike protein mutants affect viral cell entry. Virol Sin 2023; 38:595-605. [PMID: 37343929 PMCID: PMC10278895 DOI: 10.1016/j.virs.2023.06.005] [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: 01/31/2023] [Accepted: 06/15/2023] [Indexed: 06/23/2023] Open
Abstract
SARS-CoV-2 variants are constantly emerging, hampering public health measures in controlling the number of infections. While it is well established that mutations in spike proteins observed for the different variants directly affect virus entry into host cells, there remains a need for further expansion of systematic and multifaceted comparisons. Here, we comprehensively studied the effect of spike protein mutations on spike expression and proteolytic activation, binding affinity, viral entry efficiency and host cell tropism of eight variants of concern (VOC) and variants of interest (VOI). We found that both the full-length spike and its receptor-binding domain (RBD) of Omicron bind to hACE2 with an affinity similar to that of the wild-type. In addition, Alpha, Beta, Delta and Lambda pseudoviruses gained significantly enhanced cell entry ability compared to the wild-type, while the Omicron pseudoviruses showed a slightly increased cell entry, suggesting the vastly increased rate of transmission observed for Omicron variant is not associated with its affinity to hACE2. We also found that the spikes of Omicron and Mu showed lower S1/S2 cleavage efficiency and inefficiently utilized TMPRSS2 to enter host cells than others, suggesting that they prefer the endocytosis pathway to enter host cells. Furthermore, all variants' pseudoviruses we tested gained the ability to enter the animal ACE2-expressing cells. Especially the infection potential of rats and mice showed significantly increased, strongly suggesting that rodents possibly become a reservoir for viral evolution. The insights gained from this study provide valuable guidance for a targeted approach to epidemic control, and contribute to a better understanding of SARS-CoV-2 evolution.
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Affiliation(s)
- Ke Wang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yu Pan
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dianbing Wang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ye Yuan
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Min Li
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuanyuan Chen
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lijun Bi
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100101, China.
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Kim CY, Sardar Z, Ayele BA, Fleck‐Derderian S, Barrett CE, Sun Y, Clague M, Hurst HA, Boruah A, Zucker J, Maddox R, Sejvar J, Thakur KT. Neurological diagnoses in hospitalized COVID-19 patients during the B.1.1.529 surge. Ann Clin Transl Neurol 2023; 10:1433-1441. [PMID: 37350635 PMCID: PMC10424653 DOI: 10.1002/acn3.51833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
OBJECTIVE Emerging variants and sublineages of SARS-CoV-2 have differing disease severity, transmissibility, and immune evasion. The neurological conditions associated with the original strain of SARS-CoV-2 are well established. Our study assessed the neurological presentations specific to hospitalized patients during the B.1.1.529 (Omicron) variant surge in New York City. METHODS A total of 178 cases with positive RT-PCR result within 6 weeks before admission, and subsequent development of select neurological conditions during the SARS-CoV-2 B.1.1.529 (Omicron) surge between December 1, 2021 and February 28, 2022, were included from 12,800 SARS-CoV-2-positive hospital admissions. Clinical data from acute hospitalizations were compared to findings of inpatient neurological cases with COVID-19 infections from the initial surge in NYC in the same hospital system. RESULTS Compared to SARS-CoV-2 infections of the original strain, COVID-19 cases hospitalized during the Omicron surge (B.1.1.529) were associated with incidental and/or asymptomatic COVID-19 cases (96, 53.9%) and an increased incidence of pre-existing neurological and immunocompromising conditions. Encephalopathy, seizures, and stroke remained the most prevalent neurological conditions identified in hospitalized COVID-19 cases during the study period, reflecting a similar distribution of neurological presentations associated with the original strain. INTERPRETATION In our cohort of 178 admitted SARS-CoV-2-positive patients with select neurological conditions during the Omicron B.1.1.529 surge, 54% of COVID-19 cases were considered incidental and/or asymptomatic, and the identified neurological conditions resembled those associated with the original SARS-CoV-2 strain. Further studies characterizing neurological presentation in Omicron sublineages and other variants are warranted in an ongoing COVID-19 pandemic.
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Affiliation(s)
- Carla Y. Kim
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Zomer Sardar
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Biniyam A. Ayele
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | | | | | - Yifei Sun
- Department of BiostatisticsColumbia UniversityNew YorkNew YorkUSA
| | - Madison Clague
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Holly A. Hurst
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Abhilasha Boruah
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
- Case Western Reserve University School of MedicineClevelandOhioUSA
| | - Jason Zucker
- Department of Infectious DiseaseColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
| | - Ryan Maddox
- United States Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - James Sejvar
- United States Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Kiran T. Thakur
- Department of NeurologyColumbia University Irving Medical Center/New York Presbyterian HospitalNew YorkNew YorkUSA
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Xiang N, Li YJ, Liu MY, Wu QQ, Zhang YX, Jin HZ, Wang Q, Li YW, Tong DL, Xue T, Jin TC, Bao W, Chen Z. Antibody responses following the surge of SARS-CoV-2 Omicron infection among patients with systemic autoimmune rheumatic diseases. Rheumatol Adv Pract 2023; 7:rkad064. [PMID: 37547578 PMCID: PMC10398008 DOI: 10.1093/rap/rkad064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/14/2023] [Indexed: 08/08/2023] Open
Abstract
Objectives The surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron infections has affected most Chinese residents at the end of 2022, including a number of patients with systemic autoimmune rheumatic diseases (SARDs). Methods To investigate the antibody level of the Omicron variant in SARD patients after SARS-CoV-2 Omicron infection, we tested BA.5.2 and BF.7 Omicron variant IgG antibody levels using ELISA on blood samples collected from 102 SARD patients and 19 healthy controls (HCs). The type of SARD, demographics, concurrent treatment, doses of SARS-CoV-2 vaccines and outcomes were also recorded. Results A total of 102 SARD patients (mean age: 40.3 years; 89.2% female), including 60 SLE, 32 RA and 10 other SARDs, were identified. Of these, 87 (85.3%) were infected with SARS-CoV-2. We found that the BA.5.2 and BF.7 antibody levels of infected SARD patients were lower than those of HCs (P < 0.05). Sixty-five (63.7%) patients had at least one dose of a SARS-CoV-2 vaccine. SARD patients with at least two doses of SARS-CoV-2 vaccine had a higher level of BA.5.2 and BF.7 antibodies than the unvaccinated group (P < 0.05). There was no evidence for a significant inhibitory effect of glucocorticoids (GCs) on the BA.5.2 and BF.7 Omicron variant antibody levels in SARD patients. SLE patients using biologic DMARDs had a lower BA.5.2 Omicron variant antibody level than patients using GCs and/or HCQ. Conclusion These data suggest that patients with SARDs had a lower antibody response than HCs after Omicron infection.
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Affiliation(s)
| | | | - Meng-Yao Liu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qi-Qin Wu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ya-Xin Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Hui-Zhi Jin
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qian Wang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yu-Wei Li
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Da-Li Tong
- Department of Ophthalmology, The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tian Xue
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale Neurodegenerative Disorder Research Center, CAS Key Laboratory of Brain Function and Disease, CAS Key Laboratory of Innate Immunity and Chronic Disease, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Teng-Chuan Jin
- Correspondence to: Teng-Chuan Jin and Zhu Chen, Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, No. 17 Lujiang Road, Hefei, Anhui 230001, China. E-mail: ;
| | - Wei Bao
- Institute of Public Health Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhu Chen
- Correspondence to: Teng-Chuan Jin and Zhu Chen, Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, No. 17 Lujiang Road, Hefei, Anhui 230001, China. E-mail: ;
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Harthaller T, Falkensammer B, Bante D, Huber M, Schmitt M, Benainouna H, Rössler A, Fleischer V, von Laer D, Kimpel J, Würzner R, Borena W. Retained avidity despite reduced cross-binding and cross-neutralizing antibody levels to Omicron after SARS-COV-2 wild-type infection or mRNA double vaccination. Front Immunol 2023; 14:1196988. [PMID: 37545492 PMCID: PMC10401431 DOI: 10.3389/fimmu.2023.1196988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction The rapid evolution of SARS-CoV-2 has posed a challenge to long-lasting immunity against the novel virus. Apart from neutralizing function, binding antibodies induced by vaccination or infection play an important role in containing the infection. Methods To determine the proportion of wild-type (WT)-generated antibodies recognizant of more recent variants, plasma samples from either SARS-CoV-2 WT-infected (n = 336) or double-mRNA (Comirnaty)-vaccinated individuals (n = 354, age and sex matched to the convalescent group) were analyzed for binding antibody capacity against the S1 protein of the BA.1 omicron variant. Results Overall, 38.59% (95% CI, 37.01- 40.20) of WT-generated antibodies recognized Omicron BA.1 S1 protein [28.83% (95% CI, 26.73-30.91) after infection and 43.46% (95% CI, 41.61-45.31) after vaccination; p < 0.001]. Although the proportion of WT-generated binding and neutralizing antibodies also binding to BA.1 is substantially reduced, the avidity of the remaining antibodies against the Omicron variant was non-inferior to that of the ancestral virus: Omicron: 39.7% (95% CI: 38.1-41.3) as compared to the avidity to WT: 27.0% (95% CI, 25.5-28.4), respectively (p < 0.001). Furthermore, we noticed a modestly yet statistically significant higher avidity toward the Omicron epitopes among the vaccinated group (42.2%; 95% CI, 40.51-43.94) as compared to the convalescent counterparts (36.4%; 95% CI, 33.42-38.76) (p = 0.003), even after adjusting for antibody concentration. Discussion Our results suggest that an aspect of functional immunity against the novel strain was considerably retained after WT contact, speculatively counteracting the impact of immune evasion toward neutralization of the strain. Higher antibody levels and cross-binding capacity among vaccinated individuals suggest an advantage of repeated exposure in generating robust immunity.
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Affiliation(s)
- Teresa Harthaller
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Barbara Falkensammer
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - David Bante
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Maria Huber
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Melanie Schmitt
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Habib Benainouna
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Annika Rössler
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Verena Fleischer
- Department of Hygiene, Microbiology and Public Health, Institute of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - Dorothee von Laer
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Janine Kimpel
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
| | - Reinhard Würzner
- Department of Hygiene, Microbiology and Public Health, Institute of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - Wegene Borena
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Innsbruck Medical University, Innsbruck, Austria
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Tsui JLH, McCrone JT, Lambert B, Bajaj S, Inward RP, Bosetti P, Tegally H, Hill V, Pena RE, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O’Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T, Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MU. Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1. Science 2023; 381:336-343. [PMID: 37471538 PMCID: PMC10866301 DOI: 10.1126/science.adg6605] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) now arise in the context of heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron BA.1 genomes, we identified >6,000 introductions of the antigenically distinct VOC into England and analyzed their local transmission and dispersal history. We find that six of the eight largest English Omicron lineages were already transmitting when Omicron was first reported in southern Africa (22 November 2021). Multiple datasets show that importation of Omicron continued despite subsequent restrictions on travel from southern Africa as a result of export from well-connected secondary locations. Initiation and dispersal of Omicron transmission lineages in England was a two-stage process that can be explained by models of the country's human geography and hierarchical travel network. Our results enable a comparison of the processes that drive the invasion of Omicron and other VOCs across multiple spatial scales.
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Affiliation(s)
| | - John T. McCrone
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
- Helix, San Mateo, USA
| | - Ben Lambert
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Paolo Bosetti
- Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Verity Hill
- Helix, San Mateo, USA
- Yale University, New Haven, USA
| | | | | | - Thomas P. Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | - Neo Wu
- Google Research, Mountain View, USA
| | | | - Isaac I. Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | | | | | | | | | | | | | - Eduan Wilkinson
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - Thomas R. Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, UK
- Pandemic Sciences Institute, University of Oxford, UK
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Xiang Ji
- Department of Mathematics, Tulane University, New Orleans, USA
| | | | | | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Simon Cauchemez
- Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Jayna Raghwani
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | - Marc A. Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Oliver G. Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | - Moritz U.G. Kraemer
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, UK
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Laverack M, Tallmadge RL, Venugopalan R, Sheehan D, Ross S, Rustamov R, Frederici C, Potter KS, Elvinger F, Warnick LD, Koretzky GA, Lawlis R, Plocharczyk E, Diel DG. The Cornell COVID-19 Testing Laboratory: A Model to High-Capacity Testing Hubs for Infectious Disease Emergency Response and Preparedness. Viruses 2023; 15:1555. [PMID: 37515241 PMCID: PMC10385863 DOI: 10.3390/v15071555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The unprecedented COVID-19 pandemic posed major challenges to local, regional, and global economies and health systems, and fast clinical diagnostic workflows were urgently needed to contain the spread of SARS-CoV-2. Here, we describe the platform and workflow established at the Cornell COVID-19 Testing Laboratory (CCTL) for the high-throughput testing of clinical samples from the university and the surrounding community. This workflow enabled efficient and rapid detection and the successful control of SARS-CoV-2 infection on campus and its surrounding communities. Our cost-effective and fully automated workflow enabled the testing of over 8000 pooled samples per day and provided results for over 2 million samples. The automation of time- and effort-intensive sample processing steps such as accessioning and pooling increased laboratory efficiency. Customized software applications were developed to track and store samples, deconvolute positive pools, track and report results, and for workflow integration from sample receipt to result reporting. Additionally, quality control dashboards and turnaround-time tracking applications were built to monitor assay and laboratory performance. As infectious disease outbreaks pose a constant threat to both human and animal health, the highly effective workflow implemented at CCTL could be modeled to establish regional high-capacity testing hubs for infectious disease preparedness and emergency response.
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Affiliation(s)
- Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Rebecca L Tallmadge
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Roopa Venugopalan
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Daniel Sheehan
- Information Technology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Scott Ross
- Information Technology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Rahim Rustamov
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Casey Frederici
- Cayuga Medical Center, Cayuga Health System, Ithaca, NY 14850, USA
| | - Kim S Potter
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - François Elvinger
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Lorin D Warnick
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
| | - Gary A Koretzky
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Medicine, Weill Cornell Medicine, Cornell University, New York City, NY 10065, USA
| | - Robert Lawlis
- Cayuga Medical Center, Cayuga Health System, Ithaca, NY 14850, USA
| | | | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center (AHDC), College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory (CCTL), Cornell University, Ithaca, NY 14853, USA
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Franco-Luiz APM, Fernandes NMGS, Silva TBDS, Bernardes WPDOS, Westin MR, Santos TG, Fernandes GDR, Simões TC, Silva EFE, Gava SG, Alves BM, de Carvalho Melo M, da Silva-Pereira RA, Alves PA, Fonseca CT. Longitudinal study of humoral immunity against SARS-CoV-2 of health professionals in Brazil: the impact of booster dose and reinfection on antibody dynamics. Front Immunol 2023; 14:1220600. [PMID: 37520570 PMCID: PMC10376701 DOI: 10.3389/fimmu.2023.1220600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction The pandemic caused by SARS-CoV-2 has had a major impact on health systems. Vaccines have been shown to be effective in improving the clinical outcome of COVID-19, but they are not able to fully prevent infection and reinfection, especially that caused by new variants. Methods Here, we tracked for 450 days the humoral immune response and reinfection in 52 healthcare workers from Brazil. Infection and reinfection were confirmed by RT-qPCR, while IgM and IgG antibody levels were monitored by rapid test. Results Of the 52 participants, 19 (36%) got reinfected during the follow-up period, all presenting mild symptoms. For all participants, IgM levels dropped sharply, with over 47% of them becoming seronegative by the 60th day. For IgG, 90% of the participants became seropositive within the first 30 days of follow-up. IgG antibodies also dropped after this period reaching the lowest level on day 270 (68.5 ± 72.3, p<0.0001). Booster dose and reinfection increased the levels of both antibodies, with the interaction between them resulting in an increase in IgG levels of 130.3 arbitrary units. Conclusions Overall, our data indicate that acquired humoral immunity declines over time and suggests that IgM and IgG antibody levels are not associated with the prevention of reinfection.
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Affiliation(s)
- Ana Paula Moreira Franco-Luiz
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Nubia Monteiro Gonçalves Soares Fernandes
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Thais Bárbara de Souza Silva
- Grupo de Imunologia de Doenças Virais, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mateus Rodrigues Westin
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thais Garcia Santos
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel da Rocha Fernandes
- Grupo de Pesquisa em Informática de Biossistemas, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Taynãna César Simões
- Núcleo de Estudos em Saúde Pública e Envelhecimento, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo Fernandes E. Silva
- Serviço de capacitação em métodos quantitativos -SAMeQ, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Sandra Grossi Gava
- Grupo de Pesquisa em Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Breno Magalhães Alves
- Centro de Vigilância em Saúde e Segurança do Paciente, Hospital Metropolitano Doutor Célio de Castro, Belo Horizonte, Minas Gerais, Brazil
| | - Mariana de Carvalho Melo
- Serviço Especializado em Segurança e Medicina do Trabalho, Hospital Metropolitano Doutor Célio de Castro, Belo Horizonte, Minas Gerais, Brazil
| | - Rosiane A. da Silva-Pereira
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Pedro Augusto Alves
- Grupo de Imunologia de Doenças Virais, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Cristina Toscano Fonseca
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
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Lubin JH, Markosian C, Balamurugan D, Ma MT, Chen CH, Liu D, Pasqualini R, Arap W, Burley SK, Khare SD. Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion. JCI Insight 2023; 8:e168296. [PMID: 37261904 PMCID: PMC10371346 DOI: 10.1172/jci.insight.168296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/26/2023] [Indexed: 06/03/2023] Open
Abstract
Given the COVID-19 pandemic, there is interest in understanding ligand-receptor features and targeted antibody-binding attributes against emerging SARS-CoV-2 variants. Here, we developed a large-scale structure-based pipeline for analysis of protein-protein interactions regulating SARS-CoV-2 immune evasion. First, we generated computed structural models of the Spike protein of 3 SARS-CoV-2 variants (B.1.1.529, BA.2.12.1, and BA.5) bound either to a native receptor (ACE2) or to a large panel of targeted ligands (n = 282), which included neutralizing or therapeutic monoclonal antibodies. Moreover, by using the Barnes classification, we noted an overall loss of interfacial interactions (with gain of new interactions in certain cases) at the receptor-binding domain (RBD) mediated by substituted residues for neutralizing complexes in classes 1 and 2, whereas less destabilization was observed for classes 3 and 4. Finally, an experimental validation of predicted weakened therapeutic antibody binding was performed in a cell-based assay. Compared with the original Omicron variant (B.1.1.529), derivative variants featured progressive destabilization of antibody-RBD interfaces mediated by a larger set of substituted residues, thereby providing a molecular basis for immune evasion. This approach and findings provide a framework for rapidly and efficiently generating structural models for SARS-CoV-2 variants bound to ligands of mechanistic and therapeutic value.
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Affiliation(s)
- Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - D. Balamurugan
- Office of Advanced Research Computing, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Department of Radiology
| | - Minh T. Ma
- Department of Pathology, Immunology, and Laboratory Medicine
- Center for Immunity and Inflammation, and
| | - Chih-Hsiung Chen
- Department of Pathology, Immunology, and Laboratory Medicine
- Center for Immunity and Inflammation, and
| | - Dongfang Liu
- Department of Pathology, Immunology, and Laboratory Medicine
- Center for Immunity and Inflammation, and
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Stephen K. Burley
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- RCSB Protein Data Bank, San Diego Supercomputer Center, UCSD, La Jolla, California, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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147
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Acuña-Castillo C, Barrera-Avalos C, Bachelet VC, Milla LA, Inostroza-Molina A, Vidal M, Luraschi R, Vallejos-Vidal E, Mella-Torres A, Valdés D, Reyes-López FE, Imarai M, Rojas P, Sandino AM. An ecological study on reinfection rates using a large dataset of RT-qPCR tests for SARS-CoV-2 in Santiago of Chile. Front Public Health 2023; 11:1191377. [PMID: 37492136 PMCID: PMC10364051 DOI: 10.3389/fpubh.2023.1191377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/05/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction As the SARS-CoV-2 continues to evolve, new variants pose a significant threat by potentially overriding the immunity conferred by vaccination and natural infection. This scenario can lead to an upswing in reinfections, amplified baseline epidemic activity, and localized outbreaks. In various global regions, estimates of breakthrough cases associated with the currently circulating viral variants, such as Omicron, have been reported. Nonetheless, specific data on the reinfection rate in Chile still needs to be included. Methods Our study has focused on estimating COVID-19 reinfections per wave based on a sample of 578,670 RT-qPCR tests conducted at the University of Santiago of Chile (USACH) from April 2020 to July 2022, encompassing 345,997 individuals. Results The analysis reveals that the highest rate of reinfections transpired during the fourth and fifth COVID-19 waves, primarily driven by the Omicron variant. These findings hold despite 80% of the Chilean population receiving complete vaccination under the primary scheme and 60% receiving at least one booster dose. On average, the interval between initial infection and reinfection was found to be 372 days. Interestingly, reinfection incidence was higher in women aged between 30 and 55. Additionally, the viral load during the second infection episode was lower, likely attributed to Chile's high vaccination rate. Discussion This study demonstrates that the Omicron variant is behind Chile's highest number of reinfection cases, underscoring its potential for immune evasion. This vital epidemiological information contributes to developing and implementing effective public health policies.
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Affiliation(s)
- Claudio Acuña-Castillo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Carlos Barrera-Avalos
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Vivienne C. Bachelet
- Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - Luis A. Milla
- Centro de Investigaciones Biomédicas y Aplicadas, Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - Ailén Inostroza-Molina
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mabel Vidal
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Roberto Luraschi
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Eva Vallejos-Vidal
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Nanociencia y Nanotecnología CEDENNA, Universidad de Santiago de Chile, Santiago, Chile
| | - Andrea Mella-Torres
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Daniel Valdés
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe E. Reyes-López
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mónica Imarai
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Patricio Rojas
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Ana María Sandino
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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148
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Meyer-Rath G, Hounsell RA, Pulliam JR, Jamieson L, Nichols BE, Moultrie H, Silal SP. The role of modelling and analytics in South African COVID-19 planning and budgeting. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001063. [PMID: 37399174 DOI: 10.1371/journal.pgph.0001063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/24/2023] [Indexed: 07/05/2023]
Abstract
BACKGROUND The South African COVID-19 Modelling Consortium (SACMC) was established in late March 2020 to support planning and budgeting for COVID-19 related healthcare in South Africa. We developed several tools in response to the needs of decision makers in the different stages of the epidemic, allowing the South African government to plan several months ahead. METHODS Our tools included epidemic projection models, several cost and budget impact models, and online dashboards to help government and the public visualise our projections, track case development and forecast hospital admissions. Information on new variants, including Delta and Omicron, were incorporated in real time to allow the shifting of scarce resources when necessary. RESULTS Given the rapidly changing nature of the outbreak globally and in South Africa, the model projections were updated regularly. The updates reflected 1) the changing policy priorities over the course of the epidemic; 2) the availability of new data from South African data systems; and 3) the evolving response to COVID-19 in South Africa, such as changes in lockdown levels and ensuing mobility and contact rates, testing and contact tracing strategies and hospitalisation criteria. Insights into population behaviour required updates by incorporating notions of behavioural heterogeneity and behavioural responses to observed changes in mortality. We incorporated these aspects into developing scenarios for the third wave and developed additional methodology that allowed us to forecast required inpatient capacity. Finally, real-time analyses of the most important characteristics of the Omicron variant first identified in South Africa in November 2021 allowed us to advise policymakers early in the fourth wave that a relatively lower admission rate was likely. CONCLUSION The SACMC's models, developed rapidly in an emergency setting and regularly updated with local data, supported national and provincial government to plan several months ahead, expand hospital capacity when needed, allocate budgets and procure additional resources where possible. Across four waves of COVID-19 cases, the SACMC continued to serve the planning needs of the government, tracking waves and supporting the national vaccine rollout.
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Affiliation(s)
- Gesine Meyer-Rath
- Faculty of Health Sciences, Health Economics and Epidemiology Research Office, University of the Witwatersrand, Johannesburg, South Africa
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, United States of America
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Rachel A Hounsell
- Department of Statistical Sciences, Modelling and Simulation Hub, Africa, University of Cape Town, Cape Town, South Africa
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Juliet Rc Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Lise Jamieson
- Faculty of Health Sciences, Health Economics and Epidemiology Research Office, University of the Witwatersrand, Johannesburg, South Africa
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Brooke E Nichols
- Faculty of Health Sciences, Health Economics and Epidemiology Research Office, University of the Witwatersrand, Johannesburg, South Africa
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, United States of America
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Harry Moultrie
- National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sheetal P Silal
- Department of Statistical Sciences, Modelling and Simulation Hub, Africa, University of Cape Town, Cape Town, South Africa
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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Howerton E, Contamin L, Mullany LC, Qin M, Reich NG, Bents S, Borchering RK, Jung SM, Loo SL, Smith CP, Levander J, Kerr J, Espino J, van Panhuis WG, Hochheiser H, Galanti M, Yamana T, Pei S, Shaman J, Rainwater-Lovett K, Kinsey M, Tallaksen K, Wilson S, Shin L, Lemaitre JC, Kaminsky J, Hulse JD, Lee EC, McKee C, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Piontti APY, Vespignani A, Rosenstrom ET, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore S, Perkins A, Hladish T, Pillai A, Toh KB, Longini I, Chen S, Paul R, Janies D, Thill JC, Bouchnita A, Bi K, Lachmann M, Fox S, Meyers LA, Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Hurt B, Chen J, Mortveit H, Wilson A, Marathe M, Hoops S, Bhattacharya P, Machi D, Cadwell BL, Healy JM, Slayton RB, Johansson MA, Biggerstaff M, Truelove S, Runge MC, Shea K, Viboud C, Lessler J. Informing pandemic response in the face of uncertainty. An evaluation of the U.S. COVID-19 Scenario Modeling Hub. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.28.23291998. [PMID: 37461674 PMCID: PMC10350156 DOI: 10.1101/2023.06.28.23291998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Our ability to forecast epidemics more than a few weeks into the future is constrained by the complexity of disease systems, our limited ability to measure the current state of an epidemic, and uncertainties in how human action will affect transmission. Realistic longer-term projections (spanning more than a few weeks) may, however, be possible under defined scenarios that specify the future state of critical epidemic drivers, with the additional benefit that such scenarios can be used to anticipate the comparative effect of control measures. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make 6-month ahead projections of the number of SARS-CoV-2 cases, hospitalizations and deaths. The SMH released nearly 1.8 million national and state-level projections between February 2021 and November 2022. SMH performance varied widely as a function of both scenario validity and model calibration. Scenario assumptions were periodically invalidated by the arrival of unanticipated SARS-CoV-2 variants, but SMH still provided projections on average 22 weeks before changes in assumptions (such as virus transmissibility) invalidated scenarios and their corresponding projections. During these periods, before emergence of a novel variant, a linear opinion pool ensemble of contributed models was consistently more reliable than any single model, and projection interval coverage was near target levels for the most plausible scenarios (e.g., 79% coverage for 95% projection interval). SMH projections were used operationally to guide planning and policy at different stages of the pandemic, illustrating the value of the hub approach for long-term scenario projections.
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Affiliation(s)
| | | | | | | | | | - Samantha Bents
- National Institutes of Health Fogarty International Center (NIH)
| | | | | | - Sara L Loo
- Johns Hopkins University Infectious Disease Dynamics (JHU-IDD)
| | - Claire P Smith
- Johns Hopkins University Infectious Disease Dynamics (JHU-IDD)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Shi Chen
- University of North Carolina at Charlotte (UNCC)
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150
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Liu Y, Zhu J, Tuwor CP, Ling C, Yu L, Yin K. The impact of the COVID-19 pandemic on global trade-embodied carbon emissions. JOURNAL OF CLEANER PRODUCTION 2023; 408:137042. [PMID: 37077939 PMCID: PMC10074258 DOI: 10.1016/j.jclepro.2023.137042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/18/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
We evaluate the response of global supply chains to carbon emissions through compiling multi-regional input-output (MRIO) models for import and export shocks in 14 countries/territories dominated by the COVID-19 crisis. Instead of traditional production-based inventories, we achieve CO2 emissions inventories based on intermediate inputs and final consumption to analyze the connected environmental impacts. In addition, we adopt the available data up to date to construct inventories of carbon emissions involved in imports and exports from different sectors. The results show that global carbon emissions could be decreased by 6.01% during the COVID-19, while export carbon emissions remained basically unchanged. As a result, imported carbon emissions fell by 5.2%, with the energy products sector most affected by the pandemic. Transport sector witnessed 18.42% carbon emission reduction. The impact of developing countries with a large proportion of resource-based industries is comparatively higher than that of developed countries with the technological advantage. International trade plays a crucial role in the choice of supply chain partners to control carbon emissions. Building a sustainable supply chain and reducing the "trade carbon deficit" between countries/regions requires the coordination of all departments of each country/region to promote the trade of energy-saving products, environmental protection services and environmental services.
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Affiliation(s)
- Yuru Liu
- Department of Environmental Engineering, School of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Jingyu Zhu
- Department of Environmental Engineering, School of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Christopher Padi Tuwor
- Department of Environmental Engineering, School of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Chen Ling
- Department of Environmental Engineering, School of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Lei Yu
- Department of Environmental Engineering, School of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Ke Yin
- Department of Environmental Engineering, School of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
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