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Suryadevara N, Otrelo-Cardoso AR, Kose N, Hu YX, Binshtein E, Wolters RM, Greninger AL, Handal LS, Carnahan RH, Moscona A, Jardetzky TS, Crowe JE. Functional and structural basis of human parainfluenza virus type 3 neutralization with human monoclonal antibodies. Nat Microbiol 2024:10.1038/s41564-024-01722-w. [PMID: 38858594 DOI: 10.1038/s41564-024-01722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 05/02/2024] [Indexed: 06/12/2024]
Abstract
Human parainfluenza virus type 3 (hPIV3) is a respiratory pathogen that can cause severe disease in older people and infants. Currently, vaccines against hPIV3 are in clinical trials but none have been approved yet. The haemagglutinin-neuraminidase (HN) and fusion (F) surface glycoproteins of hPIV3 are major antigenic determinants. Here we describe naturally occurring potently neutralizing human antibodies directed against both surface glycoproteins of hPIV3. We isolated seven neutralizing HN-reactive antibodies and a pre-fusion conformation F-reactive antibody from human memory B cells. One HN-binding monoclonal antibody (mAb), designated PIV3-23, exhibited functional attributes including haemagglutination and neuraminidase inhibition. We also delineated the structural basis of neutralization for two HN and one F mAbs. MAbs that neutralized hPIV3 in vitro protected against infection and disease in vivo in a cotton rat model of hPIV3 infection, suggesting correlates of protection for hPIV3 and the potential clinical utility of these mAbs.
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Affiliation(s)
| | | | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yao-Xiong Hu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rachael M Wolters
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Laura S Handal
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anne Moscona
- Departments of Pediatrics, Microbiology and Immunology, and Physiology and Cellular Biophysics, and Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Theodore S Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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2
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Berry GJ, Jhaveri TA, Larkin PMK, Mostafa H, Babady NE. ADLM Guidance Document on Laboratory Diagnosis of Respiratory Viruses. J Appl Lab Med 2024; 9:599-628. [PMID: 38695489 DOI: 10.1093/jalm/jfae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 06/06/2024]
Abstract
Respiratory viral infections are among the most frequent infections experienced worldwide. The COVID-19 pandemic has highlighted the need for testing and currently several tests are available for the detection of a wide range of viruses. These tests vary widely in terms of the number of viral pathogens included, viral markers targeted, regulatory status, and turnaround time to results, as well as their analytical and clinical performance. Given these many variables, selection and interpretation of testing requires thoughtful consideration. The current guidance document is the authors' expert opinion based on the preponderance of available evidence to address key questions related to best practices for laboratory diagnosis of respiratory viral infections including who to test, when to test, and what tests to use. An algorithm is proposed to help laboratories decide on the most appropriate tests to use for the diagnosis of respiratory viral infections.
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Affiliation(s)
- Gregory J Berry
- Columbia University Vagelos College of Physicians and Surgeons, New York-Presbyterian-Columbia University Irving Medical Center, New York, NY, United States
| | - Tulip A Jhaveri
- Department of Internal Medicine, Division of Infectious Diseases, University of Mississippi Medical Center, Jackson, MS, United States
| | - Paige M K Larkin
- University of Chicago Pritzker School of Medicine, NorthShore University Health System, Chicago, IL, United States
| | - Heba Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Baltimore, MD, United States
| | - N Esther Babady
- Clinical Microbiology and Infectious Disease Services, Department of Pathology and Laboratory Medicine and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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3
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Kim SR, Waghmare A, Hijano DR. Approach to hematopoietic cell transplant candidates with respiratory viral detection. Front Pediatr 2024; 11:1339239. [PMID: 38304442 PMCID: PMC10830789 DOI: 10.3389/fped.2023.1339239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
The management of respiratory viruses prior to hematopoietic cell transplant (HCT) can be controversial and requires special consideration of host factors, transplant parameters, and the specific respiratory virus (RV). In the setting of adenovirus (ADV), human metapneumovirus (HMPV), influenza, parainfluenza virus (PIV), and respiratory syncytial virus (RSV) detection prior to hematopoietic cell transplant (HCT), clinical practice guidelines recommend transplant delay when possible; however, there is much more ambiguity when other respiratory viruses, such as seasonal coronaviruses (CoVs), human rhinovirus (HRV), and SARS-CoV-2, are detected. Our aims for this review include detailing clinical practical guidelines and reviewing current literature on pre-transplant respiratory viral infections (RVIs), including antiviral therapies and prevention strategies, when available. We will center our discussion on three representative clinical scenarios, with the goal of providing practical guidance to clinicians.
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Affiliation(s)
- Sara R. Kim
- Division of Pediatric Infectious Diseases, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Alpana Waghmare
- Division of Pediatric Infectious Diseases, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Diego R. Hijano
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, TN, United States
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4
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Pang F, Xu W, Zhao H, Chen S, Tian Y, Fu J, You Z, Song P, Xian Q, Zhao Q, Wang C, Jia X. Comprehensive evaluation of plasma microbial cell-free DNA sequencing for predicting bloodstream and local infections in clinical practice: a multicenter retrospective study. Front Cell Infect Microbiol 2024; 13:1256099. [PMID: 38362158 PMCID: PMC10868388 DOI: 10.3389/fcimb.2023.1256099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/12/2023] [Indexed: 02/17/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA (cfDNA) shows promising application for complicated infections that cannot be resolved by conventional microbiological tests (CMTs). The criteria for cfDNA sequencing are currently in need of agreement and standardization. Methods We performed a retrospective cohort observation of 653 patients who underwent plasma cfDNA mNGS, including 431 with suspected bloodstream infections (BSI) and 222 with other suspected systemic infections. Plasma mNGS and CMTs were performed simultaneously in clinical practice. The diagnostic efficacy of plasma mNGS and CMTs in the diagnosis of blood-borne and other systemic infections was evaluated using receiver operating characteristic (ROC) curves. The sensitivity and specificity of the two methods were analyzed based on the final clinical outcome as the gold standard. Results The mNGS test showed an overall positive rate of 72.3% (472/653) for detecting microorganisms in plasma cfDNA, with a range of 2 to 6 different microorganisms detected in 171 patient specimens. Patients with positive mNGS results were more immunocompromised and had a higher incidence of severe disease (P<0·05). The sensitivity of mNGS was higher for BSI (93·5%) and other systemic infections (83·6%) compared to CMTs (37·7% and 14·3%, respectively). The mNGS detected DNA from a total of 735 microorganisms, with the number of microbial DNA reads ranging from 3 to 57,969, and a higher number of reads being associated with clinical infections (P<0·05). Of the 472 patients with positive mNGS results, clinical management was positively affected in 203 (43%) cases. Negative mNGS results led to a modified clinical management regimen in 92 patients (14.1%). The study also developed a bacterial and fungal library for plasma mNGS and obtained comparisons of turnaround times and detailed processing procedures for rare pathogens. Conclusion Our study evaluates the clinical use and analytic approaches of mNGS in predicting bloodstream and local infections in clinical practice. Our results suggest that mNGS has higher positive predictive values (PPVs) for BSI and systemic infections compared to CMTs, and can positively affect clinical management in a significant number of patients. The standardized whole-process management procedure for plasma mNGS developed in this study will ensure improved pre-screening probabilities and yield clinically valuable data.
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Affiliation(s)
- Feng Pang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Wenbin Xu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Hui Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Shuai Chen
- Department of Clinical Laboratory, Liaocheng Thrid People’s Hospital, Liaocheng, Shandong, China
| | - Yaxian Tian
- Department of Center Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Juanjuan Fu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Zhiqing You
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Pingping Song
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Qingjie Xian
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Qigang Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Chengtan Wang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Xiuqin Jia
- The Key Laboratory of Molecular Pharmacology, Liaocheng People’s Hospital, Liaocheng, Shandong, China
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5
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Khawaja F, Srinivasan K, Spallone A, Feldman A, Cantu S, Ariza-Heredia E, Dvordak T, Alousi A, Ahmed S, George M, Frenzel E, Bhatti M, Chemaly RF. Nosocomial COVID-19 at a comprehensive cancer center during the first year of the pandemic: Lessons learned. Am J Infect Control 2023; 51:506-513. [PMID: 35901993 PMCID: PMC9310434 DOI: 10.1016/j.ajic.2022.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND The spread of coronavirus disease 2019 (COVID-19) in health care settings endangers patients with cancer. As knowledge of the transmission of COVID-19 emerged, strategies for preventing nosocomial COVID-19 were updated. We describe our early experience with nosocomial respiratory viral infections (RVIs) at a cancer center in the first year of the pandemic (March 2020-March 2021). METHODS Nosocomial RVIs were identified through our infection control prospective surveillance program, which conducted epidemiologic investigations of all microbiologically documented RVIs. Data was presented as frequencies and percentages or medians and ranges. RESULTS A total of 35 of 3944 (0.9%) documented RVIs were determined to have been nosocomial acquired. Majority of RVIs were due to SARS CoV-2 (13/35; 37%) or by rhinovirus/enterovirus (12/35; 34%). A cluster investigation of the first 3 patients with nosocomial COVID-19 determined that transmission most likely occurred from employees to patients. Five patients (38%) required mechanical ventilation and 4 (31%) died during the same hospital encounter. CONCLUSIONS Our investigation of the cluster led to enhancement of our infection control measures. The implications of COVID-19 vaccination on infection control policies is still unclear and further studies are needed to delineate its impact on the transmission of COVID-19 in a hospital setting.
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Affiliation(s)
- Fareed Khawaja
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Krithika Srinivasan
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Amy Spallone
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Adina Feldman
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sherry Cantu
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ella Ariza-Heredia
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tanya Dvordak
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Amin Alousi
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sairah Ahmed
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marina George
- Office of Chief Operating Officer, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Elizabeth Frenzel
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Micah Bhatti
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Roy F Chemaly
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX; Office of Chief Operating Officer, The University of Texas MD Anderson Cancer Center, Houston, TX.
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6
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Marcink TC, Zipursky G, Cheng W, Stearns K, Stenglein S, Golub K, Cohen F, Bovier F, Pfalmer D, Greninger AL, Porotto M, des Georges A, Moscona A. Subnanometer structure of an enveloped virus fusion complex on viral surface reveals new entry mechanisms. SCIENCE ADVANCES 2023; 9:eade2727. [PMID: 36763666 PMCID: PMC9917000 DOI: 10.1126/sciadv.ade2727] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Paramyxoviruses-including important pathogens like parainfluenza, measles, and Nipah viruses-use a receptor binding protein [hemagglutinin-neuraminidase (HN) for parainfluenza] and a fusion protein (F), acting in a complex, to enter cells. We use cryo-electron tomography to visualize the fusion complex of human parainfluenza virus 3 (HN/F) on the surface of authentic clinical viruses at a subnanometer resolution sufficient to answer mechanistic questions. An HN loop inserts in a pocket on F, showing how the fusion complex remains in a ready but quiescent state until activation. The globular HN heads are rotated with respect to each other: one downward to contact F, and the other upward to grapple cellular receptors, demonstrating how HN/F performs distinct steps before F activation. This depiction of viral fusion illuminates potentially druggable targets for paramyxoviruses and sheds light on fusion processes that underpin wide-ranging biological processes but have not been visualized in situ or at the present resolution.
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Affiliation(s)
- Tara C. Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gillian Zipursky
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wenjing Cheng
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kyle Stearns
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shari Stenglein
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kate Golub
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Frances Cohen
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Francesca Bovier
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Daniel Pfalmer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” 81100 Caserta, Italy
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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7
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Goldman JD, Wang K, Röltgen K, Nielsen SCA, Roach JC, Naccache SN, Yang F, Wirz OF, Yost KE, Lee JY, Chun K, Wrin T, Petropoulos CJ, Lee I, Fallen S, Manner PM, Wallick JA, Algren HA, Murray KM, Hadlock J, Chen D, Dai CL, Yuan D, Su Y, Jeharajah J, Berrington WR, Pappas GP, Nyatsatsang ST, Greninger AL, Satpathy AT, Pauk JS, Boyd SD, Heath JR. Reinfection with SARS-CoV-2 and Waning Humoral Immunity: A Case Report. Vaccines (Basel) 2022; 11:5. [PMID: 36679852 PMCID: PMC9861578 DOI: 10.3390/vaccines11010005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it is uncertain whether these confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify patients with recurrent shedding. We sequenced viruses from two distinct episodes of symptomatic COVID-19 separated by 144 days in a single patient, to conclusively describe reinfection with a different strain harboring the spike variant D614G. This case of reinfection was one of the first cases of reinfection reported in 2020. With antibody, B cell and T cell analytics, we show correlates of adaptive immunity at reinfection, including a differential response in neutralizing antibodies to a D614G pseudovirus. Finally, we discuss implications for vaccine programs and begin to define benchmarks for protection against reinfection from SARS-CoV-2.
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Affiliation(s)
- Jason D. Goldman
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Oliver F. Wirz
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E. Yost
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kelly Chun
- LabCorp Esoterix, Calabasas, CA 91301, USA
| | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA 94080, USA
| | | | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98103, USA
| | | | - Paula M. Manner
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Julie A. Wallick
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Heather A. Algren
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Kim M. Murray
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Jennifer Hadlock
- Providence St. Joseph Health, Renton, WA 98057, USA
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Daniel Chen
- Institute for Systems Biology, Seattle, WA 98103, USA
| | | | - Dan Yuan
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Joshua Jeharajah
- Division of Infectious Diseases, Polyclinic, Seattle, WA 98104, USA
| | - William R. Berrington
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - George P. Pappas
- Division of Pulmonology and Critical Care Medicine, Swedish Medical Center, Seattle, WA 98104, USA
| | - Sonam T. Nyatsatsang
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, DC 98109, USA
| | | | - John S. Pauk
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94304, USA
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8
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Mao Q, Sun G, Qian Y, Qian Y, Li W, Wang X, Shen Q, Yang S, Zhou C, Wang H, Zhang W. Viral metagenomics of pharyngeal secretions from children with acute respiratory diseases with unknown etiology revealed diverse viruses. Virus Res 2022; 321:198912. [PMID: 36058285 DOI: 10.1016/j.virusres.2022.198912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/21/2022] [Accepted: 08/31/2022] [Indexed: 12/24/2022]
Abstract
Acute respiratory tract infections are a major public health problem and the leading cause of morbidity in children younger than 5 years old. This study investigated the potential reasons of unexplained acute respiratory infections in children in Xuzhou and its environs during 2018-2019.We collected pharyngeal swab samples from 411 children under the age of five who presented with symptoms of unexplained acute respiratory infection and were negative for bacteria, mycoplasma, and influenza viruses. Using viral metagenomic techniques, viral nucleic acids were extracted, enriched, and sequenced from the samples. Results indicated that Picornaviridae, Parvoviridae, Paramyxoviridae, Coronaviridae, and Anelloviridae were the five virus families with the highest relative content of sequence reads. And we detected 35 HBoV-positive and 12 HEV-positive samples out of 411 samples by the polymerase chain reaction (PCR). Partial or nearly complete genome sequences of viruses belonging to the families Picornaviridae, Parvoviridae, and Anelloviridae were characterized, and phylogenetic trees were constructed based on the nucleic acid or amino acid sequences of the predicted viral open reading frames (ORFs), as well as genotyping of the viruses. In addition, we observed recombination events in the Saffold virus and Coxsackievirus A9 by analyzing the genetic characteristics of the viruses revealed in this study. This study provides vital information for the prevention and treatment of acute respiratory infections in children younger than five years old.
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Affiliation(s)
- Qingqing Mao
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, 212013, China; School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Guangming Sun
- Department of Clinical Laboratory, Xuzhou Central Hospital, Xuzhou 221009, Jiangsu, China
| | - Yu Qian
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Yuchen Qian
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital, Nanjing Medical University, Taizhou, Jiangsu 225300, China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Quan Shen
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital, Nanjing Medical University, Taizhou, Jiangsu 225300, China.
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China.
| | - Wen Zhang
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, 212013, China; School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
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9
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Chow EJ, Casto AM, Rogers JH, Roychoudhury P, Han PD, Xie H, Mills MG, Nguyen TV, Pfau B, Cox SN, Wolf CR, Hughes JP, Uyeki TM, Rolfes MA, Mosites E, Shim MM, Duchin JS, Sugg N, Starita LA, Englund JA, Chu HY. The clinical and genomic epidemiology of seasonal human coronaviruses in congregate homeless shelter settings: A repeated cross-sectional study. LANCET REGIONAL HEALTH. AMERICAS 2022; 15:100348. [PMID: 35996440 PMCID: PMC9387177 DOI: 10.1016/j.lana.2022.100348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Background The circulation of respiratory viruses poses a significant health risk among those residing in congregate settings. Data are limited on seasonal human coronavirus (HCoV) infections in homeless shelter settings. Methods We analysed data from a clinical trial and SARS-CoV-2 surveillance study at 23 homeless shelter sites in King County, Washington between October 2019-May 2021. Eligible participants were shelter residents aged ≥3 months with acute respiratory illness. We collected enrolment data and nasal samples for respiratory virus testing using multiplex RT-PCR platform including HCoV. Beginning April 1, 2020, eligibility expanded to shelter residents and staff regardless of symptoms. HCoV species was determined by RT-PCR with species-specific primers, OpenArray assay or genomic sequencing for samples with an OpenArray relative cycle threshold <22. Findings Of the 14,464 samples from 3281 participants between October 2019-May 2021, 107 were positive for HCoV from 90 participants (median age 40 years, range: 0·9-81 years, 38% female). HCoV-HKU1 was the most common species identified before and after community-wide mitigation. No HCoV-positive samples were identified between May 2020-December 2020. Adults aged ≥50 years had the highest detection of HCoV (11%) among virus-positive samples among all age-groups. Species and sequence data showed diversity between and within HCoV species over the study period. Interpretation HCoV infections occurred in all congregate homeless shelter site age-groups with the greatest proportion among those aged ≥50 years. Species and sequencing data highlight the complexity of HCoV epidemiology within and between shelters sites. Funding Gates Ventures, Centers for Disease Control and Prevention, National Institute of Health.
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Affiliation(s)
- Eric J. Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Amanda M. Casto
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Julia H. Rogers
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Peter D. Han
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Hong Xie
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Tien V. Nguyen
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Sarah N. Cox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Caitlin R. Wolf
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James P. Hughes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Timothy M. Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa A. Rolfes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Emily Mosites
- Office of the Deputy Director for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M. Mia Shim
- Public Health – Seattle & King County, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jeffrey S. Duchin
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Public Health – Seattle & King County, Seattle, Washington, USA
| | - Nancy Sugg
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lea A. Starita
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Janet A. Englund
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Washington, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
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10
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Reynard O, Gonzalez C, Dumont C, Iampietro M, Ferren M, Le Guellec S, Laurie L, Mathieu C, Carpentier G, Roseau G, Bovier FT, Zhu Y, Le Pennec D, Montharu J, Addetia A, Greninger AL, Alabi CA, Brisebard E, Moscona A, Vecellio L, Porotto M, Horvat B. Nebulized fusion inhibitory peptide protects cynomolgus macaques from measles virus infection. Nat Commun 2022; 13:6439. [PMID: 36307480 PMCID: PMC9616412 DOI: 10.1038/s41467-022-33832-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/03/2022] [Indexed: 12/25/2022] Open
Abstract
Measles is the most contagious airborne viral infection and the leading cause of child death among vaccine-preventable diseases. We show here that aerosolized lipopeptide fusion inhibitor, derived from heptad-repeat regions of the measles virus (MeV) fusion protein, blocks respiratory MeV infection in a non-human primate model, the cynomolgus macaque. We use a custom-designed mesh nebulizer to ensure efficient aerosol delivery of peptide to the respiratory tract and demonstrate the absence of adverse effects and lung pathology in macaques. The nebulized peptide efficiently prevents MeV infection, resulting in the complete absence of MeV RNA, MeV-infected cells, and MeV-specific humoral responses in treated animals. This strategy provides an additional means to fight against respiratory infection in non-vaccinated people, that can be readily translated to human trials. It presents a proof-of-concept for the aerosol delivery of fusion inhibitory peptides to protect against measles and other airborne viruses, including SARS-CoV-2, in case of high-risk exposure.
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Affiliation(s)
- Olivier Reynard
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007, Lyon, France
| | - Claudia Gonzalez
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007, Lyon, France
| | - Claire Dumont
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007, Lyon, France
| | - Mathieu Iampietro
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007, Lyon, France
| | - Marion Ferren
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007, Lyon, France
| | - Sandrine Le Guellec
- DTF-Aerodrug, R&D aerosolltherapy department of DTF medical (Saint Etienne, France), Faculté de médecine, Université de Tours, 37032, Tours, France
| | - Lajoie Laurie
- Université de Tours, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAe), UMR1282, Infectiologie et santé publique (ISP), Tours, France
| | - Cyrille Mathieu
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007, Lyon, France
| | | | | | - Francesca T Bovier
- Center for Host-Pathogen Interaction, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yun Zhu
- Center for Host-Pathogen Interaction, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Laboratory of Infection and Virology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Deborah Le Pennec
- INSERM, Research Center for Respiratory Diseases, CEPR U1100, Université de Tours, 37032, Tours, France
| | | | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Christopher A Alabi
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | | | - Anne Moscona
- Center for Host-Pathogen Interaction, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
- Department of Physiology & Cellular Biophysics, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
| | | | - Matteo Porotto
- Center for Host-Pathogen Interaction, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Experimental Medicine, University of Studies of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Branka Horvat
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007, Lyon, France.
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11
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Mills MG, Hajian P, Bakhash SM, Xie H, Mantzke D, Zhu H, Perchetti GA, Huang ML, Pepper G, Jerome KR, Roychoudhury P, Greninger AL. Rapid and accurate identification of SARS-CoV-2 Omicron variants using droplet digital PCR (RT-ddPCR). J Clin Virol 2022; 154:105218. [PMID: 35779343 PMCID: PMC9212762 DOI: 10.1016/j.jcv.2022.105218] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/05/2022] [Accepted: 06/10/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND Some mutations in the receptor binding domain of the SARS-CoV-2 Spike protein are associated with increased transmission or substantial reductions in vaccine efficacy, including in recently described Omicron subvariants. The changing frequencies of these mutations combined with their differing susceptibility to available therapies have posed significant problems for clinicians and public health professionals. OBJECTIVE To develop an assay capable of rapidly and accurately identifying variants including Omicron in clinical specimens to enable case tracking and/or selection of appropriate clinical treatment. STUDY DESIGN Using three duplex RT-ddPCR reactions targeting four amino acids, we tested 419 positive clinical specimens from February to December 2021 during a period of rapidly shifting variant prevalences and compared genotyping results to genome sequences for each sample, determining the sensitivity and specificity of the assay for each variant. RESULTS Mutation determinations for 99.7% of detected samples agree with NGS data for those samples, and are accurate despite wide variation in RNA concentration and potential confounding factors like transport medium, presence of additional respiratory viruses, and additional mutations in primer and probe sequences. The assay accurately identified the first 15 Omicron variants in our laboratory including the first Omicron in Washington State and discriminated against S-gene dropout Delta specimen. CONCLUSION We describe an accurate, precise, and specific RT-ddPCR assay for variant detection that remains robust despite being designed prior the emergence of Delta and Omicron variants. The assay can quickly identify mutations in current and past SARS-CoV-2 variants, and can be adapted to future mutations.
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Affiliation(s)
- Margaret G Mills
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA.
| | - Pooneh Hajian
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Shah Mohamed Bakhash
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Derrek Mantzke
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Gregory Pepper
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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12
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PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets. Life (Basel) 2022; 12:life12091345. [PMID: 36143382 PMCID: PMC9505849 DOI: 10.3390/life12091345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Over the past years, NGS has become a crucial workhorse for open-view pathogen diagnostics. Yet, long turnaround times result from using massively parallel high-throughput technologies as the analysis can only be performed after sequencing has finished. The interpretation of results can further be challenged by contaminations, clinically irrelevant sequences, and the sheer amount and complexity of the data. We implemented PathoLive, a real-time diagnostics pipeline for the detection of pathogens from clinical samples hours before sequencing has finished. Based on real-time alignment with HiLive2, mappings are scored with respect to common contaminations, low-entropy areas, and sequences of widespread, non-pathogenic organisms. The results are visualized using an interactive taxonomic tree that provides an easily interpretable overview of the relevance of hits. For a human plasma sample that was spiked in vitro with six pathogenic viruses, all agents were clearly detected after only 40 of 200 sequencing cycles. For a real-world sample from Sudan, the results correctly indicated the presence of Crimean-Congo hemorrhagic fever virus. In a second real-world dataset from the 2019 SARS-CoV-2 outbreak in Wuhan, we found the presence of a SARS coronavirus as the most relevant hit without the novel virus reference genome being included in the database. For all samples, clinically irrelevant hits were correctly de-emphasized. Our approach is valuable to obtain fast and accurate NGS-based pathogen identifications and correctly prioritize and visualize them based on their clinical significance: PathoLive is open source and available on GitLab and BioConda.
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13
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SARS-CoV-2 VOC type and biological sex affect molnupiravir efficacy in severe COVID-19 dwarf hamster model. Nat Commun 2022; 13:4416. [PMID: 35906230 PMCID: PMC9338273 DOI: 10.1038/s41467-022-32045-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
SARS-CoV-2 variants of concern (VOC) have triggered infection waves. Oral antivirals such as molnupiravir promise to improve disease management, but efficacy against VOC delta was questioned and potency against omicron is unknown. This study evaluates molnupiravir against VOC in human airway epithelium organoids, ferrets, and a lethal Roborovski dwarf hamster model of severe COVID-19-like lung injury. VOC were equally inhibited by molnupiravir in cells and organoids. Treatment reduced shedding in ferrets and prevented transmission. Pathogenicity in dwarf hamsters was VOC-dependent and highest for delta, gamma, and omicron. All molnupiravir-treated dwarf hamsters survived, showing reduction in lung virus load from one (delta) to four (gamma) orders of magnitude. Treatment effect size varied in individual dwarf hamsters infected with omicron and was significant in males, but not females. The dwarf hamster model recapitulates mixed efficacy of molnupiravir in human trials and alerts that benefit must be reassessed in vivo as VOC evolve. Molnupiravir was the first orally available SARS-CoV-2 antiviral approved for outpatient use against SARS-CoV-2, but its efficacy against variants of concern, especially delta, was questioned. Here the authors evaluate molnupiravir against variant of concern in numerous models, including human airway epithelium organoids, ferrets and Roborovski dwarf hamsters.
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14
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Shrestha L, Lin MJ, Xie H, Mills MG, Mohamed Bakhash SA, Gaur VP, Livingston RJ, Castor J, Bruce EA, Botten JW, Huang ML, Jerome KR, Greninger AL, Roychoudhury P. Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes. J Mol Diagn 2022; 24:963-976. [PMID: 35863699 PMCID: PMC9290336 DOI: 10.1016/j.jmoldx.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/24/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR. Breadth of genome recovery was evaluated across a range of CT values (11.3 to 36.7; median, 21.6). Of 428 positive samples, 413 (96.5%) generated genomes with <10% unknown bases, with a mean genome coverage of 13,545× ± SD 8382×. No genomes were recovered from PCR-negative specimens (n = 30) or from specimens positive for non–SARS-CoV-2 respiratory viruses (n = 20). Compared with whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks, with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.
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Affiliation(s)
- Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | | | - Vinod P Gaur
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Robert J Livingston
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Jared Castor
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Emily A Bruce
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT
| | - Jason W Botten
- Department of Medicine, University of Vermont, Burlington, VT
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
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15
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Wang X, Stelzer-Braid S, Scotch M, Rawlinson WD. Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use. Rev Med Virol 2022; 32:e2375. [PMID: 35775736 PMCID: PMC9539958 DOI: 10.1002/rmv.2375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022]
Abstract
Acute respiratory infection is the third most frequent cause of mortality worldwide, causing over 4.25 million deaths annually. Although most diagnosed acute respiratory infections are thought to be of viral origin, the aetiology often remains unclear. The advent of next‐generation sequencing (NGS) has revolutionised the field of virus discovery and identification, particularly in the detection of unknown respiratory viruses. We systematically reviewed the application of NGS technologies for detecting respiratory viruses from clinical samples and outline potential barriers to the routine clinical introduction of NGS. The five databases searched for studies published in English from 01 January 2010 to 01 February 2021, which led to the inclusion of 52 studies. A total of 14 different models of NGS platforms were summarised from included studies. Among these models, second‐generation sequencing platforms (e.g., Illumina sequencers) were used in the majority of studies (41/52, 79%). Moreover, NGS platforms have proven successful in detecting a variety of respiratory viruses, including influenza A/B viruses (9/52, 17%), SARS‐CoV‐2 (21/52, 40%), parainfluenza virus (3/52, 6%), respiratory syncytial virus (1/52, 2%), human metapneumovirus (2/52, 4%), or a viral panel including other respiratory viruses (16/52, 31%). The review of NGS technologies used in previous studies indicates the advantages of NGS technologies in novel virus detection, virus typing, mutation identification, and infection cluster assessment. Although there remain some technical and ethical challenges associated with NGS use in clinical laboratories, NGS is a promising future tool to improve understanding of respiratory viruses and provide a more accurate diagnosis with simultaneous virus characterisation.
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Affiliation(s)
- Xinye Wang
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Scotch
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.,Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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16
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Chow EJ, Casto AM, Roychoudhury P, Han PD, Xie H, Pfau B, Nguyen TV, Sereewit J, Rogers JH, Cox SN, Wolf CR, Rolfes MA, Mosites E, Uyeki TM, Greninger AL, Hughes JP, Shim MM, Sugg N, Duchin JS, Starita LM, Englund JA, Chu HY. The Clinical and Genomic Epidemiology of Rhinovirus in Homeless Shelters-King County, Washington. J Infect Dis 2022; 226:S304-S314. [PMID: 35749582 PMCID: PMC9384451 DOI: 10.1093/infdis/jiac239] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Rhinovirus (RV) is a common cause of respiratory illness in all people, including those experiencing homelessness. RV epidemiology in homeless shelters is unknown. METHODS We analyzed data from a cross-sectional homeless shelter study in King County, Washington, October 2019-May 2021. Shelter residents or guardians aged ≥3 months reporting acute respiratory illness completed questionnaires and submitted nasal swabs. After 1 April 2020, enrollment expanded to residents and staff regardless of symptoms. Samples were tested by multiplex RT-PCR for respiratory viruses. A subset of RV-positive samples was sequenced. RESULTS There were 1066 RV-positive samples with RV present every month of the study period. RV was the most common virus before and during the coronavirus disease 2019 (COVID-19) pandemic (43% and 77% of virus-positive samples, respectively). Participants from family shelters had the highest prevalence of RV. Among 131 sequenced samples, 33 RV serotypes were identified with each serotype detected for ≤4 months. CONCLUSIONS RV infections persisted through community mitigation measures and were most prevalent in shelters housing families. Sequencing showed a diversity of circulating RV serotypes, each detected over short periods of time. Community-based surveillance in congregate settings is important to characterize respiratory viral infections during and after the COVID-19 pandemic. CLINICAL TRIALS REGISTRATION NCT04141917.
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Affiliation(s)
- Eric J Chow
- Corresponding author: Eric J. Chow, MD, MS, MPH, Division of Allergy and Infectious Diseases, University of Washington, 1959 NE Pacific Street Box 356423, S512020125, Washington 98195, E-mail: , Ph:206-685-4456, Fax:206-616-3892
| | - Amanda M Casto
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle (98195), Washington, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle (98109), Washington, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle (98109), Washington, USA,Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle (98195), Washington, USA
| | - Peter D Han
- Brotman Baty Institute for Precision Medicine, Seattle (98195), Washington, USA,Department of Genome Sciences, University of Washington, Seattle (98195), Washington, USA
| | - Hong Xie
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle (98195), Washington, USA
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, Seattle (98195), Washington, USA,Department of Genome Sciences, University of Washington, Seattle (98195), Washington, USA
| | - Tien V Nguyen
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle (98195), Washington, USA
| | - Jaydee Sereewit
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle (98195), Washington, USA
| | - Julia H Rogers
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle (98195), Washington, USA,Department of Epidemiology, University of Washington, Seattle (98195), Washington, USA
| | - Sarah N Cox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle (98195), Washington, USA,Department of Epidemiology, University of Washington, Seattle (98195), Washington, USA
| | - Caitlin R Wolf
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle (98195), Washington, USA
| | - Melissa A Rolfes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta (30333), Georgia, USA
| | - Emily Mosites
- Office of the Deputy Director for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta (30333), Georgia, USA
| | - Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta (30333), Georgia, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle (98109), Washington, USA,Department of Laboratory Medicine and Pathology, University of Washington, Seattle (98195), Washington, USA
| | - James P Hughes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle (98109), Washington, USA,Department of Biostatistics, University of Washington, Seattle (98105), Washington, USA
| | - M Mia Shim
- Public Health – Seattle & King County, Seattle (98104), Washington, USA,Department of Medicine, University of Washington, Seattle (98195), Washington, USA
| | - Nancy Sugg
- Department of Medicine, University of Washington, Seattle (98195), Washington, USA
| | - Jeffrey S Duchin
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle (98195), Washington, USA,Public Health – Seattle & King County, Seattle (98104), Washington, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle (98195), Washington, USA,Department of Genome Sciences, University of Washington, Seattle (98195), Washington, USA
| | - Janet A Englund
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Washington, Seattle Children’s Research Institute, Seattle (98105), Washington, USA
| | - Helen Y Chu
- Alternate Corresponding Author: Helen Y. Chu, MD, MPH, Division of Allergy and Infectious Diseases, University of Washington, 750 Republican Street, Seattle, Washington 98109, Ph: 206-685-8702, E-mail:
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17
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Reynard O, Gonzalez C, Dumont C, Iampietro M, Ferren M, Le Guellec S, Laurie L, Mathieu C, Carpentier G, Roseau G, Bovier FT, Zhu Y, Le Pennec D, Montharu J, Addetia A, Greninger AL, Alabi CA, Moscona A, Vecellio L, Porotto M, Horvat B. Nebulized fusion inhibitory peptide protects cynomolgus macaques from measles virus infection. RESEARCH SQUARE 2022:rs.3.rs-1700877. [PMID: 35677066 PMCID: PMC9176655 DOI: 10.21203/rs.3.rs-1700877/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Measles is the most contagious airborne viral infection and the leading cause of child death among vaccine-preventable diseases. We show here that aerosolized lipopeptide fusion inhibitors, derived from heptad-repeat regions of the measles virus (MeV) fusion protein, block respiratory MeV infection in a non-human primate model, the cynomolgus macaque. We used a custom-designed mesh nebulizer to ensure efficient aerosol delivery of peptides to the respiratory tract and demonstrated the absence of adverse effects and lung pathology in macaques. The nebulized peptide efficiently prevented MeV infection, resulting in the complete absence of MeV RNA, MeV-infected cells, and MeV-specific humoral responses in treated animals. This strategy provides an additional shield which complements vaccination to fight against respiratory infection, presenting a proof-of-concept for the aerosol delivery of fusion inhibitory peptides to protect against measles and other airborne viruses, including SARS-CoV-2, in case of high-risk exposure, that can be readily translated to human trials.
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Affiliation(s)
- Olivier Reynard
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Claudia Gonzalez
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Claire Dumont
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Mathieu Iampietro
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Marion Ferren
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Sandrine Le Guellec
- DTF-Aerodrug, R&D aerosolltherapy department of DTF medical (Saint Etienne, France), Faculté de médecine, Université de Tours, 37032 Tours, France
| | - Lajoie Laurie
- Université de Tours, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAe), UMR1282, Infectiologie et santé publique (ISP), Tours, France
| | - Cyrille Mathieu
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
| | | | | | - Francesca T. Bovier
- Center for Host-Pathogen Interaction, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yun Zhu
- Center for Host-Pathogen Interaction, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.,Laboratory of Infection and Virology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing 100045, China
| | - Deborah Le Pennec
- INSERM, Research Center for Respiratory Diseases, CEPR U1100, Université de Tours, 37032 Tours, France
| | | | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Christopher A. Alabi
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Anne Moscona
- Center for Host-Pathogen Interaction, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.,Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA.,Department of Physiology & Cellular Biophysics, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
| | | | - Matteo Porotto
- Center for Host-Pathogen Interaction, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.,Department of Experimental Medicine, University of Studies of Campania ‘Luigi Vanvitelli’, Naples, Italy
| | - Branka Horvat
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS, UMR5308, Univ Lyon, Université Claude Bernard Lyon 1, École Normale Supérieure de Lyon, 21 Avenue Tony Garnier, 69007 Lyon, France
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18
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Kong J, Li W, Hu J, Zhao S, Yue T, Li Z, Xia Y. The Safety of Cold-Chain Food in Post-COVID-19 Pandemic: Precaution and Quarantine. Foods 2022; 11:foods11111540. [PMID: 35681292 PMCID: PMC9180738 DOI: 10.3390/foods11111540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
Since the outbreak of coronavirus disease-19 (COVID-19), cold-chain food contamination caused by the pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has attracted huge concern. Cold-chain foods provide a congenial environment for SARS-CoV-2 survival, which presents a potential risk for public health. Strengthening the SARS-CoV-2 supervision of cold-chain foods has become the top priority in many countries. Methodologically, the potential safety risks and precaution measures of SARS-CoV-2 contamination on cold-chain food are analyzed. To ensure the safety of cold-chain foods, the advances in SARS-CoV-2 detection strategies are summarized based on technical principles and target biomarkers. In particular, the techniques suitable for SARS-CoV-2 detection in a cold-chain environment are discussed. Although many quarantine techniques are available, the field-based quarantine technique on cold-chain food with characteristics of real-time, sensitive, specific, portable, and large-scale application is urgently needed.
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Affiliation(s)
- Jia Kong
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Wenxin Li
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Jinyao Hu
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Shixuan Zhao
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Ministry of Agriculture, Xianyang 712100, China
| | - Zhonghong Li
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Ministry of Agriculture, Xianyang 712100, China
| | - Yinqiang Xia
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
- Correspondence: ; Tel.: +86-151-2222-5493
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19
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Lin MJ, Rachleff VM, Xie H, Shrestha L, Lieberman NAP, Peddu V, Addetia A, Casto AM, Breit N, Mathias PC, Huang ML, Jerome KR, Greninger AL, Roychoudhury P. Host-pathogen dynamics in longitudinal clinical specimens from patients with COVID-19. Sci Rep 2022; 12:5856. [PMID: 35393464 PMCID: PMC8987511 DOI: 10.1038/s41598-022-09752-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/16/2022] [Indexed: 12/30/2022] Open
Abstract
Rapid dissemination of SARS-CoV-2 sequencing data to public repositories has enabled widespread study of viral genomes, but studies of longitudinal specimens from infected persons are relatively limited. Analysis of longitudinal specimens enables understanding of how host immune pressures drive viral evolution in vivo. Here we performed sequencing of 49 longitudinal SARS-CoV-2-positive samples from 20 patients in Washington State collected between March and September of 2020. Viral loads declined over time with an average increase in RT-QPCR cycle threshold of 0.87 per day. We found that there was negligible change in SARS-CoV-2 consensus sequences over time, but identified a number of nonsynonymous variants at low frequencies across the genome. We observed enrichment for a relatively small number of these variants, all of which are now seen in consensus genomes across the globe at low prevalence. In one patient, we saw rapid emergence of various low-level deletion variants at the N-terminal domain of the spike glycoprotein, some of which have previously been shown to be associated with reduced neutralization potency from sera. In a subset of samples that were sequenced using metagenomic methods, differential gene expression analysis showed a downregulation of cytoskeletal genes that was consistent with a loss of ciliated epithelium during infection and recovery. We also identified co-occurrence of bacterial species in samples from multiple hospitalized individuals. These results demonstrate that the intrahost genetic composition of SARS-CoV-2 is dynamic during the course of COVID-19, and highlight the need for continued surveillance and deep sequencing of minor variants.
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Affiliation(s)
- Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Victoria M Rachleff
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Program in Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Vikas Peddu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Amanda M Casto
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, USA
| | - Nathan Breit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Patrick C Mathias
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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20
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Greninger AL, Zerr DM. NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology. J Pediatric Infect Dis Soc 2021; 10:S88-S95. [PMID: 34951469 PMCID: PMC8755322 DOI: 10.1093/jpids/piab074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hospital outbreak investigations are high-stakes epidemiology. Contacts between staff and patients are numerous; environmental and community exposures are plentiful; and patients are highly vulnerable. Having the best data is paramount to understanding an outbreak in order to stop ongoing transmission and prevent future outbreaks. In the past 5 years, the high-resolution view of transmission offered by analyzing pathogen whole-genome sequencing (WGS) is increasingly part of hospital outbreak investigations. Concerns over speed and actionability, assay validation, liability, cost, and payment models lead to further opportunities for work in this area. Now accelerated by funding for COVID-19, the use of genomics in hospital outbreak investigations has firmly moved from the academic literature to more quotidian operations, with associated concerns involving regulatory affairs, data integration, and clinical interpretation. This review details past uses of WGS data in hospital-acquired infection outbreaks as well as future opportunities to increase its utility and growth in hospital infection prevention.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Corresponding Author: Alexander L. Greninger MD, PhD, MS, MPhil, 1616 Eastlake Ave East Suite 320, Seattle, WA 98102, USA. E-mail:
| | - Danielle M Zerr
- Department of Pediatrics, University of Washington Medical Center, Seattle, Washington, USA,Division of Infectious Diseases, Seattle Children’s Hospital, Seattle, Washington, USA
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21
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Charalampous T, Alcolea-Medina A, Snell LB, Williams TGS, Batra R, Alder C, Telatin A, Camporota L, Meadows CIS, Wyncoll D, Barrett NA, Hemsley CJ, Bryan L, Newsholme W, Boyd SE, Green A, Mahadeva U, Patel A, Cliff PR, Page AJ, O'Grady J, Edgeworth JD. Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units. Genome Med 2021; 13:182. [PMID: 34784976 PMCID: PMC8594956 DOI: 10.1186/s13073-021-00991-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 10/14/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity. METHODS CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave. RESULTS An 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of β-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs. CONCLUSION CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.
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Affiliation(s)
- Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Tom G S Williams
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Christopher Alder
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Luigi Camporota
- Critical Care Directorate, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | | | - Duncan Wyncoll
- Critical Care Directorate, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Nicholas A Barrett
- Critical Care Directorate, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Carolyn J Hemsley
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Lisa Bryan
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK
| | - William Newsholme
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Sara E Boyd
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Anna Green
- Department of Cellular Pathology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Ula Mahadeva
- Department of Cellular Pathology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | | | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK.
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK.
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK.
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22
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Cox RM, Wolf JD, Lieber CM, Sourimant J, Lin MJ, Babusis D, DuPont V, Chan J, Barrett KT, Lye D, Kalla R, Chun K, Mackman RL, Ye C, Cihlar T, Martinez-Sobrido L, Greninger AL, Bilello JP, Plemper RK. Oral prodrug of remdesivir parent GS-441524 is efficacious against SARS-CoV-2 in ferrets. Nat Commun 2021; 12:6415. [PMID: 34741049 PMCID: PMC8571282 DOI: 10.1038/s41467-021-26760-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/22/2021] [Indexed: 02/05/2023] Open
Abstract
Remdesivir is an antiviral approved for COVID-19 treatment, but its wider use is limited by intravenous delivery. An orally bioavailable remdesivir analog may boost therapeutic benefit by facilitating early administration to non-hospitalized patients. This study characterizes the anti-SARS-CoV-2 efficacy of GS-621763, an oral prodrug of remdesivir parent nucleoside GS-441524. Both GS-621763 and GS-441524 inhibit SARS-CoV-2, including variants of concern (VOC) in cell culture and human airway epithelium organoids. Oral GS-621763 is efficiently converted to plasma metabolite GS-441524, and in lungs to the triphosphate metabolite identical to that generated by remdesivir, demonstrating a consistent mechanism of activity. Twice-daily oral administration of 10 mg/kg GS-621763 reduces SARS-CoV-2 burden to near-undetectable levels in ferrets. When dosed therapeutically against VOC P.1 gamma γ, oral GS-621763 blocks virus replication and prevents transmission to untreated contact animals. These results demonstrate therapeutic efficacy of a much-needed orally bioavailable analog of remdesivir in a relevant animal model of SARS-CoV-2 infection. Remdesivir is an approved antiviral treatment for COVID-19, but it needs to be administered intravenously. Here, Cox et al. show that GS-621763, a prodrug of remdesivir parent nucleoside GS-441524 has good oral bioavailability and inhibits SARS-CoV-2 and variants of concerns in ferrets.
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Affiliation(s)
- Robert M Cox
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Josef D Wolf
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Carolin M Lieber
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Julien Sourimant
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Michelle J Lin
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Julie Chan
- Gilead Sciences Inc, Foster City, CA, USA
| | | | - Diane Lye
- Gilead Sciences Inc, Foster City, CA, USA
| | - Rao Kalla
- Gilead Sciences Inc, Foster City, CA, USA
| | - Kwon Chun
- Gilead Sciences Inc, Foster City, CA, USA
| | | | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | | | - Alexander L Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Richard K Plemper
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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23
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Greninger AL, Rybkina K, Lin MJ, Drew-Bear J, Marcink TC, Shean RC, Makhsous N, Boeckh M, Harder O, Bovier F, Burstein SR, Niewiesk S, Rima BK, Porotto M, Moscona A. Human parainfluenza virus evolution during lung infection of immunocompromised humans promotes viral persistence. J Clin Invest 2021; 131:150506. [PMID: 34609969 DOI: 10.1172/jci150506] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
The capacity of respiratory viruses to undergo evolution within the respiratory tract raises the possibility of evolution under the selective pressure of the host environment or drug treatment. Long-term infections in immunocompromised hosts are potential drivers of viral evolution and development of infectious variants. We show that intra-host evolution in chronic human parainfluenza virus 3 (HPIV3) infection in immunocompromised individuals elicited mutations that favor viral entry and persistence, suggesting that similar processes may operate across enveloped respiratory viruses. We profiled longitudinal HPIV3 infections from two immunocompromised individuals that persisted for 278 and 98 days. Mutations accrued in the HPIV3 attachment protein hemagglutinin-neuraminidase (HN), including the first in vivo mutation in HN's receptor binding site responsible for activating the viral fusion process. Fixation of this mutation was associated with exposure to a drug that cleaves host cell sialic acid moieties. Longitudinal adaptation of HN was associated with features that promote viral entry and persistence in cells, including greater avidity for sialic acid and more active fusion activity in vitro, but not with antibody escape. Long term infection thus led to mutations promoting viral persistence, suggesting that host-directed therapeutics may support the evolution of viruses that alter their biophysical characteristics to persist in the face of these agents in vivo.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Ksenia Rybkina
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Jennifer Drew-Bear
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Tara C Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Ryan C Shean
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Negar Makhsous
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Olivia Harder
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, United States of America
| | - Francesca Bovier
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Shana R Burstein
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Stefan Niewiesk
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, United States of America
| | - Bert K Rima
- School of Medicine Dentistry and Biomedical Sceinces, Queen's University of Belfast, Belfast, United Kingdom
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Anne Moscona
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
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24
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Braun KM, Moreno GK, Buys A, Somsen ED, Bobholz M, Accola MA, Anderson L, Rehrauer WM, Baker DA, Safdar N, Lepak AJ, O’Connor DH, Friedrich TC. Viral Sequencing to Investigate Sources of SARS-CoV-2 Infection in US Healthcare Personnel. Clin Infect Dis 2021; 73:e1329-e1336. [PMID: 33857303 PMCID: PMC8083259 DOI: 10.1093/cid/ciab281] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Healthcare personnel (HCP) are at increased risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We posit that current infection control guidelines generally protect HCP from SARS-CoV-2 infection in a healthcare setting. METHODS In this retrospective case series, we used viral genomics to investigate the likely source of SARS-CoV-2 infection in HCP at a major academic medical institution in the Upper Midwest of the United States between 25 March and 27 December 2020. We obtained limited epidemiological data through informal interviews and review of the electronic health record and combined this information with healthcare-associated viral sequences and viral sequences collected in the broader community to infer the most likely source of infection in HCP. RESULTS We investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or coworker (55 of 95 [57.9%]) and were genetically similar to viruses circulating concurrently in the community. We found that 10.5% of HCP infections (10 of 95) could be traced to a coworker. Strikingly, only 4.2% (4 of 95) could be traced to a patient source. CONCLUSIONS Infections among HCP add further strain to the healthcare system and put patients, HCP, and communities at risk. We found no evidence for healthcare-associated transmission in the majority of HCP infections evaluated. Although we cannot rule out the possibility of cryptic healthcare-associated transmission, it appears that HCP most commonly become infected with SARS-CoV-2 via community exposure. This emphasizes the ongoing importance of mask wearing, physical distancing, robust testing programs, and rapid distribution of vaccines.
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Affiliation(s)
- Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ashley Buys
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Elizabeth D Somsen
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Max Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Laura Anderson
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Alexander J Lepak
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
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25
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Assessing the potential correlation of polymorphisms in the IL6R with relative IL6 elevation in severely ill COVID-19 patients'. Cytokine 2021; 148:155662. [PMID: 34353696 PMCID: PMC8318728 DOI: 10.1016/j.cyto.2021.155662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 01/18/2023]
Abstract
Background Elevated Interleukin-6 (IL-6) may play an important role in the pathophysiology of COVID-19 yet attenuated response is not seen across all severe patients. We aimed to determine the effect of IL-6 baseline levels and other clinical variables on mortality and outcomes in hospitalized COVID-19 patients as well as to explore genetic variants associated with attenuated IL-6 response. Methods Baseline IL-6 cytokine levels were measured in hospitalized patients participating in ongoing ODYSSEY phase 3 randomized study of tradipitant and placebo in hospitalized patients with severe COVID-19 who are receiving supplemental oxygen support. Furthermore blood samples for whole genome sequencing analysis were collected from 150 participants. Results We report significantly elevated IL-6 in COVID-19 infected hospitalized patients, n = 100 (p-value < 0.0001) when compared to controls n = 324. We also report a significantly increased level of IL-6 (p-value < 0.01) between the severe and mild COVID-19 patients with severity defined on a WHO scale. Excessive IL-6 plasma levels correlate with higher mortality (p-value 0.001). Additionally, based on our classification analysis, combination of IL-6 elevation and high levels of serum glucose can identify highest risk-group of COVID19 patients. Furthermore, we explore the role of genetic regulatory variants affecting baseline IL-6 levels specifically in COVID-19 patients. We have directly tested the association between variants in the IL6 and IL6R gene region and IL6 plasma levels. We provide results for a common IL-6 variant previously associated with pneumonia, rs1800795, and rs2228145 that was previously shown to affect IL-6 plasma levels, as well as report on novel variants associated with IL-6 plasma levels detected in our study patients. Conclusions While it is unlikely that “cytokine storm” is the norm in severe COVID19, baseline elevations above 150 pg/ml may be associated with worst outcomes and as such may warrant treatment considerations. So far no clinical studies used IL-6 baseline assessment to stratify the patient population participating in clinical studies. We believe that careful examination and interpretation of the IL-6 levels and genetic variants can help to determine a patient population with a potentially very robust clinical response to IL-6 inhibition. Trial Registration: Clinicaltrials.gov: NCT04326426.
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26
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Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Ilcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Sci Transl Med 2021; 13:eabf0202. [PMID: 33941621 PMCID: PMC8158963 DOI: 10.1126/scitranslmed.abf0202] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/23/2021] [Accepted: 04/25/2021] [Indexed: 12/16/2022]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gravely affected societies around the world. Outbreaks in different parts of the globe have been shaped by repeated introductions of new viral lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State (USA) to characterize how the spread of SARS-CoV-2 in Washington State in early 2020 was shaped by differences in timing of mitigation strategies across counties and by repeated introductions of viral lineages into the state. In addition, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G but not the other variant (614D) into the state. At an individual level, we observed evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we did not find any evidence that the 614G variant affects clinical severity or patient outcomes. Overall, this suggests that with regard to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus.
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Affiliation(s)
- Nicola F Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Cassia Wagner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Chris D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Louise H Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Benjamin Pelle
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew Richardson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Victoria M Rachleff
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Elisabeth Brandstetter
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Peter D Han
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kirsten Lacombe
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Caitlin R Wolf
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | | | - Barry R Lutz
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Matthew Thompson
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey S Duchin
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Public Health - Seattle & King County, Seattle, WA98121, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Helen Y Chu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Scott Lindquist
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
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27
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Valença IN, Santos RBD, Peronni KC, Sauvage V, Vandenbogaert M, Caro V, Silva Junior WAD, Covas DT, Silva-Pinto AC, Laperche S, Kashima S, Slavov SN. Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia. Rev Inst Med Trop Sao Paulo 2021; 63:e40. [PMID: 34037156 PMCID: PMC8149102 DOI: 10.1590/s1678-9946202163040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/18/2021] [Indexed: 11/22/2022] Open
Abstract
To date, blood banks apply routine diagnosis to a specific spectrum of
transfusion-transmitted viruses. Even though this measure is considered highly
efficient to control their transmission, the threat imposed by emerging viruses
is increasing globally, which can impact transfusion safety, especially in the
light of the accelerated viral discovery by novel sequencing technologies. One
of the most important groups of patients, who may indicate the presence of
emerging viruses in the field of blood transfusion, is the group of individuals
who receive multiple transfusions due to hereditary hemoglobinopathies. It is
possible that they harbor unknown or unsuspected parenterally-transmitted
viruses. In order to elucidate this, nucleic acids from 30 patients with
beta-thalassemia were analyzed by Illumina next-generation sequencing and
bioinformatics analysis. Three major viral families:
Anelloviridae, Flaviviridae and
Hepadnaviridae were identified. Among
them, anelloviruses were the most representative, being detected with high
number of reads in all tested samples. Human Pegivirus 1 (HPgV-1, or GBV-C),
Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) were also identified. HBV
and HCV detection was expected due to the high seroprevalence in patients with
beta thalassemia. Our results do not confirm the presence of emerging or
unsuspected viruses threatening the transfusion safety at present, but can be
used to actively search for viruses that threaten blood transfusion safety. We
believe that the application of viral metagenomics in multiple-transfused
patients is highly useful to monitor possible viral transfusion threats and for
the annotation of their virome composition.
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Affiliation(s)
- Ian Nunes Valença
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Programa de Mestrado em Oncologia Clínica, Células-Tronco e Terapia Celular, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Bezerra Dos Santos
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Programa de Mestrado em Oncologia Clínica, Células-Tronco e Terapia Celular, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Kamila Chagas Peronni
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Virginie Sauvage
- Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Département d'études des Agents Transmissibles par le Sang, Paris, France
| | - Mathias Vandenbogaert
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Paris, France
| | - Valérie Caro
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Paris, France
| | - Wilson Araújo da Silva Junior
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, São Paulo, Brazil
| | - Dimas Tadeu Covas
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, São Paulo, Brazil
| | - Ana Cristina Silva-Pinto
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Syria Laperche
- Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Département d'études des Agents Transmissibles par le Sang, Paris, France
| | - Simone Kashima
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, São Paulo, Brazil
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28
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Gil P, Dupuy V, Koual R, Exbrayat A, Loire E, Fall AG, Gimonneau G, Biteye B, Talla Seck M, Rakotoarivony I, Marie A, Frances B, Lambert G, Reveillaud J, Balenghien T, Garros C, Albina E, Eloit M, Gutierrez S. A library preparation optimized for metagenomics of RNA viruses. Mol Ecol Resour 2021; 21:1788-1807. [PMID: 33713395 DOI: 10.1111/1755-0998.13378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 11/28/2022]
Abstract
Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR-based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field-caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.
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Affiliation(s)
- Patricia Gil
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Virginie Dupuy
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Rachid Koual
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Antoni Exbrayat
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Etienne Loire
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Assane G Fall
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Geoffrey Gimonneau
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France.,Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Biram Biteye
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Momar Talla Seck
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar-Hann, Senegal
| | - Ignace Rakotoarivony
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | | | | | | | - Julie Reveillaud
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France
| | - Thomas Balenghien
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Claire Garros
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Emmanuel Albina
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Centre for Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Paris, France.,École nationale vétérinaire d'Alfort, Maisons-Alfort, France
| | - Serafin Gutierrez
- ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.,Cirad, UMR ASTRE, Montpellier, F-34398, France
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29
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Nakamichi K, Shen JZ, Lee CS, Lee A, Roberts EA, Simonson PD, Roychoudhury P, Andriesen J, Randhawa AK, Mathias PC, Greninger AL, Jerome KR, Van Gelder RN. Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19. Sci Rep 2021; 11:4802. [PMID: 33637820 PMCID: PMC7910290 DOI: 10.1038/s41598-021-82850-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The COVID-19 epidemic of 2019-20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Whole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline clinical characteristics of patients and their outcome data including their hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Full length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 infections was observed (p = 0.06, Fisher's exact). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction. In summary, SARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.
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Affiliation(s)
- Kenji Nakamichi
- Department of Ophthalmology, University of Washington School of Medicine, 325 9th Avenue, Campus Box 359608, Seattle, WA, 98104, USA
| | - Jolie Z Shen
- University of Washington School of Medicine, Seattle, WA, USA
| | - Cecilia S Lee
- Department of Ophthalmology, University of Washington School of Medicine, 325 9th Avenue, Campus Box 359608, Seattle, WA, 98104, USA
| | - Aaron Lee
- Department of Ophthalmology, University of Washington School of Medicine, 325 9th Avenue, Campus Box 359608, Seattle, WA, 98104, USA
| | - Emma A Roberts
- University of Washington School of Medicine, Seattle, WA, USA
| | - Paul D Simonson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jessica Andriesen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - April K Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick C Mathias
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alex L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Russell N Van Gelder
- Department of Ophthalmology, University of Washington School of Medicine, 325 9th Avenue, Campus Box 359608, Seattle, WA, 98104, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Biological Structure, University of Washington, Seattle, WA, USA.
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30
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Hababou Y, Taleb A, Recoing A, Moreau F, Simon I, Muller de Schongor F, Gault E, Rameix-Welti MA. Molecular investigation of a RSV outbreak in a geriatric hospital. BMC Geriatr 2021; 21:120. [PMID: 33579210 PMCID: PMC7880219 DOI: 10.1186/s12877-021-02064-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acquired infections in hospitalized elderly people are a growing concern. In long-term care facilities with multiple staff and visitor contacts, virus outbreaks are a common challenge for infection prevention teams. Although several studies have reported nosocomial RSV outbreaks in long term care facilities, molecular epidemiology data are scarce. METHODS RSV RNA was detected in respiratory samples from 19 patients in a long-term care hospital for elderly in Paris in March 2019 over a 3 weeks period. Genotyping was performed using nucleotide sequencing. Sociodemographic and clinical characteristics of cases part of a unique cluster, were retrospectively reviewed. RESULTS Molecular investigation of theses RSV cases, revealed a unique cluster of 12 nosocomial cases in 2 adjacent wards. Mean age of these outbreak's cases was 89. All patients had underlying medical conditions. Seven exhibited lower respiratory symptoms and three experienced decompensation of underlying chronic heart condition. Two patients died. CONCLUSIONS This case report highlights the importance of RSV in causing substantial disease in elderly in case of nosocomial outbreak and the contributions of molecular epidemiology in investigation and management of such outbreak.
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Affiliation(s)
- Yohan Hababou
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | - Assia Taleb
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | - Amélie Recoing
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | - Frédérique Moreau
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | - Isabelle Simon
- AP-HP, Université Paris Saclay, Hôpital Sainte Perrine, Equipe opérationnelle d'hygiène, Paris, France
| | | | - Elyanne Gault
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France.,Université Paris-Saclay, INSERM, Université de Versailles St. Quentin, UMR 1173 (2I), Versailles, France
| | - Marie-Anne Rameix-Welti
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France. .,Université Paris-Saclay, INSERM, Université de Versailles St. Quentin, UMR 1173 (2I), Versailles, France.
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31
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Fang X, Cai Y, Mei J, Huang Z, Zhang C, Yang B, Li W, Zhang W. Optimizing culture methods according to preoperative mNGS results can improve joint infection diagnosis. Bone Joint J 2021; 103-B:39-45. [PMID: 33380187 DOI: 10.1302/0301-620x.103b1.bjj-2020-0771.r2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AIMS Metagenomic next-generation sequencing (mNGS) is useful in the diagnosis of infectious disease. However, while it is highly sensitive at identifying bacteria, it does not provide information on the sensitivity of the organisms to antibiotics. The purpose of this study was to determine whether the results of mNGS can be used to guide optimization of culture methods to improve the sensitivity of culture from intraoperative samples. METHODS Between July 2014 and October 2019, patients with suspected joint infection (JI) from whom synovial fluid (SF) was obtained preoperatively were enrolled. Preoperative aspirated SF was analyzed by conventional microbial culture and mNGS. In addition to samples taken for conventional microbial culture, some samples were taken for intraoperative culture to optimize the culture method according to the preoperative mNGS results. The demographic characteristics, medical history, laboratory examination, mNGS, and culture results of the patients were recorded, and the possibility of the optimized culture methods improving diagnostic efficiency was evaluated. RESULTS A total of 56 cases were included in this study. There were 35 cases of JI and 21 cases of non-joint infection (NJI). The sensitivity, specificity, and accuracy of intraoperative microbial culture after optimization of the culture method were 94.29%, 76.19%, and 87.5%, respectively, while those of the conventional microbial culture method were 60%, 80.95%, and 67.86%, respectively. CONCLUSION Preoperative aspirated SF detected via mNGS can provide more aetiological information than preoperative culture, which can guide the optimization and improve the sensitivity of intraoperative culture. Cite this article: Bone Joint J 2021;103-B(1):39-45.
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Affiliation(s)
- Xinyu Fang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yuanqing Cai
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jian Mei
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Chaofan Zhang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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32
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Lin A, Cheng B, Han X, Zhang H, Liu X, Liu X. Value of next-generation sequencing in early diagnosis of patients with tuberculous meningitis. J Neurol Sci 2021; 422:117310. [PMID: 33631643 DOI: 10.1016/j.jns.2021.117310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 11/18/2022]
Abstract
OBJECTIVES To assess the value of next-generation sequencing (NGS) technology in early diagnosis of patients with tuberculous meningitis (TBM). METHODS 56 patients with clinically suspected TBM who came to Shandong Provincial Chest Hospital from February 2, 2018 to August 2, 2018 were prospectively included, and the clinical diagnosis and treatment outcomes were followed up. NGS was performed for the cerebrospinal fluid specimens submitted for test on the BGISEQ-100 platform of Tianjin Huada Gene Research Institute and the obtained pathogen sequences were compared with the pathogen data to get the final results. The NGS results were positive for detecting the unique matching sequence of the Mycobacterium tuberculosis (MTB) complex and negative for no unique matching sequence. Patients confirmed with TBM should have at least one of the following four items: cerebrospinal fluid MTB culture positive, smear positive, Xpert MTB/RIF test positive, or MTB nucleic acid polymerase chain reaction (PCR) test positive; clinically diagnosed patients were those with clinically suspected TBM and effective anti-tuberculosis treatment; non-TBM patients were those with other pathogenic basis or clinical exclusion of TBM. The sensitivity and specificity of NGS in early diagnosis of TBM were analyzed. RESULTS 22 patients were confirmed with TBM, of which 13 were positive for Xpert MTB/RIF test, 6 were positive for cerebrospinal fluid MTB culture, 5 were positive for MTB nucleic acid PCR test, 12 patients were clinically diagnosed with TBM, and there were 16 cases of non-TBM patients. Among confirmed and clinically diagnosed patients, 20 cases of MTB complex were detected by NGS technology, with a sensitivity of 58.8% (20/34) and specificity of 100% (16/16). Among confirmed patients, the sensitivity of NGS was 63.6% (14/22). Of the 50 specimens that were simultaneously subjected to traditional methods, Xpert MTB/RIF test and NGS, the specificity of the three methods was 100% (16/16) based on clinical diagnosis, and the sensitivity was 29.4% (10/34), 38.2% (13/34), and 58.8% (20/34) respectively. The difference of sensitivity between the first two detection methods and NGS was statistically significant (McNemar test, p = 0.013, x2 = 5.786 and p = 0.065, x2 = 3.273). The sensitivity of traditional methods combined with NGS was as high as 82.4% (28/34). CONCLUSIONS NGS technology could rapidly detect the MTB complex in cerebrospinal fluid with significant sensitivity and specificity, which could be used as an early diagnosis index of TBM. NGS combined with MTB culture could increase the detection rate.
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Affiliation(s)
- Aiqing Lin
- Department of Senile Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Department of Respiratory and Critical Care Medicine, Shandong Provincial Chest Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250013, China
| | - Baotao Cheng
- Quality Control Department, Shandong Provincial Chest Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250013, China
| | - Xiaochun Han
- College of Health Sciences, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Hong Zhang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Chest Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250013, China
| | - Xiaoli Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Chest Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250013, China
| | - Xueping Liu
- Department of Senile Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.
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33
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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34
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Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Cryptic transmission of SARS-CoV-2 in Washington state. Science 2020; 370:571-575. [PMID: 32913002 PMCID: PMC7810035 DOI: 10.1126/science.abc0523] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/08/2020] [Indexed: 01/08/2023]
Abstract
After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.
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Affiliation(s)
- Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Arun Nalla
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Gregory Pepper
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Adam Reinhardt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Truong N Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Amanda Adler
- Division of Infectious Disease, Seattle Children's Hospital, Seattle, WA, USA
| | - Elisabeth Brandstetter
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Shari Cho
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Danielle Giroux
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Peter D Han
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chris D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kirsten Lacombe
- Division of Infectious Disease, Seattle Children's Hospital, Seattle, WA, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anahita Kiavand
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Matthew Richardson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Melissa Truong
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Caitlin R Wolf
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Janet A Englund
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Division of Infectious Disease, Seattle Children's Hospital, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Louise H Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nicola F Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey S Duchin
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
- Public Health - Seattle & King County, Seattle, WA, USA
| | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA, USA
| | | | - Krista Queen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ying Tao
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anna Uehara
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suxiang Tong
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Duncan MacCannell
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gregory L Armstrong
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Geoffrey S Baird
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Helen Y Chu
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
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35
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Outlaw VK, Bovier FT, Mears MC, Cajimat MN, Zhu Y, Lin MJ, Addetia A, Lieberman NAP, Peddu V, Xie X, Shi PY, Greninger AL, Gellman SH, Bente DA, Moscona A, Porotto M. Inhibition of Coronavirus Entry In Vitro and Ex Vivo by a Lipid-Conjugated Peptide Derived from the SARS-CoV-2 Spike Glycoprotein HRC Domain. mBio 2020; 11:e01935-20. [PMID: 33082259 PMCID: PMC7587434 DOI: 10.1128/mbio.01935-20] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), the etiological agent of the 2019 coronavirus disease (COVID-19), has erupted into a global pandemic that has led to tens of millions of infections and hundreds of thousands of deaths worldwide. The development of therapeutics to treat infection or as prophylactics to halt viral transmission and spread is urgently needed. SARS-CoV-2 relies on structural rearrangements within a spike (S) glycoprotein to mediate fusion of the viral and host cell membranes. Here, we describe the development of a lipopeptide that is derived from the C-terminal heptad repeat (HRC) domain of SARS-CoV-2 S that potently inhibits infection by SARS-CoV-2. The lipopeptide inhibits cell-cell fusion mediated by SARS-CoV-2 S and blocks infection by live SARS-CoV-2 in Vero E6 cell monolayers more effectively than previously described lipopeptides. The SARS-CoV-2 lipopeptide exhibits broad-spectrum activity by inhibiting cell-cell fusion mediated by SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV) and blocking infection by live MERS-CoV in cell monolayers. We also show that the SARS-CoV-2 HRC-derived lipopeptide potently blocks the spread of SARS-CoV-2 in human airway epithelial (HAE) cultures, an ex vivo model designed to mimic respiratory viral propagation in humans. While viral spread of SARS-CoV-2 infection was widespread in untreated airways, those treated with SARS-CoV-2 HRC lipopeptide showed no detectable evidence of viral spread. These data provide a framework for the development of peptide therapeutics for the treatment of or prophylaxis against SARS-CoV-2 as well as other coronaviruses.IMPORTANCE SARS-CoV-2, the causative agent of COVID-19, continues to spread globally, placing strain on health care systems and resulting in rapidly increasing numbers of cases and mortalities. Despite the growing need for medical intervention, no FDA-approved vaccines are yet available, and treatment has been limited to supportive therapy for the alleviation of symptoms. Entry inhibitors could fill the important role of preventing initial infection and preventing spread. Here, we describe the design, synthesis, and evaluation of a lipopeptide that is derived from the HRC domain of the SARS-CoV-2 S glycoprotein that potently inhibits fusion mediated by SARS-CoV-2 S glycoprotein and blocks infection by live SARS-CoV-2 in both cell monolayers (in vitro) and human airway tissues (ex vivo). Our results highlight the SARS-CoV-2 HRC-derived lipopeptide as a promising therapeutic candidate for SARS-CoV-2 infections.
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Affiliation(s)
- Victor K Outlaw
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Francesca T Bovier
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
- Center for Host-Pathogen Interaction, Columbia University Medical Center, New York, New York, USA
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli," Caserta, Italy
| | - Megan C Mears
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Maria N Cajimat
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Yun Zhu
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
- Center for Host-Pathogen Interaction, Columbia University Medical Center, New York, New York, USA
- Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Michelle J Lin
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Amin Addetia
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Vikas Peddu
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Xuping Xie
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Pei-Yong Shi
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Dennis A Bente
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Anne Moscona
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
- Center for Host-Pathogen Interaction, Columbia University Medical Center, New York, New York, USA
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York, USA
- Department of Physiology & Cellular Biophysics, Columbia University Medical Center, New York, New York, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
- Center for Host-Pathogen Interaction, Columbia University Medical Center, New York, New York, USA
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli," Caserta, Italy
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36
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Bharucha T, Oeser C, Balloux F, Brown JR, Carbo EC, Charlett A, Chiu CY, Claas ECJ, de Goffau MC, de Vries JJC, Eloit M, Hopkins S, Huggett JF, MacCannell D, Morfopoulou S, Nath A, O'Sullivan DM, Reoma LB, Shaw LP, Sidorov I, Simner PJ, Van Tan L, Thomson EC, van Dorp L, Wilson MR, Breuer J, Field N. STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies. THE LANCET. INFECTIOUS DISEASES 2020; 20:e251-e260. [PMID: 32768390 PMCID: PMC7406238 DOI: 10.1016/s1473-3099(20)30199-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.
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Affiliation(s)
- Tehmina Bharucha
- Department of Biochemistry, University of Oxford, Oxford, UK; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
| | - Clarissa Oeser
- Centre for Molecular Epidemiology and Translational Research, University College London, London, UK
| | | | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children, London, UK
| | - Ellen C Carbo
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Andre Charlett
- Statistics, Modelling and Economics Department, Public Health England, London, UK
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Marcus C de Goffau
- Wellcome Sanger Institute, Hinxton, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
| | - Susan Hopkins
- Healthcare-Associated Infection and Antimicrobial Resistance, Public Health England, London, UK; Infectious Diseases Unit, Royal Free Hospital, London, UK
| | - Jim F Huggett
- National Measurement Laboratory, LGC, Teddington, UK; School of Biosciences & Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - Duncan MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, UK
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institutes of Health, Bethesda, MD, USA
| | | | - Lauren B Reoma
- Section of Infections of the Nervous System, National Institutes of Health, Bethesda, MD, USA
| | - Liam P Shaw
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Igor Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Le Van Tan
- Emerging Infections Group, Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Michael R Wilson
- Weill Institute for Neurosciences and Department of Neurology, University of California, San Francisco, CA, USA
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK; Great Ormond Street Hospital for Children, London, UK
| | - Nigel Field
- Centre for Molecular Epidemiology and Translational Research, University College London, London, UK
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Cox RM, Sourimant J, Toots M, Yoon JJ, Ikegame S, Govindarajan M, Watkinson RE, Thibault P, Makhsous N, Lin MJ, Marengo JR, Sticher Z, Kolykhalov AA, Natchus MG, Greninger AL, Lee B, Plemper RK. Orally efficacious broad-spectrum allosteric inhibitor of paramyxovirus polymerase. Nat Microbiol 2020; 5:1232-1246. [PMID: 32661315 PMCID: PMC7529989 DOI: 10.1038/s41564-020-0752-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/09/2020] [Indexed: 12/13/2022]
Abstract
Paramyxoviruses such as human parainfluenza virus type-3 (HPIV3) and measles virus (MeV) are a substantial health threat. In a high-throughput screen for inhibitors of HPIV3 (a major cause of acute respiratory infection), we identified GHP-88309-a non-nucleoside inhibitor of viral polymerase activity that possesses unusual broad-spectrum activity against diverse paramyxoviruses including respiroviruses (that is, HPIV1 and HPIV3) and morbilliviruses (that is, MeV). Resistance profiles of distinct target viruses overlapped spatially, revealing a conserved binding site in the central cavity of the viral polymerase (L) protein that was validated by photoaffinity labelling-based target mapping. Mechanistic characterization through viral RNA profiling and in vitro MeV polymerase assays identified a block in the initiation phase of the viral polymerase. GHP-88309 showed nanomolar potency against HPIV3 isolates in well-differentiated human airway organoid cultures, was well tolerated (selectivity index > 7,111) and orally bioavailable, and provided complete protection against lethal infection in a Sendai virus mouse surrogate model of human HPIV3 disease when administered therapeutically 48 h after infection. Recoverees had acquired robust immunoprotection against reinfection, and viral resistance coincided with severe attenuation. This study provides proof of the feasibility of a well-behaved broad-spectrum allosteric antiviral and describes a chemotype with high therapeutic potential that addresses major obstacles of anti-paramyxovirus drug development.
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Affiliation(s)
- Robert M Cox
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Julien Sourimant
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Mart Toots
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Jeong-Joong Yoon
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Satoshi Ikegame
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ruth E Watkinson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patricia Thibault
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Negar Makhsous
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Michelle J Lin
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Jose R Marengo
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | - Zachary Sticher
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | | | - Michael G Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | - Alexander L Greninger
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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38
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Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Llcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.09.30.20204230. [PMID: 33024981 PMCID: PMC7536883 DOI: 10.1101/2020.09.30.20204230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.
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Affiliation(s)
| | - Cassia Wagner
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | - Pavitra Roychoudhury
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Jover Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | - Erica Ryke
- University of Washington, Seattle, WA, USA
| | - Hong Xie
- University of Washington, Seattle, WA, USA
| | | | | | - Victoria M Rachleff
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | | | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Kairsten Fay
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Misja Llcisin
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | | | - Michael Boeckh
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Janet A Englund
- University of Washington, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Barry R Lutz
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Jeffrey S Duchin
- University of Washington, Seattle, WA, USA
- Public Health - Seattle & King County, Seattle, WA, USA
| | - Lea M Starita
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Helen Y Chu
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Jay Shendure
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Keith R Jerome
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | - Alexander L Greninger
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Deborah A Nickerson
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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39
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Nakamichi K, Shen JZ, Lee CS, Lee AY, Roberts EA, Simonson PD, Roychoudhury P, Andriesen JG, Randhawa AK, Mathias PC, Greninger A, Jerome KR, Van Gelder RN. Outcomes associated with SARS-CoV-2 viral clades in COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.09.24.20201228. [PMID: 32995827 PMCID: PMC7523168 DOI: 10.1101/2020.09.24.20201228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Background The COVID-19 epidemic of 2019-20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Methods Whole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline medical data along with outcomes of hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Findings Full length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 was observed (p=0.06). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction. Conclusion SARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.
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40
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Lieberman NAP, Peddu V, Xie H, Shrestha L, Huang ML, Mears MC, Cajimat MN, Bente DA, Shi PY, Bovier F, Roychoudhury P, Jerome KR, Moscona A, Porotto M, Greninger AL. In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age. PLoS Biol 2020; 18:e3000849. [PMID: 32898168 PMCID: PMC7478592 DOI: 10.1371/journal.pbio.3000849] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/05/2020] [Indexed: 01/12/2023] Open
Abstract
Despite limited genomic diversity, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown a wide range of clinical manifestations in different patient populations. The mechanisms behind these host differences are still unclear. Here, we examined host response gene expression across infection status, viral load, age, and sex among shotgun RNA sequencing profiles of nasopharyngeal (NP) swabs from 430 individuals with PCR-confirmed SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong antiviral response with up-regulation of antiviral factors such as OAS1-3 and IFIT1-3 and T helper type 1 (Th1) chemokines CXCL9/10/11, as well as a reduction in transcription of ribosomal proteins. SARS-CoV-2 culture in human airway epithelial (HAE) cultures replicated the in vivo antiviral host response 7 days post infection, with no induction of interferon-stimulated genes after 3 days. Patient-matched longitudinal specimens (mean elapsed time = 6.3 days) demonstrated reduction in interferon-induced transcription, recovery of transcription of ribosomal proteins, and initiation of wound healing and humoral immune responses. Expression of interferon-responsive genes, including ACE2, increased as a function of viral load, while transcripts for B cell-specific proteins and neutrophil chemokines were elevated in patients with lower viral load. Older individuals had reduced expression of the Th1 chemokines CXCL9/10/11 and their cognate receptor CXCR3, as well as CD8A and granzyme B, suggesting deficiencies in trafficking and/or function of cytotoxic T cells and natural killer (NK) cells. Relative to females, males had reduced B cell-specific and NK cell-specific transcripts and an increase in inhibitors of nuclear factor kappa-B (NF-κB) signaling, possibly inappropriately throttling antiviral responses. Collectively, our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Vikas Peddu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Megan C. Mears
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Maria N. Cajimat
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dennis A. Bente
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Pei-Yong Shi
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Francesca Bovier
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Anne Moscona
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics, Columbia University Medical Center, New York, New York, United States of America
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York, United States of America
- Department of Physiology & Cellular Biophysics, Columbia University Medical Center, New York, New York, United States of America
| | - Matteo Porotto
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics, Columbia University Medical Center, New York, New York, United States of America
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” Caserta, Italy
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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41
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Casto AM, Adler AL, Makhsous N, Crawford K, Qin X, Kuypers JM, Huang ML, Zerr DM, Greninger AL. Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters. Clin Infect Dis 2020; 69:941-948. [PMID: 30576430 PMCID: PMC6735836 DOI: 10.1093/cid/ciy1020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between ongoing in-hospital transmission of the virus and new introductions from the community, and it is challenging to understand the long-term impacts of outbreak-associated viruses within medical systems using traditional epidemiological approaches alone. METHODS Real-time metagenomic sequencing during an ongoing norovirus outbreak associated with a retrospective cohort study. RESULTS We describe a hospital-associated norovirus outbreak that affected 13 patients over a 27-day period in a large, tertiary, pediatric hospital. The outbreak was chronologically associated with a spike in self-reported gastrointestinal symptoms among staff. Real-time metagenomic next-generation sequencing (mNGS) of norovirus genomes demonstrated that 10 chronologically overlapping, hospital-acquired norovirus cases were partitioned into 3 discrete transmission clusters. Sequencing data also revealed close genetic relationships between some hospital-acquired and some community-acquired cases. Finally, this data was used to demonstrate chronic viral shedding by an immunocompromised, hospital-acquired case patient. An analysis of serial samples from this patient provided novel insights into the evolution of norovirus within an immunocompromised host. CONCLUSIONS This study documents one of the first applications of real-time mNGS during a hospital-associated viral outbreak. Given its demonstrated ability to detect transmission patterns within outbreaks and elucidate the long-term impacts of outbreak-associated viral strains on patients and medical systems, mNGS constitutes a powerful resource to help infection control teams understand, prevent, and respond to viral outbreaks.
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Affiliation(s)
- Amanda M Casto
- Department of Medicine, University of Washington, Seattle
| | - Amanda L Adler
- Seattle Children's Hospital, University of Washington, Seattle
| | - Negar Makhsous
- Department of Laboratory Medicine, University of Washington, Seattle
| | | | - Xuan Qin
- Department of Medicine, University of Washington, Seattle
| | - Jane M Kuypers
- Department of Laboratory Medicine, University of Washington, Seattle
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle
| | - Danielle M Zerr
- Seattle Children's Hospital, University of Washington, Seattle.,Department of Pediatrics, University of Washington, Seattle
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42
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Zhang C, Wang C, Chen F, Huang Z, Fang X, Li W, Yang B, Zhang W. Metagenomic Next-Generation Sequencing Technique Helps Identify Cryptococcal Infection in the Rib: A Report of 2 Cases and Review of the Literature. JBJS Case Connect 2020; 9:e0367. [PMID: 31821204 DOI: 10.2106/jbjs.cc.19.00367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CASE Two patients presented with pathological lytic bone lesions in the rib and associated soft tissue mass believed initially to represent soft tissue neoplasm. However, further consideration of infectious etiologies led to the identification of cryptococcal osteomyelitis. In one case, the microbiological culture was negative, but Cryptococcus neoformans was identified with the help of the metagenomic next-generation sequencing (mNGS) technique. Both patients received oral fluconazole-only treatment, and the infections were successfully eradicated. CONCLUSIONS The mNGS technique helps identify cryptococcal infection in the rib.
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Affiliation(s)
- Chaofan Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Chaoxin Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Fei Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Zida Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Xinyu Fang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Wenbo Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
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43
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Peddu V, Shean RC, Xie H, Shrestha L, Perchetti GA, Minot SS, Roychoudhury P, Huang ML, Nalla A, Reddy SB, Phung Q, Reinhardt A, Jerome KR, Greninger AL. Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization. Clin Chem 2020; 66:966-972. [PMID: 32379863 PMCID: PMC7239240 DOI: 10.1093/clinchem/hvaa106] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 04/23/2020] [Indexed: 11/12/2022]
Abstract
BACKGROUND More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is still not widely available. Metagenomic sequencing offers the promise of unbiased detection of emerging pathogens, without requiring prior knowledge of the identity of the responsible agent or its genomic sequence. METHODS To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, WA were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2. RESULTS Within 36 h our results showed clear identification of a novel human Betacoronavirus, closely related to known Betacoronaviruses of bats, in laboratory-proven cases of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Samples negative for SARS-CoV-2 by RT-PCR were also negative by metagenomic analysis, and positive for Rhinovirus A and C. Unlike targeted SARS-CoV-2 qRT-PCR testing, metagenomic analysis of these SARS-CoV-2 negative samples identified candidate etiological agents for the patients' respiratory symptoms. CONCLUSION Taken together, these results demonstrate the value of metagenomic analysis in the monitoring and response to this and future viral pandemics.
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Affiliation(s)
- Vikas Peddu
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Ryan C Shean
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Lasata Shrestha
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | | | - Samuel S Minot
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Arun Nalla
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Shriya B Reddy
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Quynh Phung
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Adam Reinhardt
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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Liu B, Shao N, Wang J, Zhou S, Su H, Dong J, Sun L, Li L, Zhang T, Yang F. An Optimized Metagenomic Approach for Virome Detection of Clinical Pharyngeal Samples With Respiratory Infection. Front Microbiol 2020; 11:1552. [PMID: 32754134 PMCID: PMC7366072 DOI: 10.3389/fmicb.2020.01552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/16/2020] [Indexed: 12/23/2022] Open
Abstract
Respiratory virus infections are one of the major causes of acute respiratory disease or exacerbation of chronic obstructive pulmonary disease (COPD). However, next-generation sequencing has not been used for routine viral detection in clinical respiratory samples owing to its sophisticated technology. Here, several pharyngeal samples with COPD were collected to enrich viral particles using an optimized method (M3), which involved M1 with centrifugation, filtration, and concentration, M2 (magnetic beads) combined with mixed nuclease digestion, and M4 with no pretreatment as a control. Metagenomic sequencing and bioinformatics analyses showed that the M3 method for viral enrichment was superior in both viral sequencing composition and viral taxa when compared to M1, M2, and M4. M3 acquired the most viral reads and more complete sequences within 15-h performance, indicating that it might be feasible for viral detection in multiple respiratory samples in clinical practice. Based on sequence similarity analysis, 12 human viruses, including nine Anelloviruses and three coronaviruses, were characterized. Coronavirus OC43 with the largest number of viral reads accounted for nearly complete (99.8%) genome sequences, indicating that it may be a major viral pathogen involved in exacerbation of COPD.
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Affiliation(s)
- Bo Liu
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Shao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Wang
- Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - SiYu Zhou
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - HaoXiang Su
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - LiLian Sun
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Li
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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45
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Addetia A, Xie H, Roychoudhury P, Shrestha L, Loprieno M, Huang ML, Jerome KR, Greninger AL. Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates. J Clin Virol 2020; 129:104523. [PMID: 32623351 PMCID: PMC7309833 DOI: 10.1016/j.jcv.2020.104523] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 01/26/2023]
Affiliation(s)
- Amin Addetia
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | - Lasata Shrestha
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Michelle Loprieno
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
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46
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Lieberman NAP, Peddu V, Xie H, Shrestha L, Huang ML, Mears MC, Cajimat MN, Bente DA, Shi PY, Bovier F, Roychoudhury P, Jerome KR, Moscona A, Porotto M, Greninger AL. In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.22.165225. [PMID: 32607510 PMCID: PMC7325176 DOI: 10.1101/2020.06.22.165225] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Despite limited genomic diversity, SARS-CoV-2 has shown a wide range of clinical manifestations in different patient populations. The mechanisms behind these host differences are still unclear. Here, we examined host response gene expression across infection status, viral load, age, and sex among shotgun RNA-sequencing profiles of nasopharyngeal swabs from 430 individuals with PCR-confirmed SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong antiviral response with upregulation of antiviral factors such as OAS1-3 and IFIT1-3 , and Th1 chemokines CXCL9/10/11 , as well as a reduction in transcription of ribosomal proteins. SARS-CoV-2 culture in human airway epithelial cultures replicated the in vivo antiviral host response. Patient-matched longitudinal specimens (mean elapsed time = 6.3 days) demonstrated reduction in interferon-induced transcription, recovery of transcription of ribosomal proteins, and initiation of wound healing and humoral immune responses. Expression of interferon-responsive genes, including ACE2 , increased as a function of viral load, while transcripts for B cell-specific proteins and neutrophil chemokines were elevated in patients with lower viral load. Older individuals had reduced expression of Th1 chemokines CXCL9/10/11 and their cognate receptor, CXCR3 , as well as CD8A and granzyme B, suggesting deficiencies in trafficking and/or function of cytotoxic T cells and natural killer (NK) cells. Relative to females, males had reduced B and NK cell-specific transcripts and an increase in inhibitors of NF-κB signaling, possibly inappropriately throttling antiviral responses. Collectively, our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.
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47
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Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin J, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Cryptic transmission of SARS-CoV-2 in Washington State. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.04.02.20051417. [PMID: 32511596 PMCID: PMC7276023 DOI: 10.1101/2020.04.02.20051417] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding.
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Affiliation(s)
- Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Alexander L Greninger
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Pavitra Roychoudhury
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | | | | | - Arun Nalla
- University of Washington, Seattle, WA USA
| | | | | | - Hong Xie
- University of Washington, Seattle, WA USA
| | | | | | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA USA
| | | | - Shari Cho
- University of Washington, Seattle, WA USA
| | | | | | - Kairsten Fay
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | | | - Misja Ilcisin
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | | | - Jover Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | | | | | | | | | | | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Janet A Englund
- University of Washington, Seattle, WA USA
- Seattle Children's Research Institute, Seattle, WA USA
| | | | - Emma B Hodcroft
- University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - John Huddleston
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | | | | | - Richard A Neher
- University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Xianding Deng
- University of California San Francisco, San Francisco, CA USA
| | - Wei Gu
- University of California San Francisco, San Francisco, CA USA
| | - Scot Federman
- University of California San Francisco, San Francisco, CA USA
| | - Charles Chiu
- University of California San Francisco, San Francisco, CA USA
| | - Jeff Duchin
- University of Washington, Seattle, WA USA
- Public Health - Seattle & King County, Seattle, WA USA
| | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA USA
| | | | - Krista Queen
- Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Ying Tao
- Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Anna Uehara
- Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Suxiang Tong
- Centers for Disease Control and Prevention, Atlanta, GA USA
| | | | | | | | - Helen Y Chu
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
- Howard Hughes Medical Institute, Seattle, WA USA
| | - Keith R Jerome
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- University of Washington, Seattle, WA USA
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48
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Pathogenic characteristics of nosocomial infections in patients with cerebrovascular diseases and characteristics and treatment of pathogenic bacteria in different seasons. J Infect Public Health 2019; 13:800-805. [PMID: 31831394 DOI: 10.1016/j.jiph.2019.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/14/2019] [Accepted: 11/24/2019] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE The objective of this study is to explore the bacterial distribution characteristics of air and bed environment in patients with cerebrovascular diseases and to analyze the relationship between bacterial distribution and nosocomial infection in patients with cerebrovascular diseases. METHODS In this study, the inpatients with cerebrovascular diseases who suffer from nosocomial infection are taken as the research objects. The pathogenic characteristics of the air environment in the ward and the environment in the bed unit are monitored, and the samples of cerebrovascular patients are collected for identification and drug sensitivity detection. The changes of the number of pathogens in different seasons are statistically compared, and the drug sensitivity test results of various pathogens are analyzed. RESULTS In large wards, the number of pathogens in the air environment in winter is significantly higher than that in spring. In summer, the number of pathogens in pillow environment is significantly more than that in small wards. Gram-negative bacilli are the main pathogens in the four seasons, followed by Gram-positive cocci and less fungal infections. Among them, Staphylococcus aureus is the main Gram-positive coccus, which is sensitive to vancomycin and other therapeutic drugs, and resistant to erythromycin and other therapeutic drugs. Gram-negative bacteria are mainly Klebsiella pneumoniae and Pseudomonas aeruginosa. K. pneumoniae is sensitive to imipenem, tekacillin, meropenem and ceftitam, and resistant to ampicillin. P. aeruginosa is sensitive to cefuroxime ester, cefazolin and cefuroxime sodium. It is resistant to ampicillin, ceftitam, compound sinomine and ampicillin plus sulbactam. Candida albicans is the main fungus, which is sensitive to ketoconazole, fluconazole, amphotericin and nystatin. CONCLUSION The number of pathogenic bacteria in the ward environment of patients with cerebrovascular disease is affected by the size of the room and season. The main pathogenic bacteria are Gram-negative bacilli, followed by Gram-positive cocci and less fungal infections.
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Zhang C, Fang X, Huang Z, Li W, Zhang CF, Yang B, Zhang W. Value of mNGS in sonication fluid for the diagnosis of periprosthetic joint infection. ARTHROPLASTY 2019; 1:9. [PMID: 35240758 PMCID: PMC8796449 DOI: 10.1186/s42836-019-0006-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/09/2019] [Indexed: 12/24/2022] Open
Abstract
Objective To evaluate the effectiveness of metagenomics next-generation sequencing (mNGS) for the detection of pathogenic microorganisms in periprosthetic joint infection (PJI) using the sonication fluid from removed prosthesis. Methods In this prospective diagnostic cohort study, 44 patients who underwent revision arthroplasty in our hospital from December 2016 to December 2018 were screened. Seven cases were excluded due to incomplete clinical data, insufficient synovial fluid or failure of sequencing. According to the PJI diagnostic criteria recommended by the Musculoskeletal Infection Society (MSIS), the patients were defined as PJI or aseptic failure (AF). Conventional culture, sonication fluid culture and mNGS were performed, in order to assess the value of mNGS using sonication fluid for the diagnosis of PJI, and the mNGS results were analyzed and compared with the conventional and sonication fluid culture. Results Among the 37 patients, 24 were diagnosed with PJI (64.86%), while 13 were diagnosed with aseptic failure. Among the 24 patients diagnosed with PJI, 15 cases (62.5%), 17 cases (70.8%) and 24 cases (100%) yielded positive results in conventional culture, sonication fluid culture and mNGS, respectively. In addition, mNGS detected the same pathogenic microorganisms in 16 out of the 17 (94.12%) culture-positive (conventional + sonication fluid) PJI cases. In the only one discrepancy case, Enterococcus faecalis was identified in the cultures, while Enterobacter cloacae was detected by mNGS. In the AF group, the results of the conventional culture were all negative. Nevertheless, Staphylococcus epidermidis was detected in the sonication fluid culture and mNGS in one case. The diagnostic sensitivity of mNGS for PJI was 100%, which was significantly higher than 70.83% (P = 0.039) of the sonication fluid culture and 62.5% (P = 0.021) of the conventional culture. The diagnostic specificity of mNGS for PJI was 92.31%, which was not significantly different (P > 0.05) from those of the conventional culture (100%) and sonication fluid culture (92.31%). Conclusion We demonstrated that mNGS using sonication fluid can improve the detection rate of pathogenic microorganisms and provide valuable information for the diagnosis of PJI. In addition, mNGS can effectively identify pathogenic microorganisms in culture-negative PJIs cases, especially for the cases who have been treated with antibiotics before sample acquisition or have fastidious microorganisms. Therefore, this method can potentially help to guide the clinical use of antibiotics.
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50
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Ciccozzi M, Lai A, Zehender G, Borsetti A, Cella E, Ciotti M, Sagnelli E, Sagnelli C, Angeletti S. The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review. J Med Virol 2019; 91:1707-1724. [PMID: 31243773 DOI: 10.1002/jmv.25526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022]
Abstract
In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
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Affiliation(s)
- Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Roma, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
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