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Sánchez-Soliño O, Kilpatrick RD, Johnson C, Fang Y, Ye Y, Alami NN, Zarish K, Krueger WS, Dreyer N, Gray GC. Longitudinal Molecular and Serological Evidence of SARS-CoV-2 Infections and Vaccination Status: Community-Based Surveillance Study (CONTACT). Infect Dis Ther 2024; 13:633-645. [PMID: 38461480 PMCID: PMC11058157 DOI: 10.1007/s40121-024-00923-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/12/2024] [Indexed: 03/12/2024] Open
Abstract
INTRODUCTION This prospective, longitudinal, community-based study, EpidemiologiCal POpulatioN STudy of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Lake CounTy, Illinois (CONTACT), investigated coronavirus disease 2019 (COVID-19) immunity, occupational risks related to SARS-CoV-2 exposure, and long-term immunoglobulin G (IgG) seroconversion kinetics. METHODS At baseline and follow up (3, 6, and 9 months), non-hospitalized adult participants provided nasal and blood serum specimens for molecular [reverse transcription polymerase chain reaction (RT-PCR)] and serological (IgG) testing (4 November 2020-30 October 2021). RESULTS At baseline, 6.4% (65/1008) had evidence of current/prior SARS-CoV-2 infection. At 3, 6, and 9 months, positive PCR tests were obtained from 0.4% (3/781), 0.4% (3/733), and 0% (0/673) of participants, respectively. Positive IgG occurred at baseline and 3, 6, and 9 months in 4.5% (45/1008), 6.0% (48/799), 5.4% (39/733), and 2.8% (19/673) of participants, respectively. Of participants positive for IgG at baseline, 28 had a negative IgG test at a follow-up visit; of those 28, 21 had their first negative IgG test within 6 months. Participants were more likely to retain positive IgG if they were 18-29 years of age, were male, or had medium-high/high-risk occupations. A high vaccination rate (70% received ≥ 1 dose by 9 months) was observed. Influence of occupational status or characteristics on transmission and IgG, and COVID-19 vaccination trends, are shown. CONCLUSIONS This study expands on prior studies assessing COVID-19 immunity and IgG seroconversion by including both RT-PCR and serologic testing and longitudinal follow-up of study participants. We observed decreased infection rates over the 9 month follow-up period as well as a decline in IgG persistency after 6 months. The findings from this community-based study regarding vaccinate rates, infection rates by PCR, and IgG persistency over time can help improve our understanding of COVID-19 immunity, occupational risks related to SARS-CoV-2 exposure, and the kinetics of long-term IgG seroconversion, which is important to help guide local and national mitigation strategies. CLINICAL TRIAL REGISTRATION NCT04611230.
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Affiliation(s)
- Olga Sánchez-Soliño
- AbbVie Inc., 26525 Riverwoods Blvd., Mettawa, North Chicago, IL, 60045, USA.
| | | | | | | | | | | | | | | | - Nancy Dreyer
- IQVIA Real World Solutions, Cambridge, MA, USA
- Dreyer Strategies, Newton, USA
| | - Gregory C Gray
- Division of Infectious Diseases, School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
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Gray GC, Pulscher LA, Alsharif HO. Five Things Clinicians Need to Know About Zoonotic Viral Spillover and Spillback. AMA J Ethics 2024; 26:E122-131. [PMID: 38306202 DOI: 10.1001/amajethics.2024.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Since the 1990s, multiple infectious diseases have "spilled over" from nonhuman animals to infect humans and cause significant global morbidity and mortality. Despite efforts to detect and respond to such threats, surveillance and mitigation efforts have been criticized as ineffective. This article describes what "spillover" and "spillback" events are and canvasses 5 ways in which clinicians can improve emerging microbial pathogen, especially viral, detection and containment responses.
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Affiliation(s)
- Gregory C Gray
- Robert E. Shope, MD, Professor in Infectious Disease Epidemiology in the Departments of Internal Medicine (Infectious Diseases), Microbiology and Immunology, and Global Health and Emerging Diseases at the University of Texas Medical Branch in Galveston
| | - Laura A Pulscher
- Postdoctoral fellow at the University of Texas Medical Branch in Galveston
| | - Hisham O Alsharif
- Training fellow at the University of Texas Medical Branch in Galveston
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Pulscher LA, Webby RJ, Gray GC. An algorithm for the characterization of influenza A viruses from various host species and environments. Influenza Other Respir Viruses 2024; 18:e13258. [PMID: 38385997 PMCID: PMC10883340 DOI: 10.1111/irv.13258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Due to the extensive host range of influenza A viruses, it is difficult to determine the best diagnostic algorithm to efficiently screen samples from a variety of host species for influenza A viruses. While there are some influenza diagnostic algorithms that are specific to host species, to our knowledge, no single algorithm exists for the characterization of influenza A viruses across multiple host species. In this paper, we propose an algorithm that can serve as a guide for screening human, animal, and environmental samples for influenza A viruses of high human and animal health importance.
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Affiliation(s)
- Laura A Pulscher
- Department of Medicine (Infectious Diseases), University of Texas Medical Branch, Galveston, Texas, USA
| | - Richard J Webby
- Department of Infectious Disease, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gregory C Gray
- Department of Medicine (Infectious Diseases), University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas, USA
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Umar S, Ma M, Gray GC. Influenza D virus was not detected among prospectively studied swine farm in multiple provinces of China. Influenza Other Respir Viruses 2023; 17:e13223. [PMID: 37964987 PMCID: PMC10640961 DOI: 10.1111/irv.13223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/21/2023] [Indexed: 11/16/2023] Open
Affiliation(s)
- Sajid Umar
- Global Health Research Center (GHRC)Duke Kunshan UniversitySuzhouChina
- Division of Natural & Applied Sciences (DNAS)Duke Kunshan UniversitySuzhouChina
| | - Mai‐Juan Ma
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Gregory C. Gray
- Department of Medicine (Infectious Diseases)University of Texas Medical BranchGalvestonTexasUSA
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Rocha-Melogno L, Crank K, Bergin MH, Gray GC, Bibby K, Deshusses MA. Quantitative risk assessment of COVID-19 aerosol transmission indoors: a mechanistic stochastic web application. Environ Technol 2023; 44:1201-1212. [PMID: 34726128 DOI: 10.1080/09593330.2021.1998228] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
An increasing body of literature suggests that aerosol inhalation plays a primary role in COVID-19 transmission, particularly in indoor settings. Mechanistic stochastic models can help public health professionals, engineers, and space planners understand the risk of aerosol transmission of COVID-19 to mitigate it. We developed such model and a user-friendly web application to meet the need of accessible risk assessment tools during the COVID-19 pandemic. We built our model based on the Wells-Riley model of respiratory disease transmission, using quanta emission rates obtained from COVID-19 outbreak investigations. In this report, three modelled scenarios were evaluated and compared to epidemiological studies looking at similar settings: classrooms, weddings, and heavy exercise sessions. We found that the risk of long-range aerosol transmission increased 309-332% when people were not wearing masks, and 424-488% when the room was poorly ventilated in addition to no masks being worn across the scenarios. Also, the risk of transmission could be reduced by ∼40-60% with ventilation rates of 5 ACH for 1-4 h exposure events, and ∼70% with ventilation rates of 10 ACH for 4 h exposure events. Relative humidity reduced the risk of infection (inducing viral inactivation) by a maximum of ∼40% in a 4 h exposure event at 70% RH compared to a dryer indoor environment with 25% RH. Our web application has been used by more than 1000 people in 52 countries as of September 1st, 2021. Future work is needed to obtain SARS-CoV-2 dose-response functions for more accurate risk estimates.
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Affiliation(s)
- Lucas Rocha-Melogno
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
- ICF, Durham, NC, USA
| | - Katherine Crank
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN, USA
| | - Michael H Bergin
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, USA
| | - Gregory C Gray
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
- Global Health Research Center, Duke-Kunshan University, Kunshan, People's Republic of China
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore
- Division of Infectious Diseases, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN, USA
| | - Marc A Deshusses
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
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Leibler JH, Abdelgadir A, Seidel J, White RF, Johnson WE, Reynolds SJ, Gray GC, Schaeffer JW. Influenza D virus exposure among US cattle workers: A call for surveillance. Zoonoses Public Health 2023; 70:166-170. [PMID: 36370131 PMCID: PMC10099784 DOI: 10.1111/zph.13008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/27/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
Although cattle are a reservoir for influenza D virus (IDV), little is known about human exposure to IDV. We assessed IDV exposure and associated health effects among United States dairy workers, a population at heightened risk of cattle zoonoses. In prospective, cross-shift sampling of 31 workers employed at five large-herd dairy operations in two states, we found evidence of IDV in the nasal washes of 67% of participants at least once during the 5-day study period. IDV exposure was not associated with respiratory symptoms in these workers. These findings suggest that IDV is present in dairy cattle environments and can result in worker exposure.
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Affiliation(s)
- Jessica H Leibler
- Department of Environmental Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Anfal Abdelgadir
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - James Seidel
- High Plains Center for Agricultural Health and Safety, Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Roberta F White
- Department of Environmental Health, Boston University School of Public Health, Boston, Massachusetts, USA.,Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - W Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Stephen J Reynolds
- High Plains Center for Agricultural Health and Safety, Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Gregory C Gray
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Joshua W Schaeffer
- High Plains Center for Agricultural Health and Safety, Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
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Borkenhagen LK, Aung PP, Htay T, Thein ZW, Tin OS, Mon TS, Myint W, Bailey ES, Wanninger TG, Kandeil AM, Webby RJ, Gray GC. A cross-sectional study of avian influenza A virus in Myanmar live bird markets: Detection of a newly introduced H9N2? Influenza Other Respir Viruses 2023; 17:e13111. [PMID: 36843223 PMCID: PMC9970615 DOI: 10.1111/irv.13111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Zoonotic influenza surveillance in Myanmar is sparse, despite the risks of introduction of such viruses from neighboring countries that could impact the poultry industry and lead to spillover to humans. METHODS In July and August 2019, our multi-institutional partnership conducted a One Health-oriented, cross-sectional surveillance (weekly for 3 weeks) for influenza A and influenza D viruses at the three largest live bird markets in Yangon, Myanmar. RESULTS The 27 bioaerosols, 90 bird cage swabs, 90 bird oropharyngeals, and 90 human nasopharyngeal samples yielded molecular influenza A detections in 8 bioaerosols (30.0%), 16 bird cages (17.8%), 15 bird oropharyngeals (16.7%), and 1 human nasopharyngeal (1.1%) samples. No influenza D was detected. Seven of the influenza A virus detections were found to be subtype A/H9N2, and one human nasopharyngeal sample was found to be subtype A/H1pdm. Among all IAV-positive samples, three of the A/H9N2-positive samples yielded live viruses from egg culture and their whole genome sequences revealing they belonged to the G9/Y280 lineage of A/H9N2 viruses. Phylogenetic analyses showed that these A/H9N2 sequences clustered separately from A/H9N2 viruses that were previously detected in Myanmar, supporting the notion that A/H9N2 viruses similar to those seen in wider Southeast Asia may have been introduced to Myanmar on multiple occasions. CONCLUSIONS These findings call for increased surveillance efforts in Myanmar to monitor for the introduction of novel influenza viruses in poultry, as well as possible reassortment and zoonotic virus transmission.
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Affiliation(s)
- Laura K. Borkenhagen
- Duke Global Health InstituteDuke UniversityDurhamNorth CarolinaUSA
- Division of Infectious DiseasesDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Poe Poe Aung
- Duke Global Health Institute Myanmar ProgramYangonMyanmar
| | - Thura Htay
- Duke Global Health Institute Myanmar ProgramYangonMyanmar
| | - Zaw Win Thein
- Duke Global Health Institute Myanmar ProgramYangonMyanmar
| | - Ommar Swe Tin
- National Health Laboratory, Department of Medical ServicesMinistry of HealthYangonMyanmar
| | - Thet Su Mon
- Special Disease Control UnitDepartment of Public Health, Ministry of HealthNaypyitawMyanmar
| | - Win Myint
- Livestock Breeding and Veterinary DepartmentMinistry of Agriculture, Livestock and IrrigationYangonMyanmar
| | - Emily S. Bailey
- Duke Global Health InstituteDuke UniversityDurhamNorth CarolinaUSA
- Division of Infectious DiseasesDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Timothy G. Wanninger
- Department of Microbiology and ImmunologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Ahmed M. Kandeil
- Department of Infectious DiseaseSt. Jude Children's Research HospitalMemphisTennesseeUSA
- Center of Scientific Excellence for Influenza VirusesNational Research CentreGizaEgypt
| | - Richard J. Webby
- Department of Infectious DiseaseSt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - Gregory C. Gray
- Duke Global Health InstituteDuke UniversityDurhamNorth CarolinaUSA
- Division of Infectious DiseasesDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of Medicine (Infectious Diseases)University of Texas Medical BranchGalvestonTexasUSA
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8
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Umar S, Anderson BD, Chen K, Wang G, Ma M, Gray GC. Metagenomic analysis of endemic viruses in oral secretions from Chinese pigs. Vet Med Sci 2022; 8:1982-1992. [PMID: 36047475 PMCID: PMC9514493 DOI: 10.1002/vms3.869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Pigs are unique reservoirs for virus ecology. Despite the increased use of improved biosecurity measures, pig viruses readily circulate in Chinese swine farms. Objectives The main objective of this study was to examine archived swine oral secretion samples with a panel of pan‐species viral assays such that we might better describe the viral ecology of swine endemic viruses in Chinese farms. Methodology Two hundred (n = 200) swine oral secretion samples, collected during 2015 and 2016 from healthy pigs on six swine farms in two provinces in China, were screened with molecular pan‐species assays for coronaviruses (CoVs), adenoviruses (AdVs), enteroviruses (EVs), and paramyxoviruses (PMV). Samples were also screened for porcine circovirus (PCV) 3, porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV). Results Among 200 swine oral secretion samples, 152 (76.0%) were found to have at least one viral detection. Thirty‐four samples (17%) were positive for more than one virus, including 24 (70.5%) with dual detection and 10 (29.5%) with triple detection. Seventy‐eight (39.0%) samples were positive for porcine AdVs, 22 (11.0%) were positive for porcine CoVs, 21 (10.5%) were positive for IAVs, 13 (6.5%) were positive for PCV, 7 (3.5%) were positive for PMV, six (3.0%) were positive for PRRSV and five (2.5%) were positive for porcine EV. Conclusion Our findings underscore the high prevalence of numerous viruses among production pigs in China and highlight the need for routine, periodic surveillance for novel virus emergence with the goal of protecting pigs.
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Affiliation(s)
- Sajid Umar
- Global Health Research Center Duke Kunshan University Kunshan Jiangsu China
| | - Benjamin D. Anderson
- Global Health Research Center Duke Kunshan University Kunshan Jiangsu China
- Division of Natural and Applied Sciences Duke Kunshan University Kunshan Jiangsu China
| | - Kuanfu Chen
- Global Health Research Center Duke Kunshan University Kunshan Jiangsu China
| | - Guo‐Lin Wang
- State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Mai‐Juan Ma
- State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Gregory C. Gray
- Division of Infectious Diseases University of Texas Galveston USA
- Program in Emerging Infectious Diseases Duke‐NUS Medical School Singapore
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Dacso MM, Bente DA, Weaver SC, Kobinger GP, Melby PC, McLellan SL, Keiser PH, Hamer SA, Hamer GL, Parker GW, Douphrate DI, Rodriguez A, Goodman ML, XIII A, Gray GC. Texas professionals are employing a one health approach to protect the United States against biosecurity threats. One Health 2022; 15:100431. [PMID: 36277085 PMCID: PMC9582559 DOI: 10.1016/j.onehlt.2022.100431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022] Open
Abstract
Texas is a geographically large state with large human and livestock populations, many farms, a long coastal region, and extreme fluctuations in weather. During the last 15 years, the state of Texas has frequently suffered disasters or catastrophes causing extensive morbidity and economic loss. These disasters often have complicated consequences requiring multi-faceted responses. Recently, an interdisciplinary network of professionals from multiple academic institutions has emerged to collaborate in protecting Texas and the USA using a One Health approach. These experts are training the next generation of scientists in biopreparedness; increasing understanding of pathogens that cause repetitive harm; developing new therapeutics and vaccines against them; and developing novel surveillance approaches so that emerging pathogens will be detected early and thwarted before they can cause disastrous human and economic losses. These academic One Health partnerships strengthen our ability to protect human and animal health against future catastrophes that may impact the diverse ecoregions of Texas and the world. Texas has suffered from numerous disasters or catastrophes, often more than other US states. These disasters have caused tremendous morbidity, mortality, and economic loss. Texas professionals are partnering in One Health ways to mitigate such catastrophes. These numerous collaborations are important to Texas, the USA, and abroad.
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Rocha-Melogno L, Crank KC, Ginn O, Bergin MH, Brown J, Gray GC, Hamilton KA, Bibby K, Deshusses MA. Quantitative microbial risk assessment of outdoor aerosolized pathogens in cities with poor sanitation. Sci Total Environ 2022; 827:154233. [PMID: 35245543 DOI: 10.1016/j.scitotenv.2022.154233] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/08/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
The aeromicrobiological transmission pathway of enteric pathogens in places with unsafe sanitation services is poorly understood. In an attempt to partly fill this knowledge gap, we assessed the potential public health impact of bioaerosols near open waste canals (OWCs) using Quantitative Microbial Risk Assessment (QMRA). We used data acquired in La Paz, Bolivia to characterize the risk of disease that aerosolized enteric pathogens may pose through food, fomites and inhalation (all followed by ingestion). Three reference pathogens were selected to conduct the assessment: enterotoxigenic Escherichia coli (ETEC), Shigella flexneri, and Campylobacter jejuni. Inhalation followed by ingestion had the highest median infection risk per event i.e. 3 × 10-5 (3 infections for every 100,000 exposures), compared to contaminated food e.g. 5 × 10-6 and fomites e.g. 2 × 10-7, all for C. jejuni infections. Our sensitivity analysis showed that bacterial fluxes from the air were the most influential factor on risk. Our results suggest that fecal bacterial aerosols from OWCs present non-negligible risks of infection in La Paz, with median annual infection risks by C. jejuni being 18 (food), and 100 (inhalation) times greater than the EPA's standard for drinking water (1 × 10-4). We included two of the QMRA models presented here in a novel web application we developed for user-specified application in different contexts.
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Affiliation(s)
- Lucas Rocha-Melogno
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, United States; Duke Global Health Institute, Duke University, Durham, NC 27710, United States; ICF, 2635 Meridian Parkway Suite 200, Durham, NC 27713, United States
| | - Katherine C Crank
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN 46556, United States
| | - Olivia Ginn
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Michael H Bergin
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, United States
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Gregory C Gray
- Duke Global Health Institute, Duke University, Durham, NC 27710, United States; Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, United States; Global Health Research Center, Duke-Kunshan University, Kunshan, China; Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore; Division of Infectious Diseases, University of Texas Medical Branch (UTMB), Galveston, TX 77555, United States
| | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment, Arizona State University, 770 S College Ave, Tempe, AZ 85281, United States; The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, United States
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN 46556, United States
| | - Marc A Deshusses
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, United States; Duke Global Health Institute, Duke University, Durham, NC 27710, United States.
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Mielke D, Stanfield-Oakley S, Jha S, Keyes T, Zalaquett A, Dunn B, Rodgers N, Oguin T, Sempowski GD, Binder RA, Gray GC, Karuna S, Corey L, Hural J, Tomaras GD, Pollara J, Ferrari G. Development of flow cytometry-based assays to assess the ability of antibodies to bind to SARS-CoV-2-infected and Spike-transfected cells and mediate NK cell degranulation. Cytometry A 2022; 101:483-496. [PMID: 35301794 PMCID: PMC9087172 DOI: 10.1002/cyto.a.24552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/08/2022] [Accepted: 03/15/2022] [Indexed: 11/11/2022]
Abstract
Since the beginning of the SARS-CoV-2 pandemic, antibody responses and antibody effector functions targeting SARS-CoV-2-infected cells have been understudied. Consequently, the role of these types of antibodies in SARS-CoV-2 disease (COVID-19) and immunity is still undetermined. To provide tools to study these responses, we used plasma from SARS-CoV-2-infected individuals (n=50) and SARS-CoV-2 naive healthy controls (n=20) to develop four specific and reproducible flow cytometry-based assays: (i) two assessing antibody binding to, and antibody-mediated NK cell degranulation against, SARS-CoV-2-infected cells and (ii) two assessing antibody binding to, and antibody-mediated NK cell degranulation against, SARS-CoV-2 Spike-transfected cells. All four assays demonstrated the ability to detect the presence of these functional antibody responses in a specific and reproducible manner. Interestingly, we found weak to moderate correlations between the four assays (Spearman rho ranged from 0.50-0.74), suggesting limited overlap in the responses captured by the individual assays. Lastly, while we initially developed each assay with multiple dilutions in an effort to capture the full relationship between antibody titers and assay outcome, we explored the relationship between fewer antibody dilutions and the full dilution series for each assay to reduce assay costs and improve assay efficiency. We found high correlations between the full dilution series and fewer or single dilutions of plasma. Use of single or fewer sample dilutions to accurately determine the response rates and magnitudes of the responses allows for high-throughput use of these assays platforms to facilitate assessment of antibody responses elicited by SARS-CoV-2 infection and vaccination in large clinical studies. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dieter Mielke
- Department of Surgery, Duke University, Durham, NC, United States
| | | | - Shalini Jha
- Department of Surgery, Duke University, Durham, NC, United States
| | - Taylor Keyes
- Department of Surgery, Duke University, Durham, NC, United States
| | - Adam Zalaquett
- Department of Surgery, Duke University, Durham, NC, United States
| | - Brooke Dunn
- Department of Surgery, Duke University, Durham, NC, United States
| | - Nicole Rodgers
- Department of Surgery, Duke University, Durham, NC, United States
| | - Thomas Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Greg D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States.,Department of Pathology, Duke University, Durham, NC, United States.,Department of Medicine, Duke University, Durham, NC, United States
| | - Raquel A Binder
- Duke Global Health Institute, Duke University, Durham, NC, United States
| | - Gregory C Gray
- Division of Infectious Diseases, Duke University, Durham, NC, United States
| | - Shelly Karuna
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Lawrence Corey
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States.,Department of Medicine, University of Washington, Seattle, WA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - John Hural
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Georgia D Tomaras
- Department of Surgery, Duke University, Durham, NC, United States.,Department of Immunology, Duke University, Durham, NC, United States.,Deparment of Molecular and Genetic Medicine, Duke University, Durham, NC, United States
| | - Justin Pollara
- Department of Surgery, Duke University, Durham, NC, United States.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Guido Ferrari
- Department of Surgery, Duke University, Durham, NC, United States.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States.,Deparment of Molecular and Genetic Medicine, Duke University, Durham, NC, United States
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12
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Vlasova AN, Toh TH, Lee JSY, Poovorawan Y, Davis P, Azevedo MSP, Lednicky JA, Saif LJ, Gray GC. Animal alphacoronaviruses found in human patients with acute respiratory illness in different countries. Emerg Microbes Infect 2022; 11:699-702. [PMID: 35156544 PMCID: PMC8890521 DOI: 10.1080/22221751.2022.2040341] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Here we review the existing evidence of animal alphacoronaviruses (Alphacoronavirus 1 species) circulating in human patients with acute respiratory illness. Thus far, the viruses similar to canine, feline and porcine alphacoronaviruses (including the most recent CCoV-HuPn-2018 and HuCCoV_Z19) have been detected in humans in Haiti, Malaysia, Thailand, and USA. The available data suggest that these viruses emerged in different geographic locations independently and have circulated in humans for at least 20 years. Additional studies are needed to investigate their prevalence and disease impact.
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Affiliation(s)
- Anastasia N Vlasova
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, USA
| | - Teck-Hock Toh
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia.,Faculty of Medicine, SEGi University, Kota Damansara, Selangor, Malaysia
| | - Jeffrey Soon-Yit Lee
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia.,Faculty of Medicine, SEGi University, Kota Damansara, Selangor, Malaysia
| | - Yong Poovorawan
- Center of Excellence in Viral Hepatitis Research, Department of Pediatrics Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Phillip Davis
- MRIGlobal, 425 Dr Martin Luther King Jr Boulevard, Kansas City, MO, USA
| | - Marli S P Azevedo
- National Center for Toxicological Research, Division of Microbiology, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - John A Lednicky
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Linda J Saif
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, USA
| | - Gregory C Gray
- Departments of Internal Medicine (Infectious Diseases), Microbiology and Immunology, and Preventive Medicine & Population Health, University of Texas Medical Branch, Galveston, TX, USA
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13
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Vlasova AN, Diaz A, Damtie D, Xiu L, Toh TH, Lee JSY, Saif LJ, Gray GC. Novel Canine Coronavirus Isolated from a Hospitalized Patient With Pneumonia in East Malaysia. Clin Infect Dis 2022; 74:446-454. [PMID: 34013321 PMCID: PMC8194511 DOI: 10.1093/cid/ciab456] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND During the validation of a highly sensitive panspecies coronavirus (CoV) seminested reverse-transcription polymerase chain reaction (RT-PCR) assay, we found canine CoV (CCoV) RNA in nasopharyngeal swab samples from 8 of 301 patients (2.5%) hospitalized with pneumonia during 2017-2018 in Sarawak, Malaysia. Most patients were children living in rural areas with frequent exposure to domesticated animals and wildlife. METHODS Specimens were further studied with universal and species-specific CoV and CCoV 1-step RT-PCR assays, and viral isolation was performed in A72 canine cells. Complete genome sequencing was conducted using the Sanger method. RESULTS Two of 8 specimens contained sufficient amounts of CCoVs as confirmed by less-sensitive single-step RT-PCR assays, and 1 specimen demonstrated cytopathic effects in A72 cells. Complete genome sequencing of the virus causing cytopathic effects identified it as a novel canine-feline recombinant alphacoronavirus (genotype II) that we named CCoV-human pneumonia (HuPn)-2018. Most of the CCoV-HuPn-2018 genome is more closely related to a CCoV TN-449, while its S gene shared significantly higher sequence identity with CCoV-UCD-1 (S1 domain) and a feline CoV WSU 79-1683 (S2 domain). CCoV-HuPn-2018 is unique for a 36-nucleotide (12-amino acid) deletion in the N protein and the presence of full-length and truncated 7b nonstructural protein, which may have clinical relevance. CONCLUSIONS This is the first report of a novel canine-feline recombinant alphacoronavirus isolated from a human patient with pneumonia. If confirmed as a pathogen, it may represent the eighth unique coronavirus known to cause disease in humans. Our findings underscore the public health threat of animal CoVs and a need to conduct better surveillance for them.
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Affiliation(s)
- Anastasia N Vlasova
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| | - Annika Diaz
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| | - Debasu Damtie
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- The Ohio State University Global One Health LLC, Eastern Africa Regional Office, Addis Ababa, Ethiopia
| | - Leshan Xiu
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Teck-Hock Toh
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
- Faculty of Medicine, SEGi University, Kota Damansara, Selangor, Malaysia
| | - Jeffrey Soon-Yit Lee
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
- Faculty of Medicine, SEGi University, Kota Damansara, Selangor, Malaysia
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| | - Gregory C Gray
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Global Health Research Center, Duke Kunshan University, Kunshan, China
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
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14
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Kilpatrick RD, Sánchez-Soliño O, Alami NN, Johnson C, Fang Y, Wegrzyn LR, Krueger WS, Ye Y, Dreyer N, Gray GC. EpidemiologiCal POpulatioN STudy of SARS-CoV-2 in Lake CounTy, Illinois (CONTACT): Methodology and Baseline Characteristics of a Community-Based Surveillance Study. Infect Dis Ther 2022; 11:899-911. [PMID: 35107821 PMCID: PMC8808268 DOI: 10.1007/s40121-022-00593-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/18/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction EpidemiologiCal POpulatioN STudy of SARS-CoV-2 in Lake CounTy, Illinois (CONTACT) is an observational, epidemiological study with a 9-month longitudinal follow-up of nonhospitalized persons aged 18 years or older currently living or employed in Lake County, IL. We describe the study design and report baseline characteristics of the study participants, including the proportion of participants with acute or previous SARS-CoV-2 infection at enrollment. Methods At enrollment and subsequent timepoints, participants recruited through digital and paper-based advertising campaigns reported their occupational and school-based exposure, risk factors, and behaviors, and provided nasal and serum specimens. Stratified enrichment was used to enhance enrollment into medium- and higher-risk groups within four occupational risk groups for SARS-CoV-2 infection. RT-PCR and serologic (IgG) testing were conducted to detect acute or previous SARS-CoV-2 infection in participants, respectively. Results Between November 2020 and January 2021, 1008 participants (female 70.7%, mean age ± SD 51 ± 13.8 years) completed the questionnaire and diagnostic testing. Among participants, 41.8% (n = 421) were considered low risk, 24.6% (n = 248) were medium-to-low risk, 22.3% (n = 225) were medium-to-high risk, and 11.3% (n = 114) were high risk. Of 56 (5.6%) participants with evidence of acute or previous SARS-CoV-2 infection at baseline, 11 (19.6%) were RT-PCR-positive, 36 (64.3%) were IgG-seropositive, and 9 (16.1%) were positive by both assays. Participants who were adherent vs nonadherent to social distancing measures (odds ratio [95% CI] 0.8 [0.4–1.8]) were less likely, while those in higher vs lower occupational risk groups (2.0 [1.0–4.4]) were more likely to have evidence for acute or previous SARS-CoV-2 infection. Conclusion In fall/winter 2020/21, 5.6% of adults in a Lake County convenience sample had evidence for acute or previous SARS-CoV-2 infection at baseline. Nonadherence to social distancing measures and high-risk professions were associated with SARS-CoV-2 infection. The study is ongoing and future analyses will assess infection status over time. Clinical Trial Registration NCT04611230. Supplementary Information The online version contains supplementary material available at 10.1007/s40121-022-00593-0.
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Affiliation(s)
- Ryan D Kilpatrick
- AbbVie Inc., North Chicago, IL, USA. .,AbbVie, Inc., 26525 Riverwoods Blvd., Mettawa, IL, 60045, USA.
| | | | | | | | | | | | | | | | | | - Gregory C Gray
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, NC, USA.,Global Health Institute, Duke University, Durham, NC, USA.,University of Texas Medical Branch, Galveston, TX, USA
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15
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Chaorattanakawee S, Wofford RN, Takhampunya R, Poole-Smith BK, Boldbaatar B, Lkhagvatseren S, Altantogtokh D, Musih E, Nymadawa P, Davidson S, Hertz J, Fiorenzano J, Gray GC, von Fricken ME. Tracking tick-borne diseases in Mongolian livestock using next generation sequencing (NGS). Ticks Tick Borne Dis 2022; 13:101845. [PMID: 34689003 PMCID: PMC8665119 DOI: 10.1016/j.ttbdis.2021.101845] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/03/2023]
Abstract
The livestock industry in Mongolia accounts for 24% of national revenue, with one third of the population maintaining a pastoral lifestyle. This close connection between Mongolian population and livestock is a major concern for pathogen transfer, especially given the increase in vector-borne diseases globally. This study examines blood samples from livestock to assess the prevalence of tick-borne bacterial infections across three provinces in Mongolia (Dornogovi, Selenge, Töv). Whole blood samples from 243 livestock (cattle=38, camel=11, goat=85, horse=22, sheep=87) were analyzed with 16S metagenomics next-generation sequencing (NGS) to screen for bacterial pathogens. Positive-NGS samples for Anaplasma, Bartonella, Ehrlichia, Francisella, Leptospira, and Rickettsia were confirmed by conventional PCR and DNA sequencing. Prevalence rates of Anaplasma, Bartonella, and Ehrlichia were 57.6%, 12.8%, and 0.4%, respectively. A significant difference in the prevalence of Anaplasma spp. in livestock by province was observed, with a higher prevalence in Selenge (74.2%, p<0.001) and Töv (64.2% p = 0.006) compared to the semi-arid region of Dornogovi (39.8%). In contrast, no association was observed in Bartonella prevalence by provinces. All Anaplasma sequences (N = 139) were characterized as A. ovis. For Bartonella species characterization, phylogenetic analyses of gltA and rpoB genes identified three Bartonella species including B. bovis, B. melophagi and Candidatus B. ovis. Bartonella bovis was detected in all 22-positive cattle, while B. melophagi and Candidatus B. ovis were found in four and three sheep, respectively. This study identifies a high prevalence of tick-borne pathogens within the livestock population and to our knowledge, is the first time NGS methods have been used to explore tick-borne diseases in Mongolia. Further research is needed in Mongolia to better understand the clinical and economic burdens associated with tick-borne diseases in both livestock and pastoral herder populations.
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Affiliation(s)
- Suwanna Chaorattanakawee
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand,Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Rachel N. Wofford
- Department of Global and Community Health, George Mason University, Fairfax, VA, USA
| | - Ratree Takhampunya
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - B. Katherine Poole-Smith
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Bazartseren Boldbaatar
- Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, Mongolia
| | | | | | - Elisha Musih
- Department of Global and Community Health, George Mason University, Fairfax, VA, USA
| | | | - Silas Davidson
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand,Department of Chemistry and Life Science, US Military Academy, West Point, NY, USA
| | - Jeffrey Hertz
- Naval Medical Research Unit TWO (NAMRU-2), Sembawang, Singapore
| | - Jodi Fiorenzano
- Naval Medical Research Unit TWO (NAMRU-2), Sembawang, Singapore
| | - Gregory C. Gray
- Division of Infectious Diseases and Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Michael E. von Fricken
- Department of Global and Community Health, George Mason University, Fairfax, VA, USA,Corresponding Author. Michael von Fricken, PhD, Assistant Professor, George Mason University, Department of Global and Community Health, 4400 University Drive, Fairfax, VA, 22030, phone: +1 (703) 993-4677,
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16
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Wang X, Xiu L, Binder RA, Toh TH, Lee JSY, Ting J, Than ST, Qi W, Coleman KK, Perera D, Ma M, Gray GC. A pan-coronavirus RT-PCR assay for rapid viral screening of animal, human, and environmental specimens. One Health 2021; 13:100274. [PMID: 34124332 PMCID: PMC8179717 DOI: 10.1016/j.onehlt.2021.100274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
We examined a collection of 386 animal, 451 human, and 109 archived bioaerosol samples with a new pan-species coronavirus molecular assay. Thirty-eight (4.02%) of 946 specimens yielded evidence of human or animal coronaviruses. Our findings demonstrate the utility of employing the pan-CoV RT-PCR assay in detecting varied coronavirus among human, animal, and environmental specimens. This RT-PCR assay might be employed as a screening diagnostic for early detection of coronaviruses incursions or prepandemic coronavirus emergence in animal or human populations.
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Affiliation(s)
- Xinye Wang
- Global Health Research Center, Duke Kunshan University, Kunshan, China
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Leshan Xiu
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Raquel A. Binder
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Teck-Hock Toh
- Faculty of Medicine, SEGi University, Kota Damansara, Selangor, Malaysia
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | - Jeffrey Soon-Yit Lee
- Faculty of Medicine, SEGi University, Kota Damansara, Selangor, Malaysia
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | - Jakie Ting
- Faculty of Medicine, SEGi University, Kota Damansara, Selangor, Malaysia
| | - Son T. Than
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wenhao Qi
- Global Health Research Center, Duke Kunshan University, Kunshan, China
| | - Kristen K. Coleman
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - David Perera
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Maijuan Ma
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100,071, China
| | - Gregory C. Gray
- Global Health Research Center, Duke Kunshan University, Kunshan, China
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
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17
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Hii KC, Robie ER, Saihidi I, Berita A, Alarja NA, Xiu L, Merchant JA, Binder RA, Goh JKT, Guernier-Cambert V, Galán D, Gregory MJ, Gray GC. Leptospirosis infections among hospital patients, Sarawak, Malaysia. Trop Dis Travel Med Vaccines 2021; 7:32. [PMID: 34719397 PMCID: PMC8559352 DOI: 10.1186/s40794-021-00154-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/07/2021] [Indexed: 11/23/2022]
Abstract
Background Leptospirosis diagnoses have increased in Sarawak, Malaysia in recent years. Methods To better understand the burden of disease and associated risk factors, we evaluated 147 patients presenting with clinical leptospirosis to local hospitals in Sarawak, Malaysia for the presence of Leptospira and associated antibodies. Sera and urine specimens collected during the acute illness phase were assessed via a commercially available rapid diagnostic test (Leptorapide, Linnodee Ltd., Antrim, Northern Ireland), an ELISA IgM assay (Leptospira IgM ELISA, PanBio, Queensland, Australia) and a pan-Leptospira real-time PCR (qPCR) assay to estimate disease prevalence and diagnostic accuracy of each method. Microagglutination testing was performed on a subset of samples. Results Overall, 45 out of 147 patients (30.6%) showed evidence of leptospires through qPCR in either one or both sera (20 patients) or urine (33 patients), and an additional ten (6.8%) were considered positive through serological testing, for an overall prevalence of 37.4% within the study population. However, each diagnostic method individually yielded disparate prevalence estimates: rapid test 42.2% for sera and 30.5% for urine, ELISA 15.0% for sera, qPCR 13.8% for sera and 23.4% for urine. Molecular characterization of a subset of positive samples by conventional PCR identified the bacterial species as Leptospira interrogans in 4 specimens. A multivariate risk factor analysis for the outcome of leptospirosis identified having completed primary school (OR = 2.5; 95 CI% 1.0–6.4) and weekly clothes-washing in local rivers (OR = 10.6; 95 CI% 1.4–214.8) with increased likelihood of leptospirosis when compared with those who had not. Conclusion Overall, the data suggest a relatively high prevalence of leptospirosis in the study population. The low sensitivities of the rapid diagnostic test and ELISA assay against qPCR highlight a need for better screening tools. Supplementary Information The online version contains supplementary material available at 10.1186/s40794-021-00154-2.
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Affiliation(s)
- King-Ching Hii
- Department of Pediatrics, Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Emily R Robie
- Duke Global Health Institute, Duke University, Durham, NC, USA.,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA
| | - Izreena Saihidi
- Department of Pediatrics, Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Antoinette Berita
- Department of Pediatrics, Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Natalie A Alarja
- Duke Global Health Institute, Duke University, Durham, NC, USA.,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA
| | - Leshan Xiu
- Duke Global Health Institute, Duke University, Durham, NC, USA.,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA.,National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - James A Merchant
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Raquel A Binder
- Duke Global Health Institute, Duke University, Durham, NC, USA.,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA
| | - Johnny Keh-Tun Goh
- Department of Pediatrics, Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Vanina Guernier-Cambert
- Present address: Agricultural Research Service, National Animal Disease Center, United States Department of Agriculture, Ames, IA, USA
| | - Diego Galán
- Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA
| | - Michael J Gregory
- United States Naval Medical Research Center- Asia, Singapore, Singapore
| | - Gregory C Gray
- Duke Global Health Institute, Duke University, Durham, NC, USA. .,Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA. .,Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore. .,Global Health Center, Duke Kunshan University, Kunshan, China.
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18
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Ramesh A, Bailey ES, Ahyong V, Langelier C, Phelps M, Neff N, Sit R, Tato C, DeRisi JL, Greer AG, Gray GC. Metagenomic characterization of swine slurry in a North American swine farm operation. Sci Rep 2021; 11:16994. [PMID: 34417469 PMCID: PMC8379149 DOI: 10.1038/s41598-021-95804-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
Modern day large-scale, high-density farming environments are inherently susceptible to viral outbreaks, inadvertently creating conditions that favor increased pathogen transmission and potential zoonotic spread. Metagenomic sequencing has proven to be a useful tool for characterizing the microbial burden in both people, livestock, and environmental samples. International efforts have been successful at characterizing pathogens in commercial farming environments, especially swine farms, however it is unclear whether the full extent of microbial agents have been adequately captured or is representative of farms elsewhere. To augment international efforts we performed metagenomic next-generation sequencing on nine swine slurry and three environmental samples from a United States of America (U.S.A.) farm operation, characterized the microbial composition of slurry, and identified novel viruses. We assembled a remarkable total of 1792 viral genomes, of which 554 were novel/divergent. We assembled 1637 Picobirnavirus genome segments, of which 538 are novel. In addition, we discovered 10 new viruses belonging to a novel taxon: porcine Statoviruses; which have only been previously reported in human, macaques, mouse, and cows. We assembled 3 divergent Posaviruses and 3 swine Picornaviruses. In addition to viruses described, we found other eukaryotic genera such as Entamoeba and Blastocystis, and bacterial genera such as Listeria, Treponema, Peptoclostridium and Bordetella in the slurry. Of these, two species Entamoeba histolytica and Listeria monocytogenes known to cause human disease were detected. Further, antimicrobial resistance genes such as tetracycline and MLS (macrolide, lincosamide, streptogramin) were also identified. Metagenomic surveillance in swine fecal slurry has great potential for novel and antimicrobial resistant pathogen detection.
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Affiliation(s)
- Akshaya Ramesh
- Weill Institute for Neurosciences, University of California, San Francisco, CA, 94158, USA.,Department of Neurology, University of California, San Francisco, CA, 94158, USA.,Julia Jones Matthews Department of Public Health, Texas Tech University Health Sciences Center, Abilene, TX, USA
| | - Emily S Bailey
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA. .,Julia Jones Matthews Department of Public Health, Texas Tech University Health Sciences Center, Abilene, TX, USA.
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.,Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Rene Sit
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Cristina Tato
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Annette G Greer
- Department of Bioethics and Interdisciplinary Studies, Brody School of Medicine, North Carolina Agromedicine Institute, East Carolina University, Greenville, NC, USA
| | - Gregory C Gray
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA.,Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore.,Global Health Center, Duke Kunshan University, Kunshan, China
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19
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Wang X, Wang D, Umar S, Qin S, Ling Q, Gray GC, Liu Y. Molecular typing of human adenoviruses among hospitalized patients with respiratory tract infections in a tertiary Hospital in Guangzhou, China between 2017 and 2019. BMC Infect Dis 2021; 21:748. [PMID: 34344310 PMCID: PMC8330471 DOI: 10.1186/s12879-021-06412-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/18/2021] [Indexed: 12/02/2022] Open
Abstract
Background Human Adenoviruses (HAdVs) cause a wide array of illnesses in all age groups. They particularly cause frequent morbidity among children. In China, human adenovirus types 3, 4, 7, 11, 14, 21, and 55 have caused at least seven outbreaks since 2000. However, limited studies are available regarding the epidemiological patterns and diversity of HAdVs types among hospitalized patients with respiratory tract infections (RTIs). Methods To understand the epidemiology and subtype distribution of HAdV infections associated with RTIs in China, nasal swab (NS) clinical samples were collected from 4129 patients in a Guangzhou hospital between August 2017 and October 2019. PCR, sequencing, and phylogenetic analysis were performed on these specimens to identify HAdV subtypes. Results HAdV was successfully sequenced in 99 (2.4%) of the 4129 NS specimens, with the highest HAdV prevalence (6.3%) found in children between the ages of 5 and 10 years. Among HAdV-positive specimens, the most prevalent genotypes identified were HAdV-B3 (55.6%) and HAdV-B7 (25.3%). The most common symptoms in the HAdV-infected patients were fever (100%), cough (80.8%), and rhinorrhea (71.8%). HAdV infections were detected throughout the year with a relatively higher prevalence in summer. Conclusion All ages suffer adenovirus infections, but young children are at the greatest risk. This study data demonstrates that at least three species of HAdVs (species B, C, and E) are circulating in Guangzhou City, China. As antiviral therapies and type-specific vaccines become available, such epidemiological data will be useful in guiding therapy and public health interventions. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06412-0.
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Affiliation(s)
- Xinye Wang
- Global Health Research Center, Duke Kunshan University, Kunshan, China.,Faculty of Medicine, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Dawei Wang
- Emergency Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Yuexiu District, Guangzhou, China
| | - Sajid Umar
- Global Health Research Center, Duke Kunshan University, Kunshan, China
| | - Sheng Qin
- Laboratory Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiong Ling
- Laboratory Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Gregory C Gray
- Global Health Research Center, Duke Kunshan University, Kunshan, China. .,Division of Infectious Diseases, Duke University, School of Medicine, DUMC Box 102359, Durham, NC, 27710, USA. .,Duke Global Health Institute, Duke University, Durham, NC, USA. .,Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Yuntao Liu
- Emergency Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Yuexiu District, Guangzhou, China.
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Seidelman JL, Akinboyo IC, Taylor B, Henshaw NG, Abdelgadir A, Gray GC, Smith BA, Lewis SS. Pseudo-outbreak of adenovirus in bronchoscopy suite. Infect Control Hosp Epidemiol 2021; 42:1016-1017. [PMID: 33827727 PMCID: PMC8111188 DOI: 10.1017/ice.2021.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/24/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Affiliation(s)
- Jessica L. Seidelman
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University School of Medicine, Duke University, Durham, North Carolina, United States
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University Medical Center, Durham, North Carolina, United States
| | - Ibukunoluwa C. Akinboyo
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University School of Medicine, Duke University, Durham, North Carolina, United States
- Division of Infectious Diseases and International Health, Department of Pediatrics, Duke University School of Medicine, Duke University, Durham, North Carolina, United States
| | - Bonnie Taylor
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University Medical Center, Durham, North Carolina, United States
| | - Nancy G. Henshaw
- Department of Pathology, Duke University School of Medicine, Duke University, Durham, North Carolina, United States
| | - Anfal Abdelgadir
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University School of Medicine, Duke University, Durham, North Carolina, United States
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States
- Global Health Research Center, Duke Kunshan University, Kunshan, China
| | - Gregory C. Gray
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University School of Medicine, Duke University, Durham, North Carolina, United States
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States
- Global Health Research Center, Duke Kunshan University, Kunshan, China
| | - Becky A. Smith
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University School of Medicine, Duke University, Durham, North Carolina, United States
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University Medical Center, Durham, North Carolina, United States
| | - Sarah S. Lewis
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University School of Medicine, Duke University, Durham, North Carolina, United States
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University Medical Center, Durham, North Carolina, United States
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21
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El Zowalaty ME, Abdelgadir A, Borkenhagen LK, Ducatez MF, Bailey ES, Gray GC. Influenza A viruses are likely highly prevalent in South African swine farms. Transbound Emerg Dis 2021; 69:2373-2383. [PMID: 34327845 DOI: 10.1111/tbed.14255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022]
Abstract
Growth in pork production during the last decade in South Africa has escalated the risk of zoonotic pathogen emergence. This cross-sectional study was conducted to evaluate evidence for transmission of influenza A virus between pigs and swine workers. Between February and October 2018, samples from swine workers and pigs were collected from three farms in KwaZulu-Natal Province, South Africa. Workers nasal washes and serum samples, and swine oral secretion samples (rope sampling method) were studied for evidence of swine influenza A virus infection using molecular and serological methods. Among 84 human nasal washes and 51 swine oral secretion specimens, 44 (52.4%) and 6 (11.8%) had molecular evidence of influenza A virus. Microneutralization assays with workers' enrolment sera against swine H1N1 and H3N2 viruses revealed a high prevalence of elevated antibodies. Multivariate risk factor analysis showed that male workers from the age-group quartile 23-32 years, who self-reported a recent history of exposure to someone with influenza disease and seldom use of personal protective equipment were at highest risk of molecular detection of influenza A virus. These pilot study data suggest that influenza A viruses are likely highly prevalent in South African swine farms. South Africa would benefit from periodic surveillance for novel influenza viruses in swine farms as well as education and seasonal influenza vaccine programmes for swine workers.
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Affiliation(s)
- Mohamed E El Zowalaty
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Duke One Health, Duke University School of Medicine, Duke University, Durham, North Carolina, USA
| | - Anfal Abdelgadir
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Laura K Borkenhagen
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | | | - Emily S Bailey
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Gregory C Gray
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Global Health Research Center, Duke-Kunshan University, Kunshan, China.,Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
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22
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Barnes AN, Davaasuren A, Baasandavga U, Lantos PM, Gonchigoo B, Gray GC. Zoonotic enteric parasites in Mongolian people, animals, and the environment: Using One Health to address shared pathogens. PLoS Negl Trop Dis 2021; 15:e0009543. [PMID: 34237083 PMCID: PMC8266129 DOI: 10.1371/journal.pntd.0009543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/07/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Cryptosporidium spp. and Giardia duodenalis are important zoonotic enteric pathogens of One Health concern for humans, animals, and the environment. For this study, we investigated parasite prevalence and risk factors among rural, peri-urban, and urban households and environments of Mongolia. METHODS This cross-sectional study implemented a household risk factor survey at 250 home sites along with sample collection from humans, animals, flies, and drinking water. Multiplex real-time PCR analysis was conducted to look for Cryptosporidium spp. and/or Giardia duodenalis within household samples. RESULTS Lab analysis found one or both zoonotic parasites at 20% of the participating households (51/250). Human samples had a parasite prevalence of 6.4% (27/419), domestic animals at 3.3% (19/570), pooled filth flies at 14.8% (17/115), and drinking water samples at 2% (5/250). Parasite presence at the household was significantly associated with a household's use of an improved drinking water source (OR 0.27; CI 0.12-0.61; p = < 0.01), having an indoor handwashing site (OR 0.41; CI 0.19-0.92; p = 0.03), domestic animal ownership (OR 2.40; CI 1.02-5.65; p = 0.05), and rural location (OR 0.50; CI 0.25-0.98; p = 0.04). Household use of an improved drinking water source remained significant in the multivariate model (OR 0.16; CI 0.04-0.68; p = 0.01). CONCLUSION In Mongolia, public and veterinary health are intertwined, particularly for rural herding households. Increased access to safe water, sanitation and hygiene infrastructure could help prevent further transmission of zoonotic enteric parasites. Public health interventions, policy and messaging should utilize a One Health framework employing joint leadership from local human and animal health sectors.
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Affiliation(s)
- Amber N. Barnes
- Institute of Veterinary Medicine, Ulaanbaatar, Mongolia
- School of Medicine, Duke University, Durham, North Carolina, United States of America
- Department of Public Health, University of North Florida, Jacksonville, Florida, United States of America
| | - Anu Davaasuren
- Institute of Veterinary Medicine, Ulaanbaatar, Mongolia
- National Center for Communicable Disease, Ulaanbaatar, Mongolia
| | - Uyanga Baasandavga
- Institute of Veterinary Medicine, Ulaanbaatar, Mongolia
- National Center for Zoonotic Disease, Ulaanbaatar, Mongolia
| | - Paul M. Lantos
- School of Medicine, Duke University, Durham, North Carolina, United States of America
| | | | - Gregory C. Gray
- School of Medicine, Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Global Health Research Institute, Duke-Kunshan University, Kunshan, Jiangsu, China
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
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23
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Abdelgadir A, Vlasova AN, Gray GC. Susceptibility of different cell lines to the novel canine coronavirus CCoV-HuPn-2018. Influenza Other Respir Viruses 2021; 15:824-825. [PMID: 34212500 PMCID: PMC8542962 DOI: 10.1111/irv.12882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 05/30/2021] [Indexed: 12/23/2022] Open
Affiliation(s)
- Anfal Abdelgadir
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Anastasia N Vlasova
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, USA
| | - Gregory C Gray
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA.,Global Health Research Center, Duke Kunshan University, Kunshan, China.,Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
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24
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Robie ER, Abdelgadir A, Binder RA, Gray GC. Live SARS-CoV-2 is difficult to detect in patient aerosols. Influenza Other Respir Viruses 2021; 15:554-557. [PMID: 33939268 PMCID: PMC8189214 DOI: 10.1111/irv.12860] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2021] [Indexed: 01/12/2023] Open
Affiliation(s)
- Emily R Robie
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Anfal Abdelgadir
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Raquel A Binder
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Gregory C Gray
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA.,Global Health Research Center, Duke Kunshan University, Kunshan, China.,Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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25
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Trimarco JD, Heaton BE, Chaparian RR, Burke KN, Binder RA, Gray GC, Smith CM, Menachery VD, Heaton NS. TMEM41B is a host factor required for the replication of diverse coronaviruses including SARS-CoV-2. PLoS Pathog 2021; 17:e1009599. [PMID: 34043740 PMCID: PMC8189496 DOI: 10.1371/journal.ppat.1009599] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/09/2021] [Accepted: 04/29/2021] [Indexed: 12/23/2022] Open
Abstract
Antiviral therapeutics are a front-line defense against virally induced diseases. Because viruses frequently mutate to escape direct inhibition of viral proteins, there is interest in targeting the host proteins that the virus must co-opt to complete its replication cycle. However, a detailed understanding of the interactions between the virus and the host cell is necessary in order to facilitate development of host-directed therapeutics. As a first step, we performed a genome-wide loss of function screen using the alphacoronavirus HCoV-229E to better define the interactions between coronaviruses and host factors. We report the identification and validation of an ER-resident host protein, TMEM41B, as an essential host factor for not only HCoV-229E but also genetically distinct coronaviruses including the pandemic betacoronavirus SARS-CoV-2. We show that the protein is required at an early, but post-receptor engagement, stage of the viral lifecycle. Further, mechanistic studies revealed that although the protein was not enriched at replication complexes, it likely contributes to viral replication complex formation via mobilization of cholesterol and other lipids to facilitate host membrane expansion and curvature. Continued study of TMEM41B and the development of approaches to prevent its function may lead to broad spectrum anti-coronavirus therapeutics.
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Affiliation(s)
- Joseph D. Trimarco
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Ryan R. Chaparian
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Kaitlyn N. Burke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Raquel A. Binder
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | - Gregory C. Gray
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | - Clare M. Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
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26
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Borkenhagen LK, Wang GL, Simmons RA, Bi ZQ, Lu B, Wang XJ, Wang CX, Chen SH, Song SX, Li M, Zhao T, Wu MN, Park LP, Cao WC, Ma MJ, Gray GC. High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China. Clin Infect Dis 2021; 71:622-629. [PMID: 31504322 PMCID: PMC7108185 DOI: 10.1093/cid/ciz865] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/29/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND China is thought to be a hotspot for zoonotic influenza virus emergence, yet there have been few prospective studies examining the occupational risks of such infections. METHODS We present the first 2 years of data collected from a 5-year, prospective, cohort study of swine-exposed and -unexposed participants at 6 swine farms in China. We conducted serological and virological surveillance to examine evidence for swine influenza A virus infection in humans. RESULTS Of the 658 participants (521 swine-exposed and 137 swine-unexposed), 207 (31.5%) seroconverted against at least 1 swine influenza virus subtype (swine H1N1 or H3N2). Swine-exposed participants' microneutralization titers, especially those enrolled at confined animal feeding operations (CAFOs), were higher against the swine H1N1 virus than were other participants at 12 and 24 months. Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55-358.65) and swine H3N2 (OR 2.97, 95% CI 1.16-8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. CONCLUSIONS While some of the observed increased risk against swine viruses may have been explained by exposure to human influenza strains, study data suggest that even with elevated preexisting antibodies, swine-exposed workers were at high risk of infection with enzootic swine influenza A viruses.
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Affiliation(s)
- Laura K Borkenhagen
- Division of Infectious Diseases, School of Medicine, Global Health Institute, Duke University, Durham, North Carolina
| | - Guo-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology
| | - Ryan A Simmons
- Division of Infectious Diseases, School of Medicine, Global Health Institute, Duke University, Durham, North Carolina
| | - Zhen-Qiang Bi
- Shandong Provincial Center for Disease Control and Prevention.,Shandong Provincial Key Laboratory of Disease Control and Prevention, Jinan
| | - Bing Lu
- Wuxi Center for Disease Control and Prevention, Jinan
| | - Xian-Jun Wang
- Shandong Provincial Center for Disease Control and Prevention.,Shandong Provincial Key Laboratory of Disease Control and Prevention, Jinan
| | - Chuang-Xin Wang
- Licheng District Center for Disease Control and Prevention, Jinan
| | - Shan-Hui Chen
- Wuxi Center for Disease Control and Prevention, Jinan
| | - Shao-Xia Song
- Shandong Provincial Center for Disease Control and Prevention.,Shandong Provincial Key Laboratory of Disease Control and Prevention, Jinan
| | - Min Li
- Licheng District Center for Disease Control and Prevention, Jinan
| | - Teng Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology
| | - Meng-Na Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology
| | - Lawrence P Park
- Division of Infectious Diseases, School of Medicine, Global Health Institute, Duke University, Durham, North Carolina
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology
| | - Mai-Juan Ma
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology
| | - Gregory C Gray
- Division of Infectious Diseases, School of Medicine, Global Health Institute, Duke University, Durham, North Carolina.,Global Health Research Center, Duke Kunshan University, China.,Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
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27
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Nguyen NTT, Luu YTH, Hoang TD, Nguyen HX, Dao TD, Bui VN, Gray GC. An epidemiological study of Streptococcus suis prevalence among swine at industrial swine farms in Northern Vietnam. One Health 2021; 13:100254. [PMID: 33997238 PMCID: PMC8102613 DOI: 10.1016/j.onehlt.2021.100254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/26/2022] Open
Abstract
Introduction Streptococcus suis is a zoonotic pathogen found in swine that may cause systemic infection in humans. S. suis is endemic in Southeast Asia and is the leading cause of adult meningitis in Vietnam. Given Vietnam's increasing centralization of the swine industry, we sought to estimate the prevalence of S. suis on large swine farms in Northern Vietnam. Methods A cross-sectional, one-health-oriented, surveillance study for S. suis was conducted between October 2019–March 2020. Swine oral, swine worker nasal, and bioaerosol samples were collected from four large-scale swine farms (>500 swine) in three provinces in Northern Vietnam: Lao Cai, Bac Giang, and Quang Ninh. Samples were evaluated for presence of S. suis growth on blood agar plates and confirmed with conventional polymerase chain reaction. Results The authors found that 4/174 (2.3%, 95% CI: 0.6–5.8%) of swine oral samples and 1/58 (1.7%, 95% CI: 0–9.2%) bioaerosol samples were positive for S. suis by bacterial culture and conventional PCR. S. suis was not detected in any swine worker nasal wash samples. There was no significant relationship between sampling location and month of sample collection with results of swine oral or bioaerosol samples. Conclusion Compared to previous reports from slaughterhouses in Vietnam, the lower than expected prevalence of S. suis, supports the notion that that recent efforts to centralize Vietnam's pork industry through establishment of large-scale farms with better biosecurity may have been effective in limiting S. suis prevalence on these large farms.
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Affiliation(s)
- Nguyen Thao Thi Nguyen
- Duke University School of Medicine, Duke University, Durham, NC 27710, United States
- Corresponding author at: 1103 Lancaster St., Durham, NC 27701, USA.
| | - Yen Thi Hai Luu
- Bacteriology Department, National Institute of Veterinary Research, Hanoi 100000, Viet Nam
| | - Trung Duc Hoang
- Virology Department, National Institute of Veterinary Research, Hanoi 100000, Viet Nam
| | - Huyen Xuan Nguyen
- Bacteriology Department, National Institute of Veterinary Research, Hanoi 100000, Viet Nam
| | - Tung Duy Dao
- Virology Department, National Institute of Veterinary Research, Hanoi 100000, Viet Nam
| | - Vuong Nghia Bui
- Virology Department, National Institute of Veterinary Research, Hanoi 100000, Viet Nam
| | - Gregory C. Gray
- Duke University School of Medicine, Duke University, Durham, NC 27710, United States
- Duke Global Health Institute, Duke University, Durham, NC 27710, United States
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore
- Global Health Center, Duke Kunshan University, Kunshan, China
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28
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Gray GC, Robie ER, Studstill CJ, Nunn CL. Mitigating Future Respiratory Virus Pandemics: New Threats and Approaches to Consider. Viruses 2021; 13:637. [PMID: 33917745 PMCID: PMC8068197 DOI: 10.3390/v13040637] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Despite many recent efforts to predict and control emerging infectious disease threats to humans, we failed to anticipate the zoonotic viruses which led to pandemics in 2009 and 2020. The morbidity, mortality, and economic costs of these pandemics have been staggering. We desperately need a more targeted, cost-efficient, and sustainable strategy to detect and mitigate future zoonotic respiratory virus threats. Evidence suggests that the transition from an animal virus to a human pathogen is incremental and requires a considerable number of spillover events and considerable time before a pandemic variant emerges. This evolutionary view argues for the refocusing of public health resources on novel respiratory virus surveillance at human-animal interfaces in geographical hotspots for emerging infectious diseases. Where human-animal interface surveillance is not possible, a secondary high-yield, cost-efficient strategy is to conduct novel respiratory virus surveillance among pneumonia patients in these same hotspots. When novel pathogens are discovered, they must be quickly assessed for their human risk and, if indicated, mitigation strategies initiated. In this review, we discuss the most common respiratory virus threats, current efforts at early emerging pathogen detection, and propose and defend new molecular pathogen discovery strategies with the goal of preempting future pandemics.
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Affiliation(s)
- Gregory C. Gray
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, USA; (E.R.R.); (C.J.S.)
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA;
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore 169856, Singapore
- Global Health Center, Duke Kunshan University, Kunshan 215316, China
| | - Emily R. Robie
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, USA; (E.R.R.); (C.J.S.)
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA;
| | - Caleb J. Studstill
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, USA; (E.R.R.); (C.J.S.)
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA;
| | - Charles L. Nunn
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA;
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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Robie ER, Zemke JN, Toh TH, Lee JSY, Hii KC, Callahan JD, Schoepp RJ, Gray GC. Chikungunya and Zika Viruses Not Detected Among Patients With Dengue-Like Illness, Sarawak, Malaysia. Asia Pac J Public Health 2021; 33:995-996. [PMID: 33829875 DOI: 10.1177/10105395211007631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | | | - Teck-Hock Toh
- Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia.,SEGi University, Kota Damansara, Selangor, Malaysia
| | - Jeffrey Soon-Yit Lee
- Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia.,SEGi University, Kota Damansara, Selangor, Malaysia
| | - King-Ching Hii
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | | | - Randal J Schoepp
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Gregory C Gray
- Duke University, Durham, NC, USA.,Duke-NUS Medical School, Singapore.,Duke Kunshan University, Kunshan, China
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Coleman KK, Robie ER, Abdelgadir A, Kozhumam AS, Binder RA, Gray GC. Six Decades of Human Adenovirus Type 4 Infections Reviewed: Increasing Infections Among Civilians Are a Matter of Concern. Clin Infect Dis 2021; 73:740-746. [PMID: 33693635 DOI: 10.1093/cid/ciab146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/12/2021] [Indexed: 12/18/2022] Open
Abstract
Human adenovirus type 4 (HAdV-E4) frequently causes epidemics among military and civilian populations. We conducted a systematic review of 144 peer-reviewed articles reporting HAdV-E4 infections, published during the years 1960 - 2020. More than 24,500 HAdV-E4 infections, including 27 associated deaths, were documented. HAdV-E4 infections were reported from all geographic regions of the world except Central America and the Caribbean. The number of publications reporting civilian infections tripled in the last decade, with a steady increase in reported civilian infections over time. Infections commonly caused respiratory and ocular disease. North America reported the most infections, followed by Asia and Europe. The majority of deaths were reported in the USA, followed by China and Singapore. Civilians seem to increasingly suffer HAdV-E4 disease, with recent epidemics among U.S. college students. Public health officials should consider seeking emergency use authorization for the adenovirus vaccine such that it might be available to mitigate civilian epidemics.
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Affiliation(s)
- Kristen K Coleman
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Emily R Robie
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Anfal Abdelgadir
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Arthi S Kozhumam
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Raquel A Binder
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Gregory C Gray
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA.,Global Health Research Center, Duke Kunshan University, Kunshan, China
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31
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Gray GC, Abdelgadir A. While We Endure This Pandemic, What New Respiratory Virus Threats Are We Missing? Open Forum Infect Dis 2021; 8:ofab078. [PMID: 33778092 PMCID: PMC7928563 DOI: 10.1093/ofid/ofab078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
In this paper, we review recent human respiratory virus epidemics, their zoonotic nature, and our current inability to identify future prepandemic threats. We propose a cost-efficient, One Health surveillance strategy that will be more efficient and more sustainable than previous efforts.
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Affiliation(s)
- Gregory C Gray
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Global Health Research Center, Duke-Kunshan University, Kunshan, China.,Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
| | - Anfal Abdelgadir
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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32
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Gray GC. Controlling COVID-19 Spread in a Confined, High-Risk Population. JAMA Netw Open 2021; 4:e210234. [PMID: 33630082 DOI: 10.1001/jamanetworkopen.2021.0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Gregory C Gray
- Division of Infectious Diseases, Duke Global Health Institute, Durham, North Carolina
- Duke University School of Medicine, Durham, North Carolina
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33
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Gwee SXW, St John AL, Gray GC, Pang J. Animals as potential reservoirs for dengue transmission: A systematic review. One Health 2021; 12:100216. [PMID: 33598525 PMCID: PMC7868715 DOI: 10.1016/j.onehlt.2021.100216] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 12/21/2022] Open
Abstract
Dengue is a rapidly spreading mosquito-borne flavivirus infection that is prevalent in tropical and sub-tropical regions. Humans are known to be the main reservoir host maintaining the epidemic cycles of dengue but it is unclear if dengue virus is also maintained in a similar enzootic cycle. The systematic review was conducted in accordance to Cochrane's PRISMA recommendations. A search was done on PubMed, EMBASE, Scopus and Cochrane Library. Key data on animal dengue positivity was extracted and classified according to animal type and diagnostic modes. Of the 3818 articles identified, 56 articles were used in this review. A total of 16,333 animals were tested, 1817 of which were positive for dengue virus by RT-PCR or serology. Dengue positivity was detected in bats (10.1%), non-human primates (27.3%), birds (11%), bovid (4.1%), dogs (1.6%), horses (5.1%), pigs (34.1%), rodents (3.5%), marsupials (13%) and other small animals (7.3%). While majority of dengue positivity via serology suggests potential enzootic transmission, but regular dengue virus spillback cannot be excluded. With the exception of bats, acute infection among animals is limited. Further investigation on animals is critically required to better understand their role as potential reservoir in dengue transmission.
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Affiliation(s)
- Sylvia Xiao Wei Gwee
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Centre of Infectious Disease Epidemiology and Research, National University of Singapore, Singapore
| | - Ashley L St John
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Microbiology and Immunology, National University of Singapore, Singapore.,Pathology Department, Duke University, USA.,SingHealth Duke-NUS Global Health University, Singapore
| | - Gregory C Gray
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,SingHealth Duke-NUS Global Health University, Singapore.,Division of Infectious Diseases, School of Medicine, Duke University, USA.,Global Health Institute, Duke University, USA.,Duke Kunshan University, China
| | - Junxiong Pang
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Centre of Infectious Disease Epidemiology and Research, National University of Singapore, Singapore
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34
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Gray GC, Mazet JAK. To Succeed, One Health Must Win Animal Agriculture's Stronger Collaboration. Clin Infect Dis 2021; 70:535-537. [PMID: 31943052 DOI: 10.1093/cid/ciz729] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/30/2019] [Indexed: 01/28/2023] Open
Abstract
The One Health approach has received widespread international endorsements from professional, academic, and governmental organizations as the way forward in tackling complex interdisciplinary problems, such as emerging zoonotic diseases, antimicrobial resistance, and food safety. Yet conspicuously absent from US One Health training or research activities are the animal agricultural industries. Their absence is likely due to multiple factors, including the lack of appreciation for their potential problem-solving roles, as well as the industries' business-oriented fears that such engagement could cause them to suffer economic damage. As demands on the swine, poultry, egg, beef, and dairy production industries are closely linked to the above-mentioned complex problems, we must find new, nonthreatening ways to better engage and win animal agriculture's collaboration into One Health training and research partnerships for successful health problem solving. Without animal agricultural industries' improved cooperation, One Health's efforts to control these complex problems are not likely to succeed.
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Affiliation(s)
- Gregory C Gray
- Division of Infectious Diseases, Global Health Institute Durham, North Carolina.,Duke One Health Network, Duke University, Durham, North Carolina.,Emerging Infectious Disease Program, Duke-National University Singapore Medical School.,Global Health Research Center, Duke-Kunshan University, Jiangsu, China
| | - Jonna A K Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis
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35
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Binder RA, Alarja NA, Robie ER, Kochek KE, Xiu L, Rocha-Melogno L, Abdelgadir A, Goli SV, Farrell AS, Coleman KK, Turner AL, Lautredou CC, Lednicky JA, Lee MJ, Polage CR, Simmons RA, Deshusses MA, Anderson BD, Gray GC. Environmental and Aerosolized Severe Acute Respiratory Syndrome Coronavirus 2 Among Hospitalized Coronavirus Disease 2019 Patients. J Infect Dis 2020; 222:1798-1806. [PMID: 32905595 PMCID: PMC7499634 DOI: 10.1093/infdis/jiaa575] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/04/2020] [Indexed: 12/20/2022] Open
Abstract
During April and May 2020, we studied 20 patients hospitalized with coronavirus disease 2019 (COVID-19), their hospital rooms (fomites and aerosols), and their close contacts for molecular and culture evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Among >400 samples, we found molecular evidence of virus in most sample types, especially the nasopharyngeal (NP), saliva, and fecal samples, but the prevalence of molecular positivity among fomites and aerosols was low. The agreement between NP swab and saliva positivity was high (89.5%; κ = 0.79). Two NP swabs collected from patients on days 1 and 7 post-symptom onset had evidence of infectious virus (2 passages over 14 days in Vero E6 cells). In summary, the low molecular prevalence and lack of viable SARS-CoV-2 virus in fomites and air samples implied low nosocomial risk of SARS-CoV-2 transmission through inanimate objects or aerosols.
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Affiliation(s)
- Raquel A Binder
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Natalie A Alarja
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Emily R Robie
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Kara E Kochek
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Leshan Xiu
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lucas Rocha-Melogno
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina, USA
| | - Anfal Abdelgadir
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Sumana V Goli
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Amanda S Farrell
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Kristen K Coleman
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore
| | - Abigail L Turner
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Cassandra C Lautredou
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA
| | - John A Lednicky
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Mark J Lee
- Department of Pathology, Duke University, Durham, North Carolina, USA
| | | | - Ryan A Simmons
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA
| | - Marc A Deshusses
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina, USA
| | - Benjamin D Anderson
- Global Health Research Center, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Gregory C Gray
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore.,Global Health Research Center, Duke Kunshan University, Kunshan, Jiangsu, China
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36
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Gray GC. Adenovirus 4 and 7 Vaccine: New Body Armor for U.S. Marine Corps Officer Trainees. J Infect Dis 2020; 221:685-686. [PMID: 30753651 DOI: 10.1093/infdis/jiz061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 12/30/2022] Open
Affiliation(s)
- Gregory C Gray
- Division of Infectious Diseases, Duke University, Durham, North Carolina.,Global Health Institute, Duke University, Durham, North Carolina.,Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore.,Global Health Research Center, Duke-Kunshan University, China
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Vanderburg S, Wijayaratne G, Danthanarayana N, Jayamaha J, Piyasiri B, Halloluwa C, Sheng T, Amarasena S, Kurukulasooriya R, Nicholson BP, Peiris JSM, Gray GC, Gunasena S, Nagahawatte A, Bodinayake CK, Woods CW, Devasiri V, Tillekeratne LG. Outbreak of severe acute respiratory infection in Southern Province, Sri Lanka in 2018: a cross-sectional study. BMJ Open 2020; 10:e040612. [PMID: 33158834 PMCID: PMC7651749 DOI: 10.1136/bmjopen-2020-040612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVES To determine aetiology of illness among children and adults presenting during outbreak of severe respiratory illness in Southern Province, Sri Lanka, in 2018. DESIGN Prospective, cross-sectional study. SETTING 1600-bed, public, tertiary care hospital in Southern Province, Sri Lanka. PARTICIPANTS 410 consecutive patients, including 371 children and 39 adults, who were admitted with suspected viral pneumonia (passive surveillance) or who met case definition for acute respiratory illness (active surveillance) in May to June 2018. RESULTS We found that cocirculation of influenza A (22.6% of cases), respiratory syncytial virus (27.8%) and adenovirus (AdV) (30.7%; type B3) was responsible for the outbreak. Mortality was noted in 4.5% of paediatric cases identified during active surveillance. Virus type and viral coinfection were not significantly associated with mortality. CONCLUSIONS This is the first report of intense cocirculation of multiple respiratory viruses as a cause of an outbreak of severe acute respiratory illness in Sri Lanka, and the first time that AdV has been documented as a cause of a respiratory outbreak in the country. Our results emphasise the need for continued vigilance in surveying for known and emerging respiratory viruses in the tropics.
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Affiliation(s)
- Sky Vanderburg
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
| | | | | | - Jude Jayamaha
- Medical Research Institute Sri Lanka, Colombo, Sri Lanka
| | | | | | - Tianchen Sheng
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Durham, North Carolina, USA
| | | | | | | | | | - Gregory C Gray
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Durham, North Carolina, USA
| | | | - Ajith Nagahawatte
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
- Duke Global Health Institute, Durham, North Carolina, USA
| | - Champica K Bodinayake
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
- Duke Global Health Institute, Durham, North Carolina, USA
| | - Christopher W Woods
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Durham, North Carolina, USA
| | | | - L Gayani Tillekeratne
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
- Duke Global Health Institute, Durham, North Carolina, USA
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Rocha-Melogno L, Ginn O, Bailey ES, Soria F, Andrade M, Bergin MH, Brown J, Gray GC, Deshusses MA. Bioaerosol sampling optimization for community exposure assessment in cities with poor sanitation: A one health cross-sectional study. Sci Total Environ 2020; 738:139495. [PMID: 32425257 PMCID: PMC7233250 DOI: 10.1016/j.scitotenv.2020.139495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 05/20/2023]
Abstract
Evidence of exposure to enteric pathogens through the air and associated risk of infection is scarce in the literature outside of animal- or human-waste handling settings. Cities with poor sanitation are important locations to investigate this aerial exposure pathway as their rapid growth will pose unprecedented challenges in waste management. To address this issue, simple surveillance methods are needed. Therefore, the objectives of this study were to optimize a community exposure bioaerosol surveillance strategy for urban outdoor locations with poor sanitation, and to determine which bioaerosols could contribute to exposure. Passive and active bioaerosol sampling methods were used to characterize the fate and transport of sanitation-related bioaerosols during the rainy and dry seasons in La Paz, Bolivia. Median coliform bacteria fluxes were 71 CFU/(m2 × h) during the rainy season and 64 CFU/(m2 × h) during the dry season, with 38% of the dry season samples testing positive for E. coli. Wind speed, relative humidity and UVB irradiance were identified as significant covariates to consider in bioaerosol transport models in La Paz. Active sampling yielded one positive sample (10%) for human adenovirus (HadV) and one sample (10%) for influenza A virus during the rainy season. HadV was detected at the site with the highest bacterial flux. Four samples (8%) were positive for influenza A virus in the dry season. These findings suggest that aerosols can contribute to community exposure to potentially pathogenic microorganisms in cities with poor sanitation. The use of passive sampling, despite its limitations, can provide quantitative data on microorganisms' viability within realistic timeframes of personal exposure.
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Affiliation(s)
- Lucas Rocha-Melogno
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, United States
- Duke Global Health Institute, Duke University, Durham, NC 27710, United States
| | - Olivia Ginn
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Emily S Bailey
- Duke Global Health Institute, Duke University, Durham, NC 27710, United States
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, United States
| | - Freddy Soria
- Centro de Investigación en Agua, Energía y Sostenibilidad, Universidad Católica Boliviana San Pablo, La Paz, Bolivia
| | - Marcos Andrade
- Laboratory for Atmospheric Physics, Institute for Physics Research, Universidad Mayor de San Andres, La Paz, Bolivia
- Department of Atmospheric and Oceanic Sciences, University of Maryland, College Park, MD, United States
| | - Michael H Bergin
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, United States
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Gregory C Gray
- Duke Global Health Institute, Duke University, Durham, NC 27710, United States
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, United States
- Global Health Research Center, Duke-Kunshan University, Kunshan, China
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore
| | - Marc A Deshusses
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, United States
- Duke Global Health Institute, Duke University, Durham, NC 27710, United States
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Coleman KK, Wong CC, Jayakumar J, Nguyen TT, Wong AWL, Yadana S, Thoon KC, Chan KP, Low JG, Kalimuddin S, Dehghan S, Kang J, Shamsaddini A, Seto D, Su YCF, Gray GC. Adenoviral Infections in Singapore: Should New Antiviral Therapies and Vaccines Be Adopted? J Infect Dis 2020; 221:566-577. [PMID: 31563943 PMCID: PMC7107482 DOI: 10.1093/infdis/jiz489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/25/2019] [Indexed: 01/09/2023] Open
Abstract
Background A number of serious human adenovirus (HAdV) outbreaks have been recently reported: HAdV-B7 (Israel, Singapore, and USA), HAdV-B7d (USA and China), HAdV-D8, -D54, and -C2 (Japan), HAdV-B14p1 (USA, Europe, and China), and HAdV-B55 (China, Singapore, and France). Methods To understand the epidemiology of HAdV infections in Singapore, we studied 533 HAdV-positive clinical samples collected from 396 pediatric and 137 adult patients in Singapore from 2012 to 2018. Genome sequencing and phylogenetic analyses were performed to identify HAdV genotypes, clonal clusters, and recombinant or novel HAdVs. Results The most prevalent genotypes identified were HAdV-B3 (35.6%), HAdV-B7 (15.4%), and HAdV-E4 (15.2%). We detected 4 new HAdV-C strains and detected incursions with HAdV-B7 (odds ratio [OR], 14.6; 95% confidence interval [CI], 4.1–52.0) and HAdV-E4 (OR, 13.6; 95% CI, 3.9–46.7) among pediatric patients over time. In addition, immunocompromised patients (adjusted OR [aOR], 11.4; 95% CI, 3.8–34.8) and patients infected with HAdV-C2 (aOR, 8.5; 95% CI, 1.5–48.0), HAdV-B7 (aOR, 3.7; 95% CI, 1.2–10.9), or HAdV-E4 (aOR, 3.2; 95% CI, 1.1–8.9) were at increased risk for severe disease. Conclusions Singapore would benefit from more frequent studies of clinical HAdV genotypes to identify patients at risk for severe disease and help guide the use of new antiviral therapies, such as brincidofovir, and potential administration of HAdV 4 and 7 vaccine.
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Affiliation(s)
- Kristen K Coleman
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore
| | - Chui Ching Wong
- Department of Microbiology, Singapore General Hospital, Singapore
| | - Jayanthi Jayakumar
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore
| | - Tham T Nguyen
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore
| | - Abigail W L Wong
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Su Yadana
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore
| | - Koh C Thoon
- Department of Paediatrics, Infectious Disease Service, KK Women's and Children's Hospital, Singapore
| | - Kwai Peng Chan
- Department of Microbiology, Singapore General Hospital, Singapore.,Academic Clinical Programme for Pathology, Duke-NUS Medical School, Singapore
| | - Jenny G Low
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore.,Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Shirin Kalimuddin
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Shoaleh Dehghan
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA.,Chemistry Department, American University, Washington, District of Columbia, USA
| | - June Kang
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Amirhossein Shamsaddini
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Yvonne C F Su
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore
| | - Gregory C Gray
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore.,Division of Infectious Diseases, Global Health Institute, and Nicholas School of the Environment, Duke University, Durham, North Carolina, USA.,Global Health Center, Duke Kunshan University, Kunshan, China
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40
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Farrell AS, Bui VN, Dao TD, Hoang TD, Gray GC. No influenza D virus detected among pigs, northern Vietnam. Influenza Other Respir Viruses 2020; 15:315-317. [PMID: 32959521 PMCID: PMC7902251 DOI: 10.1111/irv.12812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- Amanda S Farrell
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Vuong N Bui
- Vietnam National Institute of Veterinary Research, Hanoi, Viet Nam
| | - Tung D Dao
- Vietnam National Institute of Veterinary Research, Hanoi, Viet Nam
| | - Trung D Hoang
- Vietnam National Institute of Veterinary Research, Hanoi, Viet Nam
| | - Gregory C Gray
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA.,Global Health Research Center, Duke Kunshan University, Kunshan, China.,Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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Fieldhouse JK, Bailey ES, Toh TH, Hii KC, Mallinson KA, Ting J, Lednicky JA, Berita A, Nguyen TT, Galan D, Than ST, Wong SC, Wong TM, Blair PJ, Gray GC. Panspecies molecular assays detect viral pathogens missed by real-time PCR/reverse-transcriptase PCR among pneumonia patients, Sarawak, Malaysia. Trop Dis Travel Med Vaccines 2020; 6:13. [PMID: 32817802 PMCID: PMC7422451 DOI: 10.1186/s40794-020-00114-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/27/2020] [Indexed: 11/10/2022]
Abstract
Background In a year-long pneumonia etiology study conducted June 2017 to May 2018 in Sarawak, Malaysia, 599 patients' nasopharyngeal swab specimens were studied with real-time polymerase chain reaction (rPCR)/ reverse-transcription (rRT-PCR) assays for respiratory pathogens known to contribute to the high burden of lower respiratory tract infections. The study team sought to compare real-time assay results with panspecies conventional molecular diagnostics to compare sensitivities and learn if novel viruses had been missed. Methods Specimens were studied for evidence of adenovirus (AdV), enterovirus (EV) and coronavirus (CoV) with panspecies gel-based nested PCR/RT-PCR assays. Gene sequences of specimens positive by panspecies assays were sequenced and studied with the NCBI Basic Local Alignment Search Tool software. Results There was considerable discordance between real-time and conventional molecular methods. The real-time AdV assay found a positivity of 10.4%; however, the AdV panspecies assay detected a positivity of 12.4% and the conventional AdV-Hexon assay detected a positivity of 19.6%. The CoV and EV panspecies assays similarly detected more positive specimens than the real-time assays, with a positivity of 7.8% by the CoV panspecies assay versus 4.2% by rRT-PCR, and 8.0% by the EV panspecies assay versus 1.0% by rRT-PCR. We were not able to ascertain virus viability in this setting. While most discordance was likely due to assay sensitivity for previously described human viruses, two novel, possible zoonotic AdV were detected. Conclusions The observed differences in the two modes of amplification suggest that where a problem with sensitivity is suspected, real-time assay results might be supplemented with panspecies conventional PCR/RT-PCR assays.
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Affiliation(s)
- Jane K Fieldhouse
- Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC 27710 USA.,Duke Global Health Institute, Duke University, Durham, North Carolina USA.,Institute for Global Health Sciences, University of California, San Francisco, California USA
| | - Emily S Bailey
- Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC 27710 USA.,Duke Global Health Institute, Duke University, Durham, North Carolina USA.,Department of Public Health, Texas Tech University Health Sciences Center, Abilene, TX USA
| | - Teck-Hock Toh
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak Malaysia.,Faculty of Medicine, SEGi University, Kota Damansara, Selangor Malaysia.,Department of Paediatrics, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak Malaysia
| | - King-Ching Hii
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak Malaysia
| | - Kerry A Mallinson
- Duke Global Health Institute, Duke University, Durham, North Carolina USA
| | - Jakie Ting
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak Malaysia.,Faculty of Medicine, SEGi University, Kota Damansara, Selangor Malaysia
| | - John A Lednicky
- Department of Environmental and Global Health, University of Florida, Gainesville, Florida USA.,Emerging Pathogens Institute, University of Florida, Gainesville, Florida USA
| | - Antoinette Berita
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak Malaysia
| | - Tham Thi Nguyen
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Diego Galan
- Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC 27710 USA.,Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - Son T Than
- Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
| | - See-Chang Wong
- Faculty of Medicine, SEGi University, Kota Damansara, Selangor Malaysia.,Department of Paediatrics, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak Malaysia
| | - Toh-Mee Wong
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak Malaysia.,Faculty of Medicine, SEGi University, Kota Damansara, Selangor Malaysia.,Department of Medicine, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak Malaysia
| | | | - Gregory C Gray
- Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC 27710 USA.,Duke Global Health Institute, Duke University, Durham, North Carolina USA.,Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore.,Global Health Center, Duke Kunshan University, Kunshan, China
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Abstract
Background: Worldwide, horses play critical roles in recreation, food production, transportation, and as working animals. Horses' roles differ by geographical region and the socioeconomic status of the people, but despite modern advances in transportation, which have in some ways altered humans contact with horses, potential risks for equine zoonotic pathogen transmission to humans occur globally. While previous reports have focused upon individual or groups of equine pathogens, to our knowledge, a systematic review of equine zoonoses has never been performed. Methods: Using PRISMA's systematic review guidelines, we searched the English literature and identified 233 previous reports of potential equine zoonoses found in horses. We studied and summarized their findings with a goal of identifying risk factors that favor disease transmission from horses to humans. Results: These previous reports identified 56 zoonotic pathogens that have been found in horses. Of the 233 articles, 13 involved direct transmission to humans (5.6%).The main potential routes of transmission included oral, inhalation, and cutaneous exposures. Pathogens most often manifest in humans through systemic, gastrointestinal, and dermatological signs and symptoms. Furthermore, 16.1% were classified as emerging infectious diseases and thus may be less known to both the equine and human medical community. Sometimes, these infections were severe leading to human and equine death. Conclusions: While case reports of zoonotic infections directly from horses remain low, there is a high potential for underreporting due to lack of knowledge among health professionals. Awareness of these zoonotic pathogens, their disease presentation in horses and humans, and their associated risk factors for cross-species infection are important to public health officials, clinicians, and people with recreational or occupational equid exposure.
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Affiliation(s)
- Alexandra Sack
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Tufts Clinical and Translational Science Institute, Tufts University School of Medicine Boston, Massachusetts, USA
| | - Fatai S. Oladunni
- Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
- Department of Veterinary Microbiology, University of Ilorin, Ilorin, Nigeria
| | - Battsetseg Gonchigoo
- Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, Mongolia
| | - Thomas M. Chambers
- Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Gregory C. Gray
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Global Health Research Center, Duke-Kunshan University, Kunshan, China
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore
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Anderson BD, Yondon M, Bailey ES, Duman EK, Simmons RA, Greer AG, Gray GC. Environmental bioaerosol surveillance as an early warning system for pathogen detection in North Carolina swine farms: A pilot study. Transbound Emerg Dis 2020; 68:361-367. [PMID: 32535997 DOI: 10.1111/tbed.13683] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 05/19/2020] [Accepted: 06/07/2020] [Indexed: 02/02/2023]
Abstract
Disease outbreaks can readily threaten swine production operations sometimes resulting in large economic losses. Pathogen surveillance in swine farms can be an effective approach for the early identification of new disease threats and the mitigation of transmission before broad dissemination among a herd occurs. Non-invasive environmental bioaerosol sampling could be an effective and affordable approach for conducting routine surveillance in farms, providing an additional tool for farmers to protect their animals and themselves from new disease threats. In this pilot study, we implemented a non-invasive, prospective bioaerosol sampling strategy in a swine farm located in the United States to detect economically important swine pathogens. Farm personnel collected air samples from two swine barns for 23 weeks between July and December 2017. Samples were then tested within 24 hr of collection by molecular techniques for a number of economically important swine pathogens. Of the 86 bioaerosol samples collected, 4 (4.7%) were positive for influenza A, 1 (1.2%) was positive for influenza D, 13 (15.1%) were positive for PCV2, and 13 (15.1%) were positive for PCV3. Overall, this pilot study showed that our bioaerosol surveillance strategy was feasible and able to generate data that could be quickly disseminated back to the farm stakeholders (within 24 hr). We were also able to identify PCV2, PCV3 and influenza A virus in air samples as clinical disease became apparent in the pigs, strongly suggesting that bioaerosol sampling can be used as an effective non-invasive surveillance approach for the detection of multiple pathogens in this and likely other animal production environments.
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Affiliation(s)
- Benjamin D Anderson
- Division of Infectious Disease, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA.,Global Health Research Center and Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China.,North Carolina Agromedicine Institute, Greenville, NC, USA
| | - Myagmarsukh Yondon
- Division of Infectious Disease, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Emily S Bailey
- Division of Infectious Disease, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Ege K Duman
- Global Health Research Center and Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Ryan A Simmons
- Duke Global Health Institute, Duke University, Durham, NC, USA.,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Annette G Greer
- North Carolina Agromedicine Institute, Greenville, NC, USA.,Department of Bioethics and Interdisciplinary Studies, East Carolina University, Greenville, NC, USA
| | - Gregory C Gray
- Division of Infectious Disease, School of Medicine, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA.,Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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Chia PY, Coleman KK, Tan YK, Ong SWX, Gum M, Lau SK, Lim XF, Lim AS, Sutjipto S, Lee PH, Son TT, Young BE, Milton DK, Gray GC, Schuster S, Barkham T, De PP, Vasoo S, Chan M, Ang BSP, Tan BH, Leo YS, Ng OT, Wong MSY, Marimuthu K. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients. Nat Commun 2020; 11:2800. [PMID: 32472043 DOI: 10.1101/2020.03.29.20046557] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/18/2020] [Indexed: 05/20/2023] Open
Abstract
Understanding the particle size distribution in the air and patterns of environmental contamination of SARS-CoV-2 is essential for infection prevention policies. Here we screen surface and air samples from hospital rooms of COVID-19 patients for SARS-CoV-2 RNA. Environmental sampling is conducted in three airborne infection isolation rooms (AIIRs) in the ICU and 27 AIIRs in the general ward. 245 surface samples are collected. 56.7% of rooms have at least one environmental surface contaminated. High touch surface contamination is shown in ten (66.7%) out of 15 patients in the first week of illness, and three (20%) beyond the first week of illness (p = 0.01, χ2 test). Air sampling is performed in three of the 27 AIIRs in the general ward, and detects SARS-CoV-2 PCR-positive particles of sizes >4 µm and 1-4 µm in two rooms, despite these rooms having 12 air changes per hour. This warrants further study of the airborne transmission potential of SARS-CoV-2.
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Affiliation(s)
- Po Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | | | | | - Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Marcus Gum
- DSO National Laboratories, Singapore, Singapore
| | | | | | - Ai Sim Lim
- DSO National Laboratories, Singapore, Singapore
| | - Stephanie Sutjipto
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Pei Hua Lee
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Than The Son
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Donald K Milton
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
| | - Gregory C Gray
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- School of Medicine and Global Health Institute, Duke University, Durham, NC, USA
- Global Health Research Center, Duke Kunshan University, Kunshan, China
| | - Stephan Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Timothy Barkham
- Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Partha Pratim De
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Monica Chan
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Brenda Sze Peng Ang
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Oon-Tek Ng
- National Centre for Infectious Diseases, Singapore, Singapore.
- Tan Tock Seng Hospital, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
| | | | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore, Singapore.
- Tan Tock Seng Hospital, Singapore, Singapore.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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45
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Zemke JN, Sanchez JL, Pang J, Gray GC. The Double-Edged Sword of Military Response to Societal Disruptions: A Systematic Review of the Evidence for Military Personnel as Pathogen Transmitters. J Infect Dis 2020; 220:1873-1884. [PMID: 31519020 DOI: 10.1093/infdis/jiz400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/02/2019] [Indexed: 11/12/2022] Open
Abstract
Given their lack of immunity and increased exposure, military personnel have the potential to serve as carriers or reservoirs for infectious diseases into or out of the deployment areas, but, to our knowledge, the historical evidence for such transmission events has not previously been reviewed. Using PubMed, we performed a systematic review of published literature between 1955 and 2018, which documented evidence for military personnel transporting infectious pathogens into or out of deployment areas. Of the 439 articles screened, 67 were included for final qualitative and quantitative review. The data extracted from these articles described numerous instances in which thousands of military service members demonstrated potential or actual transmission and transportation of multiple diverse pathogens. These data underscore the immense importance preventive medical professionals play in mitigating such risk, how their public health efforts must be supported, and the importance of surveillance in protecting both military and civilian populations.
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Affiliation(s)
- Juliana N Zemke
- Duke Global Health Institute, Duke University, Durham, North Carolina.,Division of Infectious Diseases, Duke University, Durham, North Carolina
| | - Jose L Sanchez
- Department of Defense, Defense Health Agency, Public Health Division, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Junxiong Pang
- Duke Global Health Institute, Duke University, Durham, North Carolina.,Centre for Infectious Disease Epidemiology & Research, Saw Swee Hock School of Public Health, National University of Singapore
| | - Gregory C Gray
- Duke Global Health Institute, Duke University, Durham, North Carolina.,Division of Infectious Diseases, Duke University, Durham, North Carolina.,Emerging Infectious Disease Program, Duke-National University of Singapore Medical School, Singapore.,Global Health Research Center, Duke-Kunshan University, Kunshan, China
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46
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Choi JY, Hii KC, Bailey ES, Chuang JY, Tang WY, Yuen Wong EK, Ti T, Pau KS, Berita A, Saihidi I, Ting J, Chua TT, Toh TH, AuCoin DP, DeShazer D, Gray GC. Burkholderia pseudomallei Detection among Hospitalized Patients, Sarawak. Am J Trop Med Hyg 2020; 102:388-391. [PMID: 31769397 DOI: 10.4269/ajtmh.19-0625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Burkholderia pseudomallei infections are prevalent in Southeast Asia and northern Australia and often misdiagnosed. Diagnostics are often neither sensitive nor rapid, contributing up to 50% mortality rate. In this 2018 pilot study, we enrolled 100 patients aged 6 months-79 years from Kapit Hospital in Sarawak, Malaysia, with symptoms of B. pseudomallei infection. We used three different methods for the detection of B. pseudomallei: a real-time polymerase chain reaction (PCR) assay, a rapid lateral flow immunoassay, and the standard-of-care bacterial culture-the gold standard. Among the 100 participants, 24 (24%) were positive for B. pseudomallei by one or more of the detection methods. Comparing the two individual diagnostic methods against the gold standard-bacterial culture-of any positive test, there was low sensitivity for each test (25-44%) but high specificity (93-98%). It seems clear that more sensitive diagnostics or a sensitive screening diagnostic followed by specific confirmatory diagnostic is needed for this disease.
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Affiliation(s)
- Jessica Y Choi
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina.,Duke Global Health Institute, Duke University, Durham, North Carolina
| | - King Ching Hii
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Emily S Bailey
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina.,Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Jia Yun Chuang
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Wei Yieng Tang
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | | | - Tiana Ti
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Kat Siong Pau
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Antoinette Berita
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Izreena Saihidi
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Jakie Ting
- Faculty of Medicine, SEGi University, Kota Damansara, Malaysia.,Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | - Tiing-Tiing Chua
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | - Teck-Hock Toh
- Faculty of Medicine, SEGi University, Kota Damansara, Malaysia.,Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | | | - David DeShazer
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Gregory C Gray
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore.,Duke Global Health Institute, Duke University, Durham, North Carolina.,Global Health Research Center, Duke-Kunshan University, Kunshan, China.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina
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47
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Le YH, Nguyen KC, Coleman KK, Nguyen TT, Than ST, Phan HH, Nguyen MD, Ngu ND, Phan DT, Hoang PVM, Trieu LP, Bailey ES, Warkentien TE, Gray GC. Virus detections among patients with severe acute respiratory illness, Northern Vietnam. PLoS One 2020; 15:e0233117. [PMID: 32396550 PMCID: PMC7217455 DOI: 10.1371/journal.pone.0233117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/28/2020] [Indexed: 01/02/2023] Open
Abstract
Severe acute respiratory illness (SARI) is a major cause of death and morbidity in low- and middle-income countries, however, the etiologic agents are often undetermined due to the lack of molecular diagnostics in hospitals and clinics. To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017–2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. Patient demographics were recorded and used to epidemiologically describe the infections. Among military and civilian cases of SARI, 184 (52.9%) tested positive for one or more respiratory viruses. Influenza A virus was the most prevalent virus detected (64.7%), followed by influenza B virus (29.3%), enterovirus (3.8%), adenovirus (1.1%), and coronavirus (1.1%). Risk factor analyses demonstrated an increased risk of influenza A virus detection among military hospital patients (adjusted OR, 2.0; 95% CI, 1.2–3.2), and an increased risk of influenza B virus detection among patients enrolled in year 2017 (adjusted OR, 7.9; 95% CI, 2.7–22.9). As influenza A and B viruses were commonly associated with SARI and are treatable, SARI patients entering these hospitals would benefit if the hospitals were able to adapt onsite molecular diagnostics.
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Affiliation(s)
- Yen H. Le
- Military Institute of Preventive Medicine, Hanoi, Vietnam
| | - Khanh C. Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Kristen K. Coleman
- Emerging Infectious Diseases Programme, Duke-National University of Singapore, Singapore
| | - Tham T. Nguyen
- Emerging Infectious Diseases Programme, Duke-National University of Singapore, Singapore
| | - Son T. Than
- Emerging Infectious Diseases Programme, Duke-National University of Singapore, Singapore
| | - Hai H. Phan
- Hai Phong Provincial Preventive Medicine Center, Hai Phong, Vietnam
| | - Manh D. Nguyen
- Military Institute of Preventive Medicine, Hanoi, Vietnam
| | - Nghia D. Ngu
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Dan T. Phan
- Military Institute of Preventive Medicine, Hanoi, Vietnam
| | | | - Long P. Trieu
- Military Institute of Preventive Medicine, Hanoi, Vietnam
| | - Emily S. Bailey
- Division of Infectious Diseases, Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | | | - Gregory C. Gray
- Emerging Infectious Diseases Programme, Duke-National University of Singapore, Singapore
- Division of Infectious Diseases, Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Global Health Center, Duke Kunshan University, Kunshan, China
- * E-mail:
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48
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Bui VN, Nguyen TT, Nguyen-Viet H, Bui AN, McCallion KA, Lee HS, Than ST, Coleman KK, Gray GC. Bioaerosol Sampling to Detect Avian Influenza Virus in Hanoi's Largest Live Poultry Market. Clin Infect Dis 2020; 68:972-975. [PMID: 30184114 DOI: 10.1093/cid/ciy583] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/11/2018] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Newly emergent and virulent strains of H7N9 avian influenza virus are rapidly spreading in China and threaten to invade Vietnam. We sought to introduce aerosol sampling for avian influenza viruses in Vietnam. METHODS During October 2017, National Institute for Occupational Safety and Health 2-stage aerosol samplers were assembled on a tripod and run for 4 hours. Concomitantly, up to 20 oropharyngeal (OP) swab samples were collected from chickens and ducks distanced at 0.2-1.5 m from each sampler. RESULTS The 3 weeks of sampling yielded 30 aerosol samples that were 90% positive for influenza A, by quantitative reverse-transcription polymerase chain reaction, and 116 OP swab sample pools (5 samples per pool) that were 47% positive. Egg cultures yielded 1 influenza A virus (not H5 or H7) from aerosol and 25 influenza A viruses from OP swab sample pools (5 were H5 positive). The association between positive sample types (over time and position) was strong, with 91.7% of positive OP pooled swab samples confirmed by positive aerosol samples and 81% of influenza A positive aerosol samples confirmed by positive OP swab samples. CONCLUSIONS We posit that aerosol sampling might be used for early warning screening of poultry markets for novel influenza virus detection, such as H7N9. Markets with positive aerosol samples might be followed up with more focused individual bird or cage swabbing, and back-tracing could be performed later to locate specific farms harboring novel virus. Culling birds in such farms could reduce highly pathogenic avian influenza virus spread among poultry and humans.
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Affiliation(s)
- Vuong N Bui
- Virology Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Tham T Nguyen
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Hung Nguyen-Viet
- International Livestock Research Institute, Hanoi, Vietnam.,Center for Public Health and Ecosystem Research, Hanoi University of Public Health, Vietnam
| | - Anh N Bui
- Virology Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Katie A McCallion
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Hu Suk Lee
- International Livestock Research Institute, Hanoi, Vietnam
| | - Son T Than
- Virology Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Kristen K Coleman
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Gregory C Gray
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Division of Infectious Diseases, Global Health Institute, and Nicholas School of the Environment, Duke University, Durham, North Carolina.,Global Health Research Center, Duke-Kunshan University, China
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49
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Wang X, Bailey ES, Qi X, Yu H, Bao C, Gray GC. Bioaerosol Sampling at a Live Animal Market in Kunshan, China: A Noninvasive Approach for Detecting Emergent Viruses. Open Forum Infect Dis 2020; 7:ofaa134. [PMID: 32462044 PMCID: PMC7240344 DOI: 10.1093/ofid/ofaa134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/16/2020] [Indexed: 12/17/2022] Open
Affiliation(s)
- Xinye Wang
- Global Health Research Center, Duke Kunshan University, Kunshan, China
| | - Emily S Bailey
- Division of Infectious Diseases, School of Medicine, Duke University, Durham Durham, North Carolina, USA.,Global Health Institute, Duke University, Durham, North Carolina, USA.,Julia Jones Matthews Department of Public Health, Texas Tech University Health Sciences Center, Abilene, Texas, USA
| | - Xian Qi
- Department of Acute Infectious Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Huiyan Yu
- Department of Acute Infectious Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Changjun Bao
- Department of Acute Infectious Disease, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Gregory C Gray
- Global Health Research Center, Duke Kunshan University, Kunshan, China.,Division of Infectious Diseases, School of Medicine, Duke University, Durham Durham, North Carolina, USA.,Nicholas School, Duke University, Durham, North Carolina, USA.,Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore
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Bailey ES, Fieldhouse JK, Alarja NA, Chen DD, Kovalik ME, Zemke JN, Choi JY, Borkenhagen LK, Toh TH, Lee JSY, Chong KS, Gray GC. First sequence of influenza D virus identified in poultry farm bioaerosols in Sarawak, Malaysia. Trop Dis Travel Med Vaccines 2020; 6:5. [PMID: 32190346 PMCID: PMC7069008 DOI: 10.1186/s40794-020-0105-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/26/2020] [Indexed: 12/28/2022]
Abstract
In 2018, our team collected aerosols samples from five poultry farms in Malaysia. Influenza D virus was detected in 14% of samples. One sample had an 86.3% identity score similar to NCBI accession number MH785020.1. This is the first molecular sequence of influenza D virus detected in Southeast Asia from a bioaerosol sample. Our findings indicate that further study of role of IDV in poultry is necessary.
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Affiliation(s)
- Emily S Bailey
- 1Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC 27710 USA.,2Duke Global Health Institute, Duke University, Durham, North Carolina USA.,3Julia Jones Matthews Department of Public Health, Texas Tech University Health Sciences Center, Abilene, TX USA
| | - Jane K Fieldhouse
- 1Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC 27710 USA.,2Duke Global Health Institute, Duke University, Durham, North Carolina USA
| | - Natalie A Alarja
- 1Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC 27710 USA.,2Duke Global Health Institute, Duke University, Durham, North Carolina USA
| | - David D Chen
- 2Duke Global Health Institute, Duke University, Durham, North Carolina USA
| | - Maria E Kovalik
- 2Duke Global Health Institute, Duke University, Durham, North Carolina USA
| | - Juliana N Zemke
- 2Duke Global Health Institute, Duke University, Durham, North Carolina USA
| | - Jessica Y Choi
- 2Duke Global Health Institute, Duke University, Durham, North Carolina USA
| | - Laura K Borkenhagen
- 1Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC 27710 USA.,2Duke Global Health Institute, Duke University, Durham, North Carolina USA
| | - Teck-Hock Toh
- 4Clinical Research Center, Sibu Hospital, Sibu, Sarawak Malaysia.,5Faculty of Medicine, SEGi University, Kota Damansara, Selangor Malaysia
| | | | - Kuek-Sen Chong
- 5Faculty of Medicine, SEGi University, Kota Damansara, Selangor Malaysia.,Divisional Health Office, Sibu, Sarawak Malaysia
| | - Gregory C Gray
- 1Division of Infectious Diseases, Duke University School of Medicine, DUMC Box 102359, Durham, NC 27710 USA.,2Duke Global Health Institute, Duke University, Durham, North Carolina USA.,7Global Health Research Center, Duke-Kunshan University, Kunshan, China.,8Emerging Infectious Disease Program, Duke-NUS Medical School, Singapore, Singapore
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