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Li P, Liu Y, Faraone JN, Hsu CC, Chamblee M, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Liu SL. Distinct patterns of SARS-CoV-2 BA.2.87.1 and JN.1 variants in immune evasion, antigenicity, and cell-cell fusion. mBio 2024:e0075124. [PMID: 38591890 DOI: 10.1128/mbio.00751-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 variants presents a constant challenge to the global vaccination effort. In this study, we conducted a comprehensive investigation into two newly emerged variants, BA.2.87.1 and JN.1, focusing on their neutralization resistance, infectivity, antigenicity, cell-cell fusion, and spike processing. Neutralizing antibody (nAb) titers were assessed in diverse cohorts, including individuals who received a bivalent mRNA vaccine booster, patients infected during the BA.2.86/JN.1-wave, and hamsters vaccinated with XBB.1.5-monovalent vaccine. We found that BA.2.87.1 shows much less nAb escape from WT-BA.4/5 bivalent mRNA vaccination and JN.1-wave breakthrough infection sera compared to JN.1 and XBB.1.5. Interestingly, BA.2.87.1 is more resistant to neutralization by XBB.1.5-monovalent-vaccinated hamster sera than BA.2.86/JN.1 and XBB.1.5, but efficiently neutralized by a class III monoclonal antibody S309, which largely fails to neutralize BA.2.86/JN.1. Importantly, BA.2.87.1 exhibits higher levels of infectivity, cell-cell fusion activity, and furin cleavage efficiency than BA.2.86/JN.1. Antigenically, we found that BA.2.87.1 is closer to the ancestral BA.2 compared to other recently emerged Omicron subvariants including BA.2.86/JN.1 and XBB.1.5. Altogether, these results highlight immune escape properties as well as biology of new variants and underscore the importance of continuous surveillance and informed decision-making in the development of effective vaccines. IMPORTANCE This study investigates the recently emerged SARS-CoV-2 variants, BA.2.87.1 and JN.1, in comparison to earlier variants and the parental D614G. Varied infectivity and cell-cell fusion activity among these variants suggest potential disparities in their ability to infect target cells and possibly pathogenesis. BA.2.87.1 exhibits lower nAb escape from bivalent mRNA vaccinee and BA.2.86/JN.1-infected sera than JN.1 but is relatively resistance to XBB.1.5-vaccinated hamster sera, revealing distinct properties in immune reason and underscoring the significance of continuing surveillance of variants and reformulation of vaccines. Antigenic differences between BA.2.87.1 and other earlier variants yield critical information not only for antibody evasion but also for viral evolution. In conclusion, this study furnishes timely insights into the spike biology and immune escape of the emerging variants BA.2.87.1 and JN.1, thus guiding effective vaccine development and informing public health interventions.
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Affiliation(s)
- Pei Li
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Yajie Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA
| | - Cheng Chih Hsu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Michelle Chamblee
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Joseph S Bednash
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, Ohio, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, Ohio, USA
| | - Jeffrey C Horowitz
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, Ohio, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, Ohio, USA
| | - Rama K Mallampalli
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, Ohio, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, Ohio, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, Ohio, USA
- Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, Ohio, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center Arthur G James Cancer Hospital and Richard J Solove Research Institute, Columbus, Ohio, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jianrong Li
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
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Silvestrini MMA, Alessio GD, Frias BED, Sales Júnior PA, Araújo MSS, Silvestrini CMA, Brito Alvim de Melo GE, Martins-Filho OA, Teixeira-Carvalho A, Martins HR. New insights into Trypanosoma cruzi genetic diversity, and its influence on parasite biology and clinical outcomes. Front Immunol 2024; 15:1342431. [PMID: 38655255 PMCID: PMC11035809 DOI: 10.3389/fimmu.2024.1342431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/26/2024] Open
Abstract
Chagas disease, caused by Trypanosoma cruzi, remains a serious public health problem worldwide. The parasite was subdivided into six distinct genetic groups, called "discrete typing units" (DTUs), from TcI to TcVI. Several studies have indicated that the heterogeneity of T. cruzi species directly affects the diversity of clinical manifestations of Chagas disease, control, diagnosis performance, and susceptibility to treatment. Thus, this review aims to describe how T. cruzi genetic diversity influences the biology of the parasite and/or clinical parameters in humans. Regarding the geographic dispersion of T. cruzi, evident differences were observed in the distribution of DTUs in distinct areas. For example, TcII is the main DTU detected in Brazilian patients from the central and southeastern regions, where there are also registers of TcVI as a secondary T. cruzi DTU. An important aspect observed in previous studies is that the genetic variability of T. cruzi can impact parasite infectivity, reproduction, and differentiation in the vectors. It has been proposed that T. cruzi DTU influences the host immune response and affects disease progression. Genetic aspects of the parasite play an important role in determining which host tissues will be infected, thus heavily influencing Chagas disease's pathogenesis. Several teams have investigated the correlation between T. cruzi DTU and the reactivation of Chagas disease. In agreement with these data, it is reasonable to suppose that the immunological condition of the patient, whether or not associated with the reactivation of the T. cruzi infection and the parasite strain, may have an important role in the pathogenesis of Chagas disease. In this context, understanding the genetics of T. cruzi and its biological and clinical implications will provide new knowledge that may contribute to additional strategies in the diagnosis and clinical outcome follow-up of patients with Chagas disease, in addition to the reactivation of immunocompromised patients infected with T. cruzi.
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Affiliation(s)
| | - Glaucia Diniz Alessio
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Bruna Estefânia Diniz Frias
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Policarpo Ademar Sales Júnior
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Márcio Sobreira Silva Araújo
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Olindo Assis Martins-Filho
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Andréa Teixeira-Carvalho
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Helen Rodrigues Martins
- Department of Pharmacy, Federal University of the Jequitinhonha and Mucuri Valleys, Diamantina, Minas Gerais, Brazil
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Trabelsi K, Ben Khalaf N, Ramadan AR, Elsharkawy A, Ashoor D, Chlif S, Boussoffara T, Ben-Ahmed M, Kumar M, Fathallah MD. A novel approach to designing viral precision vaccines applied to SARS-CoV-2. Front Cell Infect Microbiol 2024; 14:1346349. [PMID: 38628551 PMCID: PMC11018900 DOI: 10.3389/fcimb.2024.1346349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Efficient precision vaccines against several highly pathogenic zoonotic viruses are currently lacking. Proteolytic activation is instrumental for a number of these viruses to gain host-cell entry and develop infectivity. For SARS-CoV-2, this process is enhanced by the insertion of a furin cleavage site at the junction of the spike protein S1/S2 subunits upstream of the metalloprotease TMPRSS2 common proteolytic site. Here, we describe a new approach based on specific epitopes selection from the region involved in proteolytic activation and infectivity for the engineering of precision candidate vaccinating antigens. This approach was developed through its application to the design of SARS-CoV-2 cross-variant candidates vaccinating antigens. It includes an in silico structural analysis of the viral region involved in infectivity, the identification of conserved immunogenic epitopes and the selection of those eliciting specific immune responses in infected people. The following step consists of engineering vaccinating antigens that carry the selected epitopes and mimic their 3D native structure. Using this approach, we demonstrated through a Covid-19 patient-centered study of a 500 patients' cohort, that the epitopes selected from SARS-CoV-2 protein S1/S2 junction elicited a neutralizing antibody response significantly associated with mild and asymptomatic COVID-19 (p<0.001), which strongly suggests protective immunity. Engineered antigens containing the SARS-CoV-2 selected epitopes and mimicking the native epitopes 3D structure generated neutralizing antibody response in mice. Our data show the potential of this combined computational and experimental approach for designing precision vaccines against viruses whose pathogenicity is contingent upon proteolytic activation.
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Affiliation(s)
- Khaled Trabelsi
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Noureddin Ben Khalaf
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Ahmed R. Ramadan
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Amany Elsharkawy
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, United States
| | - Dana Ashoor
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Sadok Chlif
- Department of Family and Community Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Thouraya Boussoffara
- Transmission, Control and Immunobiology of Infections Laboratory, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Melika Ben-Ahmed
- Transmission, Control and Immunobiology of Infections Laboratory, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Mukesh Kumar
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, United States
| | - M-Dahmani Fathallah
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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Dzieciolowska S, Charest H, Roy T, Fafard J, Carazo S, Levade I, Longtin J, Parkes L, Beaulac SN, Villeneuve J, Savard P, Corbeil J, De Serres G, Longtin Y. Timing and Predictors of Loss of Infectivity Among Healthcare Workers With Mild Primary and Recurrent COVID-19: A Prospective Observational Cohort Study. Clin Infect Dis 2024; 78:613-624. [PMID: 37675577 PMCID: PMC10954326 DOI: 10.1093/cid/ciad535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND There is a need to understand the duration of infectivity of primary and recurrent coronavirus disease 2019 (COVID-19) and identify predictors of loss of infectivity. METHODS Prospective observational cohort study with serial viral culture, rapid antigen detection test (RADT) and reverse transcription polymerase chain reaction (RT-PCR) on nasopharyngeal specimens of healthcare workers with COVID-19. The primary outcome was viral culture positivity as indicative of infectivity. Predictors of loss of infectivity were determined using multivariate regression model. The performance of the US Centers for Disease Control and Prevention (CDC) criteria (fever resolution, symptom improvement, and negative RADT) to predict loss of infectivity was also investigated. RESULTS In total, 121 participants (91 female [79.3%]; average age, 40 years) were enrolled. Most (n = 107, 88.4%) had received ≥3 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine doses, and 20 (16.5%) had COVID-19 previously. Viral culture positivity decreased from 71.9% (87/121) on day 5 of infection to 18.2% (22/121) on day 10. Participants with recurrent COVID-19 had a lower likelihood of infectivity than those with primary COVID-19 at each follow-up (day 5 odds ratio [OR], 0.14; P < .001]; day 7 OR, 0.04; P = .003]) and were all non-infective by day 10 (P = .02). Independent predictors of infectivity included prior COVID-19 (adjusted OR [aOR] on day 5, 0.005; P = .003), an RT-PCR cycle threshold [Ct] value <23 (aOR on day 5, 22.75; P < .001) but not symptom improvement or RADT result.The CDC criteria would identify 36% (24/67) of all non-infectious individuals on day 7. However, 17% (5/29) of those meeting all the criteria had a positive viral culture. CONCLUSIONS Infectivity of recurrent COVID-19 is shorter than primary infections. Loss of infectivity algorithms could be optimized.
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Affiliation(s)
| | - Hugues Charest
- Faculté de médecine, Université de Montréal, Montréal, Canada
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | - Tonya Roy
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | - Judith Fafard
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | - Sara Carazo
- Institut National de Santé Publique du Québec, Québec City, Canada
- Université Laval, Québec City, Canada
| | - Ines Levade
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | - Jean Longtin
- CHU de Québec—Université Laval, Québec City, Canada
| | - Leighanne Parkes
- McGill University Faculty of Medicine, Montréal, Canada
- Jewish General Hospital Sir Mortimer B. Davis, Montréal, Canada
| | - Sylvie Nancy Beaulac
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | | | - Patrice Savard
- Faculté de médecine, Université de Montréal, Montréal, Canada
- Centre Hospitalier de l’Université de Montréal (CHUM) and CHUM Research Center, Montréal, Canada
| | | | - Gaston De Serres
- Institut National de Santé Publique du Québec, Québec City, Canada
- Université Laval, Québec City, Canada
| | - Yves Longtin
- McGill University Faculty of Medicine, Montréal, Canada
- Jewish General Hospital Sir Mortimer B. Davis, Montréal, Canada
- Lady Davis Research Institute, Montréal, Canada
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5
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Roederer AL, Cao Y, Denis KS, Sheehan ML, Li CJ, Lam EC, Gregory DJ, Poznansky MC, Iafrate AJ, Canaday DH, Gravenstein S, Garcia-Beltran WF, Balazs AB. Ongoing evolution of SARS-CoV-2 drives escape from mRNA vaccine-induced humoral immunity. medRxiv 2024:2024.03.05.24303815. [PMID: 38496628 PMCID: PMC10942518 DOI: 10.1101/2024.03.05.24303815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Since the COVID-19 pandemic began in 2020, viral sequencing has documented 131 individual mutations in the viral spike protein across 48 named variants. To determine the ability of vaccine-mediated humoral immunity to keep pace with continued SARS-CoV-2 evolution, we assessed the neutralization potency of sera from 76 vaccine recipients collected after 2 to 6 immunizations against a comprehensive panel of mutations observed during the pandemic. Remarkably, while many individual mutations that emerged between 2020 and 2022 exhibit escape from sera following primary vaccination, few escape boosted sera. However, progressive loss of neutralization was observed across newer variants, irrespective of vaccine doses. Importantly, an updated XBB.1.5 booster significantly increased titers against newer variants but not JN.1. These findings demonstrate that seasonal boosters improve titers against contemporaneous strains, but novel variants continue to evade updated mRNA vaccines, demonstrating the need for novel approaches to adequately control SARS-CoV-2 transmission.
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Affiliation(s)
- Alex L. Roederer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Yi Cao
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Kerri St. Denis
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | | | - Chia Jung Li
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Evan C. Lam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - David J. Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Pediatric Infectious Disease, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, 02114, USA
| | - A. John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - David H. Canaday
- Case Western Reserve University School of Medicine, Cleveland, OH
- Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Stefan Gravenstein
- Center of Innovation in Long-Term Services and Supports, Veterans Administration Medical Center, Providence, Rhode Island
- Division of Geriatrics and Palliative Medicine, Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Brown University School of Public Health Center for Gerontology and Healthcare Research, Providence, Rhode Island
| | - Wilfredo F. Garcia-Beltran
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
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Norese C, Nicosia E, Cortese K, Gentili V, Rizzo R, Rizzo S, Grasselli E, De Negri Atanasio G, Gagliani MC, Tiso M, Zinni M, Pulliero A, Izzotti A. SARS-CoV-2 presence in recreational seawater and evaluation of intestine permeability: experimental evidence of low impact on public health. Front Public Health 2024; 12:1326453. [PMID: 38500723 PMCID: PMC10944960 DOI: 10.3389/fpubh.2024.1326453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction Coastal seawater pollution poses a public health risk due to the potential ingestion of contaminated water during recreational activities. Wastewater-based epidemiology has revealed the abundant presence of SARS-CoV-2 in seawater emitted from wastewater outlets. The objective of this research was to investigate the impact of seawater on SARS-CoV-2 infectivity to assess the safety of recreational activities in seawater. Methods Wild SARS-CoV-2 was collected from oral swabs of COVID-19 affected patients and incubated for up to 90 min using the following solutions: (a) standard physiological solution (control), (b) reconstructed seawater (3.5% NaCl), and (c) authentic seawater (3.8%). Samples were then exposed to two different host systems: (a) Vero E6 cells expressing the ACE2 SARS-CoV-2 receptor and (b) 3D multi-tissue organoids reconstructing the human intestine. The presence of intracellular virus inside the host systems was determined using plaque assay, quantitative real-time PCR (qPCR), and transmission electron microscopy. Results Ultrastructural examination of Vero E6 cells revealed the presence of virus particles at the cell surface and in replicative compartments inside cells treated with seawater and/or reconstituted water only for samples incubated up to 2 min. After a 90-min incubation, the presence of the virus and its infectivity in Vero E6 cells was reduced by 90%. Ultrastructural analysis performed in 3D epi-intestinal tissue did not reveal intact viral particles or infection signs, despite the presence of viral nucleic acid detected by qPCR. Indeed, viral genes (Orf1ab and N) were found in the intestinal luminal epithelium but not in the enteric capillaries. These findings suggest that the intestinal tissue is not a preferential entry site for SARS-CoV-2 in the human body. Additionally, the presence of hypertonic saline solution did not increase the susceptibility of the intestinal epithelium to virus penetration; rather, it neutralized its infectivity. Conclusion Our results indicate that engaging in recreational activities in a seawater environment does not pose a significant risk for COVID-19 infection, despite the possible presence of viral nucleic acid deriving from degraded and fragmented viruses.
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Affiliation(s)
- Clelia Norese
- DIMES, Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Elena Nicosia
- Regione Liguria, Environmental Department, Ligurian Region, Genoa, Italy
| | - Katia Cortese
- DIMES, Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Valentina Gentili
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
- LTTA, Clinical Research Center, University of Ferrara, Ferrara, Italy
| | - Sabrina Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Elena Grasselli
- Department of Earth, Environmental, and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Giulia De Negri Atanasio
- Department of Earth, Environmental, and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | | | - Micaela Tiso
- MICAMO, Spin-Off Department of Earth Sciences, University of Genoa, Genoa, Italy
| | - Matteo Zinni
- MICAMO, Spin-Off Department of Earth Sciences, University of Genoa, Genoa, Italy
| | | | - Alberto Izzotti
- DIMES, Department of Experimental Medicine, University of Genoa, Genoa, Italy
- HSM, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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7
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Yoshida T, Kasuya Y, Yamamoto H, Kawai G, Hanaki KI, Matano T, Masuda T. HIV-1 RNAs whose transcription initiates from the third deoxyguanosine of GGG tract in the 5' long terminal repeat serve as a dominant genome for efficient provirus DNA formation. J Virol 2024; 98:e0182523. [PMID: 38289105 PMCID: PMC10878063 DOI: 10.1128/jvi.01825-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 02/21/2024] Open
Abstract
Unspliced HIV-1 RNAs function as messenger RNAs for Gag or Gag-Pol polyproteins and progeny genomes packaged into virus particles. Recently, it has been reported that fate of the RNAs might be primarily determined, depending on transcriptional initiation sites among three consecutive deoxyguanosine residues (GGG tract) downstream of TATA-box in the 5' long terminal repeat (LTR). Although HIV-1 RNA transcription starts mostly from the first deoxyguanosine of the GGG tract and often from the second or third deoxyguanosine, RNAs beginning with one guanosine (G1-form RNAs), whose transcription initiates from the third deoxyguanosine, were predominant in HIV-1 particles. Despite selective packaging of G1-form RNAs into virus particles, its biological impact during viral replication remains to be determined. In this study, we revealed that G1-form RNAs are primarily selected as a template for provirus DNA rather than other RNAs. In competitions between HIV-1 and lentiviral vector transcripts in virus-producing cells, approximately 80% of infectious particles were found to generate provirus using HIV-1 transcripts, while lentiviral vector transcripts were conversely selected when we used HIV-1 mutants in which the third deoxyguanosine in the GGG tract was replaced with deoxythymidine or deoxycytidine (GGT or GGC mutants, respectively). In the other analyses of proviral sequences after infection with an HIV-1 mutant in which the GGG tract in 3' LTR was replaced with TTT, most proviral sequences of the GGG-tract region in 5' LTR were found to be TTG, which is reasonably generated using the G1-form transcripts. Our results indicate that the G1-form RNAs serve as a dominant genome to establish provirus DNA.IMPORTANCESince the promoter for transcribing HIV-1 RNA is unique, all viral elements including genomic RNA and viral proteins have to be generated by the unique transcripts through ingenious mechanisms including RNA splicing and frameshifting during protein translation. Previous studies suggested a new mechanism for diversification of HIV-1 RNA functions by heterogeneous transcriptional initiation site usage; HIV-1 RNAs whose transcription initiates from a certain nucleotide were predominant in virus particles. In this study, we established two methods to analyze heterogenous transcriptional initiation site usage by HIV-1 during viral infection and showed that RNAs beginning with one guanosine (G1-form RNAs), whose transcription initiates from the third deoxyguanosine of the GGG tract in 5' LTR, were primarily selected as viral genome in infectious particles and thus are used as a template to generate provirus for continuous replication. This study provides insights into the mechanism for diversification of unspliced RNA functions and requisites of lentivirus infectivity.
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Affiliation(s)
- Takeshi Yoshida
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuho Kasuya
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiroyuki Yamamoto
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Ken-ichi Hanaki
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Takao Masuda
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan
- Graduate school of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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8
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Qu P, Xu K, Faraone JN, Goodarzi N, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Gumina RJ, Liu SL. Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants. Cell 2024; 187:585-595.e6. [PMID: 38194968 PMCID: PMC10872432 DOI: 10.1016/j.cell.2023.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/11/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and XBB-derived variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose-vaccinated and bivalent-vaccinated healthcare workers, XBB.1.5-wave-infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially different conformational stability of BA.2.86 spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Negin Goodarzi
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Joseph S Bednash
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Jeffrey C Horowitz
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Rama K Mallampalli
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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9
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Zhang L, Kempf A, Nehlmeier I, Cossmann A, Richter A, Bdeir N, Graichen L, Moldenhauer AS, Dopfer-Jablonka A, Stankov MV, Simon-Loriere E, Schulz SR, Jäck HM, Čičin-Šain L, Behrens GMN, Drosten C, Hoffmann M, Pöhlmann S. SARS-CoV-2 BA.2.86 enters lung cells and evades neutralizing antibodies with high efficiency. Cell 2024; 187:596-608.e17. [PMID: 38194966 DOI: 10.1016/j.cell.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
BA.2.86, a recently identified descendant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage, contains ∼35 mutations in the spike (S) protein and spreads in multiple countries. Here, we investigated whether the virus exhibits altered biological traits, focusing on S protein-driven viral entry. Employing pseudotyped particles, we show that BA.2.86, unlike other Omicron sublineages, enters Calu-3 lung cells with high efficiency and in a serine- but not cysteine-protease-dependent manner. Robust lung cell infection was confirmed with authentic BA.2.86, but the virus exhibited low specific infectivity. Further, BA.2.86 was highly resistant against all therapeutic antibodies tested, efficiently evading neutralization by antibodies induced by non-adapted vaccines. In contrast, BA.2.86 and the currently circulating EG.5.1 sublineage were appreciably neutralized by antibodies induced by the XBB.1.5-adapted vaccine. Collectively, BA.2.86 has regained a trait characteristic of early SARS-CoV-2 lineages, robust lung cell entry, and evades neutralizing antibodies. However, BA.2.86 exhibits low specific infectivity, which might limit transmissibility.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Najat Bdeir
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | | | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, 75015 Paris, France; National Reference Center for Viruses of respiratory Infections, Institut Pasteur, 75015 Paris, France
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
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Dou T, Gao F, Zhu J, Wang Z, Yang X, Hao Y, Song N, An S, Yin X, Liu X. Evolutionary analysis and biological characterization of a novel alphabaculovirus isolated from Mythimna separata. J Gen Virol 2024; 105. [PMID: 38376497 DOI: 10.1099/jgv.0.001958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Baculoviruses are insect-specific pathogens. Novel baculovirus isolates provide new options for the biological control of pests. Therefore, research into the biological characteristics of newly isolated baculoviruses, including accurate classification and nomenclature, is important. In this study, a baculovirus was isolated from Mythimna separata and its complete genome sequence was determined by next-generation sequencing. The double-stranded DNA genome was 153 882 bp in length, encoding 163 open reading frames. The virus was identified as a variant of Mamestra brassicae multiple nucleopolyhedrovirus (MbMNPV) and designated Mamestra brassicae multiple nucleopolyhedrovirus CHN1 (MbMNPV-CHN1) according to ultrastructural analysis, genome comparison and phylogenetic analysis. Phylogenetic inference placed MbMNPV-CHN1 in a clade containing isolates of MacoNPV-A, MacoNPV-B and MbMNPV, which we have designated the Mb-McNPV group. The genomes of isolates in the Mb-McNPV group exhibited a high degree of collinearity with relatively minor differences in the content of annotated open reading frames. The development of codon usage bias in the Mb-McNPV group was affected mainly by natural selection. MbMNPV-CHN1 shows high infectivity against seven species of Lepidoptera. The yield of MbMNPV-CHN1 in the fourth- and fifth-instar M. separata larvae was 6.25×109-1.23×1010 OBs/cadaver. Our data provide insights into the classification, host range and virulence differences among baculoviruses of the Mb-McNPV group, as well as a promising potential new baculoviral insecticide.
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Affiliation(s)
- Tao Dou
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Futao Gao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Junhua Zhu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Zihao Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Xifa Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Youwu Hao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
| | - Shiheng An
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
| | - Xiangyang Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
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11
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Xie Q, Sun Z, Xue X, Pan Y, Zhen S, Liu Y, Zhan J, Jiang L, Zhang J, Zhu H, Yu X, Zhang X. China-origin G1 group isolate FPV072 exhibits higher infectivity and pathogenicity than G2 group isolate FPV027. Front Vet Sci 2024; 11:1328244. [PMID: 38288138 PMCID: PMC10822907 DOI: 10.3389/fvets.2024.1328244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/02/2024] [Indexed: 01/31/2024] Open
Abstract
Introduction Feline parvovirus (FPV), a single-stranded DNA virus, is accountable for causing feline panleukopenia, a highly contagious and often lethal disease that primarily affects cats. The epidemiology prevalence and pathogenicity of FPV in certain regions of China, however, remains unclear. The aim of this research was to investigate the epidemiology of FPV in different regions of China in 2021 and compare its infectivity and pathogenicity. Methods In this research, a total of 36 FPV strains were obtained from diverse regions across China. Phylogenetic analysis was performed based on the VP2 and NS1 sequences, and two representative strains, FPV027 and FPV072, which belonged to different branches, were selected for comparative assessment of infectivity and pathogenicity. Results and discussion The results revealed that all strains were phylogenetically classified into two groups, G1 and G2, with a higher prevalence of G1 strains in China. Both in vitro and in vivo experiments demonstrated that FPV072 (G1 group) exhibited enhanced infectivity and pathogenicity compared to FPV027 (G2 Group). The structural alignment of the VP2 protein between the two viruses revealed mutations in residues 91, 232, and 300 that may contribute to differences in infectivity and pathogenicity. The findings from these observations will contribute significantly to the overall understanding of the molecular epidemiology of FPV in China and facilitate the development of an effective FPV vaccine.
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Affiliation(s)
- Qiaoqiao Xie
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Zhen Sun
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Xiu Xue
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Yajie Pan
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Shuye Zhen
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Yang Liu
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Jiuyu Zhan
- School of Life Sciences, Ludong University, Yantai, China
| | - Linlin Jiang
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Jianlong Zhang
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Hongwei Zhu
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Xin Yu
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Xingxiao Zhang
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
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Abdelnabi R, Lassaunière R, Maes P, Weynand B, Neyts J. Comparing the Infectivity of Recent SARS-CoV-2 Omicron Sub-Variants in Syrian Hamsters. Viruses 2024; 16:122. [PMID: 38257822 PMCID: PMC10819014 DOI: 10.3390/v16010122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Since the emergence of the first omicron SARS-CoV-2 variant at the end of 2021, several sub-variants have evolved and become predominant in the human population, showing enhanced transmissibility and ability to (partly) escape the adaptive immune response. The XBB sub-variants (e.g., EG.5.1) have become globally dominant. Besides the XBB sub-variants, a phylogenetically distinct variant, i.e., BA.2.86, is also circulating; it carries several mutations in the spike protein as compared to its parental BA.2 variant. Here, we explored the infectivity of the BA.2.86 and EG.5.1 sub-variants compared to the preceding BA.5 sub-variant in Syrian hamsters. Such preclinical models are important for the evaluation of updated vaccine candidates and novel therapeutic modalities. Following intranasal infection with either variant, throat swabs and lung samples were collected on days 3 and 4 post infection. No significant differences in viral RNA loads in throat swabs were observed between these sub-variants. However, the infectious virus titers in the lungs of EG.5.1- and BA.2.86-infected animals were significantly lower compared to the BA.5-infected ones. The lung pathology scores of animals infected with EG.5.1 and BA.2.86 were also markedly lower than that of BA.5 sub-variant. Together, we show that EG.5.1 and BA.2.86 sub-variants exhibit an attenuated replication in hamsters' lungs as compared to the BA.5 sub-variant.
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Affiliation(s)
- Rana Abdelnabi
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, B-3000 Leuven, Belgium;
- Department of Microbiology, Immunology and Transplantation, VirusBank Platform, KU Leuven, B-3001 Leuven, Belgium
| | | | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, Division of Translational Cell and Tissue Research, KU Leuven, B-3000 Leuven, Belgium;
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, B-3000 Leuven, Belgium;
- Department of Microbiology, Immunology and Transplantation, VirusBank Platform, KU Leuven, B-3001 Leuven, Belgium
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13
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Chung MK, Hart B, Santillana M, Patel CJ. Pediatric and Young Adult Household Transmission of the Initial Waves of SARS-CoV-2 in the United States: Administrative Claims Study. J Med Internet Res 2024; 26:e44249. [PMID: 37967280 PMCID: PMC10768807 DOI: 10.2196/44249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 07/18/2023] [Accepted: 10/29/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND The correlates responsible for the temporal changes of intrahousehold SARS-CoV-2 transmission in the United States have been understudied mainly due to a lack of available surveillance data. Specifically, early analyses of SARS-CoV-2 household secondary attack rates (SARs) were small in sample size and conducted cross-sectionally at single time points. From these limited data, it has been difficult to assess the role that different risk factors have had on intrahousehold disease transmission in different stages of the ongoing COVID-19 pandemic, particularly in children and youth. OBJECTIVE This study aimed to estimate the transmission dynamic and infectivity of SARS-CoV-2 among pediatric and young adult index cases (age 0 to 25 years) in the United States through the initial waves of the pandemic. METHODS Using administrative claims, we analyzed 19 million SARS-CoV-2 test records between January 2020 and February 2021. We identified 36,241 households with pediatric index cases and calculated household SARs utilizing complete case information. Using a retrospective cohort design, we estimated the household SARS-CoV-2 transmission between 4 index age groups (0 to 4 years, 5 to 11 years, 12 to 17 years, and 18 to 25 years) while adjusting for sex, family size, quarter of first SARS-CoV-2 positive record, and residential regions of the index cases. RESULTS After filtering all household records for greater than one member in a household and missing information, only 36,241 (0.85%) of 4,270,130 households with a pediatric case remained in the analysis. Index cases aged between 0 and 17 years were a minority of the total index cases (n=11,484, 11%). The overall SAR of SARS-CoV-2 was 23.04% (95% CI 21.88-24.19). As a comparison, the SAR for all ages (0 to 65+ years) was 32.4% (95% CI 32.1-32.8), higher than the SAR for the population between 0 and 25 years of age. The highest SAR of 38.3% was observed in April 2020 (95% CI 31.6-45), while the lowest SAR of 15.6% was observed in September 2020 (95% CI 13.9-17.3). It consistently decreased from 32% to 21.1% as the age of index groups increased. In a multiple logistic regression analysis, we found that the youngest pediatric age group (0 to 4 years) had 1.69 times (95% CI 1.42-2.00) the odds of SARS-CoV-2 transmission to any family members when compared with the oldest group (18 to 25 years). Family size was significantly associated with household viral transmission (odds ratio 2.66, 95% CI 2.58-2.74). CONCLUSIONS Using retrospective claims data, the pediatric index transmission of SARS-CoV-2 during the initial waves of the COVID-19 pandemic in the United States was associated with location and family characteristics. Pediatric SAR (0 to 25 years) was less than the SAR for all age other groups. Less than 1% (n=36,241) of all household data were retained in the retrospective study for complete case analysis, perhaps biasing our findings. We have provided measures of baseline household pediatric transmission for tracking and comparing the infectivity of later SARS-CoV-2 variants.
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Affiliation(s)
- Ming Kei Chung
- Department of Biomedical Informatics, Harvard Medical School, Harvard University, Boston, MA, United States
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China (Hong Kong)
- Institute of Environment, Energy, and Sustainability, The Chinese University of Hong Kong, Hong Kong, China (Hong Kong)
| | - Brian Hart
- Optum Labs, Eden Prairie, MN, United States
| | - Mauricio Santillana
- Machine Intelligence Group for the Betterment of Health and the Environment, Network Science Institute, Northeastern University, Boston, MA, United States
| | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Harvard University, Boston, MA, United States
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14
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Nikolaev KE, Fedorov DD, Vinogradova AA, Levakin IA, Galaktionov KV. No time to relax: Age-dependent infectivity of cercariae in marine coastal ecosystems. J Helminthol 2023; 97:e102. [PMID: 38130206 DOI: 10.1017/s0022149x2300086x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Age dynamics of the ability of cercariae of two digenean species, Himasthla elongata (Himasthlidae) and Renicola parvicaudatus (Renicolidae), to infect the second intermediate host (SIH), mussels (Mytilus edulis), was investigated experimentally. This is the first study of this kind made on cercariae transmitted in the intertidal of the northern seas. The larvae of all tested ages (from 0.5 to 6 hr) were equally successful in infecting mussels. This finding disagrees with the literature data on cercariae of several freshwater digeneans, which are practically incapable of infecting the SIH during the first 1-3 hr of life. The presence of a time delay before the attainment of the maximum infectivity (TDMI) may be associated with the need for physiological maturation of cercariae in the very beginning of their life in the environment, the need for their broad dispersion, and the prevention of superinfection of the downstream host. The absence of TDMI in the cercariae examined in our study could be associated with the instability of environmental factors in the marine intertidal (wave impact, tidal currents). These factors promote a broad dispersion of cercariae in the intertidal biotope and prevent superinfection of potential SIHs. Biological and behavioural features may also play a role. We hypothesize that the presence or absence of TDMI does not depend on the taxonomic affiliation of the cercariae but is determined by the transmission conditions.
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Affiliation(s)
- Kirill E Nikolaev
- White Sea Biological Station, Zoological Institute, Russian Academy of Sciences, St. Petersburg199034, Russia
| | - Daniil D Fedorov
- Laboratory for the Study of Parasitic Worms and Protists, Zoological Institute, Russian Academy of Sciences, St. Petersburg199034, Russia
| | - Anna A Vinogradova
- Laboratory for the Study of Parasitic Worms and Protists, Zoological Institute, Russian Academy of Sciences, St. Petersburg199034, Russia
| | - Ivan A Levakin
- Laboratory for the Study of Parasitic Worms and Protists, Zoological Institute, Russian Academy of Sciences, St. Petersburg199034, Russia
| | - Kirill V Galaktionov
- Laboratory for the Study of Parasitic Worms and Protists, Zoological Institute, Russian Academy of Sciences, St. Petersburg199034, Russia
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15
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Zeng Y, Xia F, Guo C, Hu C, Li Y, Wang X, Wu Q, Chen Z, Lu J, Wang Z. Virological Characteristics of Five SARS-CoV-2 Variants, Including Beta, Delta and Omicron BA.1, BA.2, BA.5. Viruses 2023; 15:2394. [PMID: 38140635 PMCID: PMC10747097 DOI: 10.3390/v15122394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) show increasing transmissibility and infectivity and induce substantial injuries to human health and the ecology. Therefore, it is vital to understand the related features for controlling infection. In this study, SARS-CoV-2 WIV04 (prototype) and five VOCs (Beta, Delta, Omicron BA.1, BA.2 and BA.5 variants) were inoculated in Vero cells to observe their growth activities. Apart from evaluating the environmental stability at different temperatures, residual virus titers and infectivity at different temperatures (4 °C, room temperature (RT) and 37 °C) were measured over 7 days. The experiment also assessed the infectivity for different incubation durations. The growth capacity assay suggested that the WIV04, Beta and Delta variants replicated efficiently in Vero cells compared with Omicron Variants, and BA.2 replicated more efficiently in Vero cells than BA.1 and BA.5. In addition, all variants exhibited longer survivals at 4 °C and could remain infectious after 7 days, compared to RT' survival after 5 days and at 37 °C after 1 day. The virus infection assay indicated that the Omicron variant had a weaker ability to infect cells compared to the WIV04, Beta and Delta strains, and a longer infection time was required for these strains, except for BA.2.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jia Lu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (Y.Z.); (F.X.); (C.G.); (C.H.); (Y.L.); (X.W.); (Q.W.); (Z.C.)
| | - Zejun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China; (Y.Z.); (F.X.); (C.G.); (C.H.); (Y.L.); (X.W.); (Q.W.); (Z.C.)
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16
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Macedo IS, Lara FA, Barbosa HS, Saraiva EM, Menna-Barreto RFS, Mariante RM. Human neutrophil extracellular traps do not impair in vitro Toxoplasma gondii infection. Front Immunol 2023; 14:1282278. [PMID: 38115994 PMCID: PMC10728484 DOI: 10.3389/fimmu.2023.1282278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Introduction Toxoplasma gondii, responsible for causing toxoplasmosis, is a prevalent food and waterborne pathogen worldwide. It commonly infects warm-blooded animals and affects more than a third of the global human population. Once ingested, the parasite enters the host's small intestine and rapidly disseminates throughout the body via the bloodstream, infiltrating various tissues. Leukocyte-driven responses are vital against T. gondii, with neutrophils playing a dual role: swiftly recruited to infection sites, releasing inflammatory mediators, and serving as a replication hub and Trojan horses, aiding parasite spread. Neutrophils from various hosts release extracellular traps (NETs) against the protozoan. However, gaps persist regarding the mechanisms of NETs production to parasite and their significance in infection control. This study investigates the interplay between human neutrophils and T. gondii, exploring dynamics, key molecules, and signaling pathways involved in NETs production upon protozoan challenge. Methods and Results Using confocal and electron microscopy, live cell imaging, pharmacological inhibitors, and DNA quantification assays, we find that human neutrophils promptly release both classical and rapid NETs upon pathogen stimulation. The NETs structure exhibits diverse phenotypes over time and is consistently associated with microorganisms. Mechanisms involve neutrophil elastase and peptidylarginine deiminase, along with intracellular calcium signaling and the PI3K pathway. Unexpectedly, human traps do not diminish viability or infectivity, but potentially aid in capturing parasites for subsequent neutrophil phagocytosis and elimination. Discussion By revealing NETs formation mechanisms and their nuanced impact on T. gondii infection dynamics, our findings contribute to broader insights into host-pathogen relationships.
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Affiliation(s)
- Isabela S. Macedo
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Flávio A. Lara
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Helene S. Barbosa
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Elvira M. Saraiva
- Laboratório de Imunobiologia das Leishmanioses, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Rafael M. Mariante
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
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17
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Legname G. Copper coordination modulates prion conversion and infectivity in mammalian prion proteins. Prion 2023; 17:1-6. [PMID: 36597284 PMCID: PMC9815218 DOI: 10.1080/19336896.2022.2163835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In mammals the cellular form of the prion protein (PrPC) is a ubiquitous protein involved in many relevant functions in the central nervous system. In addition to its physiological functions PrPC plays a central role in a group of invariably fatal neurodegenerative disorders collectively called prion diseases. In fact, the protein is a substrate in a process in which it converts into an infectious and pathological form denoted as prion. The protein has a unique primary structure where the unstructured N-terminal moiety possesses characteristic sequences wherein histidines are able to coordinate metal ions, in particular copper ions. These sequences are called octarepeats for their characteristic length. Moreover, a non-octarepeat fifth-copper binding site is present where copper coordination seems to control infectivity. In this review, I will argue that these sequences may play a significant role in modulating prion conversion and replication.
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Affiliation(s)
- Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy,CONTACT Giuseppe Legname Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste34136, Italy
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18
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Abhinand CS, Prabhakaran AA, Krishnamurthy A, Raju R, Keshava Prasad TS, Nair AS, Rajasekharan KN, Oommen OV, Sudhakaran PR. SARS-CoV-2 variants infectivity prediction and therapeutic peptide design using computational approaches. J Biomol Struct Dyn 2023; 41:11166-11177. [PMID: 36572420 DOI: 10.1080/07391102.2022.2160819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022]
Abstract
The outbreak of severe acute respiratory coronavirus 2 (SARS-CoV-2) has created a public health emergency globally. SARS-CoV-2 enters the human cell through the binding of the spike protein to human angiotensin converting enzyme 2 (ACE2) receptor. Significant changes have been reported in the mutational landscape of SARS-CoV-2 in the receptor binding domain (RBD) of S protein, subsequent to evolution of the pandemic. The present study examines the correlation between the binding affinity of mutated S-proteins and the rate of viral infectivity. For this, the binding affinity of SARS-CoV and variants of SARS-CoV-2 towards ACE2 was computationally determined. Subsequently, the RBD mutations were classified on the basis of the number of strains identified with respect to each mutation and the resulting variation in the binding affinity was computationally examined. The molecular docking studies indicated a significant correlation between the Z-Rank score of mutated S proteins and the rate of infectivity, suitable for predicting SARS-CoV-2 infectivity. Accordingly, a 30-mer peptide was designed and the inhibitory properties were computationally analyzed. Single amino acid-wise mutation was performed subsequently to identify the peptide with the highest binding affinity. Molecular dynamics and free energy calculations were then performed to examine the stability of the peptide-protein complexes. Additionally, selected peptides were synthesized and screened using a colorimetric assay. Together, this study developed a model to predict the rate of infectivity of SARS-CoV-2 variants and propose a potential peptide that can be used as an inhibitor for the viral entry to human.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chandran S Abhinand
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Athira A Prabhakaran
- Inter-University Centre for Genomics and Gene Technology, University of Kerala, Thiruvananthapuram, Kerala, India
| | | | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- Center for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | | | - Oommen V Oommen
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Perumana R Sudhakaran
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
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19
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Kwon JH, Bertran K, Lee DH, Criado MF, Killmaster L, Pantin-Jackwood MJ, Swayne DE. Diverse infectivity, transmissibility, and pathobiology of clade 2.3.4.4 H5Nx highly pathogenic avian influenza viruses in chickens. Emerg Microbes Infect 2023; 12:2218945. [PMID: 37309051 DOI: 10.1080/22221751.2023.2218945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Clade 2.3.4.4 Eurasian lineage H5Nx highly pathogenic avian influenza virus (HPAIV) has become the globally dominant clade and caused global outbreaks since 2014. The clade 2.3.4.4 viruses have evolved into eight hemagglutinin subgroups (2.3.4.4a-h). In this study, we evaluated the infectivity, pathobiology, and transmissibility of seven clade 2.3.4.4 viruses (two 2.3.4.4a, two 2.3.4.4b, one 2.3.4.4c and two 2.3.4.4e) in chickens. The two clade 2.3.4.4e viruses caused 100% mortality and transmissibility in chickens. However, clade 2.3.4.4a and c viruses showed 80-90% mortality and 67% transmissibility. Clade 2.3.4.4b viruses showed 100% mortality, but no transmission to co-housed chickens was observed based on lack of seroconversion. All the infected chickens died showing systemic infection, irrespective of subgroup. The results highlight that all the clade 2.3.4.4 HPAIVs used in this study caused high mortality in infected chickens, but the transmissibility of the viruses in chickens was variable in contrast to that of previous Eurasian-lineage H5N1 HPAIVs. Changes in the pathogenicity and transmissibility of clade 2.3.4.4 HPAIVs warrant careful monitoring of the viruses to establish effective control strategies.
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Affiliation(s)
- Jung-Hoon Kwon
- Agricultural Research Service, U.S. Department of Agriculture, U.S. National Poultry Research Center, Athens, GA, USA
- College of Veterinary Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Kateri Bertran
- Agricultural Research Service, U.S. Department of Agriculture, U.S. National Poultry Research Center, Athens, GA, USA
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Spain
- IRTA. Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Spain
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Miria Ferreira Criado
- Agricultural Research Service, U.S. Department of Agriculture, U.S. National Poultry Research Center, Athens, GA, USA
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Lindsay Killmaster
- Agricultural Research Service, U.S. Department of Agriculture, U.S. National Poultry Research Center, Athens, GA, USA
| | - Mary J Pantin-Jackwood
- Agricultural Research Service, U.S. Department of Agriculture, U.S. National Poultry Research Center, Athens, GA, USA
| | - David E Swayne
- Agricultural Research Service, U.S. Department of Agriculture, U.S. National Poultry Research Center, Athens, GA, USA
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20
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Locus T, Lambrecht E, Lamoral S, Willems S, Van Gucht S, Vanwolleghem T, Peeters M. A Multifaceted Approach for Evaluating Hepatitis E Virus Infectivity In Vitro: Cell Culture and Innovative Molecular Methods for Integrity Assessment. Vet Sci 2023; 10:676. [PMID: 38133227 PMCID: PMC10748075 DOI: 10.3390/vetsci10120676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Hepatitis E virus is a prominent cause of viral hepatitis worldwide. In Western countries, most infections are asymptomatic. However, acute self-limiting hepatitis and chronic cases in immunocompromised individuals can occur. Studying HEV is challenging due to its difficulty to grow in cell culture. Consequently, the detection of the virus mainly relies on RT-qPCR, which cannot differentiate between infectious and non-infectious particles. To overcome this problem, methods assessing viral integrity offer a possible solution to differentiate between intact and damaged viruses. This study aims at optimizing existing HEV cell culture models and RT-qPCR-based assays for selectively detecting intact virions to establish a reliable model for assessing HEV infectivity. In conclusion, these newly developed methods hold promise for enhancing food safety by identifying approaches for inactivating HEV in food processing, thereby increasing food safety measures.
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Affiliation(s)
- Tatjana Locus
- Fisheries and Food, Technology and Food Unit, Flemish Research Institute for Agriculture (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium or (T.L.); (E.L.)
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
- Laboratory of Experimental Medicine and Pediatrics, Viral Hepatitis Research Group, University of Antwerp, Drie Eikenstraat 655, 2650 Edegem, Belgium
| | - Ellen Lambrecht
- Fisheries and Food, Technology and Food Unit, Flemish Research Institute for Agriculture (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium or (T.L.); (E.L.)
| | - Sophie Lamoral
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
| | - Sjarlotte Willems
- Fisheries and Food, Technology and Food Unit, Flemish Research Institute for Agriculture (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium or (T.L.); (E.L.)
| | - Steven Van Gucht
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
| | - Thomas Vanwolleghem
- Laboratory of Experimental Medicine and Pediatrics, Viral Hepatitis Research Group, University of Antwerp, Drie Eikenstraat 655, 2650 Edegem, Belgium
| | - Michael Peeters
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
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21
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Nie Y, Zhang Y, Wu J. The Secondary Structure of Potato Spindle Tuber Viroid Determines Its Infectivity in Nicotiana benthamiana. Viruses 2023; 15:2307. [PMID: 38140547 PMCID: PMC10748084 DOI: 10.3390/v15122307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
The function of RNAs is determined by their structure. However, studying the relationship between RNA structure and function often requires altering RNA sequences to modify the structures, which leads to the neglect of the importance of RNA sequences themselves. In our research, we utilized potato spindle tuber viroid (PSTVd), a circular-form non-coding infectious RNA, as a model with which to investigate the role of a specific rod-like structure in RNA function. By generating linear RNA transcripts with different start sites, we established 12 PSTVd forms with different secondary structures while maintaining the same sequence. The RNA secondary structures were predicted using the mfold tool and validated through native PAGE gel electrophoresis after in vitro RNA folding. Analysis using plant infection assays revealed that the formation of a correct rod-like structure is crucial for the successful infection of PSTVd. Interestingly, the inability of PSTVd forms with non-rod-like structures to infect plants could be partially compensated by increasing the amount of linear viroid RNA transcripts, suggesting the existence of additional RNA secondary structures, such as the correct rod-like structure, alongside the dominant structure in the RNA inoculum of these forms. Our study demonstrates the critical role of RNA secondary structures in determining the function of infectious RNAs.
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Affiliation(s)
| | | | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Y.N.); (Y.Z.)
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22
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Sakuma S, Tanikawa T, Tsunekuni R, Mine J, Kumagai A, Miyazawa K, Takadate Y, Uchida Y. Experimental Infection of Chickens with H5N8 High Pathogenicity Avian Influenza Viruses Isolated in Japan in the Winter of 2020-2021. Viruses 2023; 15:2293. [PMID: 38140534 PMCID: PMC10748181 DOI: 10.3390/v15122293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
During the winter of 2020-2021, numerous outbreaks of high pathogenicity avian influenza (HPAI) were caused by viruses of the subtype H5N8 in poultry over a wide region in Japan. The virus can be divided into five genotypes-E1, E2, E3, E5, and E7. The major genotype responsible for the outbreaks was E3, followed by E2. To investigate the cause of these outbreaks, we experimentally infected chickens with five representative strains of each genotype. We found that the 50% chicken infectious dose differed by up to 75 times among the five strains, and the titer of the E3 strains (102.75 50% egg infectious dose (EID50)) was the lowest, followed by that of the E2 strains (103.50 EID50). In viral transmission experiments, in addition to the E3 and E2 strains, the E5 strain was transmitted to naïve chickens with high efficiency (>80%), whereas the other strains had low efficiencies (<20%). We observed a clear difference in the virological characteristics among the five strains isolated in the same season. The higher infectivity of the E3 and E2 viruses in chickens may have caused the large number of HPAI outbreaks in Japan during this season.
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Affiliation(s)
| | | | | | | | | | | | | | - Yuko Uchida
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba 305-0856, Ibaraki, Japan; (S.S.); (T.T.); (R.T.); (J.M.); (A.K.); (K.M.); (Y.T.)
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23
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Maeda Y, Monde K, Terasawa H, Tanaka Y, Sawa T. Interaction of TSG101 with the PTAP Motif in Distinct Locations of Gag Determines the Incorporation of HTLV-1 Env into the Retroviral Virion. Int J Mol Sci 2023; 24:16520. [PMID: 38003710 PMCID: PMC10671467 DOI: 10.3390/ijms242216520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
Human T-cell tropic virus type 1 (HTLV-1) is known to be mainly transmitted by cell-to-cell contact due to the lower infectivity of the cell-free virion. However, the reasons why cell-free HTLV-1 infection is poor remain unknown. In this study, we found that the retrovirus pseudotyped with HTLV-1 viral envelope glycoprotein (Env) was infectious when human immunodeficiency virus type 1 (HIV-1) was used to produce the virus. We found that the incorporation of HTLV-1 Env into virus-like particles (VLPs) was low when HTLV-1 Gag was used to produce VLPs, whereas VLPs produced using HIV-1 Gag efficiently incorporated HTLV-1 Env. The production of VLPs using Gag chimeras between HTLV-1 and HIV-1 Gag and deletion mutants of HIV-1 Gag showed that the p6 domain of HIV-1 Gag was responsible for the efficient incorporation of HTLV-1 Env into the VLPs. Further mutagenic analyses of the p6 domain of HIV-1 Gag revealed that the PTAP motif in the p6 domain of HIV-1 Gag facilitates the incorporation of HTLV-1 Env into VLPs. Since the PTAP motif is known to interact with tumor susceptibility gene 101 (TSG101) during the budding process, we evaluated the effect of TSG101 knockdown on the incorporation of HTLV-1 Env into VLPs. We found that TSG101 knockdown suppressed the incorporation of HTLV-1 Env into VLPs and decreased the infectivity of cell-free HIV-1 pseudotyped with HTLV-1 Env. Our results suggest that the interaction of TSG101 with the PTAP motif of the retroviral L domain is involved not only in the budding process but also in the efficient incorporation of HTLV-1 Env into the cell-free virus.
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Affiliation(s)
- Yosuke Maeda
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; (K.M.); (T.S.)
| | - Kazuaki Monde
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; (K.M.); (T.S.)
| | - Hiromi Terasawa
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; (K.M.); (T.S.)
| | - Yuetsu Tanaka
- Department of Immunology, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan;
| | - Tomohiro Sawa
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; (K.M.); (T.S.)
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Pantin-Jackwood MJ, Spackman E, Leyson C, Youk S, Lee SA, Moon LM, Torchetti MK, Killian ML, Lenoch JB, Kapczynski DR, Swayne DE, Suarez DL. Pathogenicity in Chickens and Turkeys of a 2021 United States H5N1 Highly Pathogenic Avian Influenza Clade 2.3.4.4b Wild Bird Virus Compared to Two Previous H5N8 Clade 2.3.4.4 Viruses. Viruses 2023; 15:2273. [PMID: 38005949 PMCID: PMC10674317 DOI: 10.3390/v15112273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) of subtype H5 of the Gs/GD/96 lineage remain a major threat to poultry due to endemicity in wild birds. H5N1 HPAIVs from this lineage were detected in 2021 in the United States (U.S.) and since then have infected many wild and domestic birds. We evaluated the pathobiology of an early U.S. H5N1 HPAIV (clade 2.3.4.4b, 2021) and two H5N8 HPAIVs from previous outbreaks in the U.S. (clade 2.3.4.4c, 2014) and Europe (clade 2.3.4.4b, 2016) in chickens and turkeys. Differences in clinical signs, mean death times (MDTs), and virus transmissibility were found between chickens and turkeys. The mean bird infective dose (BID50) of the 2021 H5N1 virus was approximately 2.6 log10 50% embryo infective dose (EID50) in chickens and 2.2 log10 EID50 in turkeys, and the virus transmitted to contact-exposed turkeys but not chickens. The BID50 for the 2016 H5N8 virus was also slightly different in chickens and turkeys (4.2 and 4.7 log10 EID50, respectively); however, the BID50 for the 2014 H5N8 virus was higher for chickens than turkeys (3.9 and ~0.9 log10 EID50, respectively). With all viruses, turkeys took longer to die (MDTs of 2.6-8.2 days for turkeys and 1-4 days for chickens), which increased the virus shedding period and facilitated transmission to contacts.
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Affiliation(s)
- Mary J. Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Erica Spackman
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Christina Leyson
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Sungsu Youk
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
- Department of Medicine, College of Medicine, Chungbuk National University, Cheongju-si 28644, Chungbuk, Republic of Korea
| | - Scott A. Lee
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Linda M. Moon
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Mia K. Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA 50010, USA
| | - Mary L. Killian
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA 50010, USA
| | - Julianna B. Lenoch
- Wildlife Services, National Wildlife Disease Program, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Fort Collins, CO 80521, USA
| | - Darrell R. Kapczynski
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - David E. Swayne
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - David L. Suarez
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
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25
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Vicente-Santos A, Willink B, Nowak K, Civitello DJ, Gillespie TR. Host-pathogen interactions under pressure: A review and meta-analysis of stress-mediated effects on disease dynamics. Ecol Lett 2023; 26:2003-2020. [PMID: 37804128 PMCID: PMC10874615 DOI: 10.1111/ele.14319] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
Human activities have increased the intensity and frequency of natural stressors and created novel stressors, altering host-pathogen interactions and changing the risk of emerging infectious diseases. Despite the ubiquity of such anthropogenic impacts, predicting the directionality of outcomes has proven challenging. Here, we conduct a review and meta-analysis to determine the primary mechanisms through which stressors affect host-pathogen interactions and to evaluate the impacts stress has on host fitness (survival and fecundity) and pathogen infectivity (prevalence and intensity). We assessed 891 effect sizes from 71 host species (representing seven taxonomic groups) and 78 parasite taxa from 98 studies. We found that infected and uninfected hosts had similar sensitivity to stressors and that responses varied according to stressor type. Specifically, limited resources compromised host fecundity and decreased pathogen intensity, while abiotic environmental stressors (e.g., temperature and salinity) decreased host survivorship and increased pathogen intensity, and pollution increased mortality but decreased pathogen prevalence. We then used our meta-analysis results to develop susceptible-infected theoretical models to illustrate scenarios where infection rates are expected to increase or decrease in response to resource limitations or environmental stress gradients. Our results carry implications for conservation and disease emergence and reveal areas for future work.
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Affiliation(s)
- Amanda Vicente-Santos
- Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA 30322, USA
| | - Beatriz Willink
- Department of Zoology, Stockholm University, Stockholm 106-91, Sweden
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
- School of Biology, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Kacy Nowak
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - David J. Civitello
- Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA 30322, USA
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Thomas R. Gillespie
- Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA 30322, USA
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
- Department of Environmental Sciences, Emory University, Atlanta, GA 30322, USA
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26
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Ampuero M, Martínez-Valdebenito C, Ferrés M, Soto-Rifo R, Gaggero A. Monkeypox Virus in Wastewater Samples from Santiago Metropolitan Region, Chile. Emerg Infect Dis 2023; 29:2358-2361. [PMID: 37877805 PMCID: PMC10617339 DOI: 10.3201/eid2911.230096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
Sewage surveillance provides useful epidemiologic and public health information on viral infections at the population level. We detected monkeypox virus DNA from sewage samples covering 85% of the population in Santiago Metropolitan Region Chile. We also isolated infective viruses from those samples. Wastewater surveillance could complement clinical surveillance for monkeypox virus.
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27
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Dalmat RR, Hao L, Prabhu R, Rechkina E, Hamilton D, Ikuma MH, Bauer M, Gale M, Cantera JL, Ball AS, Grant BD, Drain PK. Rapid Antigen and Antibody Microfluidic Immunofluorescence Assays Compared to Culture, PCR, and Laboratory Reference Tests: Performance in a Longitudinal Cohort. J Infect Dis 2023; 228:1066-1070. [PMID: 37353225 PMCID: PMC10582900 DOI: 10.1093/infdis/jiad231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023] Open
Abstract
We evaluated the performance of rapid antigen (RAg) and antibody (RAb) microfluidic diagnostics with serial sampling of 71 participants at 6 visits over 2 months following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Rapid tests showed strong agreement with laboratory references (κAg = 81.0%; κAb = 87.8%). RAg showed substantial concordance to both virus growth in culture and PCR positivity 0-5 days since symptom onset (κAg-culture = 60.1% and κAg-PCR = 87.1%). PCR concordance to virus growth in culture was similar (κPCR-culture = 70.0%), although agreement between RAg and culture was better overall (κAg-culture = 45.5% vs κPCR-culture = 10.0%). Rapid antigen and antibody testing by microfluidic immunofluorescence platform are highly accurate for characterization of acute infection.
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Affiliation(s)
- Ronit R Dalmat
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Linhui Hao
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, USA
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Roshni Prabhu
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, Washington, USA
| | - Elena Rechkina
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, Washington, USA
| | - Daphne Hamilton
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, Washington, USA
| | - Matthew H Ikuma
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, Washington, USA
| | - Marie Bauer
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, Washington, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
| | | | | | | | - Paul K Drain
- International Clinical Research Center, Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, USA
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28
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Thackray AM, McNulty EE, Nalls AV, Cardova A, Tran L, Telling G, Benestad SL, Gilch S, Mathiason CK, Bujdoso R. Genetic modulation of CWD prion propagation in cervid PrP Drosophila. Biochem J 2023; 480:1485-1501. [PMID: 37747806 PMCID: PMC10586768 DOI: 10.1042/bcj20230247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 09/27/2023]
Abstract
Chronic wasting disease is a fatal prion condition of cervids such as deer, elk, moose and reindeer. Secretion and excretion of prion infectivity from North American cervids with this condition causes environmental contamination and subsequent efficient lateral transmission in free-ranging and farmed cervids. Variants of cervid PrP exist that affect host susceptibility to chronic wasting disease. Cervid breeding programmes aimed at increasing the frequency of PrP variants associated with resistance to chronic wasting disease may reduce the burden of this condition in animals and lower the risk of zoonotic disease. This strategy requires a relatively rapid and economically viable model system to characterise and support selection of prion disease-modifying cervid PrP variants. Here, we generated cervid PrP transgenic Drosophila to fulfil this purpose. We have generated Drosophila transgenic for S138 wild type cervid PrP, or the N138 variant associated with resistance to chronic wasting disease. We show that cervid PrP Drosophila accumulate bona fide prion infectivity after exposure to cervid prions. Furthermore, S138 and N138 PrP fly lines are susceptible to cervid prion isolates from either North America or Europe when assessed phenotypically by accelerated loss of locomotor ability or survival, or biochemically by accumulation of prion seeding activity. However, after exposure to European reindeer prions, N138 PrP Drosophila accumulated prion seeding activity with slower kinetics than the S138 fly line. These novel data show that prion susceptibility characteristics of cervid PrP variants are maintained when expressed in Drosophila, which highlights this novel invertebrate host in modelling chronic wasting disease.
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Affiliation(s)
- Alana M. Thackray
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, U.K
| | - Erin E. McNulty
- Prion Research Center (PRC) and the Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, U.S.A
| | - Amy V. Nalls
- Prion Research Center (PRC) and the Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, U.S.A
| | - Alzbeta Cardova
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, U.K
| | - Linh Tran
- Department of Biohazard and Pathology, WOAH Reference Laboratory for CWD (SLB), National Veterinary Institute, Postboks 64, 1431 Ås, Norway
| | - Glenn Telling
- Prion Research Center (PRC) and the Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, U.S.A
| | - Sylvie L. Benestad
- Department of Biohazard and Pathology, WOAH Reference Laboratory for CWD (SLB), National Veterinary Institute, Postboks 64, 1431 Ås, Norway
| | - Sabine Gilch
- Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Candace K. Mathiason
- Prion Research Center (PRC) and the Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, U.S.A
| | - Raymond Bujdoso
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, U.K
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29
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Nogueira AM, Barbosa TMC, Quadros AFF, Orílio AF, Bigão MCJ, Xavier CAD, Ferro CG, Zerbini FM. Specific Nucleotides in the Common Region of the Begomovirus Tomato Rugose Mosaic Virus (ToRMV) Are Responsible for the Negative Interference over Tomato Severe Rugose Virus (ToSRV) in Mixed Infection. Viruses 2023; 15:2074. [PMID: 37896851 PMCID: PMC10611410 DOI: 10.3390/v15102074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Mixed infection between two or more begomoviruses is commonly found in tomato fields and can affect disease outcomes by increasing symptom severity and viral accumulation compared with single infection. Viruses that affect tomato include tomato severe rugose virus (ToSRV) and tomato rugose mosaic virus (ToRMV). Previous work showed that in mixed infection, ToRMV negatively affects the infectivity and accumulation of ToSRV. ToSRV and ToRMV share a high degree of sequence identity, including cis-elements in the common region (CR) and their specific recognition sites (iteron-related domain, IRD) within the Rep gene. Here, we investigated if divergent sites in the CR and IRD are involved in the interaction between these two begomoviruses. ToSRV clones were constructed containing the same nucleotides as ToRMV in the CR (ToSRV-A(ToR:CR)), IRD (ToSRV-A(ToR:IRD)) and in both regions (ToSRV-A(ToR:CR+IRD)). When plants were co-inoculated with ToRMV and ToSRV-A(ToR:IRD), the infectivity and accumulation of ToSRV were negatively affected. In mixed inoculation of ToRMV with ToSRV-A(ToR:CR), high infectivity of both viruses and high DNA accumulation of ToSRV-A(ToR:CR) were observed. A decrease in viral accumulation was observed in plants inoculated with ToSRV-A(ToR:CR+IRD). These results indicate that differences in the CR, but not the IRD, are responsible for the negative interference of ToRMV on ToSRV.
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Affiliation(s)
- Angélica M. Nogueira
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Departamento de Proteção Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista (UNESP), Botucatu 18610-307, SP, Brazil
| | - Tarsiane M. C. Barbosa
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Departamento de Entomologia e Acarologia, ESALQ, Universidade de São Paulo, Piracicaba 13418-900, SP, Brazil
| | - Ayane F. F. Quadros
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Anelise F. Orílio
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Marcela C. J. Bigão
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - César A. D. Xavier
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Camila G. Ferro
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Departamento de Fitopatologia e Nematologia, ESALQ, Universidade de São Paulo, Piracicaba 13418-900, SP, Brazil
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil; (A.M.N.); (T.M.C.B.); (A.F.F.Q.); (A.F.O.); (M.C.J.B.); (C.A.D.X.); (C.G.F.)
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
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30
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Hakze-van der Honing RW, van Oort S, Dirks RAM, van der Poel WHM. Development of an Ex Vivo Assay for Identification of Infectious Hepatitis E Virus in Different Kinds of Food Samples. Pathogens 2023; 12:1231. [PMID: 37887746 PMCID: PMC10610002 DOI: 10.3390/pathogens12101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/26/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
Hepatitis E virus (HEV) is a positive-sense single-stranded RNA virus and a major cause of acute viral hepatitis. HEV is responsible for 20 million infections worldwide in humans every year. HEV-3 and HEV-4 are zoonotic and are responsible for most of the HEV cases in developed countries. Consumption of contaminated pig meat or pig products is considered to be the main transmission route of HEV HEV-3 in Europe. Prevalence studies for HEV generally use PCR methods to detect the presence or absence of genomic RNA. However, these methods do not discriminate infectious virus particles from non-infectious material. Previously developed HEV cell culture systems only worked with high efficiency after cell line adaptation of the subjected virus strains. In this manuscript, the development of a culture system for the detection of infectious HEV strains is described. For this purpose, we optimized the isolation and the growth of primary hepatocytes from young piglets. Subsequently, the isolated hepatocytes were used to culture HEV of different origins, such as liver tissue samples and sausage samples. This method can be applied to better assess the risk of infection through consumption of food products associated with HEV RNA contamination.
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Affiliation(s)
- Renate W. Hakze-van der Honing
- Wageningen Bioveterinary Research (WBVR), Wageningen University and Research, Houtribweg 39, 8221 Lelystad, The Netherlands; (S.v.O.); (W.H.M.v.d.P.)
| | - Sophie van Oort
- Wageningen Bioveterinary Research (WBVR), Wageningen University and Research, Houtribweg 39, 8221 Lelystad, The Netherlands; (S.v.O.); (W.H.M.v.d.P.)
| | - René A. M. Dirks
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Akkermaalsbos 2, 6708 Wageningen, The Netherlands
| | - Wim H. M. van der Poel
- Wageningen Bioveterinary Research (WBVR), Wageningen University and Research, Houtribweg 39, 8221 Lelystad, The Netherlands; (S.v.O.); (W.H.M.v.d.P.)
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31
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Cambronne ED, Ayres C, Dowdell KS, Lawler DF, Saleh NB, Kirisits MJ. Protozoan-Priming and Magnesium Conditioning Enhance Legionella pneumophila Dissemination and Monochloramine Resistance. Environ Sci Technol 2023; 57:14871-14880. [PMID: 37756220 DOI: 10.1021/acs.est.3c04013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Opportunistic pathogens (OPs) are of concern in drinking water distribution systems because they persist despite disinfectant residuals. While many OPs garner protection from disinfectants via a biofilm lifestyle, Legionella pneumophila (Lp) also gains disinfection resistance by being harbored within free-living amoebae (FLA). It has been long established, but poorly understood, that Lp grown within FLA show increased infectivity toward subsequent FLA or human cells (i.e., macrophage), via a process we previously coined "protozoan-priming". The objectives of this study are (i) to identify in Lp a key genetic determinant of how protozoan-priming increases its infectivity, (ii) to determine the chemical stimulus within FLA to which Lp responds during protozoan-priming, and (iii) to determine if more infectious forms of Lp also exhibit enhanced disinfectant resistance. Using Acanthamoeba castellanii as a FLA host, the priming effect was isolated to Lp's sidGV locus, which is activated upon sensing elevated magnesium concentrations. Supplementing growth medium with 8 mM magnesium is sufficient to produce Lp grown in vitro with an infectivity equivalent to that of Lp grown via the protozoan-primed route. Both Lp forms with increased infectivity (FLA-grown and Mg2+-supplemented) exhibit greater monochloramine resistance than Lp grown in standard media, indicating that passage through FLA not only increases Lp's infectivity but also enhances its monochloramine resistance. Therefore, laboratory-based testing of disinfection strategies should employ conditions that simulate or replicate intracellular growth to accurately assess disinfectant resistance.
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Affiliation(s)
- Eric D Cambronne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Craig Ayres
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Katherine S Dowdell
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Desmond F Lawler
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Navid B Saleh
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Mary Jo Kirisits
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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32
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Harrison K, Snead D, Kilts A, Ammerman ML, Wigginton KR. The Protective Effect of Virus Capsids on RNA and DNA Virus Genomes in Wastewater. Environ Sci Technol 2023; 57:13757-13766. [PMID: 37656816 PMCID: PMC10516120 DOI: 10.1021/acs.est.3c03814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
Virus concentrations measured in municipal wastewater help inform both the water treatment necessary to protect human health and wastewater-based epidemiology. Wastewater measurements are typically PCR-based, and interpreting gene copy concentrations requires an understanding of the form and stability of the nucleic acids. Here, we study the persistence of model virus genomes in wastewater, the protective effects provided by the virus capsids, and the relative decay rates of the genome and infectious viruses. In benchtop batch experiments in wastewater influent at 25 °C, extraviral (+)ssRNA and dsDNA amplicons degraded by 90% within 15-19 min and 1.6-1.9 h, respectively. When encapsidated, the T90 for MS2 (+)ssRNA increased by 424× and the T90 for T4 dsDNA increased by 52×. The (+)ssRNA decay rates were similar for a range of amplicon sizes. For our model phages MS2 and T4, the nucleic acid signal in untreated wastewater disappeared shortly after the viruses lost infectivity. Combined, these results suggest that most viral genome copies measured in wastewater are encapsidated, that measured concentrations are independent of assay amplicon sizes, and that the virus genome decay rates of nonenveloped (i.e., naked) viruses are similar to inactivation rates. These findings are valuable for the interpretation of wastewater virus measurements.
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Affiliation(s)
- Katherine
R. Harrison
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Delaney Snead
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna Kilts
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Michelle L. Ammerman
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Krista R. Wigginton
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
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Lisman D, Zielińska G, Drath J, Łaszczewska A, Savochka I, Parafiniuk M, Ossowski A. Molecular Diagnosis of COVID-19 Sudden and Unexplained Deaths: The Insidious Face of the Pandemic. Diagnostics (Basel) 2023; 13:2980. [PMID: 37761347 PMCID: PMC10529476 DOI: 10.3390/diagnostics13182980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
The COVID-19 epidemic has led to a significant increase in the number of deaths. This has resulted in forensic autopsies focusing on additional diagnostic possibilities. The following article is a summary of 23 autopsies of sudden and unexplained deaths. Particularly noteworthy are the described cases of children whose deaths were originally classified as SIDS (sudden infant death syndrome). All tests were performed at the Department of Forensic Medicine and Forensic Genetics, Pomeranian Medical University in Szczecin. Autopsy analyses were extended to include diagnostics of the SARS-CoV-2 virus using molecular methods and a detailed histopathological analysis of lung tissue. The material for molecular tests consisted of a nasopharyngeal swab taken postmortem and a lung tissue homogenate. In both cases, the RT-PCR method with CT cut-off point analysis was used for diagnosis. In all analyzed cases, the lungs showed massive congestion and increased fragility and cohesion. The tested material showed the presence of the SARS-CoV-2 virus, which indicated various stages of infection. It was observed that the higher the virus expression in the lungs, the lower or undetectable it was in the nasopharyngeal swab. This may explain false negative results during life in swabs. An interesting finding is that child deaths classified as SIDS also showed the presence of the virus. This may constitute a new direction of research.
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Affiliation(s)
- Dagmara Lisman
- Forensic Genetic Department, Pomeranian Medical University, 70-204 Szczecin, Poland; (G.Z.); (J.D.); (A.Ł.); (A.O.)
| | - Grażyna Zielińska
- Forensic Genetic Department, Pomeranian Medical University, 70-204 Szczecin, Poland; (G.Z.); (J.D.); (A.Ł.); (A.O.)
| | - Joanna Drath
- Forensic Genetic Department, Pomeranian Medical University, 70-204 Szczecin, Poland; (G.Z.); (J.D.); (A.Ł.); (A.O.)
| | - Aleksandra Łaszczewska
- Forensic Genetic Department, Pomeranian Medical University, 70-204 Szczecin, Poland; (G.Z.); (J.D.); (A.Ł.); (A.O.)
| | - Ilona Savochka
- Forensic Medicine Department, Pomeranian Medical University, 70-204 Szczecin, Poland; (I.S.); (M.P.)
| | - Mirosław Parafiniuk
- Forensic Medicine Department, Pomeranian Medical University, 70-204 Szczecin, Poland; (I.S.); (M.P.)
| | - Andrzej Ossowski
- Forensic Genetic Department, Pomeranian Medical University, 70-204 Szczecin, Poland; (G.Z.); (J.D.); (A.Ł.); (A.O.)
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Blomme AK, Ackerman TL, Jones CK, Gebhardt JT, Woodworth JC, Paulk CB, Pogranichniy RM. Isolation of porcine reproductive and respiratory syndrome virus from feed ingredients and complete feed, with subsequent RT-qPCR analysis. J Vet Diagn Invest 2023; 35:464-469. [PMID: 37431822 PMCID: PMC10467466 DOI: 10.1177/10406387231185080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023] Open
Abstract
We used virus isolation (VI) to determine tissue culture infectivity and reverse-transcription quantitative PCR (RT-qPCR) to determine the stability of porcine reproductive and respiratory syndrome virus 2 (PRRSV) strain P129 in solvent-extracted soybean meal (SBM), dried distillers grains with solubles (DDGS), complete swine feed (FEED), or medium (DMEM) at 4°C, 23°C, or 37°C for up to 3 d. Samples of each treatment were taken at regular intervals and processed. Supernatant was titrated and used to inoculate confluent MARC-145 cells to determine infectivity. RNA was extracted from each supernatant sample and tested by RT-qPCR to determine any change in detectable virus RNA across matrix type, temperature, and time. An interaction (p = 0.028) was observed for matrix × temperature × hour for live virus detected by VI. At 4°C, the concentration of infectious virus was greatest in DMEM, intermediate in SBM, and lowest in DDGS and FEED. DMEM also had the greatest concentration of infectious PRRSV at 23°C over time; a higher infectious virus concentration was maintained in SBM for longer than in DDGS or FEED. At 37°C, a greater concentration of infectious virus was sustained in DMEM than in the feedstuffs, with concentrations decreasing until 48 h post-inoculation. Only matrix type influenced the quantity of viral RNA detected by RT-qPCR (p = 0.032). More viral RNA was detected in the virus control than in DDGS; SBM and FEED were intermediate. By VI, we found that infectious virus could be harbored in SBM, DDGS, and FEED for a short time.
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Affiliation(s)
- Allison K. Blomme
- Departments of Grain Science and Industry, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Tate L. Ackerman
- College of Agriculture; Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Cassandra K. Jones
- Animal Sciences and Industry, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jordan T. Gebhardt
- College of Agriculture; Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jason C. Woodworth
- Animal Sciences and Industry, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Chad B. Paulk
- Departments of Grain Science and Industry, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Roman M. Pogranichniy
- College of Agriculture; Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
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Merchioratto I, Mendes Peter C, Ramachandran A, Maggioli MF, Vicosa Bauermann F. Viability of Veterinary-Relevant Viruses in Decomposing Tissues over a 90-Day Period Using an In-Vitro System. Pathogens 2023; 12:1104. [PMID: 37764912 PMCID: PMC10537333 DOI: 10.3390/pathogens12091104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Depopulation is frequently employed during outbreaks of high-impact animal diseases. Security breaches in sites managing mortality may jeopardize pathogen control efforts as infected carcasses can serve as an infection source. This study evaluated the viability and nucleic acid detection of veterinary-relevant viruses or their surrogates in decomposing tissues. The used viruses were: Senecavirus A1 (SVA), feline calicivirus (FCV), bovine viral diarrhea virus (BVDV), porcine epidemic diarrhea virus (PEDV), bovine alphaherpesvirus 1 (BoHV-1), and swinepox virus (SwPV). Viruses were spiked in three decomposing tissues (swine bone marrow and spleen, and bovine bone marrow) and maintained for 90 days. Samples were kept under two temperature conditions resembling the average soil temperature in central Oklahoma, US, during the winter and summer (5.5 °C and 29.4 °C). At 5.5 °C, SVA and FCV remained viable over the 90 days of the study, followed by BVDV (75 days), BoHV-1 and SwPV (60 days), and PEDV (10 days). At 29.4 °C, SVA remained viable for 45 days, followed by BVDV and BoHV-1 (14 days). SwPV was viable for 10 days, whereas FCV and PEDV were viable for 5 days. Overall, viral nucleic acid detection was not significantly altered during the study. These findings support decision-making and risk management in sites overseeing animal mortality.
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Affiliation(s)
- Ingryd Merchioratto
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK 74078, USA
| | - Cristina Mendes Peter
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK 74078, USA
- Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of Sao Paulo (UNIFESP), Sao Paulo 04039-032, SP, Brazil
| | - Akhilesh Ramachandran
- Molecular Diagnostics, Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University (OSU), Stillwater, OK 74078, USA
| | - Mayara Fernanda Maggioli
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK 74078, USA
| | - Fernando Vicosa Bauermann
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK 74078, USA
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Hara S, Koike I. Survival of Bacteriophage T4 in Quasi-Pure Ionic Solutions. Viruses 2023; 15:1737. [PMID: 37632079 PMCID: PMC10459568 DOI: 10.3390/v15081737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/31/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
The preservative qualities of individual ionic compounds impacting the infectivity of T4 virions were elucidated. T4 virions were immersed in quasi-pure ionic solutions prior to the adsorption process, and the plaque forming unit (pfu) values of these were measured following the conventional method. In neutral ionic solutions, the minimum and the optimum concentrations of preservative qualities corresponded with the results obtained from the multi-ionic media/buffers. In acid and alkali solutions, phages show tolerances at a pH range of 5-11 in multi-ionic media/buffers. T4 virions show no tolerance in quasi-pure acid, neutral, and weak alkaline conditions. The preservative quality of T4 virions increased in over 10-1 mM OH- solution, equivalent to a pH value over 10, which corresponds to the pKa of the deprotonation of the DNA bases G and T. Infectivity was lost below 10-1 mM OH- and higher than 10 mM OH-. These results imply that maintaining infectivity of a virion may need the flexibility of the intra-capsid DNA by deprotonation.
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Affiliation(s)
- Seiko Hara
- Miyazaki International College, 1405 Kano, Miyazaki 889-1605, Japan
| | - Isao Koike
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan;
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Loundras EA, Netherton CL, Flannery J, Bowes MJ, Dixon L, Batten C. The Effect of Temperature on the Stability of African Swine Fever Virus BA71V Isolate in Environmental Water Samples. Pathogens 2023; 12:1022. [PMID: 37623982 PMCID: PMC10459264 DOI: 10.3390/pathogens12081022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/26/2023] Open
Abstract
African swine fever virus (ASFV) is known to be very stable and can remain infectious over long periods of time especially at low temperatures and within different matrices, particularly those containing animal-derived organic material. However, there are some gaps in our knowledge pertaining to the survivability and infectivity of ASFV in groundwater. This study aims to determine the stability and infectivity of the cell culture-adapted ASFV strain BA71V by plaque assay after incubation of the virus within river water samples at three different environmentally relevant temperatures (4 °C, 15 °C, and 21 °C) over the course of 42 days. The results from this study indicate that ASFV can remain stable and infectious when maintained at 4 °C in river water for more than 42 days, but as incubation temperatures are increased, the stability is reduced, and the virus is no longer able to form plaques after 28 days and 14 days, respectively, when stored at 15 °C and 21 °C. Characterizing the survivability of ASFV in groundwater can allow us to develop more appropriate inactivation and disinfection methods to support disease control and mitigate ASFV outbreaks.
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Affiliation(s)
- Eleni-Anna Loundras
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (E.-A.L.); (C.L.N.); (J.F.); (L.D.)
| | - Christopher L. Netherton
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (E.-A.L.); (C.L.N.); (J.F.); (L.D.)
| | - John Flannery
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (E.-A.L.); (C.L.N.); (J.F.); (L.D.)
- Department of Animal Health, Technological University of the Shannon, Athlone Campus, N37HD68 Athlone, Ireland
| | - Michael J. Bowes
- Centre for Ecology and Hydrology, Wallingford Oxon OX10 8BB, UK;
| | - Linda Dixon
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (E.-A.L.); (C.L.N.); (J.F.); (L.D.)
| | - Carrie Batten
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (E.-A.L.); (C.L.N.); (J.F.); (L.D.)
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Cook SC, Ryabov EV, Becker C, Rogers CW, Posada-Florez F, Evans JD, Chen YP. Deformed wing virus of honey bees is inactivated by cold plasma ionized hydrogen peroxide. Front Insect Sci 2023; 3:1216291. [PMID: 38469475 PMCID: PMC10926414 DOI: 10.3389/finsc.2023.1216291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/18/2023] [Indexed: 03/13/2024]
Abstract
Deformed wing virus (DWV) is a widespread pathogen of Apis mellifera honey bees, and is considered a major causative factor for the collapse of infected honey bee colonies. DWV can be horizontally transmitted among bees through various oral routes, including via food sharing and by interactions of bees with viral-contaminated solid hive substrates. Cold plasma ionized hydrogen peroxide (iHP) is used extensively by the food production, processing and medical industries to clean surfaces of microbial contaminants. In this study, we investigated the use of iHP to inactivate DWV particles in situ on a solid substrate. iHP-treated DWV sources were ~105-fold less infectious when injected into naïve honey bee pupae compared to DWV receiving no iHP treatment, matching injected controls containing no DWV. iHP treatment also greatly reduced the incidence of overt DWV infections (i.e., pupae having >109 copies of DWV). The level of DWV inactivation achieved with iHP treatment was higher than other means of viral inactivation such as gamma irradiation, and iHP treatment is likely simpler and safer. Treatment of DWV contaminated hive substrates with iHP, even with honey bees present, may be an effective way to decrease the impacts of DWV infection on honey bees.
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Affiliation(s)
- Steven C. Cook
- United States Department of Agriculture - Agricultural Research (USDA-ARS) Service, Bee Research Laboratory, Beltsville, MD, United States
| | - Eugene V. Ryabov
- United States Department of Agriculture - Agricultural Research (USDA-ARS) Service, Bee Research Laboratory, Beltsville, MD, United States
- Department of Entomology, University of Maryland, College Park, MD, United States
| | | | - Curtis W. Rogers
- United States Department of Agriculture - Agricultural Research (USDA-ARS) Service, Bee Research Laboratory, Beltsville, MD, United States
| | - Francisco Posada-Florez
- United States Department of Agriculture - Agricultural Research (USDA-ARS) Service, Bee Research Laboratory, Beltsville, MD, United States
| | - Jay D. Evans
- United States Department of Agriculture - Agricultural Research (USDA-ARS) Service, Bee Research Laboratory, Beltsville, MD, United States
| | - Yan Ping Chen
- United States Department of Agriculture - Agricultural Research (USDA-ARS) Service, Bee Research Laboratory, Beltsville, MD, United States
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Wang Z, He M, He H, Kilby K, Antueno RD, Castle E, McMullen N, Qian Z, Zeev-Ben-Mordehai T, Duncan R, Pan C. Nonenveloped Avian Reoviruses Released with Small Extracellular Vesicles Are Highly Infectious. Viruses 2023; 15:1610. [PMID: 37515296 PMCID: PMC10384003 DOI: 10.3390/v15071610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Vesicle-encapsulated nonenveloped viruses are a recently recognized alternate form of nonenveloped viruses that can avoid immune detection and potentially increase systemic transmission. Avian orthoreoviruses (ARVs) are the leading cause of various disease conditions among birds and poultry. However, whether ARVs use cellular vesicle trafficking routes for egress and cell-to-cell transmission is still poorly understood. We demonstrated that fusogenic ARV-infected quail cells generated small (~100 nm diameter) extracellular vesicles (EVs) that contained electron-dense material when observed by transmission electron microscope. Cryo-EM tomography indicated that these vesicles did not contain ARV virions or core particles, but the EV fractions of OptiPrep gradients did contain a small percent of the ARV virions released from cells. Western blotting of detergent-treated EVs revealed that soluble virus proteins and the fusogenic p10 FAST protein were contained within the EVs. Notably, virus particles mixed with the EVs were up to 50 times more infectious than virions alone. These results suggest that EVs and perhaps fusogenic FAST-EVs could contribute to ARV virulence.
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Affiliation(s)
- Zuopei Wang
- Laboratory of Molecular Virology and Immunology, Technology Innovation Center, Haid Research Institute, Guangdong Haid Group Co., Ltd., Panyu, Guangzhou 511400, China
| | - Menghan He
- Laboratory of Molecular Virology and Immunology, Technology Innovation Center, Haid Research Institute, Guangdong Haid Group Co., Ltd., Panyu, Guangzhou 511400, China
| | - Han He
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Kyle Kilby
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Roberto de Antueno
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Elizabeth Castle
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Nichole McMullen
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Zhuoyu Qian
- Department of Biochemical Engineering, University College London, London WC1E 6BT, UK
| | | | - Roy Duncan
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Chungen Pan
- Laboratory of Molecular Virology and Immunology, Technology Innovation Center, Haid Research Institute, Guangdong Haid Group Co., Ltd., Panyu, Guangzhou 511400, China
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Bouquet P, Alexandre V, De Lamballerie M, Ley D, Lesage J, Goffard A, Cocquerel L. Effect of High Hydrostatic Pressure Processing and Holder Pasteurization of Human Milk on Inactivation of Human Coronavirus 229E and Hepatitis E Virus. Viruses 2023; 15:1571. [PMID: 37515257 PMCID: PMC10384040 DOI: 10.3390/v15071571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
In preterm infants, sterilized donor milk (DM) is frequently used for feeding when breast milk is lacking. Most human milk banks use the Holder pasteurization method (HoP) to ensure the microbiological safety of DM. However, this method degrades many bioactive factors and hormones. Recently, high hydrostatic pressure (HHP) processing, which preserves bioactive factors in human milk, has been proposed as an alternative method to ensure the safety of DM. Although HHP treatment has been shown to be effective for viral inactivation, the effect of HHP on viruses that may be present in the complex nutritional matrix of human milk has not yet been defined. In the present study, we compared the efficacy of two HHP protocols (4 cycles at 350 MPa at 38 °C designated as 4xHP350 treatment, and 1 cycle at 600 MPa at 20 °C designated as 1xHP600 treatment) with the HoP method on artificially virus-infected DM. For this purpose, we used human coronavirus 229E (HCoV-229E) and hepatitis E virus (HEV) as surrogate models for enveloped and non-enveloped viruses. Our results showed that HCoV-229E is inactivated by HHP and HoP treatment. In particular, the 4xHP350 protocol is highly effective in inactivating HCoV-229E. However, our results demonstrated a matrix effect of human milk on HCoV-229E inactivation. Furthermore, we demonstrated that HEV is stable to moderate pressure HHP treatment, but the milk matrix does not protect it from inactivation by the high-pressure HHP treatment of 600 MPa. Importantly, the complex nutritional matrix of human milk protects HEV from inactivation by HoP treatment. In conclusion, we demonstrated that HHP and HoP treatments do not lead to complete inactivation of both surrogate virus models, indicating that these treatments cannot guarantee total viral safety of donor milk.
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Affiliation(s)
- Peggy Bouquet
- Unit of Clinical Microbiology, Institut Pasteur de Lille, F-59000 Lille, France
| | - Virginie Alexandre
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | | | - Delphine Ley
- CHU Lille, Division of Gastroenterology Hepatology and Nutrition, Department of Paediatrics, Jeanne de Flandre Children's Hospital, F-59000 Lille, France
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France
| | - Jean Lesage
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France
| | - Anne Goffard
- Unit of Clinical Microbiology, Institut Pasteur de Lille, F-59000 Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Laurence Cocquerel
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
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Waheed AA, Zhu Y, Agostino E, Naing L, Hikichi Y, Soheilian F, Yoo SW, Song Y, Zhang P, Slusher BS, Haughey NJ, Freed EO. Neutral sphingomyelinase 2 is required for HIV-1 maturation. Proc Natl Acad Sci U S A 2023; 120:e2219475120. [PMID: 37406093 PMCID: PMC10334776 DOI: 10.1073/pnas.2219475120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/11/2023] [Indexed: 07/07/2023] Open
Abstract
HIV-1 assembly occurs at the inner leaflet of the plasma membrane (PM) in highly ordered membrane microdomains. The size and stability of membrane microdomains is regulated by activity of the sphingomyelin hydrolase neutral sphingomyelinase 2 (nSMase2) that is localized primarily to the inner leaflet of the PM. In this study, we demonstrate that pharmacological inhibition or depletion of nSMase2 in HIV-1-producer cells results in a block in the processing of the major viral structural polyprotein Gag and the production of morphologically aberrant, immature HIV-1 particles with severely impaired infectivity. We find that disruption of nSMase2 also severely inhibits the maturation and infectivity of other primate lentiviruses HIV-2 and simian immunodeficiency virus, has a modest or no effect on nonprimate lentiviruses equine infectious anemia virus and feline immunodeficiency virus, and has no effect on the gammaretrovirus murine leukemia virus. These studies demonstrate a key role for nSMase2 in HIV-1 particle morphogenesis and maturation.
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Affiliation(s)
- Abdul A. Waheed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Eva Agostino
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Lwar Naing
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Yuta Hikichi
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Ferri Soheilian
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Seung-Wan Yoo
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Yun Song
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, DidcotOX11 0DE, United Kingdom
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, United Kingdom
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, DidcotOX11 0DE, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Barbara S. Slusher
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Norman J. Haughey
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Eric O. Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
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Wolmuth‐Gordon HS, Brown MJF. Transmission of a bumblebee parasite is robust despite parasite exposure to extreme temperatures. Ecol Evol 2023; 13:e10379. [PMID: 37502302 PMCID: PMC10368942 DOI: 10.1002/ece3.10379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
All organisms are exposed to fluctuating environmental conditions, such as temperature. How individuals respond to temperature affects their interactions with one another. Changes to the interaction between parasites and their hosts can have a large effect on disease dynamics. The gut parasite, Crithidia bombi, can be highly prevalent in the bumblebee, Bombus terrestris, and is an established epidemiological model. The parasite is transmitted between bumblebees via flowers, exposing it to a range of environmental temperatures prior to infection. We investigated whether incubation duration and temperature exposure, prior to infection, affects parasite infectivity. Prior to inoculation in B. terrestris, C. bombi was incubated at 10, 20, 30, 40 or 50°C for either 10 or 60 min. These times were chosen to reflect the length of time that the parasite remains infective when outside the host and the rate of floral visitation in bumblebees. Prevalence and infection intensity were measured in bees 1 week later. Incubation duration and the interaction between incubation temperature and duration affected the prevalence of C. bombi at 50°C, resulting in no infections after 60 min. Below 50°C, C. bombi prevalence was not affected by incubation temperature or duration. Extreme temperatures induced morphological changes in C. bombi cells; however, infection intensity was not affected by incubation duration or temperature. These results highlight that this parasite is robust to a wide range of temperatures. The parasite was not infective after being exposed to 50°C for 60 min, such temperatures likely exceed the flight abilities of bumblebees, and thus the potential for transmission. This study shows the importance of understanding the effects of environmental conditions on both hosts and parasites, which is needed to predict transmission under different environmental conditions.
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Affiliation(s)
| | - Mark J. F. Brown
- School of Life Sciences and the EnvironmentRoyal Holloway University of LondonEghamUK
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Chen P, Jin Z, Peng L, Zheng Z, Cheung YM, Guan J, Chen L, Huang Y, Fan X, Zhang Z, Shi D, Xie J, Chen R, Xiao B, Yip CH, Smith DK, Hong W, Liu Y, Li L, Wang J, Holmes EC, Lam TTY, Zhu H, Guan Y. Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health. J Virol 2023; 97:e0043423. [PMID: 37289052 PMCID: PMC10308888 DOI: 10.1128/jvi.00434-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/08/2023] [Indexed: 06/09/2023] Open
Abstract
Although influenza A viruses of several subtypes have occasionally infected humans, to date only those of the H1, H2, and H3 subtypes have led to pandemics and become established in humans. The detection of two human infections by avian H3N8 viruses in April and May of 2022 raised pandemic concerns. Recent studies have shown the H3N8 viruses were introduced into humans from poultry, although their genesis, prevalence, and transmissibility in mammals have not been fully elucidated. Findings generated from our systematic influenza surveillance showed that this H3N8 influenza virus was first detected in chickens in July 2021 and then disseminated and became established in chickens over wider regions of China. Phylogenetic analyses revealed that the H3 HA and N8 NA were derived from avian viruses prevalent in domestic ducks in the Guangxi-Guangdong region, while all internal genes were from enzootic poultry H9N2 viruses. The novel H3N8 viruses form independent lineages in the glycoprotein gene trees, but their internal genes are mixed with those of H9N2 viruses, indicating continuous gene exchange among these viruses. Experimental infection of ferrets with three chicken H3N8 viruses showed transmission through direct contact and inefficient transmission by airborne exposure. Examination of contemporary human sera detected only very limited antibody cross-reaction to these viruses. The continuing evolution of these viruses in poultry could pose an ongoing pandemic threat. IMPORTANCE A novel H3N8 virus with demonstrated zoonotic potential has emerged and disseminated in chickens in China. It was generated by reassortment between avian H3 and N8 virus(es) and long-term enzootic H9N2 viruses present in southern China. This H3N8 virus has maintained independent H3 and N8 gene lineages but continues to exchange internal genes with other H9N2 viruses to form novel variants. Our experimental studies showed that these H3N8 viruses were transmissible in ferrets, and serological data suggest that the human population lacks effective immunological protection against it. With its wide geographical distribution and continuing evolution in chickens, other spillovers to humans can be expected and might lead to more efficient transmission in humans.
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Affiliation(s)
- Peiwen Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Ziying Jin
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Liuxia Peng
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Zuoyi Zheng
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Jing Guan
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Liming Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Yiteng Huang
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, Guangxi, China
| | - Zengfeng Zhang
- Department of Microbiology, Guangxi Medical University, Nanning, Guangxi, China
| | - Dongmei Shi
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Jin Xie
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Rirong Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Boheng Xiao
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Chun Hung Yip
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - David K. Smith
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Wenshan Hong
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Yongmei Liu
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lifeng Li
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Jia Wang
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Edward C. Holmes
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tommy Tsan-Yuk Lam
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Huachen Zhu
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Yi Guan
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
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Colado Simão AN, Perugini Stadtlober N, Stinghen Garcia Lonni AA, Venâncio LM, Lerner Trigo G, de Souza Cassela PLC, Mastellini Sanches Silva T, De Fátima Oliveira Hirth Ruiz M, Batisti Lozovoy MA, Tano ZN, da Fonseca Orcina B, Vieira Vilhena F, da Silva Santos PS. Effect of phthalocyanine oral and nasal antiseptic solutions on the infectivity of SARS-CoV-2 in patients with COVID-19: a randomized controlled trial. Ger Med Sci 2023; 21:Doc07. [PMID: 37426884 PMCID: PMC10326526 DOI: 10.3205/000321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 11/16/2022] [Indexed: 07/11/2023]
Abstract
Background In individuals with coronavirus disease (COVID-19), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load (VL) plays an important role in infectivity. Objectives This study aimed to evaluate the reduction in the VL and infectivity induced by phthalocyanine mouthwash and nasal spray in patients with COVID-19. Methods Patients with mild COVID-19 were recruited to participate in a triple-blinded randomized controlled trial. Participants were assigned to one of three groups: Group 1, non-active mouthwash and saline nasal spray (SNS); Group 2, phthalocyanine mouthwash and SNS; and Group 3 phthalocyanine mouthwash and phthalocyanine nasal spray. VL was assessed in nasopharyngeal and oropharyngeal swabs collected at the time of clinical diagnosis at baseline as well as 24 and 72 hours after starting the rinsing protocols. Findings Forty-six participants were included in the analysis: 15, 16, and 15 in Groups 1, 2, and 3, respectively. After 72 hours, the reduction in VL was significantly higher in Group 3 (mean cycle threshold (Ct) decrease: 11.21) than in Group 1 (mean Ct decrease: 5.53). Additionally, only the mean VL in Group 3 was reduced to a non-contagious level after 72 hours. Main conclusions Use of phthalocyanine mouthwash and nasal spray is effective at reducing SARS-CoV-2 infectivity.
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Affiliation(s)
| | | | | | - Luiza Mara Venâncio
- Research Laboratory in Applied Immunology, State University of Londrina, Brazil
| | | | | | | | | | | | - Zuleica Naomi Tano
- Research Laboratory in Applied Immunology, State University of Londrina, Brazil
| | - Bernardo da Fonseca Orcina
- Department of Surgery, Stomatology, Pathology and Radiology, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | | | - Paulo Sérgio da Silva Santos
- Department of Surgery, Stomatology, Pathology and Radiology, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
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Bennett A, Gargas J, Kansol A, Lewis J, Hsi J, Hull J, Mietzsch M, Tartaglia L, Muzyczka N, Bhattacharya N, Chipman P, Agbandje-McKenna M, McKenna R. Structural and Biophysical Analysis of Adeno-Associated Virus Serotype 2 Capsid Assembly Variants. J Virol 2023:e0177222. [PMID: 37310260 PMCID: PMC10373557 DOI: 10.1128/jvi.01772-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
Adeno-associated virus (AAV) is a nonenveloped single-stranded DNA (ssDNA) icosahedral T=1 virus being developed as a vector for clinical gene delivery systems. Currently, there are approximately 160 AAV clinical trials, with AAV2 being the most widely studied serotype. To further understand the AAV gene delivery system, this study investigates the role of viral protein (VP) symmetry interactions on capsid assembly, genome packaging, stability, and infectivity. A total of 25 (seven 2-fold, nine 3-fold, and nine 5-fold symmetry interface) AAV2 VP variants were studied. Six 2-fold and two 5-fold variants did not assemble capsids based on native immunoblots and anti-AAV2 enzyme-linked immunosorbent assays (ELISAs). Seven of the 3-fold and seven of the 5-fold variants that assembled capsids were less stable, while the only 2-fold variant that assembled had ~2°C higher thermal stability (Tm) than recombinant wild-type AAV2 (wtAAV2). Three of the 3-fold variants (AAV2-R432A, AAV2-L510A, and N511R) had an approximately 3-log defect in genome packaging. Consistent with previous reports of the 5-fold axes, the region of the capsid is important for VP1u externalization and genome ejection, and one 5-fold variant (R404A) had a significant defect in viral infectivity. The structures of wtAAV2 packaged with a transgene (AAV2-full) and without a transgene (AAV2-empty) and one 5-fold variant (AAV2-R404A) were determined by cryo-electron microscopy and three dimensional (3D)-image reconstruction to 2.8, 2.9, and 3.6 Å resolution, respectively. These structures revealed the role of stabilizing interactions on the assembly, stability, packaging, and infectivity of the virus capsid. This study provides insight into the structural characterization and functional implications of the rational design of AAV vectors. IMPORTANCE Adeno-associated viruses (AAVs) have been shown to be useful vectors for gene therapy applications. Consequently, AAV has been approved as a biologic for the treatment of several monogenic disorders, and many additional clinical trials are ongoing. These successes have generated significant interest in all aspects of the basic biology of AAV. However, to date, there are limited data available on the importance of the capsid viral protein (VP) symmetry-related interactions required to assemble and maintain the stability of the AAV capsids and the infectivity of the AAV capsids. Characterizing the residue type and interactions at these symmetry-driven assembly interfaces of AAV2 has provided the foundation for understanding their role in AAV vectors (serotypes and engineered chimeras) and has determined the residues or regions of the capsid that can or cannot tolerate alterations.
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Affiliation(s)
- Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Joseph Gargas
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Austin Kansol
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jordyn Lewis
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jane Hsi
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Joshua Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Lawrence Tartaglia
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Nicholas Muzyczka
- Department of Molecular Genetics and Microbiology and Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, Florida, USA
- Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Nilakshee Bhattacharya
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
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Li J, Li J, Chen S, Xu W, Zhang J, Tong S. Clinical isolates of hepatitis B virus genotype C have higher in vitro transmission efficiency than genotype B isolates. J Med Virol 2023; 95:e28879. [PMID: 37314050 PMCID: PMC10404337 DOI: 10.1002/jmv.28879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023]
Abstract
Serum samples were collected from 54 hepatitis B e antigen (HBeAg)-positive Chinese patients infected with hepatitis B virus (HBV) subgenotype B2 or C2. They were compared for transmission efficiency using same volume of samples or infectivity using same genome copy number. Adding polyethylene glycol (PEG) during inoculation did not increase infectivity of fresh samples but markedly increased infectivity following prolonged sample storage. Differentiated HepaRG cells infected without PEG produced more hepatitis B surface antigen (HBsAg) and higher HBsAg/HBeAg ratio than sodium taurocholate cotransporting polypeptide (NTCP)-reconstituted HepG2 cells infected with PEG. They better supported replication of core promoter mutant in contrast to wild-type (WT) virus by HepG2/NTCP cells. Overall, subgenotype C2 samples had higher viral load than B2 samples, and in general produced more HBeAg, HBsAg, and replicative DNA following same-volume inoculation. Precore mutant was more prevalent in subgenotype B2 and had reduced transmission efficiency. When same genome copy number of viral particles was inoculated, viral signals were not necessarily higher for three WT C2 isolates than four WT B2 isolates. Using viral particles generated from cloned HBV genome, three WT C2 isolates showed slightly reduced infectivity than three B2 isolates. In conclusion, subgenotype C2 serum samples had higher transmission efficiency than B2 isolates in association with higher viral load and lower prevalence of precore mutant, but not necessarily higher infectivity. PEG-independent infection by HBV viremic serum samples is probably attributed to a labile host factor.
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Affiliation(s)
- Jing Li
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Department of Infectious Diseases, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Liver Research Center, Division of Gastroenterology, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Infectious Diseases, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Jisu Li
- Liver Research Center, Division of Gastroenterology, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Shiqi Chen
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Department of Infectious Diseases, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Weicheng Xu
- Department of Infectious Diseases, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Jiming Zhang
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Department of Infectious Diseases, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shuping Tong
- Liver Research Center, Division of Gastroenterology, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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Kuznetsova NA, Ogarkova DA, Gushchin VA, Antipyat NА, Bacalin VV, Burgasova OA, Vasilchenko LA, Samkov AA, Simakova YV, Divisenko EV, Siniavin AE, Tkachuk AP, Kolobukhina LV, Shidlovskaya EV, Tyurin IN, Kruzhkova IS, Zlobin VI, Nikiforova MA, Odnoralov MA, Gintsburg AL. [Evaluation of the dynamics of detection of viable SARS-CoV-2 (Coronaviridae: Betacoronavirus: Sarbecovirus) in biological samples obtained from patients with COVID-19 in a health care setting, as one of the indicators of the infectivity of the virus]. Vopr Virusol 2023; 68:105-116. [PMID: 37264845 DOI: 10.36233/0507-4088-160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Indexed: 06/03/2023]
Abstract
INTRODUCTION The study of the mechanisms of transmission of the SARS-CoV-2 virus is the basis for building a strategy for anti-epidemic measures in the context of the COVID-19 pandemic. Understanding in what time frame a patient can spread SARS-CoV-2 is just as important as knowing the transmission mechanisms themselves. This information is necessary to develop effective measures to prevent infection by breaking the chains of transmission of the virus. The aim of the work is to identify the infectious SARS-CoV-2 virus in patient samples in the course of the disease and to determine the duration of virus shedding in patients with varying severity of COVID-19. MATERIALS AND METHODS In patients included in the study, biomaterial (nasopharyngeal swabs) was subjected to analysis by quantitative RT-PCR and virological determination of infectivity of the virus. RESULTS We have determined the timeframe of maintaining the infectivity of the virus in patients hospitalized with severe and moderate COVID-19. Based on the results of the study, we made an analysis of the relationship between the amount of detected SARS-CoV-2 RNA and the infectivity of the virus in vitro in patients with COVID-19. The median time of the infectious virus shedding was 8 days. In addition, a comparative analysis of different protocols for the detection of the viral RNA in relation to the identification of the infectious virus was carried out. CONCLUSION The obtained data make it possible to assess the dynamics of SARS-CoV-2 detection and viral load in patients with COVID-19 and indicate the significance of these parameters for the subsequent spread of the virus and the organization of preventive measures.
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Affiliation(s)
- N A Kuznetsova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - D A Ogarkova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - V A Gushchin
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - N А Antipyat
- Infectious Clinical Hospital No. 1 of the Department of Health of the Moscow
| | | | | | - L A Vasilchenko
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - A A Samkov
- Infectious Clinical Hospital No. 1 of the Department of Health of the Moscow
| | - Y V Simakova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - E V Divisenko
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - A E Siniavin
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - A P Tkachuk
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - L V Kolobukhina
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - E V Shidlovskaya
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - I N Tyurin
- Infectious Clinical Hospital No. 1 of the Department of Health of the Moscow
| | - I S Kruzhkova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - V I Zlobin
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - M A Nikiforova
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
| | - M A Odnoralov
- Infectious Clinical Hospital No. 1 of the Department of Health of the Moscow
| | - A L Gintsburg
- National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation
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Tan MTH, Gong Z, Li D. Use of Zebrafish Embryos To Reproduce Human Norovirus and To Evaluate Human Norovirus Infectivity Decay after UV Treatment. Appl Environ Microbiol 2023; 89:e0011523. [PMID: 36943055 PMCID: PMC10132098 DOI: 10.1128/aem.00115-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
This study reports an essential improvement of the method for replication of human norovirus (HNoV) with the use of zebrafish (Danio rerio) embryos. With three HNoV genotypes and P-types GII.2[P16], GII.4[P16], and GII.17[P31], we demonstrated that this tool had higher efficiency and robustness than the zebrafish larvae as reported previously. When zebrafish larvae were injected with virus (1.6 ± 0.3 log genome copies/10 larvae), a significant increase of virus genome copies was detected at 2 days postinfection (dpi; 4.4 ± 0.8 log genome copies/10 larvae, P < 0.05) and the viral loads started to decrease gradually from 3 dpi. In comparison, when the viruses were injected into the zebrafish embryos, significant virus replication was noticed from 1 dpi and lasted to 6 dpi (P < 0.05). The virus levels detected at 3 dpi had the highest mean value and the smallest variation (7.7 ± 0.2 log genome copies/10 larvae). The high levels of virus replication enabled continuous passaging for all three strains up to four passages. The zebrafish embryo-generated HNoVs showed clear patterns of binding to human histo-blood group antigens (HBGAs) in human saliva by a simple saliva-binding reverse transcription-quantitative PCR (RT-qPCR). Last, in a disinfection study, it was shown that a dose of 6 mJ/cm2 UV254 was able induce a >2-log reduction in HNoV infectivity for all three HNoV strains tested, suggesting that HNoVs were more UV susceptible than multiple enteric viruses and commonly used HNoV surrogates as tested before. IMPORTANCE HNoVs are a leading cause of gastroenteritis outbreaks worldwide. The zebrafish embryo tool as developed in this study serves as an efficient way to generate viruses with high titers and clean background and a straightforward platform to evaluate HNoV inactivation efficacies. It is expected that this tool will not only benefit epidemiological research on HNoV but also be used to generate HNoV inactivation parameters which are highly needed by the water treatment and food industries.
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Affiliation(s)
- Malcolm Turk Hsern Tan
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Zhiyuan Gong
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Dan Li
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore, Singapore
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Faraone JN, Qu P, Evans JP, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Lozanski G, Panchal A, Saif LJ, Oltz EM, Gumina RJ, Liu SL. Neutralization escape of Omicron XBB, BR.2, and BA.2.3.20 subvariants. Cell Rep Med 2023; 4:101049. [PMID: 37148877 DOI: 10.1016/j.xcrm.2023.101049] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/17/2023] [Accepted: 04/20/2023] [Indexed: 05/08/2023]
Abstract
New Omicron subvariants continue to emerge throughout the world. In particular, the XBB subvariant, which is a recombinant virus between BA.2.10.1.1 and BA.2.75.3.1.1.1, as well as the BA.2.3.20 and BR.2 subvariants that contain mutations distinct from BA.2 and BA.2.75, are currently increasing in proportion of variants sequenced. Here we show that antibodies induced by 3-dose mRNA booster vaccination as well as BA.1- and BA.4/5-wave infection effectively neutralize BA.2, BR.2, and BA.2.3.20 but have significantly reduced efficiency against XBB. In addition, the BA.2.3.20 subvariant exhibits enhanced infectivity in the lung-derived CaLu-3 cells and in 293T-ACE2 cells. Overall, our results demonstrate that the XBB subvariant is highly neutralization resistant, which highlights the need for continued monitoring of the immune escape and tissue tropism of emerging Omicron subvariants.
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Affiliation(s)
- Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - John P Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mirela Anghelina
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick Stevens
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Soledad Fernandez
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ashish Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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50
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Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. bioRxiv 2023:2023.03.30.535005. [PMID: 37034621 PMCID: PMC10081308 DOI: 10.1101/2023.03.30.535005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and likely originated during persistent infection of immunocompromised hosts. To test the hypothesis that S:D614G facilitated emergence of such variants, S:D614G was reverted to the ancestral sequence in the context of sequential Spike sequences from an immunocompromised individual, and within each of the major SARS-CoV-2 variants of concern. In all cases, infectivity of the S:D614G revertants was severely compromised. The infectivity of atypical SARS-CoV-2 lineages that propagated in the absence of S:D614G was found to be dependent upon either S:Q613H or S:H655Y. Notably, Gamma and Omicron variants possess both S:D614G and S:H655Y, each of which contributed to infectivity of these variants. Among sarbecoviruses, S:Q613H, S:D614G, and S:H655Y are only detected in SARS-CoV-2, which is also distinguished by a polybasic S1/S2 cleavage site. Genetic and biochemical experiments here showed that S:Q613H, S:D614G, and S:H655Y each stabilize Spike on virions, and that they are dispensable in the absence of S1/S2 cleavage, consistent with selection of these mutations by the S1/S2 cleavage site. CryoEM revealed that either S:D614G or S:H655Y shift the Spike receptor binding domain (RBD) towards the open conformation required for ACE2-binding and therefore on pathway for infection. Consistent with this, an smFRET reporter for RBD conformation showed that both S:D614G and S:H655Y spontaneously adopt the conformation that ACE2 induces in the parental Spike. Data from these orthogonal experiments demonstrate that S:D614G and S:H655Y are convergent adaptations to the polybasic S1/S2 cleavage site which stabilize S1 on the virion in the open RBD conformation and act epistatically to promote the fitness of variants bearing complex combinations of clinically significant mutations.
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Affiliation(s)
- Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Shawn Egri
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- These authors contributed equally
| | - Marco A. Diaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Javier A. Jaimes
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Manish C. Choudhary
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jonathan Z. Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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