1
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Duffy SC, Marais B, Kapur V, Behr MA. Zoonotic tuberculosis in the 21st century. Lancet Infect Dis 2024; 24:339-341. [PMID: 38307096 DOI: 10.1016/s1473-3099(24)00059-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Affiliation(s)
- Shannon C Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, QC H4A 3J1, Canada; McGill International TB Centre, McGill University, Montreal, QC H4A 3J1, Canada; The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Ben Marais
- Sydney Infectious Diseases Institute, University of Sydney, NSW, Australia
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, QC H4A 3J1, Canada; McGill International TB Centre, McGill University, Montreal, QC H4A 3J1, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada; The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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2
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Fromsa A, Willgert K, Srinivasan S, Mekonnen G, Bedada W, Gumi B, Lakew M, Tadesse B, Bayissa B, Sirak A, Girma Abdela M, Gebre S, Chibssa T, Veerasami M, Vordermeier HM, Bakker D, Berg S, Ameni G, Juleff N, de Jong MCM, Wood J, Conlan A, Kapur V. BCG vaccination reduces bovine tuberculosis transmission, improving prospects for elimination. Science 2024; 383:eadl3962. [PMID: 38547287 DOI: 10.1126/science.adl3962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/24/2024] [Indexed: 04/02/2024]
Abstract
Bacillus Calmette-Guérin (BCG) is a routinely used vaccine for protecting children against Mycobacterium tuberculosis that comprises attenuated Mycobacterium bovis. BCG can also be used to protect livestock against M. bovis; however, its effectiveness has not been quantified for this use. We performed a natural transmission experiment to directly estimate the rate of transmission to and from vaccinated and unvaccinated calves over a 1-year exposure period. The results show a higher indirect efficacy of BCG to reduce transmission from vaccinated animals that subsequently become infected [74%; 95% credible interval (CrI): 46 to 98%] compared with direct protection against infection (58%; 95% CrI: 34 to 73%) and an estimated total efficacy of 89% (95% CrI: 74 to 96%). A mechanistic transmission model of bovine tuberculosis (bTB) spread within the Ethiopian dairy sector was developed and showed how the prospects for elimination may be enabled by routine BCG vaccination of cattle.
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Affiliation(s)
- Abebe Fromsa
- Aklilu Lemma Institutes of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Katriina Willgert
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, UK
| | - Sreenidhi Srinivasan
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
- The Global Health Initiative, Henry Ford Health, Detroit, MI, USA
| | | | | | - Balako Gumi
- Aklilu Lemma Institutes of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Berecha Bayissa
- Aklilu Lemma Institutes of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Musse Girma Abdela
- Aklilu Lemma Institutes of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | | | - Douwe Bakker
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Technical Consultant and Independent Researcher, Lelystad, Netherlands
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Stefan Berg
- Animal and Plant Health Agency, Weybridge, UK
| | - Gobena Ameni
- Aklilu Lemma Institutes of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, United Arab Emirates
| | - Nick Juleff
- The Bill & Melinda Gates Foundation Seattle, WA, USA
| | - Mart C M de Jong
- Quantitative Veterinary Epidemiology Group, Wageningen UR, The Netherlands
| | - James Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, UK
| | - Andrew Conlan
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, UK
| | - Vivek Kapur
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
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3
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Kumar M, Kumar T, Jangir BL, Singh M, Arora D, Bangar Y, Conlan A, Vordermeier M, Bakker D, Byregowda SM, Srinivasan S, Kapur V, Jindal N. Comparative analysis of tuberculin and defined antigen skin tests for detection of bovine tuberculosis in buffaloes (Bubalus bubalis) in Haryana state, India. BMC Vet Res 2024; 20:65. [PMID: 38395846 DOI: 10.1186/s12917-024-03913-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Bovine tuberculosis (bTB) is a chronic disease that results from infection with any member of the Mycobacterium tuberculosis complex. Infected animals are typically diagnosed with tuberculin-based intradermal skin tests according to World Organization of Animal Health which are presently in use. However, tuberculin is not suitable for use in BCG-vaccinated animals due to a high rate of false-positive reactions. Peptide-based defined skin test (DST) antigens have been identified using antigens (ESAT-6, CFP-10 and Rv3615c) which are absent from BCG, but their performance in buffaloes remains unknown. To assess the comparative performance of DST with the tuberculin-based single intradermal test (SIT) and the single intradermal comparative cervical test (SICCT), we screened 543 female buffaloes from 49 organized dairy farms in two districts of Haryana state in India. RESULTS We found that 37 (7%), 4 (1%) and 18 (3%) buffaloes were reactors with the SIT, SICCT and DST tests, respectively. Of the 37 SIT reactors, four were positive with SICCT and 12 were positive with the DST. The results show that none of the animals tested positive with all three tests, and 6 DST positive animals were SIT negative. Together, a total of 43 animals were reactors with SIT, DST, or both, and the two assays showed moderate agreement (Cohen's Kappa 0.41; 95% Confidence Interval (CI): 0.23, 0.59). In contrast, only slight agreement (Cohen's Kappa 0.18; 95% CI: 0.02, 0.34) was observed between SIT and SICCT. Using a Bayesian latent class model, we estimated test specificities of 96.5% (95% CI, 92-99%), 99.7% (95% CI: 98-100%) and 99.0% (95% CI: 97-100%) for SIT, SICCT and DST, respectively, but considerably lower sensitivities of 58% (95% CI: 35-87%), 9% (95% CI: 3-21%), and 34% (95% CI: 18-55%) albeit with broad and overlapping credible intervals. CONCLUSION Taken together, our investigation suggests that DST has a test specificity comparable with SICCT, and sensitivity intermediate between SIT and SICCT for the identification of buffaloes suspected of tuberculosis. Our study highlights an urgent need for future well-powered trials with detailed necropsy, with immunological and microbiological profiling of reactor and non-reactor animals to better define the underlying factors for the large observed discrepancies in assay performance, particularly between SIT and SICCT.
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Affiliation(s)
- Mohit Kumar
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125 004, India
| | - Tarun Kumar
- Veterinary Clinical Complex, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125 004, India
| | - Babu Lal Jangir
- Department of Veterinary Pathology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125 004, India
| | - Mahavir Singh
- College Central Laboratory, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125 004, India
| | - Devan Arora
- Regional Centre at Karnal, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125 004, India
| | - Yogesh Bangar
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125 004, India
| | - Andrew Conlan
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Douwe Bakker
- Technical Consultant and Independent Researcher, Lelystad, The Netherlands
| | - S M Byregowda
- Institute of Animal Health and Veterinary Biologicals, Bengaluru, India
| | - Sreenidhi Srinivasan
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Vivek Kapur
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, 125 004, India.
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4
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Maqsood R, Duffy SC, Bin Rashid H, Gill SS, Jabeen C, Arshad N, Umbreen G, Behr MA, Kapur V, Chaudhry M. Molecular detection and characterization of the Mycobacterium tuberculosis complex subspecies responsible for bovine tuberculosis in Punjab, Pakistan. Microbiol Spectr 2024; 12:e0269223. [PMID: 38226805 PMCID: PMC10846167 DOI: 10.1128/spectrum.02692-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/16/2023] [Indexed: 01/17/2024] Open
Abstract
Bovine tuberculosis (bTB), traditionally associated with Mycobacterium bovis, presents significant public health and economic challenges worldwide. This study investigated the causative agents of bTB in slaughtered cattle and buffalo in Lahore, Pakistan. Of the 3,581 animals screened, 34 were identified with gross TB-like lesions. The lesions were processed for culture, PCR, and Sanger sequencing to identify the causative agents of the disease. The results identified 10 Mycobacterium orygis and 8 Mycobacterium tuberculosis sensu stricto isolates. Whole-genome sequencing was performed on two M. orygis isolates, and the sequences were phylogenetically compared to 93 publicly available M. orygis sequences. The results also demonstrated that the JB21 and JB22 primers, which have been previously commonly applied to detect M. bovis in Pakistan, are unable to distinguish between M. tuberculosis complex subspecies. The identification of M. orygis and M. tuberculosis as causative agents of bTB in this slaughterhouse in Punjab may have important implications in identifying cases of zoonotic TB in humans and applying appropriate molecular tools to identify the prevalence of the disease. The data from this study align with recent findings suggesting M. orygis is the predominant cause of bTB in South Asia.IMPORTANCEThe study findings hold significant relevance to the Journal of Clinical Microbiology, as they directly impact the field. The first-time identification of Mycobacterium orygis and Mycobacterium tuberculosis as the predominant causative agents of bovine tuberculosis in Lahore, Pakistan underscores the urgent need for enhanced diagnostic methods. The study emphasizes the importance of improved assays for the accurate detection and differentiation of Mycobacterium subspecies. Additionally, the research addresses zoonotic risk assessment and public health implications, advocating for a multidisciplinary approach that integrates clinical microbiology with veterinary and human health sectors. These insights contribute to clinical microbiology knowledge, shaping effective strategies for disease prevention, surveillance, and control. The study's potential to advance the field makes it well suited for publication in the Microbiology Spectrum journal.
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Affiliation(s)
- Rubab Maqsood
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
- Institute of Continuing Education and Extension, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki, Pakistan
| | - Shannon C. Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Hamad Bin Rashid
- Department of Veterinary Surgery and Pet Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Shakera Sadiq Gill
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Chanda Jabeen
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Nimra Arshad
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Gulshan Umbreen
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Marcel A. Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Vivek Kapur
- Department of Animal Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Mamoona Chaudhry
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
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5
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Holder T, Srinivasan S, McGoldrick A, Williams GA, Palmer S, Clarke J, O'Brien A, Conlan AJK, Juleff N, Vordermeier HM, Jones GJ, Kapur V. Temporal dynamics of the early immune response following Mycobacterium bovis infection of cattle. Sci Rep 2024; 14:2600. [PMID: 38297023 PMCID: PMC10831113 DOI: 10.1038/s41598-024-52314-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024] Open
Abstract
Bovine tuberculosis is an infectious disease of global significance that remains endemic in many countries. Mycobacterium bovis infection in cattle is characterized by a cell-mediated immune response (CMI) that precedes humoral responses, however the timing and trajectories of CMI and antibody responses determined by newer generation assays remain undefined. Here we used defined-antigen interferon-gamma release assays (IGRA) and an eleven-antigen multiplex ELISA (Enferplex TB test) alongside traditional tuberculin-based IGRA and IDEXX M. bovis antibody tests to assess immune trajectories following experimental M. bovis infection of cattle. The results show CMI responses developed as early as two-weeks post-infection, with all infected cattle testing positive three weeks post-infection. Interestingly, 6 of 8 infected animals were serologically positive with the Enferplex TB assay as early as 4 weeks post-infection. As expected, application of the tuberculin skin test enhanced subsequent serological reactivity. Infrequent M. bovis faecal shedding was observed but was uncorrelated with observed immune trajectories. Together, the results show that early antibody responses to M. bovis infection are detectable in some individuals and highlight an urgent need to identify biomarkers that better predict infection outcomes, particularly for application in low-and-middle income countries where test-and-slaughter based control methods are largely unfeasible.
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Affiliation(s)
- Thomas Holder
- Animal and Plant Health Agency, Bacteriology, Addlestone, UK
| | - Sreenidhi Srinivasan
- The Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | | | | | | | - John Clarke
- Enfer Scientific, Unit T, M7 Business Park, Newhall, Naas, County Kildare, Ireland
| | - Amanda O'Brien
- Enfer Scientific, Unit T, M7 Business Park, Newhall, Naas, County Kildare, Ireland
| | - Andrew J K Conlan
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nick Juleff
- The Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Gareth J Jones
- Animal and Plant Health Agency, Bacteriology, Addlestone, UK.
| | - Vivek Kapur
- The Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
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6
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Harrison LB, Kapur V, Behr MA. An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows. Microb Genom 2024; 10:001165. [PMID: 38175684 PMCID: PMC10868604 DOI: 10.1099/mgen.0.001165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Reference-based alignment of short-reads is a widely used technique in genomic analysis of the Mycobacterium tuberculosis complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas et al. both of which are based on a lineage 4 sequence. As such, these reference sequences do not capture all of the structural variation known to be present in the ancestor of the MTBC. To better represent the base of the MTBC, we generated an imputed ancestral genomic sequence, termed MTBC0 from reference-free alignments of closed MTBC genomes. When used as a reference sequence in alignment workflows, MTBC0 mapped more short sequencing reads and called more pairwise SNPs relative to the Comas et al. sequence while exhibiting minimal impact on the overall phylogeny of MTBC. The results also show that MTBC0 provides greater fidelity in capturing genomic variation and allows for the inclusion of regions absent from H37Rv in standard MTBC workflows without additional steps. The use of MTBC0 as an ancestral reference sequence in standard workflows modestly improved read mapping, SNP calling and intuitively facilitates the study of structural variation and evolution in MTBC.
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Affiliation(s)
- Luke B. Harrison
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
- Bacterial Symbionts Evolution, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec H7V 1B7, Canada
| | - Vivek Kapur
- Department of Animal Science, The Pennsylvania State University, State College, PA 16802-3500, USA
| | - Marcel A. Behr
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec H4A 3S5, Canada
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7
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Goike J, Hsieh CL, Horton AP, Gardner EC, Zhou L, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Xie X, Xia H, Shi PY, Renberg R, Segall-Shapiro TH, Terrace CI, Wu W, Shroff R, Byrom M, Ellington AD, Marcotte EM, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Weaver SC, Dye JM, Boutz DR, McLellan JS, Gollihar JD. SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode. Commun Biol 2023; 6:1250. [PMID: 38082099 PMCID: PMC10713552 DOI: 10.1038/s42003-023-05649-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has provided unprecedented insight into mutations enabling immune escape. Understanding how these mutations affect the dynamics of antibody-antigen interactions is crucial to the development of broadly protective antibodies and vaccines. Here we report the characterization of a potent neutralizing antibody (N3-1) identified from a COVID-19 patient during the first disease wave. Cryogenic electron microscopy revealed a quaternary binding mode that enables direct interactions with all three receptor-binding domains of the spike protein trimer, resulting in extraordinary avidity and potent neutralization of all major variants of concern until the emergence of Omicron. Structure-based rational design of N3-1 mutants improved binding to all Omicron variants but only partially restored neutralization of the conformationally distinct Omicron BA.1. This study provides new insights into immune evasion through changes in spike protein dynamics and highlights considerations for future conformationally biased multivalent vaccine designs.
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Affiliation(s)
- Jule Goike
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew P Horton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Elizabeth C Gardner
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Shawn Abbassi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rebecca Renberg
- DEVCOM Army Research Laboratory, Biotechnology Branch, Adelphi, MD, USA
| | - Thomas H Segall-Shapiro
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- DEVCOM Army Research Laboratory-South, Austin, TX, USA
| | | | - Wesley Wu
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- DEVCOM Army Research Laboratory-South, Austin, TX, USA
| | - Michelle Byrom
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - James M Musser
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Suresh V Kuchipudi
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, PA, USA
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - George Georgiou
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Scott C Weaver
- University of Texas Medical Branch, World Reference Center for Emerging Viruses and Arboviruses, Galveston, TX, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Daniel R Boutz
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA.
- DEVCOM Army Research Laboratory-South, Austin, TX, USA.
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Jimmy D Gollihar
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA.
- DEVCOM Army Research Laboratory-South, Austin, TX, USA.
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8
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King S, Baron MD, Kidane M, Aklilu F, Kapur V, Herzog CM, Batten C. Complete genome of a 2014 isolate of peste des petits ruminants virus from Ethiopia. Microbiol Resour Announc 2023; 12:e0024223. [PMID: 37462384 PMCID: PMC10508127 DOI: 10.1128/mra.00242-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/01/2023] [Indexed: 09/20/2023] Open
Abstract
This report describes the complete genome sequence of a peste des petits ruminants virus (PPRV) isolate from Ethiopia in 2014. The strain (PPRV/Ethiopia/Habru/2014), which showed a normal virulence and relatively low morbidity in the field, belongs to the North African subclade of Lineage IV.
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Affiliation(s)
- Simon King
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | | | | | | | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Catherine M. Herzog
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carrie Batten
- The Pirbright Institute, Woking, Surrey, United Kingdom
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9
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Sumanth LJ, Suresh CR, Venkatesan M, Manesh A, Behr MA, Kapur V, Michael JS. Clinical features of human tuberculosis due to Mycobacterium orygis in Southern India. J Clin Tuberc Other Mycobact Dis 2023; 32:100372. [PMID: 37168873 PMCID: PMC10164920 DOI: 10.1016/j.jctube.2023.100372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Mycobacterium orygis is a member of the Mycobacterium tuberculosis complex (MTBC) and causes tuberculosis in a variety of animals, including humans in South Asia. Here, we describe the clinical features associated with 8 human cases of whole genome sequence (WGS) confirmed M. orygis from a tertiary care hospital in South India during 2018-2019. The patient ages ranged from 9 to 51 years, with 5 females and 3 males included. All the patients had extrapulmonary disease with 2 having concomitant pulmonary involvement. Clinical improvement was documented after a full course of anti-tuberculosis therapy in 6 cases for whom follow-up was available. Taken together, the results show that M. orygis causes human tuberculosis in India, with a predominant extrapulmonary disease. Standardized molecular assays of this emerging member of the MTBC are needed to provide further information on the frequency of M. orygis infection in India and other countries where it is found in livestock and domestic wildlife.
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Affiliation(s)
- Lydia Jennifer Sumanth
- Associate Physician, Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | | | - Manigandan Venkatesan
- Research Associate, Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Abi Manesh
- Associate Professor, Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Marcel A. Behr
- Professor of Medicine, McGill International TB Centre, Montreal, Quebec H4A 3S5, Canada
| | - Vivek Kapur
- Professor, Infectious Diseases and Microbiology, The Pennsylvania State University, State College, PA 16802-3500, USA
| | - Joy Sarojini Michael
- Professor, Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu 632004, India
- Corresponding author.
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10
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Sharma M, Mathesh K, Dandapat P, Mariappan AK, Kumar R, Kumari S, Kapur V, Maan S, Jindal N, Bansal N, Kadiwar R, Kumar A, Gupta N, Pawde AM, Sharma AK. Emergence of Mycobacterium orygis-Associated Tuberculosis in Wild Ruminants, India. Emerg Infect Dis 2023; 29:661-663. [PMID: 36823735 PMCID: PMC9973683 DOI: 10.3201/eid2903.221228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Tuberculosis caused by Mycobacterium orygis was detected in 2 spotted deer from a wildlife sanctuary in western India and an Indian bison from a national park in central India. Nationwide surveillance is urgently required to clarify the epidemiology of the Mycobacterium tuberculosis complex at the human-livestock-wildlife interface.
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11
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Bakker D, Buza JJ, Álvarez J, Kapur V. Editorial: Advancing the development and implementation of regional, national tuberculosis control programs in livestock in Africa, Asia, and Latin America. Front Vet Sci 2023; 10:1192091. [PMID: 37143495 PMCID: PMC10151898 DOI: 10.3389/fvets.2023.1192091] [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: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 05/06/2023] Open
Affiliation(s)
- Douwe Bakker
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
- School of Life Sciences and Bioengineering, The Pennsylvania State University (PSU), University Park, State College, PA, United States
- *Correspondence: Douwe Bakker
| | - Joram Josephat Buza
- Huck Institutes of the Life Sciences, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Julio Álvarez
- VISAVET Health Surveillance Centre (UCM), Madrid, Spain
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Vivek Kapur
- School of Life Sciences and Bioengineering, The Pennsylvania State University (PSU), University Park, State College, PA, United States
- Huck Institutes of the Life Sciences, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
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12
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Willgert K, da Silva S, Li R, Dandapat P, Veerasami M, Maity H, Papanna M, Srinivasan S, Wood JLN, Kapur V, Conlan AJK. Is bovine density and ownership associated with human tuberculosis in India? PLoS One 2023; 18:e0283357. [PMID: 36947560 PMCID: PMC10032477 DOI: 10.1371/journal.pone.0283357] [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] [Received: 07/11/2022] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Abstract
Zoonotic tuberculosis in humans is caused by infection with bacteria of the Mycobacterium tuberculosis complex acquired from animals, most commonly cattle. India has the highest burden of human tuberculosis in the world and any zoonotic risk posed by tuberculosis in bovines needs to be managed at the source of infection as a part of efforts to end human tuberculosis. Zoonotic tuberculosis in humans can be severe and is clinically indistinguishable from non-zoonotic tuberculosis. As a consequence, zoonotic tuberculosis remains under-recognised and the significance of its contribution to human tuberculosis is poorly understood. This study aimed to explore any association between bovine density, bovine ownership, and human tuberculosis reporting in India using self-reported tuberculosis data in households and officially reported tuberculosis cases while controlling for common confounders for human tuberculosis. We find an association between human tuberculosis reporting, bovine density and bovine ownership in India. Buffalo density was significantly associated with an increased risk of self-reported tuberculosis in households (odds ratio (OR) = 1.23 (95% credible interval (CI): 1.10-1.39) at household level; incidence rate ratio (IRR) = 1.17 (95% CI: 1.04-1.33) at district level), while cattle density (OR = 0.80, 95% CI: 0.71-0.89; IRR = 0.78, 95% CI: 0.70-0.87) and ownership of bovines in households (OR = 0.94, 95% CI: 0.9-0.99; IRR = 0.67, 95% CI: 0.57-0.79) had a protective association with tuberculosis reporting. It is unclear whether this relates to differences in tuberculosis transmission dynamics, or perhaps an association between bovines and other unexplored confounders for tuberculosis reporting in humans. Our study highlights a need for structured surveillance to estimate the prevalence of tuberculosis in cattle and buffaloes, characterisation of Mycobacterium tuberculosis complex species present in bovines and transmission analyses at the human-animal interface to better assess the burden and risk pathways of zoonotic tuberculosis in India.
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Affiliation(s)
- Katriina Willgert
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Susie da Silva
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ruoran Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Premanshu Dandapat
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, West Bengal, India
| | | | - Hindol Maity
- CisGen Biotech Discoveries Pvt Ltd, Chennai, India
| | - Mohan Papanna
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America
| | - Sreenidhi Srinivasan
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America
| | - James L N Wood
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Vivek Kapur
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States of America
| | - Andrew J K Conlan
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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13
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Vandegrift KJ, Yon M, Surendran Nair M, Gontu A, Ramasamy S, Amirthalingam S, Neerukonda S, Nissly RH, Chothe SK, Jakka P, LaBella L, Levine N, Rodriguez S, Chen C, Sheersh Boorla V, Stuber T, Boulanger JR, Kotschwar N, Aucoin SG, Simon R, Toal KL, Olsen RJ, Davis JJ, Bold D, Gaudreault NN, Dinali Perera K, Kim Y, Chang KO, Maranas CD, Richt JA, Musser JM, Hudson PJ, Kapur V, Kuchipudi SV. SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City. Viruses 2022; 14:v14122770. [PMID: 36560774 PMCID: PMC9785669 DOI: 10.3390/v14122770] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/19/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
There is mounting evidence of SARS-CoV-2 spillover from humans into many domestic, companion, and wild animal species. Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City. Between December 2021 and February 2022, 155 deer on Staten Island, New York, were anesthetized and examined for gross abnormalities and illnesses. Paired nasopharyngeal swabs and blood samples were collected and analyzed for the presence of SARS-CoV-2 RNA and antibodies. Of 135 serum samples, 19 (14.1%) indicated SARS-CoV-2 exposure, and 11 reacted most strongly to the wild-type B.1 lineage. Of the 71 swabs, 8 were positive for SARS-CoV-2 RNA (4 Omicron and 4 Delta). Two of the animals had active infections and robust neutralizing antibodies, revealing evidence of reinfection or early seroconversion in deer. Variants of concern continue to circulate among and may reinfect US deer populations, and establish enzootic transmission cycles in the wild: this warrants a coordinated One Health response, to proactively surveil, identify, and curtail variants of concern before they can spill back into humans.
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Affiliation(s)
- Kurt J. Vandegrift
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (K.J.V.); (V.K.); (S.V.K.); Tel.: +1-814-574-9852 (K.J.V.); +1-814-865-9788 (V.K.); +1-814-863-4436 (S.V.K.)
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Santhamani Ramasamy
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Saranya Amirthalingam
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shubhada K. Chothe
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Padmaja Jakka
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lindsey LaBella
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nicole Levine
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sophie Rodriguez
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, IA 50010, USA
| | | | | | | | - Richard Simon
- City of New York Parks & Recreation, New York, NY 10029, USA
| | - Katrina L. Toal
- City of New York Parks & Recreation, New York, NY 10029, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Peter J. Hudson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Vivek Kapur
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (K.J.V.); (V.K.); (S.V.K.); Tel.: +1-814-574-9852 (K.J.V.); +1-814-865-9788 (V.K.); +1-814-863-4436 (S.V.K.)
| | - Suresh V. Kuchipudi
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (K.J.V.); (V.K.); (S.V.K.); Tel.: +1-814-574-9852 (K.J.V.); +1-814-865-9788 (V.K.); +1-814-863-4436 (S.V.K.)
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14
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Willgert K, Didelot X, Surendran-Nair M, Kuchipudi SV, Ruden RM, Yon M, Nissly RH, Vandegrift KJ, Nelli RK, Li L, Jayarao BM, Levine N, Olsen RJ, Davis JJ, Musser JM, Hudson PJ, Kapur V, Conlan AJK. Transmission history of SARS-CoV-2 in humans and white-tailed deer. Sci Rep 2022; 12:12094. [PMID: 35840592 PMCID: PMC9284484 DOI: 10.1038/s41598-022-16071-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human–animal interface.
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Affiliation(s)
- Katriina Willgert
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - Meera Surendran-Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Rachel M Ruden
- Wildlife Bureau, Iowa Department of Natural Resources, Des Moines, IA, USA.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Kurt J Vandegrift
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Rahul K Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Lingling Li
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Bhushan M Jayarao
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nicole Levine
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Animal Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - James J Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, USA.,Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - Peter J Hudson
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Vivek Kapur
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Animal Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Andrew J K Conlan
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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15
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Gontu A, Marlin EA, Ramasamy S, Neerukonda S, Anil G, Morgan J, Quraishi M, Chen C, Boorla VS, Nissly RH, Jakka P, Chothe SK, Ravichandran A, Kodali N, Amirthalingam S, LaBella L, Kelly K, Natesan P, Minns AM, Rossi RM, Werner JR, Hovingh E, Lindner SE, Tewari D, Kapur V, Vandegrift KJ, Maranas CD, Surendran Nair M, Kuchipudi SV. Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken. Viruses 2022; 14:v14071358. [PMID: 35891340 PMCID: PMC9317974 DOI: 10.3390/v14071358] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
Multiple domestic and wild animal species are susceptible to SARS-CoV-2 infection. Cattle and swine are susceptible to experimental SARS-CoV-2 infection. The unchecked transmission of SARS-CoV-2 in animal hosts could lead to virus adaptation and the emergence of novel variants. In addition, the spillover and subsequent adaptation of SARS-CoV-2 in livestock could significantly impact food security as well as animal and public health. Therefore, it is essential to monitor livestock species for SARS-CoV-2 spillover. We developed and optimized species-specific indirect ELISAs (iELISAs) to detect anti-SARS-CoV-2 antibodies in cattle, swine, and chickens using the spike protein receptor-binding domain (RBD) antigen. Serum samples collected prior to the COVID-19 pandemic were used to determine the cut-off threshold. RBD hyperimmunized sera from cattle (n = 3), swine (n = 6), and chicken (n = 3) were used as the positive controls. The iELISAs were evaluated compared to a live virus neutralization test using cattle (n = 150), swine (n = 150), and chicken (n = 150) serum samples collected during the COVID-19 pandemic. The iELISAs for cattle, swine, and chicken were found to have 100% sensitivity and specificity. These tools facilitate the surveillance that is necessary to quickly identify spillovers into the three most important agricultural species worldwide.
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Affiliation(s)
- Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Erika A. Marlin
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Clinical & Diagnostic Assay Development Group, Pfizer, Pearl River, NY 10965, USA
| | - Santhamani Ramasamy
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | | | - Gayatri Anil
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Jasmine Morgan
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Meysoon Quraishi
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (C.C.); (V.S.B.); (C.D.M.)
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (C.C.); (V.S.B.); (C.D.M.)
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Padmaja Jakka
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Shubhada K. Chothe
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Abirami Ravichandran
- Department of Integrative and Biomedical Physiology, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Nishitha Kodali
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
| | - Saranya Amirthalingam
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
| | - Lindsey LaBella
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Kathleen Kelly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Pazhanivel Natesan
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India;
| | - Allen M. Minns
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Randall M. Rossi
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
| | - Jacob R. Werner
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Ernest Hovingh
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Scott E. Lindner
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Deepanker Tewari
- Pennsylvania Department of Agriculture, Pennsylvania Veterinary Laboratory, Harrisburg, PA 17110, USA;
| | - Vivek Kapur
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA;
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kurt J. Vandegrift
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (C.C.); (V.S.B.); (C.D.M.)
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
- Correspondence: (M.S.N.); (S.V.K.)
| | - Suresh V. Kuchipudi
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (M.S.N.); (S.V.K.)
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16
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Tan CCS, Lam SD, Richard D, Owen CJ, Berchtold D, Orengo C, Nair MS, Kuchipudi SV, Kapur V, van Dorp L, Balloux F. Transmission of SARS-CoV-2 from humans to animals and potential host adaptation. Nat Commun 2022; 13:2988. [PMID: 35624123 PMCID: PMC9142586 DOI: 10.1038/s41467-022-30698-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/13/2022] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2, the causative agent of the COVID-19 pandemic, can infect a wide range of mammals. Since its spread in humans, secondary host jumps of SARS-CoV-2 from humans to multiple domestic and wild populations of mammals have been documented. Understanding the extent of adaptation to these animal hosts is critical for assessing the threat that the spillback of animal-adapted SARS-CoV-2 into humans poses. We compare the genomic landscapes of SARS-CoV-2 isolated from animal species to that in humans, profiling the mutational biases indicative of potentially different selective pressures in animals. We focus on viral genomes isolated from mink (Neovison vison) and white-tailed deer (Odocoileus virginianus) for which multiple independent outbreaks driven by onward animal-to-animal transmission have been reported. We identify five candidate mutations for animal-specific adaptation in mink (NSP9_G37E, Spike_F486L, Spike_N501T, Spike_Y453F, ORF3a_L219V), and one in deer (NSP3a_L1035F), though they appear to confer a minimal advantage for human-to-human transmission. No considerable changes to the mutation rate or evolutionary trajectory of SARS-CoV-2 has resulted from circulation in mink and deer thus far. Our findings suggest that minimal adaptation was required for onward transmission in mink and deer following human-to-animal spillover, highlighting the ‘generalist’ nature of SARS-CoV-2 as a mammalian pathogen. Here, Tan et al. find that the rapid spread of SARS-CoV-2 in mink and deer required minimal adaptation, has only caused moderate changes to the evolutionary trajectory of the virus, and has not led to viral mutations that greatly improve human transmission thus far.
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Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, London, UK. .,Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - Su Datt Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.,Department of Structural and Molecular Biology, University College London, London, UK
| | - Damien Richard
- UCL Genetics Institute, University College London, London, UK.,Division of Infection and Immunity, University College London, London, UK
| | | | | | - Christine Orengo
- Department of Structural and Molecular Biology, University College London, London, UK
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA, Pennsylvania, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, PA, Pennsylvania, USA
| | - Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA, Pennsylvania, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, PA, Pennsylvania, USA
| | - Vivek Kapur
- Huck Institutes of the Life Sciences, The Pennsylvania State University, PA, Pennsylvania, USA.,Department of Animal Science, The Pennsylvania State University, PA, Pennsylvania, USA
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
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17
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Arnold CRK, Srinivasan S, Rodriguez S, Rydzak N, Herzog CM, Gontu A, Bharti N, Small M, Rogers CJ, Schade MM, Kuchipudi SV, Kapur V, Read AF, Ferrari MJ. A longitudinal study of the impact of university student return to campus on the SARS-CoV-2 seroprevalence among the community members. Sci Rep 2022; 12:8586. [PMID: 35597780 PMCID: PMC9124192 DOI: 10.1038/s41598-022-12499-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/04/2022] [Indexed: 12/02/2022] Open
Abstract
Returning university students represent large-scale, transient demographic shifts and a potential source of transmission to adjacent communities during the COVID-19 pandemic. In this prospective longitudinal cohort study, we tested for IgG antibodies against SARS-CoV-2 in a non-random cohort of residents living in Centre County prior to the Fall 2020 term at the Pennsylvania State University and following the conclusion of the Fall 2020 term. We also report the seroprevalence in a non-random cohort of students collected at the end of the Fall 2020 term. Of 1313 community participants, 42 (3.2%) were positive for SARS-CoV-2 IgG antibodies at their first visit between 07 August and 02 October 2020. Of 684 student participants who returned to campus for fall instruction, 208 (30.4%) were positive for SARS-CoV-2 antibodies between 26 October and 21 December. 96 (7.3%) community participants returned a positive IgG antibody result by 19 February. Only contact with known SARS-CoV-2-positive individuals and attendance at small gatherings (20-50 individuals) were significant predictors of detecting IgG antibodies among returning students (aOR, 95% CI 3.1, 2.07-4.64; 1.52, 1.03-2.24; respectively). Despite high seroprevalence observed within the student population, seroprevalence in a longitudinal cohort of community residents was low and stable from before student arrival for the Fall 2020 term to after student departure. The study implies that heterogeneity in SARS-CoV-2 transmission can occur in geographically coincident populations.
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Affiliation(s)
- Callum R K Arnold
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Sreenidhi Srinivasan
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sophie Rodriguez
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Natalie Rydzak
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Catherine M Herzog
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Nita Bharti
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Meg Small
- College of Health and Human Development, Pennsylvania State University, University Park, PA, 16802, USA
- Social Science Research Institute, Pennsylvania State University, University Park, PA, 16802, USA
| | - Connie J Rogers
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Margeaux M Schade
- College of Health and Human Development, Pennsylvania State University, University Park, PA, 16802, USA
| | - Suresh V Kuchipudi
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Animal Science, Pennsylvania State University, University Park, PA, 16802, USA
| | - Andrew F Read
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Matthew J Ferrari
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA.
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18
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Bansal N, Singh R, Chaudhary D, Mahajan NK, Joshi VG, Maan S, Ravishankar C, Sahoo N, Mor SK, Radzio-Basu J, Kapur V, Jindal N, Goyal SM. Prevalence of Newcastle Disease Virus in Wild and Migratory Birds in Haryana, India. Avian Dis 2022; 66:141-147. [PMID: 35510471 DOI: 10.1637/aviandiseases-d-21-00115] [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: 12/01/2021] [Accepted: 02/20/2022] [Indexed: 11/05/2022]
Abstract
Newcastle disease virus (NDV) can infect approximately 250 avian species and causes highly contagious Newcastle disease (ND) in domestic poultry, leading to huge economic losses. There are three different pathotypes of NDV, i.e., lentogenic, mesogenic, and velogenic. Wild resident (wild) and migratory birds are natural reservoirs of NDV and are believed to play a key role in transmitting the virus to domestic poultry. The present study was conducted to determine the prevalence of NDV in wild and migratory birds in the state of Haryana, India, during two migratory seasons (2018-19 and 2019-20). In total 1379 samples (1368 choanal swabs and 11 tissue samples) were collected from live (n = 1368) or dead birds (n = 4) belonging to 53 different avian species. These samples belonged to apparently healthy (n = 1338), sick (n = 30), and dead (n = 4) birds. All samples were tested for NDV by real-time reverse transcription-PCR using M gene specific primers and probe. Of the 1379 samples, 23 samples from wild birds [Columba livia domestica (n = 12, 52.17%), Pavo cristatus (n = 9, 39.13%), and Psittaciformes (n = 2, 8.69%)] were found positive for NDV. Only one of the 23 samples (from P. cristatus) was positive for F gene, indicating it to be a mesogenic/velogenic strain. These results indicate that both lentogenic and velogenic strains of NDV are circulating in wild birds in Haryana and that further studies are needed to characterize NDV strains from wild/migratory birds and domestic poultry to determine the extent of virus transmission among these populations. This study considers the disease transmission risk from domestic pigeons and parrots to commercial poultry and vice versa, and the results emphasize the need for strict biosecurity strategies to protect commercial poultry in the region.
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Affiliation(s)
- Nitish Bansal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Renu Singh
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Deepika Chaudhary
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Nand K Mahajan
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Vinay G Joshi
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Sushila Maan
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Chintu Ravishankar
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Pookode, Kerala, India
| | - Niranjana Sahoo
- College of Veterinary Science and Animal Husbandry, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Sunil K Mor
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN 55455
| | - Jessica Radzio-Basu
- The Huck Institute of the Life Sciences, The Pennsylvania State University, State College, PA 16801.,Department of Animal Science, The Pennsylvania State University, State College, PA 16801
| | - Vivek Kapur
- The Huck Institute of the Life Sciences, The Pennsylvania State University, State College, PA 16801.,Department of Animal Science, The Pennsylvania State University, State College, PA 16801
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India,
| | - Sagar M Goyal
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN 55455
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19
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Subramanian S, Srinivasan S, Ramaiyan Selvaraju K, Vinoli PM, Selladurai S, Ramasamy B, Kumaragurubaran K, Bakker D, Vordermeier M, Kapur V, Gopal DR. Defined Antigen Skin Test for Bovine Tuberculosis Retains Specificity on Revaccination With Bacillus Calmette–Guérin. Front Vet Sci 2022; 9:814227. [PMID: 35498753 PMCID: PMC9043861 DOI: 10.3389/fvets.2022.814227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 11/12/2021] [Accepted: 02/17/2022] [Indexed: 11/15/2022] Open
Abstract
The Bacillus Calmette–Guérin (BCG) vaccination provides partial protection against, and reduces severity of pathological lesions associated with bovine tuberculosis (bTB) in cattle. Accumulating evidence also suggests that revaccination with BCG may be needed to enhance the duration of immune protection. Since BCG vaccine cross-reacts with traditional tuberculin-based diagnostic tests, a peptide-based defined antigen skin test (DST) comprising of ESAT-6, CFP-10, and Rv3615c to detect the infected among the BCG-vaccinated animals (DIVA) was recently described. The DST reliably identifies bTB-infected animals in experimental challenge models and in natural infection settings, and differentiated these from animals immunized with a single dose of BCG in both skin tests and interferon-gamma release assay (IGRA). The current investigation sought to assess the diagnostic specificity of DST in calves (Bos taurus ssp. taurus × B. t. ssp. indicus; n = 15) revaccinated with BCG 6 months after primary immunization. The results show that none of the 15 BCG-revaccinated calves exhibited a delayed hypersensitivity response when skin tested with DST 61 days post-revaccination, suggesting 100% diagnostic specificity (one-tailed lower 95% CI: 82). In contrast, 8 of 15 (diagnostic specificity = 47%; 95% CI: 21, 73) BCG-revaccinated calves were positive per the single cervical tuberculin (SCT) test using bovine tuberculin. Together, these results show that the DST retains its specificity even after revaccination with BCG and confirms the potential for implementation of BCG-based interventions in settings where test-and-slaughter are not economically or culturally feasible.
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Affiliation(s)
- Saraswathi Subramanian
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Sreenidhi Srinivasan
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Kathiravan Ramaiyan Selvaraju
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Priyadharshini Michael Vinoli
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Suganya Selladurai
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Boominathan Ramasamy
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Karthik Kumaragurubaran
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Douwe Bakker
- Technical Consultant and Independent Researcher, Lelystad, Netherlands
| | - Martin Vordermeier
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
- Centre for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Vivek Kapur
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States
| | - Dhinakar Raj Gopal
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
- *Correspondence: Dhinakar Raj Gopal
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20
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Lakew M, Srinivasan S, Mesele B, Olani A, Koran T, Tadesse B, Mekonnen GA, Almaw G, Sahlu T, Seyoum B, Beyecha K, Gumi B, Ameni G, Ashenafi H, Bakker D, Kapur V, Gebre S. Utility of the Intradermal Skin Test in a Test-and-Cull Approach to Control Bovine Tuberculosis: A Pilot Study in Ethiopia. Front Vet Sci 2022; 9:823365. [PMID: 35330613 PMCID: PMC8940234 DOI: 10.3389/fvets.2022.823365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/17/2022] [Indexed: 11/30/2022] Open
Abstract
Bovine tuberculosis (bTB) is one of the top three, high-priority, livestock diseases in Ethiopia and hence, the need for evaluation of potential control strategies is critical. Here, we applied the test-and-segregate followed by cull strategy for the control of bTB in the intensive Alage dairy farm in Ethiopia. All cattle reared on this farm were repeatedly skin tested using the Comparative Cervical Tuberculin (CCT) test for a total of five times between 2015 and 2021. During the first (October 2015) and second (March 2017) rounds of testing, all reactor animals (>4 mm) were culled, while those that were deemed as inconclusive (1–4 mm) were segregated and retested. At retest, animals with CCT >2 mm were removed from the herd. In the third (December 2017) and fourth (June 2018) rounds of tuberculin testing, a more stringent approach was taken wherein all reactors per the severe mode of CCT test interpretation (>2 mm) were culled. A final herd status check was performed in May 2021. In summary, the number of CCT positives (>4 mm) in the farm dropped from 23.1% (31/134) in October 2015 to 0% in December 2017 and remained 0% until May 2021. In contrast, the number of Single Cervical Tuberculin (SCT) test positives (≥4 mm) increased from 1.8 to 9.5% (from 2017 to 2021), indicating that CCT test might not be sufficient to effectively clear the herd of bTB. However, a more stringent approach would result in a drastic increase in the number of false positives. The total cost of the bTB control effort in this farm holding 134–200 cattle at any given time was conservatively estimated to be ~US$48,000. This, together with the need for culling an unacceptably high number of animals based on skin test status, makes the test-and-cull strategy impractical for nationwide implementation in Ethiopia and other low- and middle-income countries (LMICs) where the infection is endemic. Hence, there is an increased emphasis on the need to explore alternate, affordable measures such as vaccination alongside accurate diagnostics to help control bTB in endemic settings.
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Affiliation(s)
- Matios Lakew
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- *Correspondence: Matios Lakew
| | - Sreenidhi Srinivasan
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Beruhtesfa Mesele
- Alage Agricultural Technical and Vocational Education Training (ATVET) College, Alage, Ethiopia
| | - Abebe Olani
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Tafesse Koran
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Biniam Tadesse
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | | | - Gizat Almaw
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Temertu Sahlu
- Alage Agricultural Technical and Vocational Education Training (ATVET) College, Alage, Ethiopia
| | - Bekele Seyoum
- Alage Agricultural Technical and Vocational Education Training (ATVET) College, Alage, Ethiopia
| | - Kebede Beyecha
- Alage Agricultural Technical and Vocational Education Training (ATVET) College, Alage, Ethiopia
| | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hagos Ashenafi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Douwe Bakker
- Independent Researcher and Technical Consultant, Lelystad, Netherlands
| | - Vivek Kapur
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States
| | - Solomon Gebre
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
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21
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Sahoo N, Bhuyan K, Panda B, Behura NC, Biswal S, Samal L, Chaudhary D, Bansal N, Singh R, Joshi VG, Jindal N, Mahajan NK, Maan S, Ravishankar C, Rajasekhar R, Radzio-Basu J, Herzog CM, Kapur V, Mor SK, Goyal SM. Prevalence of Newcastle disease and associated risk factors in domestic chickens in the Indian state of Odisha. PLoS One 2022; 17:e0264028. [PMID: 35171961 PMCID: PMC8849498 DOI: 10.1371/journal.pone.0264028] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/31/2022] [Indexed: 11/27/2022] Open
Abstract
Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a contagious disease that affects a variety of domestic and wild avian species. Though ND is vaccine-preventable, it is a persistent threat to poultry industry across the globe. The disease represents a leading cause of morbidity and mortality in chickens. To better understand the epidemiology of NDV among commercial and backyard chickens of Odisha, where chicken farming is being prioritized to assist with poverty alleviation, a cross-sectional study was conducted in two distinct seasons during 2018. Choanal swabs (n = 1361) from live birds (commercial layers, broilers, and backyard chicken) and tracheal tissues from dead birds (n = 10) were collected and tested by real-time reverse transcription polymerase chain reaction (RT-PCR) for the presence of matrix (M) and fusion (F) genes of NDV. Risk factors at the flock and individual bird levels (health status, ND vaccination status, geographical zone, management system, and housing) were assessed using multivariable logistic regression analyses. Of the 1371 samples tested, 160 were positive for M gene amplification indicating an overall apparent prevalence of 11.7% (95% CI 10.1–13.5%). Circulation of virulent NDV strains was also evident with apparent prevalence of 8.1% (13/160; 95% CI: 4.8–13.4%). In addition, commercial birds had significantly higher odds (75%) of being infected with NDV as compared to backyard poultry (p = 0.01). This study helps fill a knowledge gap in the prevalence and distribution of NDV in apparently healthy birds in eastern India, and provides a framework for future longitudinal research of NDV risk and mitigation in targeted geographies—a step forward for effective control of ND in Odisha.
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Affiliation(s)
- Niranjana Sahoo
- Department of Epidemiology & Preventive Medicine and Poultry Science, College of Veterinary Science & Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
- * E-mail:
| | - Kashyap Bhuyan
- Department of Epidemiology & Preventive Medicine and Poultry Science, College of Veterinary Science & Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Biswaranjan Panda
- Department of Epidemiology & Preventive Medicine and Poultry Science, College of Veterinary Science & Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Nrushingha Charan Behura
- Department of Epidemiology & Preventive Medicine and Poultry Science, College of Veterinary Science & Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Sangram Biswal
- Department of Epidemiology & Preventive Medicine and Poultry Science, College of Veterinary Science & Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Lipismita Samal
- Department of Epidemiology & Preventive Medicine and Poultry Science, College of Veterinary Science & Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Deepika Chaudhary
- Departments of Veterinary Public Health & Epidemiology and Animal Biotechnology, College of Veterinary Sciences, LalaLajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Nitish Bansal
- Departments of Veterinary Public Health & Epidemiology and Animal Biotechnology, College of Veterinary Sciences, LalaLajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Renu Singh
- Departments of Veterinary Public Health & Epidemiology and Animal Biotechnology, College of Veterinary Sciences, LalaLajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Vinay G. Joshi
- Departments of Veterinary Public Health & Epidemiology and Animal Biotechnology, College of Veterinary Sciences, LalaLajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Naresh Jindal
- Departments of Veterinary Public Health & Epidemiology and Animal Biotechnology, College of Veterinary Sciences, LalaLajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Nand K. Mahajan
- Departments of Veterinary Public Health & Epidemiology and Animal Biotechnology, College of Veterinary Sciences, LalaLajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Sushila Maan
- Departments of Veterinary Public Health & Epidemiology and Animal Biotechnology, College of Veterinary Sciences, LalaLajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Chintu Ravishankar
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Pookode, Kerala, India
| | - Ravindran Rajasekhar
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Pookode, Kerala, India
| | - Jessica Radzio-Basu
- The Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Catherine M. Herzog
- The Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Vivek Kapur
- The Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Animal Science, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sunil K. Mor
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Sagar M. Goyal
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
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22
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Ravishankar C, Ravindran R, John AA, Divakar N, Chandy G, Joshi V, Chaudhary D, Bansal N, Singh R, Sahoo N, Mor SK, Mahajan NK, Maan S, Jindal N, Schilling MA, Herzog CM, Basu S, Radzio-Basu J, Kapur V, Goyal SM. Detection of Newcastle disease virus and assessment of associated relative risk in backyard and commercial poultry in Kerala, India. Vet Med Sci 2022; 8:1146-1156. [PMID: 35199954 PMCID: PMC9122440 DOI: 10.1002/vms3.747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background Newcastle disease (ND) is an economically important viral disease affecting the poultry industry. In Kerala, a state in South India, incidences of ND in commercial and backyard poultry have been reported. But a systematic statewide study on the prevalence of the disease has not been carried out. Objectives A cross‐sectional survey was performed to detect the presence of Newcastle disease virus (NDV) in suspect cases and among apparently healthy commercial flocks and backyard poultry, in the state and to identify risk factors for NDV infection. Methods Real‐time reverse transcription‐PCR (RT‐PCR) was used to detect the M gene of NDV in choanal swabs and tissue samples collected from live and dead birds, respectively and the results were statistically analysed. Results The predominant clinical signs of the examined birds included mild respiratory signs, huddling together and greenish diarrhoea. Nervous signs in the form of torticollis were noticed in birds in some of the affected flocks. On necropsy, many birds had haemorrhages in the proventriculus and caecal tonsils which were suggestive of ND. Of the 2079 samples tested, 167 (8.0%) were positive for the NDV M‐gene by RT‐PCR. Among 893 samples collected from diseased flocks, 129 (14.5%), were positive for M gene with pairwise relative risk (RR) of 15.6 as compared to apparently healthy flocks where 6 out of 650 (0.9%) samples were positive. All positive samples were from poultry; none of the ducks, pigeons, turkey and wild birds were positive. Commercial broilers were at higher risk of infection than commercial layers (RR: 4.5) and backyard poultry (RR: 4.9). Similarly, birds reared under intensive housing conditions were at a higher risk of being infected as compared to those reared under semi‐intensive (RR: 6.7) or backyard housing (RR: 2.1). Multivariable analysis indicated that significantly higher risk of infection exists during migratory season and during ND outbreaks occurring nearby. Further, lower risk was observed with flock vaccination and backyard or semi‐intensive housing when compared to intensive housing. When the M gene positive samples were tested by RT‐PCR to determine whether the detected NDV were mesogenic/velogenic, 7 (4.2%) were positive. Conclusions In Kerala, NDV is endemic in poultry with birds reared commercially under intensive rearing systems being affected the most. The outcome of this study also provides a link between epidemiologic knowledge and the development of successful disease control measures. Statistical analysis suggests that wild bird migration season and presence of migratory birds influences the prevalence of the virus in the State. Further studies are needed to genotype and sub‐genotype the detected viruses and to generate baseline data on the prevalence of NDV strains, design better detection strategies, and determine patterns of NDV transmission across domestic poultry and wild bird populations in Kerala. A study was carried out to detect Newcastle disease virus in commercial and backyard chicken in Kerala, India, by employing real time RT‐PCR. The overall percentage positivity obtained was 8%. Risk analysis revealed significantly higher risk for broiler birds and intensive type of housing. The risk was also higher for birds housed in facilities in areas with a history of occurrence of the disease, if migratory birds were present in the area, and during bird migration season. It was also observed that vaccination had a protective effect as indicated by lower relative risk values.
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Affiliation(s)
- Chintu Ravishankar
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, and Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Pookode, Kerala, India
| | - Rajasekhar Ravindran
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, and Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Pookode, Kerala, India
| | - Anneth Alice John
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, and Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Pookode, Kerala, India
| | - Nithin Divakar
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, and Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Pookode, Kerala, India
| | - George Chandy
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, and Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Pookode, Kerala, India
| | - Vinay Joshi
- Departments of Veterinary Public Health and Epidemiology and Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science, Hisar, India
| | - Deepika Chaudhary
- Departments of Veterinary Public Health and Epidemiology and Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science, Hisar, India
| | - Nitish Bansal
- Departments of Veterinary Public Health and Epidemiology and Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science, Hisar, India
| | - Renu Singh
- Departments of Veterinary Public Health and Epidemiology and Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science, Hisar, India
| | - Niranjana Sahoo
- College of Veterinary Science and Animal Husbandry, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Sunil K Mor
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota
| | - Nand K Mahajan
- Departments of Veterinary Public Health and Epidemiology and Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science, Hisar, India
| | - Sushila Maan
- Departments of Veterinary Public Health and Epidemiology and Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science, Hisar, India
| | - Naresh Jindal
- Departments of Veterinary Public Health and Epidemiology and Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science, Hisar, India
| | - Megan A Schilling
- Department of Animal Sciences, The Pennsylvania State University, University Park, Pennsylvania.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Catherine M Herzog
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Saurabh Basu
- Department of Industrial and Manufacturing Engineering, College of Engineering, The Pennsylvania State University, University Park, Pennsylvania
| | - Jessica Radzio-Basu
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Vivek Kapur
- Department of Animal Sciences, The Pennsylvania State University, University Park, Pennsylvania.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Sagar M Goyal
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota
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23
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Vandegrift KJ, Yon M, Surendran-Nair M, Gontu A, Amirthalingam S, Nissly RH, Levine N, Stuber T, DeNicola AJ, Boulanger JR, Kotschwar N, Aucoin SG, Simon R, Toal K, Olsen RJ, Davis JJ, Bold D, Gaudreault NN, Richt JA, Musser JM, Hudson PJ, Kapur V, Kuchipudi SV. Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer. bioRxiv 2022:2022.02.04.479189. [PMID: 35169802 PMCID: PMC8845426 DOI: 10.1101/2022.02.04.479189] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
White-tailed deer ( Odocoileus virginianus ) are highly susceptible to infection by SARS-CoV-2, with multiple reports of widespread spillover of virus from humans to free-living deer. While the recently emerged SARS-CoV-2 B.1.1.529 Omicron variant of concern (VoC) has been shown to be notably more transmissible amongst humans, its ability to cause infection and spillover to non-human animals remains a challenge of concern. We found that 19 of the 131 (14.5%; 95% CI: 0.10-0.22) white-tailed deer opportunistically sampled on Staten Island, New York, between December 12, 2021, and January 31, 2022, were positive for SARS-CoV-2 specific serum antibodies using a surrogate virus neutralization assay, indicating prior exposure. The results also revealed strong evidence of age-dependence in antibody prevalence. A significantly (χ 2 , p < 0.001) greater proportion of yearling deer possessed neutralizing antibodies as compared with fawns (OR=12.7; 95% CI 4-37.5). Importantly, SARS-CoV-2 nucleic acid was detected in nasal swabs from seven of 68 (10.29%; 95% CI: 0.0-0.20) of the sampled deer, and whole-genome sequencing identified the SARS-CoV-2 Omicron VoC (B.1.1.529) is circulating amongst the white-tailed deer on Staten Island. Phylogenetic analyses revealed the deer Omicron sequences clustered closely with other, recently reported Omicron sequences recovered from infected humans in New York City and elsewhere, consistent with human to deer spillover. Interestingly, one individual deer was positive for viral RNA and had a high level of neutralizing antibodies, suggesting either rapid serological conversion during an ongoing infection or a "breakthrough" infection in a previously exposed animal. Together, our findings show that the SARS-CoV-2 B.1.1.529 Omicron VoC can infect white-tailed deer and highlights an urgent need for comprehensive surveillance of susceptible animal species to identify ecological transmission networks and better assess the potential risks of spillback to humans. KEY FINDINGS These studies provide strong evidence of infection of free-living white-tailed deer with the SARS-CoV-2 B.1.1.529 Omicron variant of concern on Staten Island, New York, and highlight an urgent need for investigations on human-to-animal-to-human spillovers/spillbacks as well as on better defining the expanding host-range of SARS-CoV-2 in non-human animals and the environment.
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Affiliation(s)
- Kurt J. Vandegrift
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Meera Surendran-Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Saranya Amirthalingam
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Nicole Levine
- Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
| | | | | | | | - Sarah Grimké Aucoin
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Richard Simon
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Katrina Toal
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - James J. Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago and Division of Data Science and Learning, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - Peter J. Hudson
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Vivek Kapur
- Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
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24
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Joshi VG, Chaudhary D, Bansal N, Singh R, Maan S, Mahajan NK, Ravishankar C, Sahoo N, Mor SK, Radzio-Basu J, Herzog CM, Kapur V, Goel P, Jindal N, Goyal SM. Prevalence of Newcastle Disease Virus in Commercial and Backyard Poultry in Haryana, India. Front Vet Sci 2021; 8:725232. [PMID: 34805330 PMCID: PMC8600042 DOI: 10.3389/fvets.2021.725232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Newcastle disease virus (NDV) causes Newcastle disease (ND) in poultry. The ND is a highly contagious disease, which is endemic in several countries despite regular vaccination with live or killed vaccines. Studies on NDV in India are mostly targeted toward its detection and characterization from disease outbreaks. A surveillance study was undertaken to determine NDV prevalence throughout the state of Haryana from March 2018 to March 2020 using a stratified sampling scheme. The state was divided into three different zones and a total of 4,001 choanal swab samples were collected from backyard poultry, commercial broilers, and layers. These samples were tested for the M gene of NDV using real-time RT-PCR. Of the 4,001 samples tested, 392 were positive (9.8% apparent prevalence; 95% CI: 8.9–10.8%) for the M gene. Of these 392 M gene positive samples, 35 (8.9%; 95% CI: 6.4–12.3%) were found to be positive based on F gene real-time RT-PCR. Circulation of NDV in commercial and backyard poultry highlights the importance of surveillance studies even in apparently healthy flocks. The information generated in this study should contribute to better understanding of NDV epidemiology in India and may help formulate appropriate disease control strategies for commercial and backyard birds.
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Affiliation(s)
- Vinay G Joshi
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Deepika Chaudhary
- Department of Veterinary Public Health & Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Nitish Bansal
- Department of Veterinary Public Health & Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Renu Singh
- Department of Veterinary Public Health & Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Sushila Maan
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Nand K Mahajan
- Department of Veterinary Public Health & Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Chintu Ravishankar
- Department of Veterinary Microbiology, Kerala Veterinary and Animal Sciences University, Pookode, India
| | - Niranjana Sahoo
- College of Veterinary Science and Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Sunil K Mor
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN, United States
| | - Jessica Radzio-Basu
- The Huck Institute of the Life Sciences, University Park, PA, United States.,Department of Animal Science, The Pennsylvania State University, University Park, PA, United States
| | - Catherine M Herzog
- The Huck Institute of the Life Sciences, University Park, PA, United States
| | - Vivek Kapur
- The Huck Institute of the Life Sciences, University Park, PA, United States.,Department of Animal Science, The Pennsylvania State University, University Park, PA, United States
| | - Parveen Goel
- Directorate of Research, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Naresh Jindal
- Department of Veterinary Public Health & Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Sagar M Goyal
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN, United States
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25
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Kumar R, Christensen ND, Kaddis Maldonado RJ, Bewley MC, Ostman A, Sudol M, Chen EC, Buchkovich NW, Gontu A, Surendran Nair M, Nissly RH, Minns AM, Kapur V, Rossi R, Kuchipudi SV, Lindner SE, Parent LJ, Flanagan JM, Buchkovich NJ. Monoclonal Antibodies to S and N SARS-CoV-2 Proteins as Probes to Assess Structural and Antigenic Properties of Coronaviruses. Viruses 2021; 13:v13101899. [PMID: 34696329 PMCID: PMC8537396 DOI: 10.3390/v13101899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 01/18/2023] Open
Abstract
Antibodies targeting the spike (S) and nucleocapsid (N) proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential tools. In addition to important roles in the treatment and diagnosis of infection, the availability of high-quality specific antibodies for the S and N proteins is essential to facilitate basic research of virus replication and in the characterization of mutations responsible for variants of concern. We have developed panels of mouse and rabbit monoclonal antibodies (mAbs) to the SARS-CoV-2 spike receptor-binding domain (S-RBD) and N protein for functional and antigenic analyses. The mAbs to the S-RBD were tested for neutralization of native SARS-CoV-2, with several exhibiting neutralizing activity. The panels of mAbs to the N protein were assessed for cross-reactivity with the SARS-CoV and Middle East respiratory syndrome (MERS)-CoV N proteins and could be subdivided into sets that showed unique specificity for SARS-CoV-2 N protein, cross-reactivity between SARS-CoV-2 and SARS-CoV N proteins only, or cross-reactivity to all three coronavirus N proteins tested. Partial mapping of N-reactive mAbs were conducted using truncated fragments of the SARS-CoV-2 N protein and revealed near complete coverage of the N protein. Collectively, these sets of mouse and rabbit monoclonal antibodies can be used to examine structure/function studies for N proteins and to define the surface location of virus neutralizing epitopes on the RBD of the S protein.
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Affiliation(s)
- Rinki Kumar
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
| | - Neil D. Christensen
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Correspondence: (N.D.C.); (N.J.B.)
| | - Rebecca J. Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - Maria C. Bewley
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Alexandria Ostman
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
| | - Malgorzata Sudol
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - Eunice C. Chen
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - Natalie W. Buchkovich
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Ruth H. Nissly
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Allen M. Minns
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Animal Science, Penn State University, University Park, PA 16802, USA
| | - Vivek Kapur
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Animal Science, Penn State University, University Park, PA 16802, USA
| | - Randall Rossi
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
| | - Suresh V. Kuchipudi
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Scott E. Lindner
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Leslie J. Parent
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - John M. Flanagan
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Nicholas J. Buchkovich
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
- Correspondence: (N.D.C.); (N.J.B.)
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26
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Arnold CR, Srinivasan S, Rodriguez S, Rydzak N, Herzog CM, Gontu A, Bharti N, Small M, Rogers CJ, Schade MM, Kuchipudi SV, Kapur V, Read A, Ferrari MJ. SARS-CoV-2 Seroprevalence in a University Community: A Longitudinal Study of the Impact of Student Return to Campus on Infection Risk Among Community Members. medRxiv 2021:2021.02.17.21251942. [PMID: 33619497 PMCID: PMC7899462 DOI: 10.1101/2021.02.17.21251942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Returning university students represent large-scale, transient demographic shifts and a potential source of transmission to adjacent communities during the COVID-19 pandemic. METHODS In this prospective longitudinal cohort study, we tested for IgG antibodies against SARS-CoV-2 in a non-random cohort of residents living in Centre County prior to the Fall 2020 term at the Pennsylvania State University and following the conclusion of the Fall 2020 term. We also report the seroprevalence in a non-random cohort of students collected at the end of the Fall 2020 term. RESULTS Of 1313 community participants, 42 (3.2%) were positive for SARS-CoV-2 IgG antibodies at their first visit between 07 August and 02 October 2020. Of 684 student participants who returned to campus for fall instruction, 208 (30.4%) were positive for SARS-CoV-2 antibodies between 26 October and 21 December. 96 (7.3%) community participants returned a positive IgG antibody result by 19 February. Only contact with known SARS-CoV-2-positive individuals and attendance at small gatherings (20-50 individuals) were significant predictors of detecting IgG antibodies among returning students (aOR, 95% CI: 3.1, 2.07-4.64; 1.52, 1.03-2.24; respectively). CONCLUSIONS Despite high seroprevalence observed within the student population, seroprevalence in a longitudinal cohort of community residents was low and stable from before student arrival for the Fall 2020 term to after student departure. The study implies that heterogeneity in SARS-CoV-2 transmission can occur in geographically coincident populations.
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Affiliation(s)
- Callum R.K. Arnold
- Department of Biology, Pennsylvania State University, University Park, PA, USA 16802
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802
| | - Sreenidhi Srinivasan
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA 16802
| | - Sophie Rodriguez
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA 16802
| | - Natalie Rydzak
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA 16802
| | - Catherine M. Herzog
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA 16802
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA 16802
| | - Nita Bharti
- Department of Biology, Pennsylvania State University, University Park, PA, USA 16802
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802
| | - Meg Small
- College of Health and Human Development, Pennsylvania State University, University Park, PA, USA 16802
- Social Science Research Institute, Pennsylvania State University, University Park, PA, USA 16802
| | - Connie J. Rogers
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA, USA 16802
| | - Margeaux M. Schade
- Social Science Research Institute, Pennsylvania State University, University Park, PA, USA 16802
| | - Suresh V Kuchipudi
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA 16802
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA 16802
- Department of Animal Science, Pennsylvania State University, University Park, PA, USA 16802
| | - Andrew Read
- Department of Biology, Pennsylvania State University, University Park, PA, USA 16802
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA 16802
| | - Matthew J. Ferrari
- Department of Biology, Pennsylvania State University, University Park, PA, USA 16802
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA 16802
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27
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Kumar T, Singh M, Jangir BL, Arora D, Srinivasan S, Bidhan D, Yadav DC, Veerasami M, Bakker D, Kapur V, Jindal N. A Defined Antigen Skin Test for Diagnosis of Bovine Tuberculosis in Domestic Water Buffaloes ( Bubalus bubalis). Front Vet Sci 2021; 8:669898. [PMID: 34490387 PMCID: PMC8418101 DOI: 10.3389/fvets.2021.669898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
Bovine tuberculosis (bTB) remains endemic in domestic water buffaloes (Bubalus bubalis) in India and elsewhere, with limited options for control other than testing and slaughter. The prescribed tuberculin skin tests with purified protein derivative (PPD) for diagnosis of bTB preclude the use of Bacille Calmette-Guérin (BCG)-based vaccination because of the antigenic cross-reactivity of vaccine strains with Mycobacterium bovis and related pathogenic members of the M. tuberculosis complex (MTBC). For the diagnosis of bTB in domestic water buffaloes, we here assessed a recently described defined-antigen skin test (DST) that comprises overlapping peptides representing the ESAT-6, CFP-10 and Rv3615c antigens, present in disease-causing members of the MTBC but missing in BCG strains. The performance characteristics of three doses (5, 10 or 20 μg/peptide) of the DST were assessed in natural tuberculin skin test reactor (n = 11) and non-reactor (n = 35) water buffaloes at an organized dairy farm in Hisar, India, and results were compared with the single intradermal skin test (SIT) using standard bovine tuberculin (PPD-B). The results showed a dose-dependent response of DST in natural reactor water buffaloes, although the SIT induced a significantly greater (P < 0.001) skin test response than the highest dose of DST used. However, using a cut-off of 2 mm or greater, the 5, 10, and 20 μg DST cocktail correctly classified eight, 10 and all 11 of the SIT-positive reactors, respectively, suggesting that the 20 μg DST cocktail has a diagnostic sensitivity (Se) of 1.0 (95% CI: 0.72-1.0) identical to that of the SIT. Importantly, none of the tested DST doses induced any measurable skin induration responses in the 35 SIT-negative animals, suggesting a specificity point estimate of 1.0 (95% CI: 0.9-1.0), also identical to that of the SIT and compares favorably with that of the comparative cervical test (Se = 0.85; 95% CI: 0.55-0.98). Overall, the results suggest that similar to tuberculin, the DST enables sensitive and specific diagnosis of bTB in water buffaloes. Future field trials to explore the utility of DST as a defined antigen replacement for tuberculin in routine surveillance programs and to enable BCG vaccination of water buffaloes are warranted.
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Affiliation(s)
- Tarun Kumar
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Mahavir Singh
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Babu Lal Jangir
- Department of Veterinary Pathology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Devan Arora
- Haryana Pashu Vigyan Kendra, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Sreenidhi Srinivasan
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Devender Bidhan
- Department of Livestock Production Management, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Dipin Chander Yadav
- Department of Livestock Production Management, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | | | | | - Vivek Kapur
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States.,Department of Animal Science, The Pennsylvania State University, University Park, PA, United States
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
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28
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Islam SS, Rumi TB, Kabir SML, van der Zanden AGM, Kapur V, Rahman AKMA, Ward MP, Bakker D, Ross AG, Rahim Z. Correction: Bovine tuberculosis prevalence and risk factors in selected districts of Bangladesh. PLoS One 2021; 16:e0256042. [PMID: 34352029 PMCID: PMC8341511 DOI: 10.1371/journal.pone.0256042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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29
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Srinivasan S, Conlan AJK, Easterling LA, Herrera C, Dandapat P, Veerasami M, Ameni G, Jindal N, Raj GD, Wood J, Juleff N, Bakker D, Vordermeier M, Kapur V. Corrigendum: A Meta-Analysis of the Effect of Bacillus Calmette-Guérin Vaccination Against Bovine Tuberculosis: Is Perfect the Enemy of Good? Front Vet Sci 2021; 8:716565. [PMID: 34395582 PMCID: PMC8359737 DOI: 10.3389/fvets.2021.716565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/22/2021] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fvets.2021.637580.].
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Affiliation(s)
- Sreenidhi Srinivasan
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Andrew J K Conlan
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Laurel A Easterling
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Christian Herrera
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Premanshu Dandapat
- Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | | | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Gopal Dhinakar Raj
- Translational Research Platform for Veterinary Biological, Tamil Nadu University of Veterinary and Animal Sciences, Chennai, India
| | - James Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nick Juleff
- The Bill & Melinda Gates Foundation, Seattle, WA, United States
| | - Douwe Bakker
- Technical Consultant and Independent Researcher, Lelystad, Netherlands
| | - Martin Vordermeier
- Animal and Plant Health Agency, Addlestone, United Kingdom.,Centre for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Vivek Kapur
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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30
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Katani R, Kudva IT, Srinivasan S, Stasko JB, Schilling M, Li L, Cote R, DebRoy C, Arthur TM, Sokurenko EV, Kapur V. Strain and host-cell dependent role of type-1 fimbriae in the adherence phenotype of super-shed Escherichia coli O157:H7. Int J Med Microbiol 2021; 311:151511. [PMID: 33975122 PMCID: PMC8605689 DOI: 10.1016/j.ijmm.2021.151511] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/14/2021] [Accepted: 05/03/2021] [Indexed: 02/04/2023] Open
Abstract
Super-shed (SS) Escherichia coli O157 (E. coli O157) demonstrate a strong, aggregative, locus of enterocyte effacement (LEE)-independent adherence phenotype on bovine recto-anal junction squamous epithelial (RSE) cells, and harbor polymorphisms in non-LEE-adherence-related loci, including in the type 1 fimbriae operon. To elucidate the role of type 1 fimbriae in strain- and host-specific adherence, we evaluated the entire Fim operon (FimB-H) and its adhesion (FimH) deletion mutants in four E. coli O157 strains, SS17, SS52, SS77 and EDL933, and evaluated the adherence phenotype in bovine RSE and human HEp-2 adherence assays. Consistent with the prevailing dogma that fimH expression is genetically switched off in E. coli O157, the ΔfimHSS52, ΔfimB-HSS52, ΔfimB-HSS17, and ΔfimHSS77 mutants remained unchanged in adherence phenotype to RSE cells. In contrast, the ΔfimHSS17 and ΔfimB-HSS77 mutants changed from a wild-type strong and aggregative, to a moderate and diffuse adherence phenotype, while both ΔfimHEDL933 and ΔfimB-HEDL933 mutants demonstrated enhanced binding to RSE cells (p < 0.05). Additionally, both ΔfimHSS17 and ΔfimHEDL933 were non-adherent to HEp-2 cells (p < 0.05). Complementation of the mutant strains with their respective wild-type genes restored parental phenotypes. Microscopy revealed that the SS17 and EDL933 strains indeed carry type 1 fimbriae-like structures shorter than those seen in uropathogenic E. coli. Taken together, these results provide compelling evidence for a strain and host cell type-dependent role of fimH and the fim operon in E. coli O157 adherence that needs to be further evaluated.
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Affiliation(s)
- Robab Katani
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Indira T Kudva
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, IA, USA.
| | - Sreenidhi Srinivasan
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Judith B Stasko
- Microscopy Services, National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, IA, USA
| | - Megan Schilling
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Lingling Li
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Rebecca Cote
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chitrita DebRoy
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Terrance M Arthur
- Roman L. Hruska U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, NE, USA
| | | | - Vivek Kapur
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA; Department of Animal Science, The Pennsylvania State University, University Park, PA, USA.
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31
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Liu X, Wang Y, Wu J, Qi J, Zeng Z, Wan Q, Chen Z, Manandhar P, Cavener VS, Boyle NR, Fu X, Salazar E, Kuchipudi SV, Kapur V, Zhang X, Umetani M, Sen M, Willson RC, Chen S, Zu Y. Neutralizing Aptamers Block S/RBD-ACE2 Interactions and Prevent Host Cell Infection. Angew Chem Int Ed Engl 2021; 60:10273-10278. [PMID: 33684258 PMCID: PMC8250721 DOI: 10.1002/anie.202100345] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [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: 01/08/2021] [Indexed: 12/23/2022]
Abstract
The receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 spike (S) protein plays a central role in mediating the first step of virus infection to cause disease: virus binding to angiotensin-converting enzyme 2 (ACE2) receptors on human host cells. Therefore, S/RBD is an ideal target for blocking and neutralization therapies to prevent and treat coronavirus disease 2019 (COVID-19). Using a target-based selection approach, we developed oligonucleotide aptamers containing a conserved sequence motif that specifically targets S/RBD. Synthetic aptamers had high binding affinity for S/RBD-coated virus mimics (KD ≈7 nM) and also blocked interaction of S/RBD with ACE2 receptors (IC50 ≈5 nM). Importantly, aptamers were able to neutralize S protein-expressing viral particles and prevent host cell infection, suggesting a promising COVID-19 therapy strategy.
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Affiliation(s)
- Xiaohui Liu
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Yi‐ling Wang
- Center for Immunotherapy ResearchHouston Methodist Research InstituteHoustonTX77030USA
| | - Jacky Wu
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell SignallingUniversity of HoustonHoustonTX77204USA
| | - Jianjun Qi
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Zihua Zeng
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Quanyuan Wan
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Zhenghu Chen
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Pragya Manandhar
- Department of Biology and BiochemistryUniversity of HoustonHoustonTX77204USA
| | - Victoria S. Cavener
- Animal Diagnostic LaboratoryDept. of Veterinary and Biomedical SciencesHuck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Nina R. Boyle
- Animal Diagnostic LaboratoryDept. of Veterinary and Biomedical SciencesHuck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Xinping Fu
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell SignallingUniversity of HoustonHoustonTX77204USA
| | - Eric Salazar
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic LaboratoryDept. of Veterinary and Biomedical SciencesHuck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Vivek Kapur
- Dept. of Animal Science and Huck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Xiaoliu Zhang
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell SignallingUniversity of HoustonHoustonTX77204USA
| | - Michihisa Umetani
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell SignallingUniversity of HoustonHoustonTX77204USA
| | - Mehmet Sen
- Department of Biology and BiochemistryUniversity of HoustonHoustonTX77204USA
| | - Richard C. Willson
- Chemical and Biomolecular EngineeringUniversity of HoustonHoustonTX77204USA
| | - Shu‐hsia Chen
- Center for Immunotherapy ResearchHouston Methodist Research InstituteHoustonTX77030USA
| | - Youli Zu
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
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32
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Liu X, Wang Y, Wu J, Qi J, Zeng Z, Wan Q, Chen Z, Manandhar P, Cavener VS, Boyle NR, Fu X, Salazar E, Kuchipudi SV, Kapur V, Zhang X, Umetani M, Sen M, Willson RC, Chen S, Zu Y. Neutralizing Aptamers Block S/RBD-ACE2 Interactions and Prevent Host Cell Infection. Angew Chem Weinheim Bergstr Ger 2021; 133:10361-10366. [PMID: 34230707 PMCID: PMC8250357 DOI: 10.1002/ange.202100345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 12/23/2022]
Abstract
The receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 spike (S) protein plays a central role in mediating the first step of virus infection to cause disease: virus binding to angiotensin-converting enzyme 2 (ACE2) receptors on human host cells. Therefore, S/RBD is an ideal target for blocking and neutralization therapies to prevent and treat coronavirus disease 2019 (COVID-19). Using a target-based selection approach, we developed oligonucleotide aptamers containing a conserved sequence motif that specifically targets S/RBD. Synthetic aptamers had high binding affinity for S/RBD-coated virus mimics (K D≈7 nM) and also blocked interaction of S/RBD with ACE2 receptors (IC50≈5 nM). Importantly, aptamers were able to neutralize S protein-expressing viral particles and prevent host cell infection, suggesting a promising COVID-19 therapy strategy.
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Affiliation(s)
- Xiaohui Liu
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Yi‐ling Wang
- Center for Immunotherapy ResearchHouston Methodist Research InstituteHoustonTX77030USA
| | - Jacky Wu
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell SignallingUniversity of HoustonHoustonTX77204USA
| | - Jianjun Qi
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Zihua Zeng
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Quanyuan Wan
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Zhenghu Chen
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Pragya Manandhar
- Department of Biology and BiochemistryUniversity of HoustonHoustonTX77204USA
| | - Victoria S. Cavener
- Animal Diagnostic LaboratoryDept. of Veterinary and Biomedical SciencesHuck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Nina R. Boyle
- Animal Diagnostic LaboratoryDept. of Veterinary and Biomedical SciencesHuck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Xinping Fu
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell SignallingUniversity of HoustonHoustonTX77204USA
| | - Eric Salazar
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic LaboratoryDept. of Veterinary and Biomedical SciencesHuck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Vivek Kapur
- Dept. of Animal Science and Huck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Xiaoliu Zhang
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell SignallingUniversity of HoustonHoustonTX77204USA
| | - Michihisa Umetani
- Department of Biology and Biochemistry and Center for Nuclear Receptor and Cell SignallingUniversity of HoustonHoustonTX77204USA
| | - Mehmet Sen
- Department of Biology and BiochemistryUniversity of HoustonHoustonTX77204USA
| | - Richard C. Willson
- Chemical and Biomolecular EngineeringUniversity of HoustonHoustonTX77204USA
| | - Shu‐hsia Chen
- Center for Immunotherapy ResearchHouston Methodist Research InstituteHoustonTX77030USA
| | - Youli Zu
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTX77030USA
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33
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Goike J, Hsieh CL, Horton A, Gardner EC, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Renberg R, Johanson MJ, Cardona JA, Segall-Shapiro T, Zhou L, Nissly RH, Gontu A, Byrom M, Maranhao AC, Battenhouse AM, Gejji V, Soto-Sierra L, Foster ER, Woodard SL, Nikolov ZL, Lavinder J, Voss WN, Annapareddy A, Ippolito GC, Ellington AD, Marcotte EM, Finkelstein IJ, Hughes RA, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Dye JM, Boutz DR, McLellan JS, Gollihar JD. Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality. bioRxiv 2021:2021.04.07.438849. [PMID: 33851158 PMCID: PMC8043448 DOI: 10.1101/2021.04.07.438849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.
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Affiliation(s)
- Jule Goike
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Horton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Elizabeth C. Gardner
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Shawn Abbassi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Rebecca Renberg
- CCDC Army Research Laboratory, Biotechnology Branch, Adelphi, MD, USA
| | - Michael J. Johanson
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Jose A. Cardona
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | | | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ruth H. Nissly
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michelle Byrom
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andre C. Maranhao
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Anna M. Battenhouse
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Varun Gejji
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Laura Soto-Sierra
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Emma R. Foster
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Susan L. Woodard
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Zivko L. Nikolov
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Jason Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Will N. Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ankur Annapareddy
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - Gregory C. Ippolito
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J. Finkelstein
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Randall A. Hughes
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Suresh V. Kuchipudi
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - George Georgiou
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Daniel R. Boutz
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D. Gollihar
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
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Srinivasan S, Conlan AJK, Easterling LA, Herrera C, Dandapat P, Veerasami M, Ameni G, Jindal N, Raj GD, Wood J, Juleff N, Bakker D, Vordermeier M, Kapur V. A Meta-Analysis of the Effect of Bacillus Calmette-Guérin Vaccination Against Bovine Tuberculosis: Is Perfect the Enemy of Good? Front Vet Sci 2021; 8:637580. [PMID: 33681334 PMCID: PMC7930010 DOI: 10.3389/fvets.2021.637580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/27/2021] [Indexed: 01/10/2023] Open
Abstract
More than 50 million cattle are likely exposed to bovine tuberculosis (bTB) worldwide, highlighting an urgent need for bTB control strategies in low- and middle-income countries (LMICs) and other regions where the disease remains endemic and test-and-slaughter approaches are unfeasible. While Bacillus Calmette-Guérin (BCG) was first developed as a vaccine for use in cattle even before its widespread use in humans, its efficacy against bTB remains poorly understood. To address this important knowledge gap, we conducted a systematic review and meta-analysis to determine the direct efficacy of BCG against bTB challenge in cattle, and performed scenario analyses with transmission dynamic models incorporating direct and indirect vaccinal effects (“herd-immunity”) to assess potential impact on herd level disease control. The analysis shows a relative risk of infection of 0.75 (95% CI: 0.68, 0.82) in 1,902 vaccinates as compared with 1,667 controls, corresponding to a direct vaccine efficacy of 25% (95% CI: 18, 32). Importantly, scenario analyses considering both direct and indirect effects suggest that disease prevalence could be driven down close to Officially TB-Free (OTF) status (<0.1%), if BCG were introduced in the next 10-year time period in low to moderate (<15%) prevalence settings, and that 50–95% of cumulative cases may be averted over the next 50 years even in high (20–40%) disease burden settings with immediate implementation of BCG vaccination. Taken together, the analyses suggest that BCG vaccination may help accelerate control of bTB in endemic settings, particularly with early implementation in the face of dairy intensification in regions that currently lack effective bTB control programs.
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Affiliation(s)
- Sreenidhi Srinivasan
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Andrew J K Conlan
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Laurel A Easterling
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Christian Herrera
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Premanshu Dandapat
- Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | | | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Gopal Dhinakar Raj
- Translational Research Platform for Veterinary Biological, Tamil Nadu University of Veterinary and Animal Sciences, Chennai, India
| | - James Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nick Juleff
- The Bill & Melinda Gates Foundation, Seattle, WA, United States
| | - Douwe Bakker
- Technical Consultant and Independent Researcher, Lelystad, Netherlands
| | - Martin Vordermeier
- Animal and Plant Health Agency, Addlestone, United Kingdom.,Centre for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Vivek Kapur
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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35
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Rufai SB, McIntosh F, Poojary I, Chothe S, Sebastian A, Albert I, Praul C, Venkatesan M, Mahata G, Maity H, Dandapat P, Michael JS, Katani R, Kapur V, Behr MA. Complete Genome Sequence of Mycobacterium orygis Strain 51145. Microbiol Resour Announc 2021; 10:e01279-20. [PMID: 33414309 PMCID: PMC8407732 DOI: 10.1128/mra.01279-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
We report the complete 4,352,172-bp genome sequence of Mycobacterium orygis strain 51145 assembled into a single circular chromosome. Comparative genomic analyses with other lineages of the Mycobacterium tuberculosis complex can provide insights into the biology, evolution, and epidemiology of this important group of pathogenic mycobacteria.
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Affiliation(s)
- Syed Beenish Rufai
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- McGill International TB Centre, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Fiona McIntosh
- McGill International TB Centre, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Indira Poojary
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shubhada Chothe
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Craig Praul
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Manigandan Venkatesan
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Gibarni Mahata
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Hindol Maity
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Cisgen Biotech Discoveries, Chennai, India
| | - Premanshu Dandapat
- Indian Veterinary Research Institute, Eastern Region Station, Kolkata, West Bengal, India
| | - Joy Sarojini Michael
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Robab Katani
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- Department of Animal Science and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Vivek Kapur
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- Department of Animal Science and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- McGill International TB Centre, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
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36
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Salazar E, Kuchipudi SV, Christensen PA, Eagar T, Yi X, Zhao P, Jin Z, Long SW, Olsen RJ, Chen J, Castillo B, Leveque C, Towers D, Lavinder J, Gollihar J, Cardona J, Ippolito G, Nissly R, Bird I, Greenawalt D, Rossi RM, Gontu A, Srinivasan S, Poojary I, Cattadori IM, Hudson PJ, Josleyn NM, Prugar L, Huie K, Herbert A, Bernard DW, Dye JM, Kapur V, Musser JM. Convalescent plasma anti-SARS-CoV-2 spike protein ectodomain and receptor-binding domain IgG correlate with virus neutralization. J Clin Invest 2020; 130:6728-6738. [PMID: 32910806 PMCID: PMC7685744 DOI: 10.1172/jci141206] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the urgent need for assays that detect protective levels of neutralizing antibodies. We studied the relationship among anti-spike ectodomain (anti-ECD), anti-receptor-binding domain (anti-RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by 2 in vitro assays using convalescent plasma samples from 68 patients with COVID-19. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers and in vitro VN titers. The probability of a VN titer of ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment, was ≥80% when anti-RBD or anti-ECD titers were ≥1:1350. Of all donors, 37% lacked VN titers of ≥160. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease VN or IgG titers. Analysis of 2814 asymptomatic adults found 73 individuals with anti-ECD IgG titers of ≥1:50 and strong positive correlation with anti-RBD and VN titers. Fourteen of these individuals had VN titers of ≥1:160, and all of them had anti-RBD titers of ≥1:1350. We conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titers of ≥1:1350 may provide critical information about protection against COVID-19 disease.
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Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Suresh V. Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Paul A. Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Todd Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Zhicheng Jin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Dalton Towers
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Jimmy Gollihar
- Combat Capabilities Development Command Army Research Laboratory — South, University of Texas, Austin, Texas, USA
| | - Jose Cardona
- Combat Capabilities Development Command Army Research Laboratory — South, University of Texas, Austin, Texas, USA
| | - Gregory Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas, USA
| | - Ruth Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | - Ian Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | - Denver Greenawalt
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | | | - Abhinay Gontu
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | | | | | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Nicole M. Josleyn
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Laura Prugar
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Kathleen Huie
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Andrew Herbert
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - David W. Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - John M. Dye
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences and
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, USA
| | - James M. Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
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37
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Kini A, Okamoto N, Barman N, Vengrenyuk Y, Yasumura K, Bhatheja S, Kapur V, Hasan C, Sweeny J, Baber U, Mehran R, Stone G, Sharma S. Side branch FFR after provisional stenting: simplified approach based on OCT frame count. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.1467] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background/Introduction
Treatment of bifurcation coronary artery lesions remains a major challenge in interventional cardiology. Side branch (SB) stenoses are frequently observed after stent implantation in bifurcation lesions, although angiographically narrowed SBs may not be functionally significant. Fractional flow reserve (FFR), a pressure-derived index of the hemodynamic significance of a coronary artery stenosis, may be useful in determining whether additional intervention is required in jailed SBs. Angiography and intravascular ultrasound (IVUS) derived parameters have showed poor diagnostic accuracy in predicting the functional significance of jailed SBs.
Purpose
The aim of the present study was to use high resolution optical coherence tomography (OCT) imaging to predict functionally significant SB stenoses after provisional stenting defined as SB FFR ≤0.80.
Methods
Seventy-one patients with 71 calcified bifurcation lesions with angiographically intermediate SB stenoses undergoing provisional stenting were enrolled in the prospective study. OCT pullbacks were performed before and after stent placement, and SB FFR was measured after main vessel stenting. SB ostium area (SBOA) was assessed using three-dimensional OCT cut-plane analysis off-line. In addition, we developed a simplified approach to SB ostium assessment based on SB ostium frame count using two-dimensional OCT pullback not requiring off-line 3D reconstruction. For the analysis, consecutive frames were counted between the most distal and most proximal take-off of the SB frames.
Results
Similar to previous studies, quantitative coronary angiography findings were not associated with the functional significance of SBs after main vessel stenting. In contrast, SBOA assessed by 3D-OCT after provisional stenting strongly correlated with post-procedure SB FFR. The optimal cut-off value for the SBOA area to predict a SB FFR ≤0.80 was 0.76 mm2 (sensitivity 82%, specificity 89% and area under the curve of 0.92 (95% CI: 0.84–0.99). A simplified approach to SB ostium assessment using OCT frame count yielded a sensitivity of 82%, specificity 89% and area under the curve 0.92 (95% CI: 0.84 to 0.99) with a cut-off of 4.5 frames allowing detection of functionally significant SB stenoses during the procedure in real time. Figure 1 shows a receiver-operating characteristic curve for SB FFR ≤0.8 and a representative case with SB FFR = 0.66 after provisional stenting and SB ostium frame count equal 3 (Frame 1 to 3)
Conclusion(s)
Assessment of SB using either 3D OCT off-line reconstruction or a simplified approach based on OCT frame count can detect SB branches with FFR ≤0.80 with high sensitivity and specificity. The developed approaches may represent a useful tool to assess provisional stent outcomes.
Figure 1
Funding Acknowledgement
Type of funding source: Private grant(s) and/or Sponsorship. Main funding source(s): Boston Scientific; St. Jude Medical
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Affiliation(s)
- A Kini
- Mount Sinai Medical Center, New York, United States of America
| | - N Okamoto
- Mount Sinai Medical Center, New York, United States of America
| | - N Barman
- Mount Sinai Medical Center, New York, United States of America
| | - Y Vengrenyuk
- Mount Sinai Medical Center, New York, United States of America
| | - K Yasumura
- Mount Sinai Medical Center, New York, United States of America
| | - S Bhatheja
- Mount Sinai Medical Center, New York, United States of America
| | - V Kapur
- Mount Sinai Medical Center, New York, United States of America
| | - C Hasan
- Mount Sinai Medical Center, New York, United States of America
| | - J Sweeny
- Mount Sinai Medical Center, New York, United States of America
| | - U Baber
- Mount Sinai Medical Center, New York, United States of America
| | - R Mehran
- Mount Sinai Medical Center, New York, United States of America
| | - G Stone
- Mount Sinai Medical Center, New York, United States of America
| | - S Sharma
- Mount Sinai Medical Center, New York, United States of America
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38
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Duffy SC, Srinivasan S, Michael JS, Behr MA, Kapur V. Mycobacterium orygis: a zoonosis, zooanthroponosis, or both? – Authors' reply. The Lancet Microbe 2020; 1:e241. [DOI: 10.1016/s2666-5247(20)30145-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 11/29/2022] Open
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39
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Herzog CM, de Glanville WA, Willett BJ, Cattadori IM, Kapur V, Hudson PJ, Buza J, Swai ES, Cleaveland S, Bjørnstad ON. Peste des petits ruminants Virus Transmission Scaling and Husbandry Practices That Contribute to Increased Transmission Risk: An Investigation among Sheep, Goats, and Cattle in Northern Tanzania. Viruses 2020; 12:E930. [PMID: 32847058 PMCID: PMC7552010 DOI: 10.3390/v12090930] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 11/22/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) causes an infectious disease of high morbidity and mortality among sheep and goats which impacts millions of livestock keepers globally. PPRV transmission risk varies by production system, but a deeper understanding of how transmission scales in these systems and which husbandry practices impact risk is needed. To investigate transmission scaling and husbandry practice-associated risk, this study combined 395 household questionnaires with over 7115 cross-sectional serosurvey samples collected in Tanzania among agropastoral and pastoral households managing sheep, goats, or cattle (most managed all three, n = 284, 71.9%). Although self-reported compound-level herd size was significantly larger in pastoral than agropastoral households, the data show no evidence that household herd force of infection (FOI, per capita infection rate of susceptible hosts) increased with herd size. Seroprevalence and FOI patterns observed at the sub-village level showed significant spatial variation in FOI. Univariate analyses showed that household herd FOI was significantly higher when households reported seasonal grazing camp attendance, cattle or goat introduction to the compound, death, sale, or giving away of animals in the past 12 months, when cattle were grazed separately from sheep and goats, and when the household also managed dogs or donkeys. Multivariable analyses revealed that species, production system type, and goat or sheep introduction or seasonal grazing camp attendance, cattle or goat death or sales, or goats given away in the past 12 months significantly increased odds of seroconversion, whereas managing pigs or cattle attending seasonal grazing camps had significantly lower odds of seroconversion. Further research should investigate specific husbandry practices across production systems in other countries and in systems that include additional atypical host species to broaden understanding of PPRV transmission.
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Affiliation(s)
- Catherine M. Herzog
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
| | - William A. de Glanville
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; (W.A.d.G.); (S.C.)
| | - Brian J. Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK;
| | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
| | - Joram Buza
- Nelson Mandela African Institute of Science and Technology, Arusha Box 447, Tanzania;
| | - Emmanuel S. Swai
- Department of Veterinary Services, Ministry of Livestock and Fisheries, Dodoma Box 2870, Tanzania;
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; (W.A.d.G.); (S.C.)
| | - Ottar N. Bjørnstad
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA; (I.M.C.); (V.K.); (P.J.H.); (O.N.B.)
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40
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Srinivasan S, Subramanian S, Shankar Balakrishnan S, Ramaiyan Selvaraju K, Manomohan V, Selladurai S, Jothivelu M, Kandasamy S, Gopal DR, Kathaperumal K, Conlan AJK, Veerasami M, Bakker D, Vordermeier M, Kapur V. A Defined Antigen Skin Test That Enables Implementation of BCG Vaccination for Control of Bovine Tuberculosis: Proof of Concept. Front Vet Sci 2020; 7:391. [PMID: 32793643 PMCID: PMC7393633 DOI: 10.3389/fvets.2020.00391] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/01/2020] [Indexed: 01/25/2023] Open
Abstract
In most low- and middle-income countries (LMICs), bovine tuberculosis (bTB) remains endemic due to the absence of control programs. This is because successful bTB control and eradication programs have relied on test-and-slaughter strategies that are socioeconomically unfeasible in LMICs. While Bacillus Calmette–Guérin (BCG) vaccine-induced protection for cattle has long been documented in experimental and field trials, its use in control programs has been precluded by the inability to differentiate BCG-vaccinated from naturally infected animals using the OIE-prescribed purified protein derivative (PPD)-based tuberculin skin tests. In the current study, the diagnostic specificity and capability for differentiating infected from vaccinated animals (DIVA) of a novel defined antigen skin test (DST) in BCG-vaccinated (Bos taurus ssp. taurus x B. t. ssp. indicus) calves were compared with the performance of traditional PPD-tuberculin in both the skin test and in vitro interferon-gamma release assay (IGRA). The IFN-γ production from whole blood cells stimulated with both PPDs increased significantly from the 0 week baseline levels, while DST induced no measurable IFN-γ production in BCG-vaccinated calves. None of the 15 BCG-vaccinated calves were reactive with the DST skin test (100% specificity; one-tailed lower 95% CI: 82). In contrast, 10 of 15 BCG-vaccinated calves were classified as reactors with the PPD-based single intradermal test (SIT) (specificity in vaccinated animals = 33%; 95% CI: 12, 62). Taken together, the results provide strong evidence that the DST is highly specific and enables DIVA capability in both skin and IGRA assay format, thereby enabling the implementation of BCG vaccine-based bTB control, particularly in settings where test and slaughter remain unfeasible.
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Affiliation(s)
- Sreenidhi Srinivasan
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Saraswathi Subramanian
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Sai Shankar Balakrishnan
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Kathiravan Ramaiyan Selvaraju
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Vandana Manomohan
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Suganya Selladurai
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Monika Jothivelu
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Srinivasan Kandasamy
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Dhinakar Raj Gopal
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Kumanan Kathaperumal
- Translational Research Platform for Veterinary Biologicals, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Andrew J K Conlan
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Douwe Bakker
- Independent Researcher and Technical Consultant, Lelystad, Netherlands
| | - Martin Vordermeier
- Animal and Plant Health Agency, Weybridge, United Kingdom.,Centre for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Vivek Kapur
- Department of Animal Science, The Pennsylvania State University, University Park, PA, United States.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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41
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Salazar E, Kuchipudi SV, Christensen PA, Eagar TN, Yi X, Zhao P, Jin Z, Long SW, Olsen RJ, Chen J, Castillo B, Leveque C, Towers DM, Lavinder J, Gollihar JD, Cardona J, Ippolito GC, Nissly RH, Bird IM, Greenawalt D, Rossi RM, Gontu A, Srinivasan S, Poojary IB, Cattadori IM, Hudson PJ, Joselyn N, Prugar L, Huie K, Herbert A, Bernard DW, Dye J, Kapur V, Musser JM. Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma. bioRxiv 2020:2020.06.08.138990. [PMID: 32577662 PMCID: PMC7302218 DOI: 10.1101/2020.06.08.138990] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ectodomain (ECD) and anti-receptor binding domain (RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by two different in vitro assays using convalescent plasma samples obtained from 68 COVID-19 patients, including 13 who donated plasma multiple times. Only 23% (16/68) of donors had been hospitalized. We also studied 16 samples from subjects found to have anti-spike protein IgG during surveillance screening of asymptomatic individuals. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers, and in vitro VN titer. Anti-RBD plasma IgG correlated slightly better than anti-ECD IgG titer with VN titer. The probability of a VN titer ≥160 was 80% or greater with anti-RBD or anti-ECD titers of ≥1:1350. Thirty-seven percent (25/68) of convalescent plasma donors lacked VN titers ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease either VN or IgG titers. Analysis of 2,814 asymptomatic adults found 27 individuals with anti-RBD or anti-ECD IgG titers of ≥1:1350, and evidence of VN ≥1:160. Taken together, we conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titer of ≥1:1350 may provide critical information about protection against COVID-19 disease.
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Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Suresh V. Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
| | - Paul A. Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Todd N. Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Zhicheng Jin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Dalton M. Towers
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jimmy D. Gollihar
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Jose Cardona
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, University of Texas at Austin
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Ruth H. Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Ian M. Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Denver Greenawalt
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Randall M. Rossi
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Abinhay Gontu
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Sreenidhi Srinivasan
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Indira B. Poojary
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Nicole Joselyn
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Laura Prugar
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Kathleen Huie
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Andrew Herbert
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - David W. Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - John Dye
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - James M. Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
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42
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Duffy SC, Srinivasan S, Schilling MA, Stuber T, Danchuk SN, Michael JS, Venkatesan M, Bansal N, Maan S, Jindal N, Chaudhary D, Dandapat P, Katani R, Chothe S, Veerasami M, Robbe-Austerman S, Juleff N, Kapur V, Behr MA. Reconsidering Mycobacterium bovis as a proxy for zoonotic tuberculosis: a molecular epidemiological surveillance study. Lancet Microbe 2020; 1:e66-e73. [PMID: 32642742 PMCID: PMC7325494 DOI: 10.1016/s2666-5247(20)30038-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Zoonotic tuberculosis is defined as human infection with Mycobacterium bovis. Although globally, India has the largest number of human tuberculosis cases and the largest cattle population, in which bovine tuberculosis is endemic, the burden of zoonotic tuberculosis is unknown. The aim of this study was to obtain estimates of the human prevalence of animal-associated members of the Mycobacterium tuberculosis complex (MTBC) at a large referral hospital in India. Methods We did a molecular epidemiological surveillance study of 940 positive mycobacteria growth indicator tube (MGIT) cultures, collected from patients visiting the outpatient department at Christian Medical College (Vellore, India) with suspected tuberculosis between Oct 1, 2018, and March 31, 2019. A PCR-based approach was applied to subspeciate cultures. Isolates identified as MTBC other than M tuberculosis or as inconclusive on PCR were subject to whole-genome sequencing (WGS), and phylogenetically compared with publicly available MTBC sequences from south Asia. Sequences from WGS were deposited in the National Center for Biotechnology Information Sequence Read Archive, accession number SRP226525 (BioProject database number PRJNA575883). Findings The 940 MGIT cultures were from 548 pulmonary and 392 extrapulmonary samples. A conclusive identification was obtained for all 940 isolates; wild-type M bovis was not identified. The isolates consisted of M tuberculosis (913 [97·1%] isolates), Mycobacterium orygis (seven [0·7%]), M bovis BCG (five [0·5%]), and non-tuberculous mycobacteria (15 [1·6%]). Subspecies were assigned for 25 isolates by WGS, which were analysed against 715 MTBC sequences from south Asia. Among the 715 genomes, no M bovis was identified. Four isolates of cattle origin were dispersed among human sequences within M tuberculosis lineage 1, and the seven M orygis isolates from human MGIT cultures were dispersed among sequences from cattle. Interpretation M bovis prevalence in humans is an inadequate proxy of zoonotic tuberculosis. The recovery of M orygis from humans highlights the need to use a broadened definition, including MTBC subspecies such as M orygis, to investigate zoonotic tuberculosis. The identification of M tuberculosis in cattle also reinforces the need for One Health investigations in countries with endemic bovine tuberculosis. Funding Bill & Melinda Gates Foundation, Canadian Institutes for Health Research.
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Affiliation(s)
- Shannon C Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International Tuberculosis Centre, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Sreenidhi Srinivasan
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Megan A Schilling
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, US Department of Agriculture, Ames, IA, USA
| | - Sarah N Danchuk
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International Tuberculosis Centre, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Joy S Michael
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Manigandan Venkatesan
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Nitish Bansal
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Sushila Maan
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Deepika Chaudhary
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Premanshu Dandapat
- Eastern Regional Station, Indian Veterinary Research Institute, Indian Council of Agricultural Research, Kolkata, India
| | - Robab Katani
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Shubhada Chothe
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | | | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, US Department of Agriculture, Ames, IA, USA
| | | | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International Tuberculosis Centre, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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43
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Katani R, Schilling MA, Lyimo B, Tonui T, Cattadori IM, Eblate E, Martin A, Estes AB, Buza T, Rentsch D, Davenport KW, Hovde BT, Lyimo S, Munuo L, Stomeo F, Tiambo C, Radzio-Basu J, Mosha F, Hudson PJ, Buza JJ, Kapur V. Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania. Sci Rep 2019; 9:18086. [PMID: 31792246 PMCID: PMC6888819 DOI: 10.1038/s41598-019-53969-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023] Open
Abstract
Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.
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Affiliation(s)
- Robab Katani
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Megan A Schilling
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Beatus Lyimo
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Triza Tonui
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Isabella M Cattadori
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ernest Eblate
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.,Tanzania Wildlife Research Institute, Arusha, Tanzania
| | - Andimile Martin
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Anna B Estes
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.,Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Teresia Buza
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | | | - Blake T Hovde
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Samson Lyimo
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Lydia Munuo
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Francesca Stomeo
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Christian Tiambo
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Jessica Radzio-Basu
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Fausta Mosha
- Ministry of Health Community Development Gender Elderly and Children, Dar es Salaam, Tanzania
| | - Peter J Hudson
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Joram J Buza
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Vivek Kapur
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA. .,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA. .,Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, USA. .,Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
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44
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Li L, Bannantine JP, Campo JJ, Randall A, Grohn YT, Schilling MA, Katani R, Radzio-Basu J, Easterling L, Kapur V. Identification of Sero-Diagnostic Antigens for the Early Diagnosis of Johne's Disease using MAP Protein Microarrays. Sci Rep 2019; 9:17573. [PMID: 31772281 PMCID: PMC6879513 DOI: 10.1038/s41598-019-53973-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 11/07/2019] [Indexed: 01/20/2023] Open
Abstract
Considerable effort has been directed toward controlling Johne’s disease (JD), a chronic granulomatous intestinal inflammatory disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) in cattle and other ruminants. However, progress in controlling the spread of MAP infection has been impeded by the lack of reliable diagnostic tests that can identify animals early in the infection process and help break the transmission chain. To identify reliable antigens for early diagnosis of MAP infection, we constructed a MAP protein array with 868 purified recombinant MAP proteins, and screened a total of 180 well-characterized serum samples from cows assigned to 4 groups based on previous serological and fecal test results: negative low exposure (NL, n = 30); negative high exposure (NH, n = 30); fecal-positive, ELISA-negative (F + E−, n = 60); and both fecal- and ELISA-positive (F + E+, n = 60). The analyses identified a total of 49 candidate antigens in the NH, F + E−, and F + E+ with reactivity compared with the NL group (p < 0.01), a majority of which have not been previously identified. While some of the antigens were identified as reactive in only one of the groups, others showed reactivity in multiple groups, including NH (n = 28), F + E− (n = 26), and F + E+ (n = 17) groups. Using combinations of top reactive antigens in each group, the results reveal sensitivities of 60.0%, 73.3%, and 81.7% in the NH, F + E−, and F + E+, respectively at 90% specificity, suggesting that early detection of infection in animals may be possible and enable better opportunities to reduce within herd transmission that may be otherwise missed by traditional serological assays that are biased towards more heavily infected animals. Together, the results suggest that several of the novel candidate antigens identified in this study, particularly those that were reactive in the NH and F + E− groups, have potential utility for the early sero-diagnosis of MAP infection.
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Affiliation(s)
- Lingling Li
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America
| | - John P Bannantine
- National Animal Disease Center, USDA-ARS, Ames, IA, United States of America
| | - Joseph J Campo
- Antigen Discovery, Inc., Irvine, CA, United States of America
| | - Arlo Randall
- Antigen Discovery, Inc., Irvine, CA, United States of America
| | - Yrjo T Grohn
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, United States of America
| | - Megan A Schilling
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Department of Animal Science, Pennsylvania State University, University Park, PA, United States of America
| | - Robab Katani
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Department of Animal Science, Pennsylvania State University, University Park, PA, United States of America.,Applied Biological and Biosafety Research Laboratory, The Pennsylvania State University, University Park, PA, United States of America
| | - Jessica Radzio-Basu
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Applied Biological and Biosafety Research Laboratory, The Pennsylvania State University, University Park, PA, United States of America
| | - Laurel Easterling
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America.,Department of Animal Science, Pennsylvania State University, University Park, PA, United States of America
| | - Vivek Kapur
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States of America. .,Department of Animal Science, Pennsylvania State University, University Park, PA, United States of America. .,Applied Biological and Biosafety Research Laboratory, The Pennsylvania State University, University Park, PA, United States of America.
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45
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Buza TM, Tonui T, Stomeo F, Tiambo C, Katani R, Schilling M, Lyimo B, Gwakisa P, Cattadori IM, Buza J, Kapur V. iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics 2019; 20:374. [PMID: 31269897 PMCID: PMC6610863 DOI: 10.1186/s12859-019-2965-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 01/29/2019] [Accepted: 06/24/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essential requirements of modern microbiome research. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. However, most of these tools are built with many functions that require an in-depth understanding of their implementation and the choice of additional tools for visualizing the final output. Furthermore, microbiome analysis can be time-consuming and may even require more advanced programming skills which some investigators may be lacking. RESULTS We have developed a wrapper named iMAP (Integrated Microbiome Analysis Pipeline) to provide the microbiome research community with a user-friendly and portable tool that integrates bioinformatics analysis and data visualization. The iMAP tool wraps functionalities for metadata profiling, quality control of reads, sequence processing and classification, and diversity analysis of operational taxonomic units. This pipeline is also capable of generating web-based progress reports for enhancing an approach referred to as review-as-you-go (RAYG). For the most part, the profiling of microbial community is done using functionalities implemented in Mothur or QIIME2 platform. Also, it uses different R packages for graphics and R-markdown for generating progress reports. We have used a case study to demonstrate the application of the iMAP pipeline. CONCLUSIONS The iMAP pipeline integrates several functionalities for better identification of microbial communities present in a given sample. The pipeline performs in-depth quality control that guarantees high-quality results and accurate conclusions. The vibrant visuals produced by the pipeline facilitate a better understanding of the complex and multidimensional microbiome data. The integrated RAYG approach enables the generation of web-based reports, which provides the investigators with the intermediate output that can be reviewed progressively. The intensively analyzed case study set a model for microbiome data analysis.
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Affiliation(s)
- Teresia M. Buza
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, State College, PA USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA USA
| | - Triza Tonui
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Francesca Stomeo
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Present Address: The European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Christian Tiambo
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Robab Katani
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, State College, PA USA
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, State College, PA USA
| | - Megan Schilling
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, State College, PA USA
- Department of Animal Science, Pennsylvania State University, University Park, State College, PA USA
| | - Beatus Lyimo
- Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
| | - Paul Gwakisa
- Sokoine University of Agriculture, Morogoro, Tanzania
| | - Isabella M. Cattadori
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, State College, PA USA
- Department of Biology, Pennsylvania State University, University Park, State College, PA USA
| | - Joram Buza
- Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
| | - Vivek Kapur
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, State College, PA USA
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, State College, PA USA
- Department of Animal Science, Pennsylvania State University, University Park, State College, PA USA
- Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
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Srinivasan S, Jones G, Veerasami M, Steinbach S, Holder T, Zewude A, Fromsa A, Ameni G, Easterling L, Bakker D, Juleff N, Gifford G, Hewinson RG, Vordermeier HM, Kapur V. A defined antigen skin test for the diagnosis of bovine tuberculosis. Sci Adv 2019; 5:eaax4899. [PMID: 31328169 PMCID: PMC6636981 DOI: 10.1126/sciadv.aax4899] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/13/2019] [Indexed: 06/10/2023]
Abstract
Bovine tuberculosis (bTB) is a major zoonotic disease of cattle that is endemic in much of the world, limiting livestock productivity and representing a global public health threat. Because the standard tuberculin skin test precludes implementation of Bacille Calmette-Guérin (BCG) vaccine-based control programs, we here developed and evaluated a novel peptide-based defined antigen skin test (DST) to diagnose bTB and to differentiate infected from vaccinated animals (DIVA). The results, in laboratory assays and in experimentally or naturally infected animals, demonstrate that the peptide-based DST provides DIVA capability and equal or superior performance over the extant standard tuberculin surveillance test. Together with the ease of chemical synthesis, quality control, and lower burden for regulatory approval compared with recombinant antigens, the results of our studies show that the DST considerably improves a century-old standard and enables the development and implementation of critically needed surveillance and vaccination programs to accelerate bTB control.
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Affiliation(s)
- Sreenidhi Srinivasan
- Department of Animal Sciences, Pennsylvania State University, University Park, PA, USA
- The Huck Institutes, Pennsylvania State University, University Park, PA, USA
| | | | - Maroudam Veerasami
- Department of Animal Sciences, Pennsylvania State University, University Park, PA, USA
- Cisgen Biotech Discoveries, Chennai, India
| | | | | | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abebe Fromsa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Laurel Easterling
- Department of Animal Sciences, Pennsylvania State University, University Park, PA, USA
- The Huck Institutes, Pennsylvania State University, University Park, PA, USA
| | - Douwe Bakker
- Department of Animal Sciences, Pennsylvania State University, University Park, PA, USA
- Independent Researcher, Lelystad, Netherlands
| | | | - Glen Gifford
- World Organization for Animal Health, Paris, France
| | - R. G. Hewinson
- Centre for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, UK
| | - H. Martin Vordermeier
- Animal and Plant Health Agency, Surrey, UK
- Centre for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, UK
| | - Vivek Kapur
- Department of Animal Sciences, Pennsylvania State University, University Park, PA, USA
- The Huck Institutes, Pennsylvania State University, University Park, PA, USA
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47
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Schilling MA, Memari S, Cattadori IM, Katani R, Muhairwa AP, Buza JJ, Kapur V. Innate Immune Genes Associated With Newcastle Disease Virus Load in Chick Embryos From Inbred and Outbred Lines. Front Microbiol 2019; 10:1432. [PMID: 31281305 PMCID: PMC6596324 DOI: 10.3389/fmicb.2019.01432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/06/2019] [Indexed: 12/21/2022] Open
Abstract
Newcastle disease virus (NDV) causes substantial economic losses to smallholder farmers in low- and middle-income countries with high levels of morbidity and mortality in poultry flocks. Previous investigations have suggested differing levels of susceptibility to NDV between specific inbred lines and amongst breeds of chickens, however, the mechanisms contributing to this remain poorly understood. Studies have shown that some of these differences in levels of susceptibility to NDV infection may be accounted for by variability in the innate immune response amongst various breeds of poultry to NDV infection. Recent studies, in inbred Fayoumi and Leghorn lines, uncovered conserved, breed-dependent, and subline-dependent responses. To better understand the role of innate immune genes in engendering a protective immune response, we assessed the transcriptional responses to NDV of three highly outbred Tanzanian local chicken ecotypes, the Kuchi, the Morogoro Medium, and the Ching’wekwe. Hierarchical clustering and principal coordinate analysis of the gene expression profiles of 21-day old chick embryos infected with NDV clustered in an ecotype-dependent manner and was consistent with the relative viral loads for each of the three ecotypes. The Kuchi and Morogoro Medium exhibit significantly higher viral loads than the Ching’wekwe. The results show that the outbred ecotypes with increased levels of expression of CCL4, NOS2, and SOCS1 also had higher viral loads. The higher expression of SOCS1 is inconsistent with the expression in inbred lines. These differences may uncover new mechanisms or pathways in these populations that may have otherwise been overlooked when examining the response in highly inbred lines. Taken together, our findings provide insights on the specific conserved and differentially expressed innate immune-related genes involved the response of highly outbred chicken lines to NDV. This also suggests that several of the specific innate immunity related genes identified in the current investigation may serve as markers for the selection of chickens with reduced susceptibility to NDV.
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Affiliation(s)
- Megan A Schilling
- Animal Science Department, Pennsylvania State University, University Park, PA, United States.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States.,School of Life Sciences and Bioengineering, The Nelson Mandela African Institution of Science and Technology, Arusha, TZ, United States
| | - Sahar Memari
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Isabella M Cattadori
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States.,Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, PA, United States.,Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Robab Katani
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States.,Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Amandus P Muhairwa
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, TZ, United States
| | - Joram J Buza
- School of Life Sciences and Bioengineering, The Nelson Mandela African Institution of Science and Technology, Arusha, TZ, United States
| | - Vivek Kapur
- Animal Science Department, Pennsylvania State University, University Park, PA, United States.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States.,School of Life Sciences and Bioengineering, The Nelson Mandela African Institution of Science and Technology, Arusha, TZ, United States.,Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, PA, United States
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48
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Schilling MA, Memari S, Cavanaugh M, Katani R, Deist MS, Radzio-Basu J, Lamont SJ, Buza JJ, Kapur V. Conserved, breed-dependent, and subline-dependent innate immune responses of Fayoumi and Leghorn chicken embryos to Newcastle disease virus infection. Sci Rep 2019; 9:7209. [PMID: 31076577 PMCID: PMC6510893 DOI: 10.1038/s41598-019-43483-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/24/2019] [Indexed: 11/13/2022] Open
Abstract
Newcastle disease virus (NDV) is a threat to the global poultry industry, but particularly for smallholder farmers in low- and middle-income countries. Previous reports suggest that some breeds of chickens are less susceptible to NDV infection, however, the mechanisms contributing to this are unknown. We here examined the comparative transcriptional responses of innate immune genes to NDV infection in inbred sublines of the Fayoumi and Leghorn breeds known to differ in their relative susceptibility to infection as well as at the microchromosome bearing the major histocompatability complex (MHC) locus. The analysis identified a set of five core genes, Mx1, IRF1, IRF7, STAT1, and SOCS1, that are up-regulated regardless of subline. Several genes were differentially expressed in a breed- or subline-dependent manner. The breed-dependent response involved TLR3, NOS2, LITAF, and IFIH1 in the Fayoumi versus IL8, CAMP, and CCL4 in the Leghorn. Further analysis identified subline-dependent differences in the pro-inflammatory response within the Fayoumi breed that are likely influenced by the MHC. These results have identified conserved, breed-dependent, and subline-dependent innate immune responses to NDV infection in chickens, and provide a strong framework for the future characterization of the specific roles of genes and pathways that influence the susceptibility of chickens to NDV infection.
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Affiliation(s)
- Megan A Schilling
- The Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA, 16802, USA.,The Pennsylvania State University, Animal Science Department, University Park, PA, 16802, USA.,The Nelson Mandela African Institution of Science and Technology, School of Life Science and Bioengineering, Arusha, Tanzania
| | - Sahar Memari
- The Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA, 16802, USA.,The Pennsylvania State University, Animal Science Department, University Park, PA, 16802, USA
| | - Meredith Cavanaugh
- The Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA, 16802, USA.,The Pennsylvania State University, Animal Science Department, University Park, PA, 16802, USA
| | - Robab Katani
- The Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA, 16802, USA.,The Pennsylvania State University, Animal Science Department, University Park, PA, 16802, USA.,The Pennsylvania State University, Applied Biological and Biosafety Research Laboratory, University Park, PA, 16802, USA
| | - Melissa S Deist
- The Iowa State University, Department of Animal Science, Ames, IA, 50011, USA
| | - Jessica Radzio-Basu
- The Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA, 16802, USA.,The Pennsylvania State University, Applied Biological and Biosafety Research Laboratory, University Park, PA, 16802, USA
| | - Susan J Lamont
- The Iowa State University, Department of Animal Science, Ames, IA, 50011, USA
| | - Joram J Buza
- The Nelson Mandela African Institution of Science and Technology, School of Life Science and Bioengineering, Arusha, Tanzania
| | - Vivek Kapur
- The Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA, 16802, USA. .,The Pennsylvania State University, Animal Science Department, University Park, PA, 16802, USA. .,The Nelson Mandela African Institution of Science and Technology, School of Life Science and Bioengineering, Arusha, Tanzania. .,The Pennsylvania State University, Applied Biological and Biosafety Research Laboratory, University Park, PA, 16802, USA.
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49
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Srinivasan S, Easterling L, Rimal B, Niu XM, Conlan AJK, Dudas P, Kapur V. Prevalence of Bovine Tuberculosis in India: A systematic review and meta-analysis. Transbound Emerg Dis 2018; 65:1627-1640. [PMID: 29885021 PMCID: PMC6282864 DOI: 10.1111/tbed.12915] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/17/2018] [Accepted: 05/01/2018] [Indexed: 12/11/2022]
Abstract
Bovine tuberculosis (bTB) is a chronic disease of cattle that impacts productivity and represents a major public health threat. Despite the considerable economic costs and zoonotic risk consequences associated with the disease, accurate estimates of bTB prevalence are lacking in many countries, including India, where national control programmes are not yet implemented and the disease is considered endemic. To address this critical knowledge gap, we performed a systematic review of the literature and a meta-analysis to estimate bTB prevalence in cattle in India and provide a foundation for the future formulation of rational disease control strategies and the accurate assessment of economic and health impact risks. The literature search was performed in accordance with PRISMA guidelines and identified 285 cross-sectional studies on bTB in cattle in India across four electronic databases and handpicked publications. Of these, 44 articles were included, contributing a total of 82,419 cows and buffaloes across 18 states and one union territory in India. Based on a random-effects (RE) meta-regression model, the analysis revealed a pooled prevalence estimate of 7.3% (95% CI: 5.6, 9.5), indicating that there may be an estimated 21.8 million (95% CI: 16.6, 28.4) infected cattle in India-a population greater than the total number of dairy cows in the United States. The analyses further suggest that production system, species, breed, study location, diagnostic technique, sample size and study period are likely moderators of bTB prevalence in India and need to be considered when developing future disease surveillance and control programmes. Taken together with the projected increase in intensification of dairy production and the subsequent increase in the likelihood of zoonotic transmission, the results of our study suggest that attempts to eliminate tuberculosis from humans will require simultaneous consideration of bTB control in cattle population in countries such as India.
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Affiliation(s)
- Sreenidhi Srinivasan
- Department of Animal ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Laurel Easterling
- Department of Animal ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Bipin Rimal
- The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Xiaoyue Maggie Niu
- Department of StatisticsEberly College of ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Andrew J. K. Conlan
- Disease Dynamics UnitDepartment of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Patrick Dudas
- The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Vivek Kapur
- Department of Animal ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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50
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Schilling MA, Katani R, Memari S, Cavanaugh M, Buza J, Radzio-Basu J, Mpenda FN, Deist MS, Lamont SJ, Kapur V. Transcriptional Innate Immune Response of the Developing Chicken Embryo to Newcastle Disease Virus Infection. Front Genet 2018. [PMID: 29535762 PMCID: PMC5835104 DOI: 10.3389/fgene.2018.00061] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Traditional approaches to assess the immune response of chickens to infection are through animal trials, which are expensive, require enhanced biosecurity, compromise welfare, and are frequently influenced by confounding variables. Since the chicken embryo becomes immunocompetent prior to hatch, we here characterized the transcriptional response of selected innate immune genes to Newcastle disease virus (NDV) infection in chicken embryos at days 10, 14, and 18 of embryonic development. The results suggest that the innate immune response 72 h after challenge of 18-day chicken embryo is both consistent and robust. The expression of CCL5, Mx1, and TLR3 in lung tissues of NDV challenged chicken embryos from the outbred Kuroiler and Tanzanian local ecotype lines showed that their expression was several orders of magnitude higher in the Kuroiler than in the local ecotypes. Next, the expression patterns of three additional innate-immunity related genes, IL-8, IRF-1, and STAT1, were examined in the highly congenic Fayoumi (M5.1 and M15.2) and Leghorn (Ghs6 and Ghs13) sublines that differ only at the microchromosome bearing the major histocompatibility locus. The results show that the Ghs13 Leghorn subline had a consistently higher expression of all genes except IL-8 and expression seemed to be subline-dependent rather than breed-dependent, suggesting that the innate immune response of chicken embryos to NDV infection may be genetically controlled by the MHC-locus. Taken together, the results suggest that the chicken embryo may represent a promising model to studying the patterns and sources of variation of the avian innate immune response to infection with NDV and related pathogens.
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Affiliation(s)
- Megan A Schilling
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States.,Department of Animal Science, Pennsylvania State University, University Park, PA, United States.,School of Life Sciences and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Robab Katani
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States.,Department of Animal Science, Pennsylvania State University, University Park, PA, United States.,Applied Biological Research Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Sahar Memari
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Meredith Cavanaugh
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Joram Buza
- School of Life Sciences and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Jessica Radzio-Basu
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Fulgence N Mpenda
- School of Life Sciences and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Melissa S Deist
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Vivek Kapur
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States.,Department of Animal Science, Pennsylvania State University, University Park, PA, United States.,School of Life Sciences and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
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