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Jiao C, Liang X, Wu X, Shang Y, Wu Y, Zhang F, Liu X, Zeng J, Yang C. SERS Platform for Integrated Enrichment, Isolation, and Identification of Multiple Respiratory Viruses in a Single Assay Using 3D Stereoscopic SERS Tags and Flocked Swabs. Anal Chem 2024. [PMID: 39092994 DOI: 10.1021/acs.analchem.4c01243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Influenza (flu) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibit similar clinical symptoms, complicating the diagnosis and clinical management of these critical respiratory infections. Thus, there is an urgent need for rapid on-site detection technologies that can simultaneously detect SARS-CoV-2 and influenza A viruses. Here, we have developed the first platform that combines in situ sampling with immune swabs and multichannel surface-enhanced Raman spectroscopy (SERS) for simultaneous screening of these two respiratory viruses in a single assay. A seed-mediated growth method was used to assemble a number of silver spheres on the surface of Fe3O4@SiO2 spheres, which not only creates extensive Raman hotspots but also provides numerous sites for Raman signaling molecules, enhancing the sensing sensitivity. Integrating two specific Raman signaling molecules into the nanospheres allows for the parallel detection of both viruses, improving the efficiency of SERS signal read-out. Rapid quantitative screening of both SARS-CoV-2 and H1N1 is achievable within 15 min, with detection limits of 7.76, and 8.13 pg·mL-1 for their respective target proteins. The platform demonstrated excellent performance in testing and analyzing 98 clinical samples (SARS-CoV-2:50; influenza A:48), achieving sensitivities of 88.00, and 95.83% for SARS-CoV-2 and influenza A, respectively. Pearson's correlation analysis revealed a significant correlation with the clinical CT values (P < 0.0001), underscoring the great potential of this platform for the early, rapid, and simultaneous diagnostic discrimination of multiple pathogens.
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Affiliation(s)
- Chunpeng Jiao
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xinyi Liang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xian Wu
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Department of Clinical Laboratory, Peking University First Hospital, Beijing 100034, P. R. China
| | - Yanxue Shang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Yanfang Wu
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Fangdou Zhang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiangyi Liu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P. R. China
| | - Jingbin Zeng
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Chaoyong Yang
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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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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Pellegrinelli L, Galli C, Seiti A, Primache V, Hirvonen A, Schiarea S, Salmoiraghi G, Castiglioni S, Ammoni E, Cereda D, Binda S, Pariani E. Wastewater-based epidemiology revealed in advance the increase of enterovirus circulation during the Covid-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166539. [PMID: 37625729 DOI: 10.1016/j.scitotenv.2023.166539] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Wastewater-based epidemiology (WBE) was conducted to track Enteroviruses (EVs) circulation in the Milan metropolitan area (Northern Italy) during Covid-19 pandemic (March 2020-December 2022). 202 composite 24-hour wastewater samples (WWSs) were collected weekly from March 24, 2020, to December 29, 2022 at the inlet of two wastewater treatment plants (WWTP) in Milan (1.5 million inhabitants). EV-RNA was quantified and molecular characterization of non-polio EVs (NPEV) was performed by Sanger sequence analysis. Data from WWS were matched with virological data collected in the framework of Influenza-Like Illness (ILI) surveillance in the same place and time. EV-RNA was identified in 88.2 % of WWSs. The peak in EVs circulation was observed in late August 2020 (upon conclusion of the first national lockdown), in late August 2021, and in mid-April 2022. EV-RNA concentration in WWS (normalized as copies/d/1000 people) at peak of circulation presented a yearly increase (2020: 2.47 × 1010; 2021: 6.81 × 1010; 2022: 2.14 × 1011). This trend overlapped with trend in EV-positivity rate in ILI cases, expanded from 21.7 % in 2021 to 55.6 % in 2022. EV trends in WWS preceded clinical sample detections in 2021 and 2022 by eight and five weeks, respectively, acting as an early warning of outbreak. Although sequencing of EV-positive WWSs revealed the presence of multiple EV strains, typing remained inconclusive. Molecular characterization of EVs in clinical samples revealed the co-circulation of several genotypes: EV-A accounted for 60 % of EVs, EV-B for 16.7 %, EV-D68 for 23.3 %. EVs were circulating in Milan metropolitan area between March 2020 and December 2022. The epidemiological trends unfolded the progressive accumulation of EV transmission in the population after removal of Covid-19 restrictions. The increased circulation of EVs in 2021-2022 was identified at least 35 days in advance compared to the analysis of clinical data. The inconclusive results of Sanger sequencing lookout for improvement and innovative molecular approaches to deepen track EVs.
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Affiliation(s)
- Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Arlinda Seiti
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Valeria Primache
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Aurora Hirvonen
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Silvia Schiarea
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giulia Salmoiraghi
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Sara Castiglioni
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Emanuela Ammoni
- Directorate General for Health, Lombardy Region, Milan, Italy
| | - Danilo Cereda
- Directorate General for Health, Lombardy Region, Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
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Fall A, Han L, Yunker M, Gong YN, Li TJ, Norton JM, Abdullah O, Rothman RE, Fenstermacher KZJ, Morris CP, Pekosz A, Klein E, Mostafa HH. Evolution of Influenza A(H3N2) Viruses in 2 Consecutive Seasons of Genomic Surveillance, 2021-2023. Open Forum Infect Dis 2023; 10:ofad577. [PMID: 38088981 PMCID: PMC10715682 DOI: 10.1093/ofid/ofad577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Background The circulation and the genomic evolution of influenza A(H3N2) viruses during the 2021/2022 and 2022/2023 seasons were studied and associated with infection outcomes. Methods Remnant influenza A-positive samples following standard-of-care testing from patients across the Johns Hopkins Health System (JHHS) were used for the study. Samples were randomly selected for whole viral genome sequencing. The sequence-based pEpitope model was used to estimate the predicted vaccine efficacy (pVE) for circulating H3N2 viruses. Clinical data were collected and associated with viral genomic data. Results A total of 121 683 respiratory specimens were tested for influenza at JHHS between 1 September 2021 and 31 December 2022. Among them, 6071 (4.99%) tested positive for influenza A. Of these, 805 samples were randomly selected for sequencing, with hemagglutinin (HA) segments characterized for 610 samples. Among the characterized samples, 581 were H3N2 (95.2%). Phylogenetic analysis of HA segments revealed the exclusive circulation of H3N2 viruses with HA segments of the 3C.2a1b.2a.2 clade. Analysis of a total of 445 complete H3N2 genomes revealed reassortments; 200 of 227 of the 2022/2023 season genomes (88.1%) were found to have reassorted with clade 3C.2a1b.1a. The pVE was estimated to be -42.53% for the 2021/2022 season and 30.27% for the 2022/2023 season. No differences in clinical presentations or admissions were observed between the 2 seasons. Conclusions The increased numbers of cases and genomic diversity of influenza A(H3N2) during the 2022/2023 season were not associated with a change in disease severity compared to the previous influenza season.
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Affiliation(s)
- Amary Fall
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Lijie Han
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Madeline Yunker
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Tai-Jung Li
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Julie M Norton
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Omar Abdullah
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Richard E Rothman
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | | | - C Paul Morris
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Andrew Pekosz
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- W.Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Eili Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, District of Columbia, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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de Campos GM, de La-Roque DGL, Lima ARJ, Zucherato VS, de Carvalho E, de Lima LPO, de Queiroz Cattony Neto P, dos Santos MM, Ciccozzi M, Giovanetti M, Haddad R, Alcantara LCJ, Elias MC, Sampaio SC, Covas DT, Kashima S, Slavov SN. Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2. Microorganisms 2023; 11:2744. [PMID: 38004755 PMCID: PMC10672962 DOI: 10.3390/microorganisms11112744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 11/26/2023] Open
Abstract
The emergence of SARS-CoV-2 and the subsequent pandemic have prompted extensive diagnostic and clinical efforts to mitigate viral spread. However, these strategies have largely overlooked the presence of other respiratory viruses. Acute respiratory diseases in pediatric patients can be caused by a diverse range of viral agents, and metagenomics represents a powerful tool for their characterization. This study aimed to investigate the viral abundance in pediatric patients with acute respiratory symptoms who tested negative for SARS-CoV-2 during the Omicron pandemic wave. To achieve this, viral metagenomics and next-generation sequencing were employed on 96 nasopharyngeal swab samples, which were organized into 12 pools, with each pool consisting of eight individual samples. Metagenomic analysis revealed that the most prevalent viruses associated with acute disease in pediatric patients were respiratory syncytial virus (detected in all pools) and enteroviruses, which are known to cause significant morbidity and mortality in children. Additionally, clinically significant viruses such as mumps orthorubulavirus, human metapneumovirus, influenza A, and a wide array of human herpesviruses (1, 3-7) were identified. These findings highlight the extensive potential of viral metagenomics in identifying viruses other than SARS-CoV-2 that contribute to acute infections in children. Consequently, this methodology should garner clinical attention in terms of differential diagnosis and the development of public policies to address such conditions in the global pediatric population.
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Affiliation(s)
- Gabriel Montenegro de Campos
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
| | - Debora Glenda Lima de La-Roque
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
| | - Alex Ranieri Jerônimo Lima
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Victória Simionatto Zucherato
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
| | - Eneas de Carvalho
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Loyze Paola Oliveira de Lima
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Pedro de Queiroz Cattony Neto
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Murilo Marconi dos Santos
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Marta Giovanetti
- Instututo Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil; (M.G.); (L.C.J.A.)
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Rodrigo Haddad
- Campus Ceilândia, University of Brasília, Federal District of Brazil, Brasília 70910-900, Brazil;
| | | | - Maria Carolina Elias
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Sandra Coccuzzo Sampaio
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Dimas Tadeu Covas
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, Brazil; (G.M.d.C.); (D.G.L.d.L.-R.); (V.S.Z.); (S.K.)
- Center for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, Brazil; (A.R.J.L.); (E.d.C.); (L.P.O.d.L.); (P.d.Q.C.N.); (M.M.d.S.); (M.C.E.); (S.C.S.); (D.T.C.)
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Fall A, Forman M, Morris CP, Gniazdowski V, Luo CH, Hanlon A, Miller H, Bergman Y, Mostafa HH. Enterovirus characterized from cerebrospinal fluid in a cohort from the Eastern United States. J Clin Virol 2023; 161:105401. [PMID: 36805602 DOI: 10.1016/j.jcv.2023.105401] [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: 09/19/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND Enteroviruses (EVs) are predominant causes of a spectrum of neurological diseases. To better understand the origins of the outbreaks of disease associated with EV, it is essential to develop an efficient surveillance system that identifies the circulating EVs and correlate their genomic evolution with the disease presentations. METHODS The clinical presentations of patients with positive EV from cerebrospinal fluid (CSF) between 2014 and 2022, diagnosed at the Johns Hopkins Medical Microbiology Laboratory, were compared from year to year. EV typing and whole genome sequencing were performed and correlated to the spectrum of disease. RESULTS A total of 95 CSF specimens were positive for EV between 2014 and 2022. The percentage positivity ranged from the lowest of 1.1% in 2020 to the highest of 3.2% in 2015. The median ages declined from 22 years in 2014 to less than one year starting in 2016 to 34 in 2022. Typing using VP1 sequencing revealed that E30 and E6 were associated with meningitis in adults but coxsackieviruses (CVs-B3 and B5) were detected from pediatric patients with fever. Whole genome sequencing revealed multiple recombination events. In 2020, a recombinant CV-A9 was detected in a CSF sample associated with unusual presentation of sepsis, profound acute bilateral sensory neural hearing loss, and myofasciitis. CONCLUSIONS EV genomic surveillance is needed for a better understanding of the genetic determinants of neurovirulence. Whole genome sequencing can reveal recombination events missed by traditional molecular surveillance methods.
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Affiliation(s)
- Amary Fall
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Michael Forman
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - C Paul Morris
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA; National Institute of Allergy and Infectious Disease, National Institutes of Health, Frederick, MD, USA
| | - Victoria Gniazdowski
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Chun Huai Luo
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Ann Hanlon
- Johns Hopkins Hospital Medical Microbiology Laboratory, Meyer B-130, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Heather Miller
- Johns Hopkins Hospital Medical Microbiology Laboratory, Meyer B-130, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Yehudit Bergman
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA.
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7
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Hayes LJ, Uri H, Bojkova D, Cinatl J, Wass MN, Michaelis M. Impact of the COVID-19 pandemic on the circulation of other pathogens in England. J Med Virol 2023; 95:e28401. [PMID: 36512325 PMCID: PMC9877778 DOI: 10.1002/jmv.28401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/28/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Affiliation(s)
| | - Hannah Uri
- School of BiosciencesUniversity of KentCanterburyUK
| | - Denisa Bojkova
- Institute for Medical VirologyUniversity Hospital, Goethe UniversityFrankfurt am MainGermany
| | - Jindrich Cinatl
- Institute for Medical VirologyUniversity Hospital, Goethe UniversityFrankfurt am MainGermany,Dr. Petra Joh‐ForschungshausFrankfurt am MainGermany
| | - Mark N. Wass
- School of BiosciencesUniversity of KentCanterburyUK
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8
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Lai HC, Hsu YL, Lin CH, Wei HM, Chen JA, Low YY, Chiu YT, Lin HC, Hwang KP. Bacterial coinfections in hospitalized children with COVID-19 during the SARS-CoV-2 Omicron BA.2 variant pandemic in Taiwan. Front Med (Lausanne) 2023; 10:1178041. [PMID: 37144031 PMCID: PMC10151712 DOI: 10.3389/fmed.2023.1178041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/04/2023] [Indexed: 05/06/2023] Open
Abstract
Background Bacterial coinfections have been widely recognized in adults with coronavirus disease 2019 (COVID-19). However, bacterial coinfections in hospitalized children with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have not been sufficiently researched. This study aimed to determine the clinical presentations and risk factors for bacterial coinfections of pediatric inpatients during the SARS-CoV-2 Omicron BA.2 variant pandemic. Methods This retrospective, observational study included patients younger than 18 years of age who were hospitalized for COVID-19 confirmed by polymerase chain reaction (PCR) or antigen rapid tests during the SARS-CoV-2 Omicron BA.2 variant pandemic. Data and outcomes of these patients with or without bacterial coinfections were compared. Results During this study period, 161 children with confirmed COVID-19 were hospitalized. Twenty-four had bacterial coinfections. The most frequently reported concurrent diagnosis was bacterial enteritis, followed by lower respiratory tract infections. Children with bacterial coinfections had higher white blood cell (WBC) counts and PCR cycle threshold values. The bacterial coinfection group comprised a relatively greater proportion of patients who required high-flow nasal cannula oxygen and remdesivir. The length of stay in the hospital and that in the intensive care unit were longer for children with COVID-19 with bacterial coinfections. Mortality was not observed in either group. Abdominal pain, diarrhea, and comorbidity with neurologic illnesses were risk factors for bacterial coinfections with COVID-19. Conclusion This study provides clinicians with reference points for the detection of COVID-19 in children and its possible association with bacterial infections. Children with COVID-19 and neurologic diseases who present with abdominal pain or diarrhea are at risk of bacterial coinfections. Prolonged fever duration and higher PCR test cycle threshold values, WBC levels, and high-sensitivity C-reactive protein (hsCRP) levels may indicate bacterial coinfections in children with COVID-19.
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Affiliation(s)
- Huan-Cheng Lai
- Division of Pediatric Infectious Diseases, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
| | - Yu-Lung Hsu
- Division of Pediatric Infectious Diseases, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Chien-Heng Lin
- Division of Pediatric Pulmonology, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
- Department of Biomedical Imaging and Radiological Science, College of Medicine, China Medical University, Taichung, Taiwan
| | - Hsiu-Mei Wei
- Division of Pediatric Infectious Diseases, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
| | - Jiun-An Chen
- Division of Pediatric Infectious Diseases, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
| | - Yan-Yi Low
- Division of Pediatric Infectious Diseases, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
| | - Yu-Ting Chiu
- Division of Pediatric Infectious Diseases, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
| | - Hsiao-Chuan Lin
- Division of Pediatric Infectious Diseases, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
- *Correspondence: Hsiao-Chuan Lin,
| | - Kao-Pin Hwang
- Division of Pediatric Infectious Diseases, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
- Kao-Pin Hwang,
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