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Guo Z, Xing G, Wang L, Jin Q, Lu Q, Zhang G. Potential Pathogenicity and Genetic Characteristics of a Live-Attenuated Classical Swine Fever Virus Vaccine Derivative Variant. Transbound Emerg Dis 2024; 2024:1-6. [DOI: 10.1155/2024/7244445] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] [Imported: 04/14/2024]
Abstract
Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease affecting pigs and causing massive pig production losses with severe global economic recession. The immunization of live-attenuated vaccines is still one of the key measures to CSFV management in endemic countries. However, there are also strong controversies about the usage of live-attenuated vaccines, particularly in pregnant sows and young pigs, such as in Europe, where domestic pigs are routinely not vaccinated until severe outbreaks occur. Here, we report a CSF outbreak in a pig farm in China, which affected more than 90% of the delivery sows and led to ∼45% birth loss. Surprisingly, phylogenetic analysis showed that the CSFV isolate (named CSFV/HeNLY2022, GenBank No. OR195698) was clustered into subgenotype 1.1a, closely together with the live-attenuated vaccine strains. Further genomic analysis also revealed that the isolate CSFV/HeNLY2022 shared the highest nucleotide identity of 99.7% with the C/HVRI vaccine strain (C-strain, GenBank No. AY805221). Moreover, compared to the C/HVRI strain, a total of eight amino acid mutations, distributed in Erns (H436thY and S476thR), E1 (T502thI and P581thT), E2 (M979thK and A1061thS), NS5A (A2980thT), and NS5B (I3818thM), were characterized in the CSFV/HeNLY2022 isolate. Our results suggested that the CSF outbreak was most likely caused by the live-attenuated CSFV vaccine or its derivative. It raises concern that the unscientific application of CSFV vaccines could potentially lead to CSFV spread in pigs. It is needed to perform a more rigorous evaluation of the safety of the C-strain-derived vaccines in combination with other different live-attenuated vaccines.
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Affiliation(s)
- Zhenhua Guo
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Institute for Animal Health, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Guangxu Xing
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Institute for Animal Health, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Qianyue Jin
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Institute for Animal Health, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qingxia Lu
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Institute for Animal Health, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Gaiping Zhang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Institute for Animal Health, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Longhu Modern Immunity Laboratory, Zhengzhou, Henan, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
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2
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Savard C, Wang L. Identification and Genomic Characterization of Bovine Boosepivirus A in the United States and Canada. Viruses 2024; 16:307. [DOI: https:/doi.org/10.3390/v16020307] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] [Imported: 02/21/2024] Open
Abstract
Boosepivirus is a new genus in the Picornaviridae family. Boosepiviruses (BooVs) are genetically classified into three species: A, B, and C. Initially, Boosepivirus A and B were identified in cattle, whereas Boosepivirus C was detected in sheep. Recent evidence showed that Boosepivirus B was detected in sheep and Boosepivirus C was identified in goats, suggesting that Boosepvirus might cross the species barrier to infect different hosts. Different from BooV B, BooV A is less studied. In the present study, we reported identification of two North American BooV A strains from cattle. Genomic characterization revealed that US IL33712 (GenBank accession #PP035161) and Canada 1087562 (GenBank accession #PP035162) BooV A strains are distantly related to each other, and US IL33712 is more closely correlated to two Asian BooV A strains. US-strain-specific insertions, NorthAmerican-strain-specific insertions, and species A-specific insertions are observed and could contribute to viral pathogenicity and host adaptation. Our findings highlight the importance of continued surveillance of BooV A in animals.
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Affiliation(s)
- Christian Savard
- Biovet Inc., 4375, Avenue Beaudry, Saint-Hyacinthe, QC J2S 8W2, Canada
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
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3
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Drozd M, Ritter JM, Samuelson JP, Parker M, Wang L, Sander SJ, Yoshicedo J, Wright L, Odani J, Shrader T, Lee E, Lockhart SR, Ghai RR, Terio KA. Mortality associated with SARS-CoV-2 in nondomestic felids. Vet Pathol 2024. [DOI: https:/doi.org/10.1177/03009858231225500] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] [Imported: 02/21/2024]
Abstract
Between September and November 2021, 5 snow leopards ( Panthera uncia) and 1 lion ( Panthera leo) were naturally infected with severe acute respiratory coronavirus 2 (SARS-CoV-2) and developed progressive respiratory disease that resulted in death. Severe acute respiratory syndrome coronavirus 2 sequencing identified the delta variant in all cases sequenced, which was the predominant human variant at that time. The time between initial clinical signs and death ranged from 3 to 45 days. Gross lesions in all 6 cats included nasal turbinate hyperemia with purulent discharge and marked pulmonary edema. Ulcerative tracheitis and bronchitis were noted in 4 cases. Histologically, there was necrotizing and ulcerative rhinotracheitis and bronchitis with fibrinocellular exudates and fibrinosuppurative to pyogranulomatous bronchopneumonia. The 4 cats that survived longer than 8 days had fungal abscesses. Concurrent bacteria were noted in 4 cases, including those with more acute disease courses. Severe acute respiratory syndrome coronavirus 2 was detected by in situ hybridization using probes against SARS-CoV-2 spike and nucleocapsid genes and by immunohistochemistry. Viral nucleic acid and protein were variably localized to mucosal and glandular epithelial cells, pneumocytes, macrophages, and fibrinocellular debris. Based on established criteria, SARS-CoV-2 was considered a contributing cause of death in all 6 cats. While mild clinical infections are more common, these findings suggest that some SARS-CoV-2 variants may cause more severe disease and that snow leopards may be more severely affected than other felids.
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Affiliation(s)
- Mary Drozd
- University of Nebraska–Lincoln, Lincoln, NE
| | | | | | | | - Leyi Wang
- University of Illinois Urbana-Champaign, Urbana, IL
| | | | | | - Louden Wright
- Great Plain Zoo, Sioux Falls, SD
- Nashville Zoo at Grassmere, Nashville, TN
| | - Jenee Odani
- University of Hawai‘i at Mānoa, Honolulu, HI
| | | | - Elizabeth Lee
- Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Ria R. Ghai
- Centers for Disease Control and Prevention, Atlanta, GA
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4
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Tewari D, Miller R, Livengood J, Wang L, Killian ML, Bustamante F, Kessler C, Thirumalapura N, Terio K, Torchetti M, Lantz K, Rosenberg J. SARS-CoV-2 Infection Dynamics in the Pittsburgh Zoo Wild Felids with Two Viral Variants (Delta and Alpha) during the 2021-2022 Pandemic in the United States. Animals (Basel) 2023; 13:3094. [PMID: 37835700 PMCID: PMC10571823 DOI: 10.3390/ani13193094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/17/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] [Imported: 10/19/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported in multiple animal species besides humans. The goal of this study was to report clinical signs, infection progression, virus detection and antibody response in a group of wild felids housed in adjacent but neighboring areas at the Pittsburgh Zoo. Initially, five African lions (Panthera leo krugeri) housed together exhibited respiratory clinical signs with viral shedding in their feces in March of 2021 coinciding with infection of an animal keeper. During the second infection wave in December 2021, four Amur tigers (Panthera tigris altaica) and a Canadian lynx (Lynx canadensis) showed clinical signs and tested positive for viral RNA in feces. In infected animals, viral shedding in feces was variable lasting up to 5 weeks and clinical signs were observed for up to 4 weeks. Despite mounting an antibody response to initial exposure, lions exhibited respiratory clinical signs during the second infection wave, but none shed the virus in their feces. The lions were positive for alpha variant (B.1.1.7 lineage) during the first wave and the tiger and lynx were positive for delta variant (AY.25.1. lineage) during the second wave. The viruses recovered from felids were closely related to variants circulating in human populations at the time of the infection. Cheetahs (Acinonyx jubatus) in the park did not show either the clinical signs or the antibody response.
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Affiliation(s)
- Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Ryan Miller
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Julia Livengood
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Leyi Wang
- Illinois Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA;
| | - Mary Lea Killian
- National Veterinary Services Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.T.); (K.L.)
| | - Felipe Bustamante
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Candy Kessler
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Nagaraja Thirumalapura
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Karen Terio
- Zoological Pathology Program, University of Illinois, Brookfield, IL 60513, USA;
| | - Mia Torchetti
- National Veterinary Services Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.T.); (K.L.)
| | - Kristina Lantz
- National Veterinary Services Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.T.); (K.L.)
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Bartlett SL, Koeppel KN, Cushing AC, Bellon HF, Almagro V, Gyimesi ZS, Thies T, Hård T, Denitton D, Fox KZ, Vodička R, Wang L, Calle PP. GLOBAL RETROSPECTIVE REVIEW OF SEVERE ACUTE RESPIRATORY SYNDROME SARS COV-2 INFECTIONS IN NONDOMESTIC FELIDS: MARCH 2020-FEBRUARY 2021. J Zoo Wildl Med 2023; 54:607-616. [PMID: 37817628 DOI: 10.1638/2022-0141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 10/12/2023] [Imported: 10/19/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in nondomestic felids have been documented in North America, South America, Africa, Europe, and Asia. Between March 2020 and February 2021, at nine institutions across three continents, infection was confirmed in 16 tigers (Panthera tigris), 14 lions (Panthera leo), three snow leopards (Panthera uncia), one cougar (Puma concolor), and one Amur leopard cat (Prionailurus bengalensis euptilurus) ranging from 2 to 21 yr old (average, 10 yr). Infection was suspected in an additional 12 tigers, 4 lions, and 9 cougars. Clinical signs (in order of most to least common) included coughing, ocular and/or nasal discharge, wheezing, sneezing, decreased appetite, lethargy, diarrhea, and vomiting. Most felids recovered uneventfully, but one geriatric tiger with comorbidities developed severe dyspnea and neurologic signs necessitating euthanasia. Clinical signs lasted 1-19 d (average, 8 d); one tiger was asymptomatic. Infection was confirmed by various methods, including antigen tests and/or polymerase chain reaction (PCR) of nasal or oral swabs, tracheal wash, and feces, or virus isolation from feces or tracheal wash. Infection status and resolution were determined by testing nasal swabs from awake animals, fecal PCR, and observation of clinical signs. Shedding of fecal viral RNA was significantly longer than duration of clinical signs. Postinfection seropositivity was confirmed by four institutions including 11 felids (5 lions, 6 tigers). In most instances, asymptomatic or presymptomatic keepers were the presumed or confirmed source of infection, although in some instances the infection source remains uncertain. Almost all infections occurred despite using cloth facemasks and disposable gloves when in proximity to the felids and during food preparation. Although transmission may have occurred during momentary lapses in personal protective equipment compliance, it seems probable that cloth masks are insufficient at preventing transmission of SARS-CoV-2 from humans to nondomestic felids. Surgical or higher grade masks may be warranted when working with nondomestic felids.
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Affiliation(s)
- Susan L Bartlett
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY 10460, USA,
| | - Katja N Koeppel
- Department of Production Animal Studies and Centre for Veterinary Wildlife Research, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Andrew C Cushing
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA
| | | | | | | | - Tammy Thies
- The Wildcat Sanctuary, Sandstone, MN 55072, USA
| | | | | | - Kami Z Fox
- Fort Wayne Children's Zoo, Fort Wayne, IN 46808, USA
| | - Roman Vodička
- Zoologická zahrada hl. m. Prahy, Prague Zoo, 171 00 Praha 7-Trója, Czech Republic
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Paul P Calle
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY 10460, USA
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6
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Wu J, Ding J, Wang L. Editorial: Livestock and poultry infectious diseases: pathogenesis and immune mechanisms. Front Cell Infect Microbiol 2023; 13:1249034. [PMID: 37496807 PMCID: PMC10368184 DOI: 10.3389/fcimb.2023.1249034] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/28/2023] [Imported: 10/19/2023] Open
Affiliation(s)
- Jiaqiang Wu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jiabo Ding
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States
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7
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Li C, Wang L, Zheng S. Editorial: Immunosuppressive disease in poultry. Front Immunol 2023; 14:1215513. [PMID: 37377969 PMCID: PMC10292216 DOI: 10.3389/fimmu.2023.1215513] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] [Imported: 10/19/2023] Open
Affiliation(s)
- Charles Li
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States
| | - Shijun Zheng
- College of Veterinary Medicine, China Agricultural University, Beijing, China
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8
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Wang L. Diagnostics for Viral Pathogens in Veterinary Diagnostic Laboratories. Vet Clin North Am Food Anim Pract 2023; 39:129-140. [PMID: 36731993 DOI: 10.1016/j.cvfa.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Laboratory testing is one part of clinical diagnosis, and quick and reliable testing results provide important data to support treatment decision and develop control strategies. Clinical viral testing has been shifting from traditional virus isolation and electron microscopy to molecular polymerase chain reaction and point-of-care antigen tests. This shift in diagnostic methodology also means change from looking for infectious virions or viral particles to hunting viral antigens and genomes. With technological development, it is predicted that metagenomic sequencing will be commonly used in veterinary clinical diagnosis for unveiling the whole picture of microbes involved in diseases in the future.
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Affiliation(s)
- Leyi Wang
- Department of Veterinary Clinical Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, VMBSB Room 1222A, Urbana, IL 61802, USA.
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Allender MC, Adkesson MJ, Langan JN, Delk KW, Meehan T, Aitken‐Palmer C, McEntire MM, Killian ML, Torchetti M, Morales SA, Austin C, Fredrickson R, Olmstead C, Ke R, Smith R, Hostnik ET, Terio K, Wang L. Multi-species outbreak of SARS-CoV-2 Delta variant in a zoological institution, with the detection in two new families of carnivores. Transbound Emerg Dis 2022; 69:e3060-e3075. [PMID: 35839756 PMCID: PMC9349917 DOI: 10.1111/tbed.14662] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 02/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a worldwide distribution in humans and many other mammalian species. In late September 2021, 12 animals maintained by the Chicago Zoological Society's Brookfield Zoo were observed with variable clinical signs. The Delta variant of SARS-CoV-2 was detected in faeces and nasal swabs by qRT-PCR, including the first detection in animals from the families Procyonidae and Viverridae. Test positivity rate was 12.5% for 35 animals tested. All animals had been vaccinated with at least one dose of a recombinant vaccine designed for animals and all recovered with variable supportive treatment. Sequence analysis showed that six zoo animal strains were closely correlated with 18 human SARS-CoV-2 strains, suggestive of potential human-to-animal transmission events. This report documents the expanding host range of COVID-19 during the ongoing pandemic.
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Affiliation(s)
- Matthew C. Allender
- Brookfield ZooChicago Zoological SocietyBrookfieldIllinoisUSA
- Veterinary Diagnostic LabUniversity of Illinois Wildlife Epidemiology LaboratoryUrbanaIllinoisUSA
| | | | - Jennifer N. Langan
- Brookfield ZooChicago Zoological SocietyBrookfieldIllinoisUSA
- Department of Veterinary Clinical Medicine, College of Veterinary MedicineUniversity of IllinoisUrbanaIllinoisUSA
| | - Katie W. Delk
- Brookfield ZooChicago Zoological SocietyBrookfieldIllinoisUSA
| | - Thomas Meehan
- Brookfield ZooChicago Zoological SocietyBrookfieldIllinoisUSA
| | | | - Michael M. McEntire
- Illinois Zoological and Aquatic Animal ResidencyUniversity of IllinoisUrbanaIllinoisUSA
| | - Mary L. Killian
- National Veterinary Services Laboratories, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureAmesIowaUSA
| | - Mia Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureAmesIowaUSA
| | | | - Connie Austin
- Illinois Department of Public HealthSpringfieldIllinoisUSA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary MedicineUniversity of IllinoisUrbanaIllinoisUSA
| | - Colleen Olmstead
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary MedicineUniversity of IllinoisUrbanaIllinoisUSA
| | - Ruian Ke
- T‐6, Theoretical Biology and Biophysics, T DivisionLos Alamos National LaboratoryLos AlamosNew MexicoUSA
| | - Rebecca Smith
- Department of PathobiologyUniversity of Illinois at Urbana–ChampaignUrbanaIllinoisUSA
| | - Eric T. Hostnik
- Brookfield ZooChicago Zoological SocietyBrookfieldIllinoisUSA
- Department of Veterinary Clinical SciencesOhio State UniversityColumbusOhioUSA
| | - Karen Terio
- Zoological Pathology Program, College of Veterinary MedicineUniversity of IllinoisBrookfieldIllinoisUSA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary MedicineUniversity of IllinoisUrbanaIllinoisUSA
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10
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Wang L, Lim A, Fredrickson R. Genomic characterization of a new bovine picornavirus (boosepivirus) in diarrheal cattle and detection in different states of the United States, 2019. Transbound Emerg Dis 2022; 69:3109-3114. [PMID: 34761864 DOI: 10.1111/tbed.14390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 02/05/2023]
Abstract
The Boosepivirus is a newly proposed genus in the family Picornaviridae in 2020. Bovine boosepiviruses (BooV) were initially identified in diarrheal cattle through deep sequencing in Japan in 2009. These diarrheal cases were either BooV alone positive or coinfection with other viruses, suggesting that BooV is an enteric pathogen. In 2019, through metagenomic sequencing, a US BooV strain IL41203-19 was identified in the fecal sample of a 10-day old calf with diarrhea and characterized in the present study. Genomic characterization revealed that IL41203-19 share the highest identities with the Japan BooV strain (Bo-12-7/2009/JPN) at both the complete nucleotide and amino acid levels, belonging to Boosepivirus B species in the genus Boosepivirus. Further real-time RT-PCR testing of 84 clinical samples from the diarrheal testing panel showed that five were positive for BooV and were all coinfected with one to four other enteric pathogens. Our data provided further evidence that BooV might contribute to cattle diarrhea observed in different states. Future studies on epidemiology and pathogenesis of bovine BooV are warranted.
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Affiliation(s)
- Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Ailam Lim
- Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
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11
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Savard C, Provost C, Ariel O, Morin S, Fredrickson R, Gagnon CA, Broes A, Wang L. First report and genomic characterization of a bovine-like coronavirus causing enteric infection in an odd-toed non-ruminant species (Indonesian tapir, Acrocodia indica) during an outbreak of winter dysentery in a zoo. Transbound Emerg Dis 2022; 69:3056-3065. [PMID: 34427399 PMCID: PMC8943714 DOI: 10.1111/tbed.14300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 02/05/2023]
Abstract
Bovine coronavirus (BCoV) is associated with three distinct clinical syndromes in cattle that is, neonatal diarrhoea, haemorrhagic diarrhoea in adults (the so-called winter dysentery syndrome, WD) and respiratory infections in cattle of different ages. In addition, bovine-like CoVs have been detected in various species including domestic and wild ruminants. However, bovine-like CoVs have not been reported so far in odd-toed ungulates. We describe an outbreak of WD associated with a bovine-like CoV affecting several captive wild ungulates, including Indonesian tapirs (Acrocodia indica) an odd-toed ungulate species (Perissodactyla) which, with even-toed ungulates species (Artiodactyla) form the clade Euungulata. Genomic characterization of the CoV revealed that it was closely related to BCoVs previously reported in America. This case illustrates the adaptability of bovine-like CoVs to new species and the necessity of continued surveillance of bovine-like CoVs in various species.
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Affiliation(s)
| | - Chantale Provost
- Molecular diagnostic laboratory, Centre de diagnostic vétérinaire de l’Université de Montréal (CDVUM), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | | | - Samuel Morin
- Bureau vétérinaire Iberville, Saint-Jean-sur-Richelieu, Québec, Canada
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Carl A. Gagnon
- Molecular diagnostic laboratory, Centre de diagnostic vétérinaire de l’Université de Montréal (CDVUM), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - André Broes
- Biovet Inc., Saint-Hyacinthe, Québec, Canada
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
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12
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Ke R, Martinez PP, Smith RL, Gibson LL, Achenbach CJ, McFall S, Qi C, Jacob J, Dembele E, Bundy C, Simons LM, Ozer EA, Hultquist JF, Lorenzo-Redondo R, Opdycke AK, Hawkins C, Murphy RL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Zhou R, Farjo M, Rendon G, Fields CJ, Wang L, Fredrickson R, Baughman ME, Chiu KK, Choi H, Scardina KR, Owens AN, Broach J, Barton B, Lazar P, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution. Open Forum Infect Dis 2022; 9:ofac192. [PMID: 35791353 PMCID: PMC9047214 DOI: 10.1093/ofid/ofac192] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023] Open
Abstract
Background The global effort to vaccinate people against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during an ongoing pandemic has raised questions about how vaccine breakthrough infections compare with infections in immunologically naive individuals and the potential for vaccinated individuals to transmit the virus. Methods We examined viral dynamics and infectious virus shedding through daily longitudinal sampling in 23 adults infected with SARS-CoV-2 at varying stages of vaccination, including 6 fully vaccinated individuals. Results The durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases. Conclusions Vaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.
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Affiliation(s)
- Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Pamela P Martinez
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Laura L Gibson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Chad J Achenbach
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sally McFall
- Center for Innovation in Point-of-Care Technologies for HIV/AIDS at Northwestern University, Evanston, Illinois, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, USA
| | - Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joshua Jacob
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Etienne Dembele
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Camille Bundy
- Institute for Sexual and Gender Minority Health and Wellbeing, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lacy M Simons
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A Ozer
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Judd F Hultquist
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ramon Lorenzo-Redondo
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Anita K Opdycke
- Department of Health Service, Northwestern University, Evanston, Illinois, USA
| | - Claudia Hawkins
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Robert L Murphy
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Junko Jarrett
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Karen K Chiu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hannah Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin R Scardina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alyssa N Owens
- Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - John Broach
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- UMass Memorial Medical Center, Worcester, Massachusetts, USA
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Bruce Barton
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Peter Lazar
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Matthew L Robinson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yukari C Manabe
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - David D McManus
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Wang L, Gyimesi ZS, Killian ML, Torchetti M, Olmstead C, Fredrickson R, Terio KA. Detection of SARS‐CoV‐2 clade B.1.2 in three snow leopards. Transbound Emerg Dis 2022. [DOI: doi.org/10.1111/tbed.14625] [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: 02/05/2023]
Affiliation(s)
- Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary Medicine University of Illinois Urbana Illinois USA
| | - Zoltan S. Gyimesi
- Louisville Zoological Garden 1100 Trevilian Way Louisville Kentucky USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service United States Department of Agriculture Ames Iowa USA
| | - Mia Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service United States Department of Agriculture Ames Iowa USA
| | - Colleen Olmstead
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary Medicine University of Illinois Urbana Illinois USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary Medicine University of Illinois Urbana Illinois USA
| | - Karen A. Terio
- Zoological Pathology Program, College of Veterinary Medicine University of Illinois Brookfield Illinois USA
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14
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Ranoa DRE, Holland RL, Alnaji FG, Green KJ, Wang L, Fredrickson RL, Wang T, Wong GN, Uelmen J, Maslov S, Weiner ZJ, Tkachenko AV, Zhang H, Liu Z, Ibrahim A, Patel SJ, Paul JM, Vance NP, Gulick JG, Satheesan SP, Galvan IJ, Miller A, Grohens J, Nelson TJ, Stevens MP, Hennessy PM, Parker RC, Santos E, Brackett C, Steinman JD, Fenner MR, Dohrer K, DeLorenzo M, Wilhelm-Barr L, Brauer BR, Best-Popescu C, Durack G, Wetter N, Kranz DM, Breitbarth J, Simpson C, Pryde JA, Kaler RN, Harris C, Vance AC, Silotto JL, Johnson M, Valera EA, Anton PK, Mwilambwe L, Bryan SP, Stone DS, Young DB, Ward WE, Lantz J, Vozenilek JA, Bashir R, Moore JS, Garg M, Cooper JC, Snyder G, Lore MH, Yocum DL, Cohen NJ, Novakofski JE, Loots MJ, Ballard RL, Band M, Banks KM, Barnes JD, Bentea I, Black J, Busch J, Conte A, Conte M, Curry M, Eardley J, Edwards A, Eggett T, Fleurimont J, Foster D, Fouke BW, Gallagher N, Gastala N, Genung SA, Glueck D, Gray B, Greta A, Healy RM, Hetrick A, Holterman AA, Ismail N, Jasenof I, Kelly P, Kielbasa A, Kiesel T, Kindle LM, Lipking RL, Manabe YC, Mayes J́, McGuffin R, McHenry KG, Mirza A, Moseley J, Mostafa HH, Mumford M, Munoz K, Murray AD, Nolan M, Parikh NA, Pekosz A, Pflugmacher J, Phillips JM, Pitts C, Potter MC, Quisenberry J, Rear J, Robinson ML, Rosillo E, Rye LN, Sherwood M, Simon A, Singson JM, Skadden C, Skelton TH, Smith C, Stech M, Thomas R, Tomaszewski MA, Tyburski EA, Vanwingerden S, Vlach E, Watkins RS, Watson K, White KC, Killeen TL, Jones RJ, Cangellaris AC, Martinis SA, Vaid A, Brooke CB, Walsh JT, Elbanna A, Sullivan WC, Smith RL, Goldenfeld N, Fan TM, Hergenrother PJ, Burke MD. Mitigation of SARS-CoV-2 transmission at a large public university. Nat Commun 2022. [DOI: doi.org/10.1038/s41467-022-30833-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
AbstractIn Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university.
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15
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Shen H, Zhang J, Gauger PC, Burrough ER, Zhang J, Harmon K, Wang L, Zheng Y, Petznick T, Li G. Genetic characterization of porcine sapoviruses identified from pigs during a diarrhoea outbreak in Iowa, 2019. Transbound Emerg Dis 2022; 69:1246-1255. [PMID: 33780163 DOI: 10.1111/tbed.14087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
Porcine sapovirus (SaV) was first identified by electron microscopy in the United States in 1980 and has since been reported from both asymptomatic and diarrhoeic pigs usually in mixed infection with other enteric pathogens. SaV as the sole aetiological agent of diarrhoea in naturally infected pigs has not previously been reported in the United States. Here, we used four independent lines of evidence including metagenomics analysis, real-time RT-PCR (rRT-PCR), histopathology, and in situ hybridization to confirm porcine SaV genogroup III (GIII) as the sole cause of enteritis and diarrhoea in pigs. A highly sensitive and specific rRT-PCR was established to detect porcine SaV GIII. Examination of 184 faecal samples from an outbreak of diarrhoea on a pig farm showed that pigs with clinical diarrhoea had significantly lower Ct values (15.9 ± 0.59) compared to clinically unaffected pigs (35.8 ± 0.71). Further survey of 336 faecal samples from different states in the United States demonstrated that samples from pigs with clinical diarrhoea had a comparable positive rate (45.3%) with those from asymptomatic pigs (43.1%). However, the SaV-positive pigs with clinical diarrhoea had significantly higher viral loads (Ct = 26.0 ± 0.5) than the SAV-positive but clinically healthy pigs (Ct = 33.2 ± 0.9). Phylogenetic analysis of 20 field SaVs revealed that all belonged to SaV GIII and recombination analysis indicated that intragenogroup recombination had occurred within the field isolates of SaV GIII. These results suggest that porcine SaV GIII plays an important aetiologic role in swine enteritis and diarrhoea and rRT-PCR is a reliable method to detect porcine SaV. Our findings provide significant insights to better understand the epidemiology and pathogenicity of porcine SaV infection.
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Affiliation(s)
- Huigang Shen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jianfeng Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Eric R Burrough
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Ying Zheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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16
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Savard C, Ariel O, Fredrickson R, Wang L, Broes A. Detection and genome characterization of bovine kobuvirus (BKV) in faecal samples from diarrhoeic calves in Quebec, Canada. Transbound Emerg Dis 2022; 69:1649-1655. [PMID: 33788413 PMCID: PMC8938984 DOI: 10.1111/tbed.14086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
Kobuviruses are known to infect the gastrointestinal tract of different animal species. Since its discovery in 2003, bovine kobuvirus (BKV) has been identified in faecal samples from diarrhoeic cattle in many countries, but only recently in North America. Although its possible role as an agent of calf diarrhoea remains to be determined, evidence is mounting. Our study reports for the first time the detection of BKV in faecal samples from diarrhoeic calves raised in Quebec, Canada. BKV was more commonly identified than eight known and common enteric calf pathogens. Further sequence analysis revealed that Canada BKV strain 1,043,507 was more closely correlated with the US BKV IL35164 strain than other BKV strains with complete genome. Continued surveillance and genomic characterization are needed to monitor BKV in the cattle around the world.
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Affiliation(s)
| | | | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
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17
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Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Zhou R, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Nat Microbiol 2022; 7:640-652. [PMID: 35484231 PMCID: PMC9084242 DOI: 10.1038/s41564-022-01105-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [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: 08/06/2021] [Accepted: 03/15/2022] [Indexed: 02/07/2023]
Abstract
The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to 'superspreading'. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant-of-concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be explained simply by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
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Affiliation(s)
- Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Pamela P Martinez
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Laura L Gibson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Junko Jarrett
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tongyu Liu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kimberly K O Walden
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Darci C Edmonson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karen K Chiu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hannah Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kevin R Scardina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shannon Bradley
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stacy L Gloss
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Crystal Reinhart
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jagadeesh Yedetore
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jessica Quicksall
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alyssa N Owens
- Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - John Broach
- UMass Memorial Medical Center, Worcester, MA, USA
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruce Barton
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, USA
| | - Peter Lazar
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - William J Heetderks
- National Institute for Biomedical Imaging and Bioengineering, Bethesda, MD, USA
| | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David D McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Oh C, Sashittal P, Zhou A, Wang L, El-Kebir M, Nguyen TH. Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Appl Environ Microbiol 2022; 88:e0228921. [PMID: 35285246 PMCID: PMC9004361 DOI: 10.1128/aem.02289-21] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Monitoring the prevalence of SARS-CoV-2 variants is necessary to make informed public health decisions during the COVID-19 pandemic. PCR assays have received global attention, facilitating a rapid understanding of variant dynamics because they are more accessible and scalable than genome sequencing. However, as PCR assays target only a few mutations, their accuracy could be reduced when these mutations are not exclusive to the target variants. Here we introduce PRIMES, an algorithm that evaluates the sensitivity and specificity of SARS-CoV-2 variant-specific PCR assays across different geographical regions by incorporating sequences deposited in the GISAID database. Using PRIMES, we determined that the accuracy of several PCR assays decreased when applied beyond the geographic scope of the study in which the assays were developed. Subsequently, we used this tool to design Alpha and Delta variant-specific PCR assays for samples from Illinois, USA. In silico analysis using PRIMES determined the sensitivity/specificity to be 0.99/0.99 for the Alpha variant-specific PCR assay and 0.98/1.00 for the Delta variant-specific PCR assay in Illinois, respectively. We applied these two variant-specific PCR assays to six local sewage samples and determined the dominant SARS-CoV-2 variant of either the wild type, the Alpha variant, or the Delta variant. Using next-generation sequencing (NGS) of the spike (S) gene amplicons of the Delta variant-dominant samples, we found six mutations exclusive to the Delta variant (S:T19R, S:Δ156/157, S:L452R, S:T478K, S:P681R, and S:D950N). The consistency between the variant-specific PCR assays and the NGS results supports the applicability of PRIMES. IMPORTANCE Monitoring the introduction and prevalence of variants of concern (VOCs) and variants of interest (VOIs) in a community can help the local authorities make informed public health decisions. PCR assays can be designed to keep track of SARS-CoV-2 variants by measuring unique mutation markers that are exclusive to the target variants. However, the mutation markers may not be exclusive to the target variants because of regional and temporal differences in variant dynamics. We introduce PRIMES, an algorithm that enables the design of reliable PCR assays for variant detection. Because PCR is more accessible, scalable, and robust for sewage samples than sequencing technology, our findings will contribute to improving global SARS-CoV-2 variant surveillance.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Palash Sashittal
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
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19
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Oh C, Kim K, Araud E, Wang L, Shisler JL, Nguyen TH. A novel approach to concentrate human and animal viruses from wastewater using receptors-conjugated magnetic beads. Water Res 2022; 212:118112. [PMID: 35091223 DOI: 10.1016/j.watres.2022.118112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/04/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023]
Abstract
Viruses are present at low concentrations in wastewater; therefore, an effective method for concentrating virus particles is necessary for accurate wastewater-based epidemiology (WBE). We designed a novel approach to concentrate human and animal viruses from wastewater using porcine gastric mucin-conjugated magnetic beads (PGM-MBs). We systematically evaluated the performances of the PGM-MBs method (sensitivity, specificity, and robustness to environmental inhibitors) with six viral species, including Tulane virus (a surrogate for human norovirus), rotavirus, adenovirus, porcine coronavirus (transmissible gastroenteritis virus or TGEV), and two human coronaviruses (NL63 and SARS-CoV-2) in influent wastewater and raw sewage samples. We determined the multiplication factor (the ratio of genome concentration of the final solution to that of the initial solution) for the PGM-MBs method, which ranged from 1.3 to 64.0 depending on the viral species. Because the recovery efficiency was significantly higher when calculated with virus titers than it was with genome concentration, the PGM-MBs method could be an appropriate tool for assessing the risk to humans who are inadvertently exposed to wastewater contaminated with infectious viruses. Furthermore, PCR inhibitors were not concentrated by PGM-MBs, suggesting that this tool will be successful for use with environmental samples. In addition, the PGM-MBs method is cost-effective (0.5 USD/sample) and has a fast turnaround time (3 h from virus concentration to genome quantification). Thus, this method can be implemented in high throughput facilities. Because of its strong performance, intrinsic characteristics of targeting the infectious virus, robustness to wastewater, and adaptability to high throughput systems, the PGM-MBs method can be successfully applied to WBE and ultimately provides valuable public health information.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, United States.
| | - Kyukyoung Kim
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, United States
| | - Elbashir Araud
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana-Champaign
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, United States
| | - Joanna L Shisler
- Department of Microbiology, University of Illinois at Urbana-Champaign, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, United States; Institute of Genomic Biology, University of Illinois at Urbana-Champaign, United States
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20
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Mitchell PK, Wang L, Stanhope BJ, Cronk BD, Anderson R, Mohan S, Zhou L, Sanchez S, Bartlett P, Maddox C, DeShambo V, Mani R, Hengesbach LM, Gresch S, Wright K, Mor S, Zhang S, Shen Z, Yan L, Mackey R, Franklin-Guild R, Zhang Y, Prarat M, Shiplett K, Ramachandran A, Narayanan S, Sanders J, Hunkapiller AA, Lahmers K, Carbonello AA, Aulik N, Lim A, Cooper J, Jones A, Guag J, Nemser SM, Tyson GH, Timme R, Strain E, Reimschuessel R, Ceric O, Goodman LB. Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria. Microb Genom 2022; 8:000717. [PMID: 35113783 PMCID: PMC8942033 DOI: 10.1099/mgen.0.000717] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitoring antimicrobial resistance (AMR) and protecting the safety of people and animals. With the availability of smaller and more affordable sequencing platforms coupled with well-defined bioinformatic protocols, the technological capability to incorporate this technique for real-time surveillance and genomic epidemiology has greatly expanded. There is a need, however, to ensure that data are of high quality. The goal of this study was to assess the utility of a small benchtop sequencing platform using a multi-laboratory verification approach. Thirteen laboratories were provided the same equipment, reagents, protocols and bacterial reference strains. The Illumina DNA Prep and Nextera XT library preparation kits were compared, and 2×150 bp iSeq i100 chemistry was used for sequencing. Analyses comparing the sequences produced from this study with closed genomes from the provided strains were performed using open-source programs. A detailed, step-by-step protocol is publicly available via protocols.io (https://www.protocols.io/view/iseq-bacterial-wgs-protocol-bij8kcrw). The throughput for this method is approximately 4-6 bacterial isolates per sequencing run (20-26 Mb total load). The Illumina DNA Prep library preparation kit produced high-quality assemblies and nearly complete AMR gene annotations. The Prep method produced more consistent coverage compared to XT, and when coverage benchmarks were met, nearly all AMR, virulence and subtyping gene targets were correctly identified. Because it reduces the technical and financial barriers to generating WGS data, the iSeq platform is a viable option for small laboratories interested in genomic surveillance of microbial pathogens.
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Affiliation(s)
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
- *Correspondence: Leyi Wang,
| | | | | | - Renee Anderson
- Cornell University, College of Veterinary Medicine, Ithaca, NY, USA
| | - Shipra Mohan
- Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA
| | - Lijuan Zhou
- Bronson Animal Disease Diagnostic Laboratory, Kissimmee, FL, USA
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, The University of Georgia, College of Veterinary Medicine,, GA, USA
| | - Paula Bartlett
- Athens Veterinary Diagnostic Laboratory, The University of Georgia, College of Veterinary Medicine,, GA, USA
| | - Carol Maddox
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Vanessa DeShambo
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Rinosh Mani
- Michigan State University, Veterinary Diagnostic Laboratory, Lansing, MI, USA
| | | | - Sarah Gresch
- University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA
| | - Katie Wright
- University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA
| | - Sunil Mor
- University of Minnesota, Veterinary Diagnostic Lboratory, Saint Paul, MN, USA
| | - Shuping Zhang
- University of Missouri Veterinary Medical Diagnostic Laboratory, Columbia, MO, USA
| | - Zhenyu Shen
- University of Missouri Veterinary Medical Diagnostic Laboratory, Columbia, MO, USA
| | - Lifang Yan
- Mississippi State University, Veterinary Diagnostic Laboratory, MS, USA
| | - Rebecca Mackey
- Mississippi State University, Veterinary Diagnostic Laboratory, MS, USA
| | | | - Yan Zhang
- Ohio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA
| | - Melanie Prarat
- Ohio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA
| | - Katherine Shiplett
- Ohio Department of Agriculture, Animal Disease Diagnostic Laboratory, Reynoldsburg, OH, USA
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University, Stillwater, OK, USA
| | - Sai Narayanan
- Oklahoma Animal Disease Diagnostic Laboratory, Oklahoma State University, Stillwater, OK, USA
| | - Justin Sanders
- Oregon Veterinary Diagnostic Laboratory, Oregon State University, College of Veterinary Medicine, Corvallis, OR, USA
| | - Andree A. Hunkapiller
- Oregon Veterinary Diagnostic Laboratory, Oregon State University, College of Veterinary Medicine, Corvallis, OR, USA
| | - Kevin Lahmers
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | | | - Nicole Aulik
- University of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA
| | - Ailam Lim
- University of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA
| | - Jennifer Cooper
- University of Wisconsin-Madison Veterinary Diagnostic Laboratory, Madison, WI, USA
| | - Angelica Jones
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Jake Guag
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Sarah M. Nemser
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Gregory H. Tyson
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Ruth Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Silver Spring, MD, USA
| | - Errol Strain
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Renate Reimschuessel
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Olgica Ceric
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Silver Spring, MD, USA
| | - Laura B. Goodman
- Cornell University, College of Veterinary Medicine, Ithaca, NY, USA
- *Correspondence: Laura B. Goodman,
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21
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Hu H, Wang L, Zhao Q. Editorial: Molecular insight of chronic infections. Front Microbiol 2022; 13:1112456. [PMID: 36687589 PMCID: PMC9846801 DOI: 10.3389/fmicb.2022.1112456] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Affiliation(s)
- Honghua Hu
- Jinhua Institute of Zhejiang University, Jinhua, Zhejiang, China
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- *Correspondence: Honghua Hu ✉ ; ✉
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, Liaoning, China
- Qi Zhao ✉
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22
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Cole AL, Kirk NM, Wang L, Hung CC, Samuelson JP. Mycobacterium fortuitum abortion in a sow. J Vet Diagn Invest 2022; 34:116-120. [PMID: 34448422 PMCID: PMC8689021 DOI: 10.1177/10406387211042289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Two aborted Chester White pig fetuses were presented to a veterinary diagnostic laboratory in Illinois. Postmortem examination identified no gross abnormalities. Histologic evaluation revealed multifocal necrosis of chorionic epithelial cells, coalescing areas of mineralization in the placenta, and focal accumulations of viable and degenerate neutrophils in the lung. Intra- and extracellular acid-fast bacilli were identified in the lesions in both the placenta and lungs. Bacterial culture of stomach contents yielded heavy growth of Mycobacterium fortuitum, a rapidly growing nontuberculous mycobacterium (NTM), which was further confirmed through whole-genome sequencing. NTM are opportunistic pathogens commonly found in the soil and in contaminated water supplies. In animals, M. fortuitum is typically introduced through cutaneous wounds leading to infections limited to the skin, with systemic infection being uncommon. To our knowledge, abortion caused by M. fortuitum has not been reported previously.
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Affiliation(s)
- Allysa L. Cole
- College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Natalie M. Kirk
- Departments of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Current address: Department of Veterinary Population Medicine, University of Minnesota Twin Cities, St. Paul, MN, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chien-Che Hung
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan P. Samuelson
- Jonathan P. Samuelson, Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, 2001 S Lincoln, M/C 002, Urbana, IL 61802, USA.
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23
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Wu J, Wang L, Wei Y, Yang J, Chen Z, Hao P, Lv Y, Wang M, Liao F, Chang L, Liu Y, Chen Z. Editorial: Multi-Omics Study on Gut Microbiota Related to Faecal Microbiota Transplantation. Front Microbiol 2022; 13:944879. [PMID: 35814686 PMCID: PMC9257269 DOI: 10.3389/fmicb.2022.944879] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jingtong Wu
- Department of Gastroenterology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, China
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States
| | - Yanling Wei
- Department of Teaching Support, Army Medical University, Chongqing, China
| | | | - Zeyou Chen
- College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Pei Hao
- Department of Gastroenterology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, China
| | - Yinyin Lv
- Department of Gastroenterology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, China
| | - Min Wang
- Inner Mongolia Shuangqi Pharmaceutical Co., Ltd., Huhhot, China
| | - Feng Liao
- Shenzhen Wedge Microbiology Research Co., Ltd., Shenzhen, China
| | - Longgang Chang
- Shenzhen Wedge Microbiology Research Co., Ltd., Shenzhen, China
| | - Yanmin Liu
- Inner Mongolia Shuangqi Pharmaceutical Co., Ltd., Huhhot, China
| | - Zhangran Chen
- Department of Gastroenterology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, China
- Inner Mongolia Shuangqi Pharmaceutical Co., Ltd., Huhhot, China
- Shenzhen Wedge Microbiology Research Co., Ltd., Shenzhen, China
- *Correspondence: Zhangran Chen
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24
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Pitman JL, Morris AJ, Grice S, Walsh JT, Wang L, Burke MD, Dixon-McIver A. Validation of a molecular assay to detect SARS-CoV-2 in saliva. N Z Med J 2021; 134:34-47. [PMID: 35728108 DOI: pmid/35728108] [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] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AIM To validate a reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) assay to detect SARS-CoV-2 in saliva in two independent Aotearoa New Zealand laboratories. METHODS An RT-qPCR assay developed at University of Illinois Urbana-Champaign, USA, was validated in two New Zealand laboratories. Analytical measures, such as limit of detection (LOD) and cross-reactivity, were performed. One hundred and forty-seven saliva samples, each paired with a contemporaneously collected nasal swab, mainly of nasopharyngeal origin, were received. Positive (N=33) and negative (N=114) samples were tested blindly in each laboratory. Diagnostic sensitivity and specificity were then calculated. RESULTS The LOD was <0.75 copy per µL and no cross-reactivity with MERS-CoV was detected. There was complete concordance between laboratories for all saliva samples with the quantification cycle values for all three genes in close agreement. Saliva had 98.7% concordance with paired nasal samples: and a sensitivity, specificity and accuracy of 97.0%, 99.1% and 99.1%, respectively. CONCLUSION This saliva RT-qPCR assay produces reproducible results with a low LOD. High sensitivity and specificity make it a reliable option for SARS-CoV-2 testing, including for asymptomatic people requiring regular screening.
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Affiliation(s)
- Janet L Pitman
- Associate Professor, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington
| | | | - Stephen Grice
- Director, Rako Science Ltd, Level 7, 76 Manners Street, Te Aro, Wellington
| | - Joseph T Walsh
- Office of the Vice President for Economic Development and Innovation, University of Illinois System, Urbana, IL, USA
| | - Leyi Wang
- Clinical Assistant Professor, Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Martin D Burke
- Professor, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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25
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Yuan F, Wang L, Fang Y, Wang L. Global SNP analysis of 11,183 SARS-CoV-2 strains reveals high genetic diversity. Transbound Emerg Dis 2021; 68:3288-3304. [PMID: 33207070 PMCID: PMC7753349 DOI: 10.1111/tbed.13931] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/19/2020] [Accepted: 11/13/2020] [Indexed: 02/05/2023]
Abstract
Since first identified in December of 2019, COVID-19 has been quickly spreading to the world in few months and COVID-19 cases are still undergoing rapid surge in most countries worldwide. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), adapts and evolves rapidly in nature. With the availability of 16,092 SARS-CoV-2 full genomes in GISAID as of 13 May, we removed the poor-quality genomes and performed mutational profiling analysis for the remaining 11,183 viral genomes. Global analysis of all sequences identified all single nucleotide polymorphisms (SNPs) across the whole genome and critical SNPs with high mutation frequency that contributes to five-clade classification of global strains. A total of 119 SNPs were found with 74 non-synonymous mutations, 43 synonymous mutations and two mutations in intergenic regions. Analysis of geographic pattern of mutational profiling for the whole genome reveals differences between each continent. A transition mutation from C to T represents the most mutation types across the genome, suggesting rapid evolution and adaptation of the virus in host. Amino acid (AA) deletions and insertions found across the genome results in changes in viral protein length and potential function alteration. Mutational profiling for each gene was analysed, and results show that nucleocapsid gene demonstrates the highest mutational frequency, followed by Nsp2, Nsp3 and Spike gene. We further focused on non-synonymous mutational distributions on four key viral proteins, spike with 75 mutations, RNA-dependent-RNA-polymerase with 41 mutations, 3C-like protease with 22 mutations and Papain-like protease with 10 mutations. Results show that non-synonymous mutations on critical sites of these four proteins pose great challenge for development of anti-viral drugs and other countering measures. Overall, this study provides more understanding of genetic diversity/variability of SARS-CoV-2 and insights for development of anti-viral therapeutics.
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Affiliation(s)
- Fangfeng Yuan
- Department of PathobiologyCollege of Veterinary MedicineUniversity of Illinois at Urbana ChampaignUrbanaIllinoisUSA
| | - Liping Wang
- Department of Diagnostic Medicine and PathobiologyCollege of Veterinary MedicineKansas State UniversityManhattanKansasUSA
| | - Ying Fang
- Department of PathobiologyCollege of Veterinary MedicineUniversity of Illinois at Urbana ChampaignUrbanaIllinoisUSA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical MedicineCollege of Veterinary MedicineUniversity of IllinoisUrbanaIllinoisUSA
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26
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Smith RL, Gibson LL, Martinez PP, Ke R, Mirza A, Conte M, Gallagher N, Conte A, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Jensen TW, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Owens AN, Broach J, Barton B, Lazar P, Henness D, Young T, Dunnett A, Robinson ML, Mostafa HH, Pekosz A, Manabe YC, Heetderks WJ, McManus DD, Brooke CB. Longitudinal Assessment of Diagnostic Test Performance Over the Course of Acute SARS-CoV-2 Infection. J Infect Dis 2021; 224:976-982. [PMID: 34191025 PMCID: PMC8448437 DOI: 10.1093/infdis/jiab337] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [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: 04/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Serial screening is critical for restricting spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by facilitating timely identification of infected individuals to interrupt transmission. Variation in sensitivity of different diagnostic tests at different stages of infection has not been well documented. METHODS In a longitudinal study of 43 adults newly infected with SARS-CoV-2, all provided daily saliva and nasal swabs for quantitative reverse transcription polymerase chain reaction (RT-qPCR), Quidel SARS Sofia antigen fluorescent immunoassay (FIA), and live virus culture. RESULTS Both RT-qPCR and Quidel SARS Sofia antigen FIA peaked in sensitivity during the period in which live virus was detected in nasal swabs, but sensitivity of RT-qPCR tests rose more rapidly prior to this period. We also found that serial testing multiple times per week increases the sensitivity of antigen tests. CONCLUSIONS RT-qPCR tests are more effective than antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (given timely results reporting). All tests showed >98% sensitivity for identifying infected individuals if used at least every 3 days. Daily screening using antigen tests can achieve approximately 90% sensitivity for identifying infected individuals while they are viral culture positive.
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Affiliation(s)
- Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Laura L Gibson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Pamela P Martinez
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Darci C Edmonson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Karen K Chiu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hannah Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Tor W Jensen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin R Scardina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Shannon Bradley
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Stacy L Gloss
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Crystal Reinhart
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jagadeesh Yedetore
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alyssa N Owens
- Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - John Broach
- UMass Memorial Medical Center, Worcester, Massachusetts, USA
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Bruce Barton
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Peter Lazar
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Todd Young
- Carle Foundation Hospital, Urbana, Illinois, USA
| | | | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - William J Heetderks
- National Institute for Biomedical Imaging and Bioengineering, Bethesda, Maryland, USA
| | - David D McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher B Brooke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Correspondence: Christopher Brooke, PhD, 390 Burrill Hall, Urbana, IL 61801 ()
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27
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Abstract
An 8-y-old jenny was presented because of anorexia and mild depression. The jenny had weaned her colt 10 d before the admission. Upon arrival at the University of Illinois Veterinary Teaching Hospital, the heart rate was elevated, and the right udder was painful and swollen on palpation. Milk stripping of the affected side revealed purulent content; the contralateral udder had normal-appearing milk. Cytology of mammary gland secretions from the affected side revealed a large number of hypersegmented reactive neutrophils with phagocytized bacteria. Complete blood count, serum chemistry, and fibrinogen were within normal limits. A diagnosis of clinical mastitis was made, and the jenny was started on a 5-d course of broad-spectrum antibiotics, a non-steroidal anti-inflammatory, hydrotherapy, and milk stripping. Clinical signs reduced over time, and the cure was attained by 96 h post-admission. Aerobic culture and subsequent MALDI-TOF MS analysis identified a bacterium of the Streptococcus genus but not the species. Whole-genome analysis was performed, and 16S rDNA sequencing and analysis determined that our isolate 20-37394 clustered with 2 other Streptococcus strains (27284-01 and 28462). Single-nucleotide variations and phylogenetic tree analysis revealed that Streptococcus 20-37394 had 96.8% and 94.9% identities to Streptococcus strains 27284-01 and 28462, respectively; therefore, the bacteria isolated in our case was deemed as a new Streptococcus species.
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Affiliation(s)
- Giorgia Podico
- Department of Veterinary Clinical Medicine (Podico, Gray, Canisso), College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Sarah M. Gray
- Department of Veterinary Clinical Medicine (Podico, Gray, Canisso), College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory (Wang), College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Igor F. Canisso
- Igor F. Canisso, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois Urbana-Champaign, 1008 W. Hazelwood Dr, Urbana, IL 61801, USA.
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28
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Abstract
Atypical porcine pestivirus (APPV) is an emerging virus discovered in 2014 and it can cause congenital tremors in pigs. Molecular epidemiology serves as an essential tool in monitoring and controlling the disease. Virus epidemiology mainly relies on genome sequencing and phylogenetic characterization. Previous molecular epidemiology studies have been using different genes/regions for phylogeny, namely whole genome, Npro, and E2 coding sequences. However, with increasing number of APPV sequences available in GenBank, no systemic studies have been performed for detailed classification of APPV strains around the globe. The goal of this study is to propose a classification strategy or taxonomy of APPV strains at genotype, subgenotype, and isolate levels. A total of 76 whole genomes and 16 partial polyprotein coding sequences were analyzed for genetic variability and suitability of all individual genes for viral phylogenies. Our results revealed that, among all the viral genes, NS5a coding sequences were proved to be the most suitable alternative for tracing APPV strains supported by its capability of reproducing the same phylogenetic and evolutionary information as the whole viral genome did. Also, a reliable cutoff to accurately classify APPV at different levels is established. We propose a genotyping scheme with three well-defined genotypes (1-3) and 7 subgenotypes for genotype 1 (1.1-1.7). For whole genome analysis, a threshold value of 84%-91% pairwise identity allows separation of all APPV subgenotypes, whereas 80% identity clearly segregate the three major APPV genotypes. For NS5a gene analysis, 82%-91% identity allows subgenotype separation and 76% identity segregate APPV genotypes. Additionally, genetic distance of whole genome exhibits ≤8% in isolate level, 9%-14% in subgenotype level, and 17%-22% in genotype level, while for NS5a encoding sequences the genetic distance displays ≤9% in isolate level, 9.9%-19.1% in subgenotype level, and 21.6%-29.7% in genotype level. These allow a clear segregation among APPV genotypes, subgenotypes, and isolates. Therefore, the proposed strategy in this study provides a solid and improved basis for molecular phylogenetics to understand APPV genetic diversity, trace the origins and control the spread of new disease outbreaks.
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Affiliation(s)
- Fangfeng Yuan
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA.
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29
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Hu R, Wang L, Liu Q, Hua L, Huang X, Zhang Y, Fan J, Chen H, Song W, Liang W, Ding N, Li Z, Ding Z, Tang X, Peng Z, Wu B. Whole-Genome Sequence Analysis of Pseudorabies Virus Clinical Isolates from Pigs in China between 2012 and 2017 in China. Viruses 2021; 13:v13071322. [PMID: 34372529 PMCID: PMC8310123 DOI: 10.3390/v13071322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and evolution is still limited. Here, we sequenced 54 genomes of novel PRV variants isolated in China from 2012 to 2017. Phylogenetic analysis revealed that China strains and US/Europe strains were classified into two separate genotypes. PRV strains isolated from 2012 to 2017 in China are highly related to each other and genetically close to classic China strains such as Ea, Fa, and SC. RDP analysis revealed 23 recombination events within novel PRV variants, indicating that recombination contributes significantly to the viral evolution. The selection pressure analysis indicated that most ORFs were under evolutionary constraint, and 19 amino acid residue sites in 15 ORFs were identified under positive selection. Additionally, 37 unique mutations were identified in 19 ORFs, which distinguish the novel variants from classic strains. Overall, our study suggested that novel PRV variants might evolve from classical PRV strains through point mutation and recombination mechanisms.
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Affiliation(s)
- Ruiming Hu
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
- Department of Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (N.D.); (Z.D.)
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang 330045, China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA;
| | - Qingyun Liu
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
| | - Lin Hua
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
| | - Xi Huang
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
| | - Yue Zhang
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
| | - Jie Fan
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
| | - Hongjian Chen
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
| | - Wenbo Song
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
| | - Wan Liang
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
| | - Nengshui Ding
- Department of Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (N.D.); (Z.D.)
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
- State Key Laboratory of Food Safety Technology for Meat Products, Xiamen 360000, China
| | - Zuohua Li
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China;
| | - Zhen Ding
- Department of Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (N.D.); (Z.D.)
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xibiao Tang
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
| | - Zhong Peng
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
- Correspondence: (Z.P.); (B.W.)
| | - Bin Wu
- State Key Laboratory of Agricultural Microbiology, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (R.H.); (Q.L.); (L.H.); (X.H.); (Y.Z.); (J.F.); (H.C.); (W.S.); (W.L.); (X.T.)
- Correspondence: (Z.P.); (B.W.)
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30
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Hao L, Chen C, Bailey K, Wang L. Bovine kobuvirus-A comprehensive review. Transbound Emerg Dis 2021; 68:1886-1894. [PMID: 33146459 DOI: 10.1111/tbed.13909] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/14/2020] [Accepted: 10/30/2020] [Indexed: 02/05/2023]
Abstract
Bovine kobuvirus (BKV) is a single-stranded, positive sense, non-enveloped RNA virus in genus Kobuvirus of family Picornavirus. BKV was first identified in the culture media of HeLa cell containing calf serum in 2003. Since then, BKV has been detected in 13 countries of four different continents, suggesting widespread in the world. Herein, we review the detection and genomic characterization of BKV in 13 countries. All studies tested bovine faecal samples for BKV. These studies provide evidence that BKV might be a causative agent for neonatal calf diarrhoea. Therefore, further efforts including animal challenge study are urgently needed to unveil the pathogenicity of BKV.
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Affiliation(s)
- Lili Hao
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Chaoxi Chen
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Keith Bailey
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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31
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Su CM, Wang L, Yoo D. Activation of NF-κB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. Sci Rep 2021; 11:13464. [PMID: 34188167 PMCID: PMC8242070 DOI: 10.1038/s41598-021-92941-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [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: 04/13/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19) that emerged in human populations recently. Severely ill COVID-19 patients exhibit the elevation of proinflammatory cytokines, and such an unbalanced production of proinflammatory cytokines is linked to acute respiratory distress syndrome with high mortality in COVID-19 patients. Our study provides evidence that the ORF3a, M, ORF7a, and N proteins of SARS-CoV-2 were NF-κB activators. The viral sequence from infected zoo lions belonged to clade V, and a single mutation of G251V is found for ORF3a gene compared to all other clades. No significant functional difference was found for clade V ORF3a, indicating the NF-κB activation is conserved among COVID-19 variants. Of the four viral proteins, the ORF7a protein induced the NF-κB dictated proinflammatory cytokines including IL-1α, IL-1β, IL-6, IL-8, IL-10, TNF-α, and IFNβ. The ORF7a protein also induced IL-3, IL-4, IL-7, IL-23. Of 15 different chemokines examined in the study, CCL11, CCL17, CCL19, CCL20, CCL21, CCL22, CCL25, CCL26, CCL27, and CXCL9 were significantly upregulated by ORF7. These cytokines and chemokines were frequently elevated in severely ill COVID-19 patients. Our data provide an insight into how SARS-CoV-2 modulates NF-κB signaling and inflammatory cytokine expressions. The ORF7a protein may be a desirable target for strategic developments to minimize uncontrolled inflammation in COVID-19 patients.
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Affiliation(s)
- Chia-Ming Su
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 Lincoln Ave, Urbana, IL, 61802, USA
| | - Leyi Wang
- Department of Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dongwan Yoo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 Lincoln Ave, Urbana, IL, 61802, USA.
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32
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Li T, Huang T, Guo C, Wang A, Shi X, Mo X, Lu Q, Sun J, Hui T, Tian G, Wang L, Yang J. Genomic variation, origin tracing, and vaccine development of SARS-CoV-2: A systematic review. Innovation (N Y) 2021; 2:100116. [PMID: 33997827 PMCID: PMC8110321 DOI: 10.1016/j.xinn.2021.100116] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 10/31/2020] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
COVID-19 has spread globally to over 200 countries with more than 40 million confirmed cases and one million deaths as of November 1, 2020. The SARS-CoV-2 virus, leading to COVID-19, shows extremely high rates of infectivity and replication, and can result in pneumonia, acute respiratory distress, or even mortality. SARS-CoV-2 has been found to continue to rapidly evolve, with several genomic variants emerging in different regions throughout the world. In addition, despite intensive study of the spike protein, its origin, and molecular mechanisms in mediating host invasion are still only partially resolved. Finally, the repertoire of drugs for COVID-19 treatment is still limited, with several candidates still under clinical trial and no effective therapeutic yet reported. Although vaccines based on either DNA/mRNA or protein have been deployed, their efficacy against emerging variants requires ongoing study, with multivalent vaccines supplanting the first-generation vaccines due to their low efficacy against new strains. Here, we provide a systematic review of studies on the epidemiology, immunological pathogenesis, molecular mechanisms, and structural biology, as well as approaches for drug or vaccine development for SARS-CoV-2.
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Affiliation(s)
- Tianbao Li
- Genetic Testing Center, Academician Workstation, Changsha Medical University, Changsha 410219, China
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng Guo
- Center for Infection and Immunity, School of Public Health, Columbia University, New York, NY 10032, USA
| | - Ailan Wang
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Xiaoli Shi
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Xiaofei Mo
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Qingqing Lu
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Jing Sun
- Department of Pathology, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Tingting Hui
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
- Corresponding author
| | - Jialiang Yang
- Genetic Testing Center, Academician Workstation, Changsha Medical University, Changsha 410219, China
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
- Corresponding author
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33
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Tyson GH, Ceric O, Guag J, Nemser S, Borenstein S, Slavic D, Lippert S, McDowell R, Krishnamurthy A, Korosec S, Friday C, Pople N, Saab ME, Fairbrother JH, Janelle I, McMillan D, Bommineni YR, Simon D, Mohan S, Sanchez S, Phillips A, Bartlett P, Naikare H, Watson C, Sahin O, Stinman C, Wang L, Maddox C, DeShambo V, Hendrix K, Lubelski D, Burklund A, Lubbers B, Reed D, Jenkins T, Erol E, Patel M, Locke S, Fortner J, Peak L, Balasuriya U, Mani R, Kettler N, Olsen K, Zhang S, Shen Z, Landinez MP, Thornton JK, Thachil A, Byrd M, Jacob M, Krogh D, Webb B, Schaan L, Patil A, Dasgupta S, Mann S, Goodman LB, Franklin-Guild RJ, Anderson RR, Mitchell PK, Cronk BD, Aprea M, Cui J, Jurkovic D, Prarat M, Zhang Y, Shiplett K, Campos DD, Rubio JVB, Ramanchandran A, Talent S, Tewari D, Thirumalapura N, Kelly D, Barnhart D, Hall L, Rankin S, Dietrich J, Cole S, Scaria J, Antony L, Lawhon SD, Wu J, McCoy C, Dietz K, Wolking R, Alexander T, Burbick C, Reimschuessel R. Genomics accurately predicts antimicrobial resistance in Staphylococcus pseudintermedius collected as part of Vet-LIRN resistance monitoring. Vet Microbiol 2021; 254:109006. [PMID: 33581494 DOI: 10.1016/j.vetmic.2021.109006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/28/2021] [Indexed: 02/07/2023]
Abstract
Whole-genome sequencing (WGS) has changed our understanding of bacterial pathogens, aiding outbreak investigations and advancing our knowledge of their genetic features. However, there has been limited use of genomics to understand antimicrobial resistance of veterinary pathogens, which would help identify emerging resistance mechanisms and track their spread. The objectives of this study were to evaluate the correlation between resistance genotypes and phenotypes for Staphylococcus pseudintermedius, a major pathogen of companion animals, by comparing broth microdilution antimicrobial susceptibility testing and WGS. From 2017-2019, we conducted antimicrobial susceptibility testing and WGS on S. pseudintermedius isolates collected from dogs in the United States as a part of the Veterinary Laboratory Investigation and Response Network (Vet-LIRN) antimicrobial resistance monitoring program. Across thirteen antimicrobials in nine classes, resistance genotypes correlated with clinical resistance phenotypes 98.4 % of the time among a collection of 592 isolates. Our findings represent isolates from diverse lineages based on phylogenetic analyses, and these strong correlations are comparable to those from studies of several human pathogens such as Staphylococcus aureus and Salmonella enterica. We uncovered some important findings, including that 32.3 % of isolates had the mecA gene, which correlated with oxacillin resistance 97.0 % of the time. We also identified a novel rpoB mutation likely encoding rifampin resistance. These results show the value in using WGS to assess antimicrobial resistance in veterinary pathogens and to reveal putative new mechanisms of resistance.
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Affiliation(s)
- Gregory H Tyson
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States.
| | - Olgica Ceric
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
| | - Jake Guag
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
| | - Sarah Nemser
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
| | - Stacey Borenstein
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
| | - Durda Slavic
- University of Guelph - Animal Health Laboratory, Canada
| | - Sarah Lippert
- University of Guelph - Animal Health Laboratory, Canada
| | | | | | - Shannon Korosec
- Manitoba Agriculture and Resource Development - Veterinary Diagnostic Services, Canada
| | - Cheryl Friday
- Manitoba Agriculture and Resource Development - Veterinary Diagnostic Services, Canada
| | - Neil Pople
- Manitoba Agriculture and Resource Development - Veterinary Diagnostic Services, Canada
| | - Matthew E Saab
- Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Canada
| | | | - Isabelle Janelle
- Complexe de diagnostic et d'épidémiosurveillance vétérinaires du Québec, Canada
| | - Deanna McMillan
- University of Saskatchewan - Prairie Diagnostic Services Inc, Canada
| | | | - David Simon
- Bronson Animal Disease Diagnostic Laboratory, United States
| | - Shipra Mohan
- Bronson Animal Disease Diagnostic Laboratory, United States
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, The University of Georgia, United States
| | - Ashley Phillips
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, The University of Georgia, United States
| | - Paula Bartlett
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, The University of Georgia, United States
| | - Hemant Naikare
- University of Georgia - Tifton Veterinary Diagnostic & Investigational Laboratory, United States
| | - Cynthia Watson
- University of Georgia - Tifton Veterinary Diagnostic & Investigational Laboratory, United States
| | | | | | - Leyi Wang
- University of Illinois Veterinary Diagnostic Laboratory - College of Veterinary Medicine, United States
| | - Carol Maddox
- University of Illinois Veterinary Diagnostic Laboratory - College of Veterinary Medicine, United States
| | - Vanessa DeShambo
- University of Illinois Veterinary Diagnostic Laboratory - College of Veterinary Medicine, United States
| | | | - Debra Lubelski
- Indiana Animal Disease Diagnostic Laboratory, United States
| | | | | | - Debbie Reed
- Murray State University Breathitt Veterinary Center, United States
| | - Tracie Jenkins
- Murray State University Breathitt Veterinary Center, United States
| | | | | | | | | | - Laura Peak
- Louisiana State University, United States
| | | | | | | | - Karen Olsen
- University of Minnesota Veterinary Diagnostic Lab, United States
| | - Shuping Zhang
- University of Missouri Veterinary Medical Diagnostic Laboratory, United States
| | - Zhenyu Shen
- University of Missouri Veterinary Medical Diagnostic Laboratory, United States
| | - Martha Pulido Landinez
- Mississippi State University, Veterinary Research and Diagnostic Lab System, United States
| | - Jay Kay Thornton
- Mississippi State University, Veterinary Research and Diagnostic Lab System, United States
| | - Anil Thachil
- North Carolina Veterinary Diagnostic Lab System, United States
| | | | - Megan Jacob
- North Carolina State University, United States
| | - Darlene Krogh
- North Dakota State University Veterinary Diagnostic Laboratory, United States
| | - Brett Webb
- North Dakota State University Veterinary Diagnostic Laboratory, United States
| | - Lynn Schaan
- North Dakota State University Veterinary Diagnostic Laboratory, United States
| | - Amar Patil
- New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory, United States
| | - Sarmila Dasgupta
- New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory, United States
| | - Shannon Mann
- New Jersey Department of Agriculture, Animal Health Diagnostic Laboratory, United States
| | - Laura B Goodman
- Cornell University, College of Veterinary Medicine, United States
| | | | - Renee R Anderson
- Cornell University, College of Veterinary Medicine, United States
| | | | - Brittany D Cronk
- Cornell University, College of Veterinary Medicine, United States
| | - Missy Aprea
- Cornell University, College of Veterinary Medicine, United States
| | - Jing Cui
- Ohio Animal Disease Diagnostic Lab, United States
| | | | | | - Yan Zhang
- Ohio Animal Disease Diagnostic Lab, United States
| | | | - Dubra Diaz Campos
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, United States
| | - Joany Van Balen Rubio
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, United States
| | - Akhilesh Ramanchandran
- Oklahoma Animal Disease Diagnostic Laboraotry, College of Veterinary Medicine, Oklahoma State University, United States
| | - Scott Talent
- Oklahoma Animal Disease Diagnostic Laboraotry, College of Veterinary Medicine, Oklahoma State University, United States
| | - Deepanker Tewari
- PA Veterinary Laboratory, Pennsylvania Department of Agriculture, United States
| | | | - Donna Kelly
- University of Pennsylvania, New Bolton Center, United States
| | - Denise Barnhart
- University of Pennsylvania, New Bolton Center, United States
| | - Lacey Hall
- University of Pennsylvania, New Bolton Center, United States
| | - Shelley Rankin
- University of Pennsylvania, Ryan Veterinary Hospital, United States
| | - Jaclyn Dietrich
- University of Pennsylvania, Ryan Veterinary Hospital, United States
| | - Stephen Cole
- University of Pennsylvania, Ryan Veterinary Hospital, United States
| | - Joy Scaria
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, United States
| | - Linto Antony
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, United States
| | - Sara D Lawhon
- Texas A&M University, College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Pathobiology, United States
| | - Jing Wu
- Texas A&M University, College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Pathobiology, United States
| | - Christine McCoy
- Virginia Department of Agriculture and Consumer Services- Lynchburg Regional Animal Health Laboratory, United States
| | - Kelly Dietz
- Virginia Department of Agriculture and Consumer Services- Lynchburg Regional Animal Health Laboratory, United States
| | | | | | | | - Renate Reimschuessel
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States
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Yang C, Wang L, Schwartz K, Burrough E, Groeltz-Thrush J, Chen Q, Zheng Y, Shen H, Li G. Case Report and Genomic Characterization of a Novel Porcine Nodavirus in the United States. Viruses 2021; 13:v13010073. [PMID: 33430224 PMCID: PMC7825704 DOI: 10.3390/v13010073] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Nodaviruses are small bisegmented RNA viruses belonging to the family Nodaviridae. Nodaviruses have been identified in different hosts, including insects, fishes, shrimps, prawns, dogs, and bats. A novel porcine nodavirus was first identified in the United States by applying next-generation sequencing on brain tissues of pigs with neurological signs, including uncontrollable shaking. RNA1 of the porcine nodavirus had the highest nucleotide identity (51.1%) to the Flock House virus, whereas its RNA2 shared the highest nucleotide identity (48%) with the RNA2 segment of caninovirus (Canine nodavirus). Genetic characterization classified porcine nodavirus as a new species under the genus Alphanodavirus. Further studies are needed to understand the pathogenicity and clinical impacts of this virus.
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Affiliation(s)
- Chenghuai Yang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (C.Y.); (K.S.); (E.B.); (J.G.-T.); (Q.C.); (Y.Z.); (H.S.)
- China Institute of Veterinary Drug Control, Beijing 100081, China
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA;
| | - Kent Schwartz
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (C.Y.); (K.S.); (E.B.); (J.G.-T.); (Q.C.); (Y.Z.); (H.S.)
| | - Eric Burrough
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (C.Y.); (K.S.); (E.B.); (J.G.-T.); (Q.C.); (Y.Z.); (H.S.)
| | - Jennifer Groeltz-Thrush
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (C.Y.); (K.S.); (E.B.); (J.G.-T.); (Q.C.); (Y.Z.); (H.S.)
| | - Qi Chen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (C.Y.); (K.S.); (E.B.); (J.G.-T.); (Q.C.); (Y.Z.); (H.S.)
| | - Ying Zheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (C.Y.); (K.S.); (E.B.); (J.G.-T.); (Q.C.); (Y.Z.); (H.S.)
| | - Huigang Shen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (C.Y.); (K.S.); (E.B.); (J.G.-T.); (Q.C.); (Y.Z.); (H.S.)
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (C.Y.); (K.S.); (E.B.); (J.G.-T.); (Q.C.); (Y.Z.); (H.S.)
- Correspondence: ; Tel.: +1-515-2943-358
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Bartlett SL, Diel DG, Wang L, Zec S, Laverack M, Martins M, Caserta LC, Killian ML, Terio K, Olmstead C, Delaney MA, Stokol T, Ivančić M, Jenkins-Moore M, Ingerman K, Teegan T, McCann C, Thomas P, McAloose D, Sykes JM, Calle PP. SARS-COV-2 INFECTION AND LONGITUDINAL FECAL SCREENING IN MALAYAN TIGERS ( PANTHERA TIGRIS JACKSONI), AMUR TIGERS ( PANTHERA TIGRIS ALTAICA ), AND AFRICAN LIONS ( PANTHERA LEO KRUGERI) AT THE BRONX ZOO, NEW YORK, USA. J Zoo Wildl Med 2021; 51:733-744. [PMID: 33480553 DOI: 10.1638/2020-0171] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged as the cause of a global pandemic in 2019-2020. In March 2020, New York City became the epicenter in the United States for the pandemic. On 27 March 2020, a Malayan tiger (Panthera tigris jacksoni) at the Bronx Zoo in New York City developed a cough and wheezing with subsequent inappetence. Over the next week, an additional Malayan tiger and two Amur tigers (Panthera tigris altaica) in the same building and three lions (Panthera leo krugeri) in a separate building also became ill. The index case was anesthetized for diagnostic workup. Physical examination and bloodwork results were unremarkable. Thoracic radiography and ultrasonography revealed a bronchial pattern with peribronchial cuffing and mild lung consolidation with alveolar-interstitial syndrome, respectively. SARS-CoV-2 RNA was identified by real-time, reverse transcriptase PCR (rRT-PCR) on oropharyngeal and nasal swabs and tracheal wash fluid. Cytologic examination of tracheal wash fluid revealed necrosis, and viral RNA was detected in necrotic cells by in situ hybridization, confirming virus-associated tissue damage. SARS-CoV-2 was isolated from the tracheal wash fluid of the index case, as well as the feces from one Amur tiger and one lion. Fecal viral RNA shedding was confirmed in all seven clinical cases and an asymptomatic Amur tiger. Respiratory signs abated within 1-5 days for most animals, although they persisted intermittently for 16 days in the index case. Fecal RNA shedding persisted for as long as 35 days beyond cessation of respiratory signs. This case series describes the clinical presentation, diagnostic evaluation, and management of tigers and lions infected with SARS-CoV-2 and describes the duration of viral RNA fecal shedding in these cases. This report documents the first known natural transmission of SARS-CoV-2 from humans to nondomestic felids.
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Affiliation(s)
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | | | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Leonardo Cardia Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Veterinary Services, United States Department of Agriculture, Ames, IA 50010, USA
| | - Karen Terio
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois, Brookfield, IL 60513, USA
| | - Colleen Olmstead
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Martha A Delaney
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois, Brookfield, IL 60513, USA
| | - Tracy Stokol
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Melinda Jenkins-Moore
- National Veterinary Services Laboratories, Veterinary Services, United States Department of Agriculture, Ames, IA 50010, USA
| | | | - Taryn Teegan
- Wildlife Conservation Society, Bronx, NY 10460, USA
| | | | | | | | - John M Sykes
- Wildlife Conservation Society, Bronx, NY 10460, USA
| | - Paul P Calle
- Wildlife Conservation Society, Bronx, NY 10460, USA
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36
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Ding Z, Luo S, Gong W, Wang L, Ding N, Chen J, Chen J, Wang T, Ye Y, Song D, Kong L, Zhang J, Tang Y. Subcellular localization of the porcine deltacoronavirus nucleocapsid protein. Virus Genes 2020; 56:687-695. [PMID: 32944812 PMCID: PMC7497858 DOI: 10.1007/s11262-020-01790-0] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
Abstract
Porcine deltacoronavirus (PDCoV) has been recently identified as an emerging enteropathogenic coronavirus that mainly infects newborn piglets and causes enteritis, diarrhea and high mortality. Although coronavirus N proteins have multifarious activities, the subcellular localization of the PDCoV N protein is still unknown. Here, we produced mouse monoclonal antibodies against the PDCoV N protein. Experiments using anti-haemagglutinin antibodies and these monoclonal antibodies revealed that the PDCoV N protein is shuttled into the nucleolus in both ectopic PDCoV N-expressing cells and PDCoV-infected cells. The results of deletion mutagenesis experiments demonstrated that the predicted nucleolar localization signal at amino acids 295-318 is critical for nucleolar localization. Cumulatively, our study yielded a monoclonal antibody against the PDCoV N protein and revealed a mechanism by which the PDCoV N protein translocated into the nucleolus. The tolls and findings from this work will facilitate further investigations on the functions of the PDCoV N protein.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/biosynthesis
- Antibodies, Monoclonal/chemistry
- Antibodies, Viral/biosynthesis
- Antibodies, Viral/chemistry
- Cell Line
- Cell Nucleolus/genetics
- Cell Nucleolus/metabolism
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Coronavirus Nucleocapsid Proteins/genetics
- Coronavirus Nucleocapsid Proteins/metabolism
- Deltacoronavirus/genetics
- Deltacoronavirus/growth & development
- Deltacoronavirus/metabolism
- Epithelial Cells/metabolism
- Epithelial Cells/ultrastructure
- Epithelial Cells/virology
- Gastroenteritis, Transmissible, of Swine/pathology
- Gastroenteritis, Transmissible, of Swine/virology
- Gene Expression
- Hemagglutinins, Viral/genetics
- Hemagglutinins, Viral/metabolism
- Host-Pathogen Interactions/genetics
- Kidney/pathology
- Kidney/virology
- Mice
- Nuclear Localization Signals
- Protein Transport
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Deletion
- Swine
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Affiliation(s)
- Zhen Ding
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, 1101 Zhimin Dadao, Qingshan Lake District, Nanchang, 330045, Jiangxi, China
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Suxian Luo
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, 1101 Zhimin Dadao, Qingshan Lake District, Nanchang, 330045, Jiangxi, China
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Wang Gong
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, 1101 Zhimin Dadao, Qingshan Lake District, Nanchang, 330045, Jiangxi, China
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Nengshui Ding
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jun Chen
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, 1101 Zhimin Dadao, Qingshan Lake District, Nanchang, 330045, Jiangxi, China
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jiajia Chen
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, 1101 Zhimin Dadao, Qingshan Lake District, Nanchang, 330045, Jiangxi, China
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ting Wang
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yu Ye
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, 1101 Zhimin Dadao, Qingshan Lake District, Nanchang, 330045, Jiangxi, China
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Deping Song
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, 1101 Zhimin Dadao, Qingshan Lake District, Nanchang, 330045, Jiangxi, China
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lingbao Kong
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jinghua Zhang
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, 1101 Zhimin Dadao, Qingshan Lake District, Nanchang, 330045, Jiangxi, China.
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Yuxing Tang
- Department of Veterinary Preventive Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, 1101 Zhimin Dadao, Qingshan Lake District, Nanchang, 330045, Jiangxi, China.
- Jiangxi Provincial Key Laboratory for Animal Health, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
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Kim H, Seiler P, Jones JC, Ridout G, Camp KP, Fabrizio TP, Jeevan T, Miller LA, Throm RE, Ferrara F, Fredrickson RL, Lowe JF, Wang L, Odemuyiwa SO, Wan XF, Webby RJ. Antibody Responses to SARS-CoV-2 Antigens in Humans and Animals. Vaccines (Basel) 2020; 8:vaccines8040684. [PMID: 33207583 PMCID: PMC7712576 DOI: 10.3390/vaccines8040684] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023] Open
Abstract
To optimize the public health response to coronavirus disease 2019 (COVID-19), we must first understand the antibody response to individual proteins on the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and the antibody's cross reactivity to other coronaviruses. Using a panel of 37 convalescent COVID-19 human serum samples, we showed that the magnitude and specificity of responses varied across individuals, independent of their reactivity to seasonal human coronaviruses (HCoVs). These data suggest that COVID-19 vaccines will elicit primary humoral immune responses in naïve individuals and variable responses in those previously exposed to SARS-CoV-2. Unlike the limited cross-coronavirus reactivities in humans, serum samples from 96 dogs and 10 cats showed SARS-CoV-2 protein-specific responses focused on non-S1 proteins. The correlation of this response with those to other coronaviruses suggests that the antibodies are cross-reactive and generated to endemic viruses within these hosts, which must be considered in seroepidemiologic studies. We conclude that substantial variation in antibody generation against coronavirus proteins will influence interpretations of serologic data in the clinical and veterinary settings.
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Affiliation(s)
- Hyunsuh Kim
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.K.); (P.S.); (J.C.J.); (T.P.F.); (T.J.); (L.A.M.)
| | - Patrick Seiler
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.K.); (P.S.); (J.C.J.); (T.P.F.); (T.J.); (L.A.M.)
| | - Jeremy C. Jones
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.K.); (P.S.); (J.C.J.); (T.P.F.); (T.J.); (L.A.M.)
| | - Granger Ridout
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | | | - Thomas P. Fabrizio
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.K.); (P.S.); (J.C.J.); (T.P.F.); (T.J.); (L.A.M.)
| | - Trushar Jeevan
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.K.); (P.S.); (J.C.J.); (T.P.F.); (T.J.); (L.A.M.)
| | - Lance A. Miller
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.K.); (P.S.); (J.C.J.); (T.P.F.); (T.J.); (L.A.M.)
| | - Robert E. Throm
- Vector Development & Production, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.T.); (F.F.)
| | - Francesca Ferrara
- Vector Development & Production, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.T.); (F.F.)
| | - Richard L. Fredrickson
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA;
| | - James F. Lowe
- Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA;
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA;
| | - Solomon O. Odemuyiwa
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (S.O.O.); (X.-F.W.)
| | - Xiu-Feng Wan
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; (S.O.O.); (X.-F.W.)
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.K.); (P.S.); (J.C.J.); (T.P.F.); (T.J.); (L.A.M.)
- Department of Microbiology, Immunology & Biochemistry, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: ; Tel.: +1-901-595-3014
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38
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McAloose D, Laverack M, Wang L, Killian ML, Caserta LC, Yuan F, Mitchell PK, Queen K, Mauldin MR, Cronk BD, Bartlett SL, Sykes JM, Zec S, Stokol T, Ingerman K, Delaney MA, Fredrickson R, Ivančić M, Jenkins-Moore M, Mozingo K, Franzen K, Bergeson NH, Goodman L, Wang H, Fang Y, Olmstead C, McCann C, Thomas P, Goodrich E, Elvinger F, Smith DC, Tong S, Slavinski S, Calle PP, Terio K, Torchetti MK, Diel DG. From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo. mBio 2020; 11:mBio.02220-20. [PMID: 33051368 PMCID: PMC7554670 DOI: 10.1128/mbio.02220-20] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [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] [Indexed: 02/07/2023] Open
Abstract
Despite numerous barriers to transmission, zoonoses are the major cause of emerging infectious diseases in humans. Among these, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and ebolaviruses have killed thousands; the human immunodeficiency virus (HIV) has killed millions. Zoonoses and human-to-animal cross-species transmission are driven by human actions and have important management, conservation, and public health implications. The current SARS-CoV-2 pandemic, which presumably originated from an animal reservoir, has killed more than half a million people around the world and cases continue to rise. In March 2020, New York City was a global epicenter for SARS-CoV-2 infections. During this time, four tigers and three lions at the Bronx Zoo, NY, developed mild, abnormal respiratory signs. We detected SARS-CoV-2 RNA in respiratory secretions and/or feces from all seven animals, live virus in three, and colocalized viral RNA with cellular damage in one. We produced nine whole SARS-CoV-2 genomes from the animals and keepers and identified different SARS-CoV-2 genotypes in the tigers and lions. Epidemiologic and genomic data indicated human-to-tiger transmission. These were the first confirmed cases of natural SARS-CoV-2 animal infections in the United States and the first in nondomestic species in the world. We highlight disease transmission at a nontraditional interface and provide information that contributes to understanding SARS-CoV-2 transmission across species.IMPORTANCE The human-animal-environment interface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important aspect of the coronavirus disease 2019 (COVID-19) pandemic that requires robust One Health-based investigations. Despite this, few reports describe natural infections in animals or directly link them to human infections using genomic data. In the present study, we describe the first cases of natural SARS-CoV-2 infection in tigers and lions in the United States and provide epidemiological and genetic evidence for human-to-animal transmission of the virus. Our data show that tigers and lions were infected with different genotypes of SARS-CoV-2, indicating two independent transmission events to the animals. Importantly, infected animals shed infectious virus in respiratory secretions and feces. A better understanding of the susceptibility of animal species to SARS-CoV-2 may help to elucidate transmission mechanisms and identify potential reservoirs and sources of infection that are important in both animal and human health.
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Affiliation(s)
- Denise McAloose
- Wildlife Conservation Society, Bronx Zoo, Bronx, New York, USA
| | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service (APHIS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | - Leonardo C Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Fangfeng Yuan
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Patrick K Mitchell
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Krista Queen
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Brittany D Cronk
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | - John M Sykes
- Wildlife Conservation Society, Bronx Zoo, Bronx, New York, USA
| | - Stephanie Zec
- Wildlife Conservation Society, Bronx Zoo, Bronx, New York, USA
| | - Tracy Stokol
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Karen Ingerman
- Wildlife Conservation Society, Bronx Zoo, Bronx, New York, USA
| | - Martha A Delaney
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois, Brookfield, Illinois, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | | | - Melinda Jenkins-Moore
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service (APHIS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | - Katie Mozingo
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service (APHIS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | - Kerrie Franzen
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service (APHIS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | - Nichole Hines Bergeson
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service (APHIS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | - Laura Goodman
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Haibin Wang
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ying Fang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Colleen Olmstead
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Colleen McCann
- Wildlife Conservation Society, Bronx Zoo, Bronx, New York, USA
| | - Patrick Thomas
- Wildlife Conservation Society, Bronx Zoo, Bronx, New York, USA
| | - Erin Goodrich
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - François Elvinger
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - David C Smith
- New York State Department of Agriculture and Markets, Albany, New York, USA
| | - Suxiang Tong
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sally Slavinski
- New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Paul P Calle
- Wildlife Conservation Society, Bronx Zoo, Bronx, New York, USA
| | - Karen Terio
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois, Brookfield, Illinois, USA
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service (APHIS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Oh C, Araud E, Puthussery JV, Bai H, Clark GG, Wang L, Verma V, Nguyen TH. Dry Heat as a Decontamination Method for N95 Respirator Reuse. Environ Sci Technol Lett 2020; 7:677-682. [PMID: 37566356 PMCID: PMC7374934 DOI: 10.1021/acs.estlett.0c00534] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023]
Abstract
A pandemic such as COVID-19 can cause a sudden depletion of the worldwide supply of respirators, forcing healthcare providers to reuse them. In this study, we systematically evaluated dry heat treatment as a viable option for the safe decontamination of N95 respirators (1860, 3M) before their reuse. We found that the dry heat generated by an electric cooker (100 °C, 5% relative humidity, 50 min) effectively inactivated Tulane virus (TV, >5.2-log10 reduction), rotavirus (RV, >6.6-log10 reduction), adenovirus (AdV, >4.0-log10 reduction), and transmissible gastroenteritis virus (TGEV, >4.7-log10 reduction). The respirator integrity (determined on the basis of the particle filtration efficiency and quantitative fit testing) was not compromised after 20 cycles of a 50 min dry heat treatment. On the basis of these results, dry heat decontamination generated by an electric cooker (e.g., rice cookers, instant pots, and ovens) could be an effective and accessible decontamination method for the safe reuse of N95 respirators. We recommend users measure the temperature during decontamination to ensure the respirator temperature can be maintained at 100 °C for 50 min.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering,
University of Illinois at Urbana-Champaign, Urbana, Illinois
61801, United States
| | - Elbashir Araud
- Holonyak Micro & Nanotechnology Lab,
University of Illinois at Urbana-Champaign, Urbana, Illinois
61801, United States
| | - Joseph V. Puthussery
- Department of Civil and Environmental Engineering,
University of Illinois at Urbana-Champaign, Urbana, Illinois
61801, United States
| | - Hezi Bai
- Department of Civil and Environmental Engineering,
University of Illinois at Urbana-Champaign, Urbana, Illinois
61801, United States
| | - Gemma G. Clark
- Department of Civil and Environmental Engineering,
University of Illinois at Urbana-Champaign, Urbana, Illinois
61801, United States
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of
Veterinary Clinical Medicine, College of Veterinary Medicine, University of
Illinois at Urbana-Champaign, Urbana, Illinois 61802, United
States
| | - Vishal Verma
- Department of Civil and Environmental Engineering,
University of Illinois at Urbana-Champaign, Urbana, Illinois
61801, United States
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering,
University of Illinois at Urbana-Champaign, Urbana, Illinois
61801, United States
- Carl R. Woese Institute for Genomic Biology,
University of Illinois at Urbana-Champaign, Urbana, Illinois
61801, United States
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40
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Yang S, Li Y, Wang B, Yang N, Huang X, Chen Q, Geng S, Zhou Y, Shi H, Wang L, Brugman S, Savelkoul H, Liu G. Acute porcine epidemic diarrhea virus infection reshapes the intestinal microbiota. Virology 2020; 548:200-212. [PMID: 32763491 PMCID: PMC7353907 DOI: 10.1016/j.virol.2020.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota is crucial to intestinal homeostasis. Porcine epidemic diarrhea virus (PEDV) is high pathogenic to intestines, causing diarrhea, even death in piglets. To investigate the detailed relationship between PEDV infection and intestinal microbiota, the composition and distribution of intestinal microbiota from pigs were first analyzed using 16S rRNA sequencing technology. The results demonstrated that the composition and distribution of microbes in different intestinal segments were quite similar between 1-week-old and 2-week-old piglets but different from 4-week-old (weaned) piglets. Then piglets at different ages were inoculated with PEDV. The results showed that the 1-week-old piglets exhibited the most severe pathogenicity comparing to the other age groups. Further investigations indicated that Lactobacillus, Escherichia coli, and Lactococcus in the intestinal microbiota of piglets were significantly changed by PEDV infection. These results strengthen our understanding of viruses influencing intestinal microbes and remind us of the potential association between PEDV and intestinal microbes.
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Affiliation(s)
- Shanshan Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China; Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Yang Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Bin Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Ning Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Xin Huang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Qingbo Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Shuxian Geng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Yawei Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Han Shi
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, 61802, USA
| | - Sylvia Brugman
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Huub Savelkoul
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Guangliang Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China.
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41
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Gu W, Shi Q, Wang L, Zhang J, Yuan G, Chen S, Zuo Y, Fan J. Detection and phylogenetic analysis of porcine circovirus 3 in part of northern China from 2016 to 2018. Arch Virol 2020; 165:2003-2011. [PMID: 32594321 DOI: 10.1007/s00705-020-04709-0] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 05/20/2020] [Indexed: 02/07/2023]
Abstract
Porcine circovirus 3 (PCV3) is a recently identified virus that is associated with reproductive failure, porcine dermatitis and nephropathy syndrome, and multi-systemic inflammation. To investigate the molecular epidemic characteristics and genetic evolution of PCV3 in northern China, a commercial TaqMan-based real-time quantitative PCR kit was used to detect PCV3 in 435 tissue specimens collected from pigs with various clinical signs from 105 different swine farms in northern China. The results showed that 48 out of 105 (45.7%) farms and 97 out of 435 (22.3%) samples tested positive for PCV3. Of the 97 PCV3-positive samples, 80 (82.5%) tested positive for other pathogens. PCV3 was found more frequently in pigs with reproductive failure than in those with other clinical signs. This study is the first to detect PCV3 in Tianjin. The complete genome sequences of six PCV3 isolates and the capsid (Cap) protein gene sequences of 11 isolates were determined. Based on the predicted amino acids at positions 24 and 27 of the Cap protein and their evolutionary relationships, the 17 PCV3 strains obtained from northern China and 49 reference strains downloaded from the GenBank database were divided into four major groups (3a-3d). An analysis of selection pressure and polymorphism indicated that the PCV3 Cap protein seems to be evolving under balancing selection, that the population is in dynamic equilibrium, and that no population expansion occurred during the study period. Our results provide new information about the molecular epidemiology and evolution of PCV3.
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Affiliation(s)
- Wenyuan Gu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
- Animal Diseases Control Center of Hebei, Shijiazhuang, 050053, China
| | - Qiankai Shi
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, 61802, USA
| | - Jianlou Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Guangfu Yuan
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Shaojie Chen
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Yuzhu Zuo
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China.
| | - Jinghui Fan
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China.
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42
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Guo Z, Wang L, Qiao S, Deng R, Zhang G. Genetic characterization and recombination analysis of atypical porcine pestivirus. Infect Genet Evol 2020; 81:104259. [PMID: 32087344 DOI: 10.1016/j.meegid.2020.104259] [Citation(s) in RCA: 12] [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: 11/24/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Atypical porcine pestivirus (APPV) is recognised as the etiology of congenital tremor (CT) Type A-II and poses a challenge to pig production. Here, we described a CT case in piglets caused by APPV infection in central China in 2017. Interestingly, different from a previous report, more CT litters were observed in the second and third parity sows compared to the first and fourth parity. Evolutionary analysis and recombination evaluation were conducted for the isolate and 61 APPV genomes were available in GenBank. Phylogenetic analysis revealed a high level of genetic variation of APPV and the coexistence of three clades (Clades I-III) in China. The isolate was clustered into Clade I, which seemed to be prevalent worldwide and displayed higher genetic variability (Subgroups 1-4) compared with Clade II and Clade III, both of which were only reported in China. Notably, three putative recombinants were identified and characterized in APPV. The recombination events occurred in inter-clades (Clade II and III) or intra-clades (Clade I). To the best of our knowledge, this study presents the first evidence of homologous recombination within Pestivirus K. These results provide new clinical presentations of APPV infection and may be helpful in better understanding the large amount of genetic variations in this genus.
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Affiliation(s)
- Zhenhua Guo
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, PR China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Songlin Qiao
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, PR China
| | - Ruiguang Deng
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, PR China
| | - Gaiping Zhang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, PR China; College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, PR China.
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43
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Wang L, Maddox C, Terio K, Lanka S, Fredrickson R, Novick B, Parry C, McClain A, Ross K. Detection and Characterization of New Coronavirus in Bottlenose Dolphin, United States, 2019. Emerg Infect Dis 2020; 26:1610-1612. [PMID: 32568058 PMCID: PMC7323548 DOI: 10.3201/eid2607.200093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We characterized novel coronaviruses detected in US bottlenose dolphins (BdCoVs) with diarrhea. These viruses are closely related to the other 2 known cetacean coronaviruses, Hong Kong BdCoV and beluga whale CoV. A deletion in the spike gene and insertions in the membrane gene and untranslated regions were found in US BdCoVs (unrelated to severe acute respiratory syndrome coronavirus 2).
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44
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Wang Z, Zhang Y, Wang L, Wei J, Liu K, Shao D, Li B, Liu L, Widén F, Ma Z, Qiu Y. Comparative genomic analysis of Bordetella bronchiseptica isolates from the lungs of pigs with porcine respiratory disease complex (PRDC). Infect Genet Evol 2020; 81:104258. [PMID: 32087347 DOI: 10.1016/j.meegid.2020.104258] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/16/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Bordetella bronchiseptica (B. bronchiseptica), as an opportunistic pathogen, can cause respiratory diseases in a variety of animals, including humans. In additional to being involved in porcine atrophic rhinitis through coinfection with Pasteurella multocida, B. bronchiseptica is associated with porcine respiratory disease complex (PRDC). While there are genomic data available from different host species, little is known about B. bronchiseptica isolates from pig lungs, especially from lungs characterized as having PRDC. RESULTS A total of five B. bronchiseptica isolates were identified from pig lungs characterized as PRDC. The draft genomes of these strains were generated. In comparison with the other reported genomes, these five isolates showed the similar general characteristic including G+C content, rRNAs/tRNA, and clusters of orthologous groups of proteins (COGs). Phylogenetic analysis of all B. Bronchiseptica isolates of different species available at GenBank based on core genome multilocus sequence typing (cgMLST) classified them into two genogroups. All five isolates from this study, with the other isolates from pigs, were placed into a subclade of genogroup I consisting of only mammalian isolates. By contrast, genogroup II contained the isolates from an avian species (turkey) and some mammals (human and dog). Moreover, genome annotation revealed the presence of antibiotic resistance genes and virulence genes among these five genomes, consistent with the similarity and variety in genomic traits. Finally, comparative analysis of insertion sequence (IS) and prophages in five genomes further showed the similarity and variety in genomic characteristic. CONCLUSIONS This is the first study to provide comparative genomics of B. bronchiseptica strains from pig lungs characterized as having PRDC. Importantly, the findings presented in this study reveal novel genomic characteristic of B. bronchiseptica, which should provide insightful information on genome evolution.
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Affiliation(s)
- Zhitao Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 518, Ziyue Road, Shanghai 200241, PR China
| | - Yanbing Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 518, Ziyue Road, Shanghai 200241, PR China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 518, Ziyue Road, Shanghai 200241, PR China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 518, Ziyue Road, Shanghai 200241, PR China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 518, Ziyue Road, Shanghai 200241, PR China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 518, Ziyue Road, Shanghai 200241, PR China
| | - Lihong Liu
- Department of Virology, Immunobiology and Parasitology (VIP), The Notional Veterinary Institute (SVA), Uppsala, Sweden
| | - Frederik Widén
- Department of Virology, Immunobiology and Parasitology (VIP), The Notional Veterinary Institute (SVA), Uppsala, Sweden
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 518, Ziyue Road, Shanghai 200241, PR China.
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 518, Ziyue Road, Shanghai 200241, PR China.
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45
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Zheng LL, Cui JT, Han HY, Hou HL, Wang L, Liu F, Chen HY. Development of a duplex SYBR GreenⅠ based real-time PCR assay for detection of porcine epidemic diarrhea virus and porcine bocavirus3/4/5. Mol Cell Probes 2020; 51:101544. [PMID: 32109535 DOI: 10.1016/j.mcp.2020.101544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/07/2020] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
The duplex real-time PCR assay based on SYBR Green І was developed for detection of porcine epidemic diarrhea virus (PEDV) and porcine bocavirus (PBoV) 3/4/5 genotypes simultaneously. Two pairs of specific primers were designed targeting the N gene sequence of PEDV and VP1 gene sequence of PBoV3/4/5. PEDV and PBoV3/4/5 could be distinguished by their different melting temperatures (Tm) in one sample. The Tm value of PEDV was 83.5 °C, and the Tm value of PBoV3/4/5 was 78.5 °C, while other swine pathogens showed no specific melting peaks. The detection limits of this assay were 10 copies/μL for both PEDV and PBoV3/4/5. A total of sixty-three intestinal tissue samples were collected from piglets suffering from diarrhea, and the viral nucleic acids detected and identified by the real-time PCR assay and conventional PCR assay. The duplex real-time PCR detection results showed that the prevalence of PEDV and PBoV3/4/5 was 85.7% and 46%, respectively, and the co-infection rate of the two viruses was 28.6%. These results indicated that this duplex real-time PCR assay was a sensitive, specific and reproducible method for differentiating PEDV and PBoV3/4/5 or their co-infection.
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Affiliation(s)
- Lan-Lan Zheng
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Jian-Tao Cui
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Hao-Ying Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Hua-Lin Hou
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan Province, People's Republic of China; College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, People's Republic of China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Fang Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan Province, People's Republic of China.
| | - Hong-Ying Chen
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan Province, People's Republic of China.
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46
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Briggs K, Wang L, Nagashima K, Zengel J, Tripp RA, He B. Regulation of Mumps Virus Replication and Transcription by Kinase RPS6KB1. J Virol 2020; 94:JVI.00387-20. [PMID: 32295907 PMCID: PMC7307103 DOI: 10.1128/jvi.00387-20] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023] Open
Abstract
Mumps virus (MuV) caused the most viral meningitis before mass immunization. Unfortunately, MuV has reemerged in the United States in the past several years. MuV is a member of the genus Rubulavirus, in the family Paramyxoviridae, and has a nonsegmented negative-strand RNA genome. The viral RNA-dependent RNA polymerase (vRdRp) of MuV consists of the large protein (L) and the phosphoprotein (P), while the nucleocapsid protein (NP) encapsulates the viral RNA genome. These proteins make up the replication and transcription machinery of MuV. The P protein is phosphorylated by host kinases, and its phosphorylation is important for its function. In this study, we performed a large-scale small interfering RNA (siRNA) screen targeting host kinases that regulated MuV replication. The human kinase ribosomal protein S6 kinase beta-1 (RPS6KB1) was shown to play a role in MuV replication and transcription. We have validated the role of RPS6KB1 in regulating MuV using siRNA knockdown, an inhibitor, and RPS6KB1 knockout cells. We found that MuV grows better in cells lacking RPS6KB1, indicating that it downregulates viral growth. Furthermore, we detected an interaction between the MuV P protein and RPS6KB1, suggesting that RPS6KB1 directly regulates MuV replication and transcription.IMPORTANCE Mumps virus is an important human pathogen. In recent years, MuV has reemerged in the United State, with outbreaks occurring in young adults who have been vaccinated. Our work provides insight into a previously unknown mumps virus-host interaction. RPS6KB1 negatively regulates MuV replication, likely through its interaction with the P protein. Understanding virus-host interactions can lead to novel antiviral drugs and enhanced vaccine production.
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Affiliation(s)
- Kelsey Briggs
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Leyi Wang
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Kaito Nagashima
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - James Zengel
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Ralph A Tripp
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Biao He
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
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47
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Wang L, Mitchell PK, Calle PP, Bartlett SL, McAloose D, Killian ML, Yuan F, Fang Y, Goodman LB, Fredrickson R, Elvinger F, Terio K, Franzen K, Stuber T, Diel DG, Torchetti MK. Complete Genome Sequence of SARS-CoV-2 in a Tiger from a U.S. Zoological Collection. Microbiol Resour Announc 2020; 9:9/22/e00468-20. [PMID: 32467283 PMCID: PMC7256270 DOI: 10.1128/mra.00468-20] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
This report describes the identification and characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a Malayan tiger in a U.S. zoo.
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Affiliation(s)
- Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Patrick K Mitchell
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Paul P Calle
- Wildlife Conservation Society, Zoological Health Program, Bronx Zoo, Bronx, New York, USA
| | - Susan L Bartlett
- Wildlife Conservation Society, Zoological Health Program, Bronx Zoo, Bronx, New York, USA
| | - Denise McAloose
- Wildlife Conservation Society, Zoological Health Program, Bronx Zoo, Bronx, New York, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
| | - Fangfeng Yuan
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Ying Fang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - Laura B Goodman
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, USA
| | - François Elvinger
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Karen Terio
- Zoological Pathology Program, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois, Brookfield, Illinois, USA
| | - Kerrie Franzen
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
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48
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Kong WH, Li Y, Peng MW, Kong DG, Yang XB, Wang L, Liu MQ. SARS-CoV-2 detection in patients with influenza-like illness. Nat Microbiol 2020; 5:675-678. [PMID: 32265517 DOI: 10.1038/s41564-020-0713-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first reported in Wuhan, Hubei Province, China in late December 2019. We re-analysed 640 throat swabs collected from patients in Wuhan with influenza-like-illness from 6 October 2019 to 21 January 2020 and found that 9 of the 640 throat swabs were positive for SARS-CoV-2 RNA by quantitative PCR, suggesting community transmission of SARS-CoV2 in Wuhan in early January 2020.
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Affiliation(s)
- Wen-Hua Kong
- Wuhan Center for Disease Control & Prevention, Wuhan, Hubei, China
| | - Yao Li
- Wuhan Center for Disease Control & Prevention, Wuhan, Hubei, China
| | - Ming-Wei Peng
- Wuhan Center for Disease Control & Prevention, Wuhan, Hubei, China
| | - De-Guang Kong
- Wuhan Center for Disease Control & Prevention, Wuhan, Hubei, China
| | - Xiao-Bing Yang
- Wuhan Center for Disease Control & Prevention, Wuhan, Hubei, China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Man-Qing Liu
- Wuhan Center for Disease Control & Prevention, Wuhan, Hubei, China.
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Zheng HH, Zhang SJ, Cui JT, Zhang J, Wang L, Liu F, Chen HY. Simultaneous detection of classical swine fever virus and porcine circovirus 3 by SYBR green I-based duplex real-time fluorescence quantitative PCR. Mol Cell Probes 2020; 50:101524. [PMID: 31972226 DOI: 10.1016/j.mcp.2020.101524] [Citation(s) in RCA: 14] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 01/07/2020] [Accepted: 01/18/2020] [Indexed: 02/07/2023]
Abstract
In the present study, the SYBR green I-based duplex quantitative polymerase chain reaction (qPCR) was developed for simultaneous detection of classical swine fever virus (CSFV) and porcine circovirus 3 (PCV3). The assay was used to detect both CSFV and PCV3 in one sample by their distinct melting temperatures (melting peaks at 87°C for CSFV and 81.5 °C for PCV3), and no specific fluorescence signals were detected for other non-targeted porcine pathogens. The assay had a high degree of linearity (R2 > 0.998) with the detection limits of 23 copies/μL for CSFV and 36 copies/μL for PCV3, and exhibited high repeatability and reproducibility with a low coefficient of variation below 2.0% in both intra- and inter-assay. In this study, 130 clinical samples collected from sick pigs in the field were tested by this assay with the positive rates of 9.23% (12/130) for CSFV and 21.54% (28/130) for PCV3 respectively, and the positive rate of CSFV and PCV3 co-infection was 6.92% (9/130). Our results showed that the developed method was a reliable diagnostic tool to monitor and survey CSFV, PCV3 and CSFV/PCV3 co-infection in the field.
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Affiliation(s)
- Hui-Hua Zheng
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, Henan Province, People's Republic of China
| | - Shu-Jian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, Henan Province, People's Republic of China
| | - Jian-Tao Cui
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, Henan Province, People's Republic of China
| | - Jia Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, Henan Province, People's Republic of China
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Fang Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, Henan Province, People's Republic of China.
| | - Hong-Ying Chen
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, Henan Province, People's Republic of China; Zhengzhou Major Pig Disease Prevention and Control Laboratory, Henan Province, Zhengzhou, 450046, Henan Province, People's Republic of China.
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Abstract
We report the identification of astrovirus WI65268 in a white-tailed deer with respiratory disease in the United States in 2018. This virus is a recombinant of Kagoshima1-7 and Kagoshima2-3-2 (both bovine astroviruses from Japan) and was characterized as a potential new genotype. Further surveillance of deer might help identify related isolates.
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