Source: UNIV OF TEXAS - MEDICAL BRANCH submitted to
PARTNERSHIP: RAPID DETECTION OF INCURSIONS OF SARS-COV-2 AND NOVEL CORONAVIRUSES ON TEXAS MEAT AND DAIRY FARMS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1030125
Grant No.
2023-70432-39558
Cumulative Award Amt.
$797,322.00
Proposal No.
2022-11245
Multistate No.
(N/A)
Project Start Date
Sep 1, 2023
Project End Date
Aug 31, 2028
Grant Year
2023
Program Code
[A1181]- Tactical Sciences for Agricultural Biosecurity
Recipient Organization
UNIV OF TEXAS - MEDICAL BRANCH
(N/A)
GALVESTON,TX 77550
Performing Department
(N/A)
Non Technical Summary
Emergent viruses that cause epidemics and are often at first not detected by routine veterinary or human diagnostics. It is only after these viruses cause much disease that they are discovered, characterized, and commercial tests are developed to detect them.One group of viruses that is particularly likely to change and cause epidemics is the coronavirus family. These viruses have caused multiple severe epidemics in humans and livestock. Coronaviruses include the SARS-CoV-2 virus which causes COVID-19. Coronaviruses often move back and forth between different species. When they do so, they often further change. Sometimes these changes cause severe disease in the new animal host and sometimes they change and can cause new types of disease if they return to their original host. Often the changes in coronaviruses that lead to epidemics take dozens of years to occur but if we can detect such new coronaviruses early, we have an opportunity to stop their spread.Today there are no commercial laboratory tests to detect such new coronaviruses. Our laboratory diagnostics are finely tuned to pick up only the previously well-studied coronaviruses. We have developed a test that picks nearly 100% of all coronaviruses, both previously recognized and newly generated. We have recently used it to detect a novel canine-like coronavirus that is causing human respiratory illness in both Malaysia and Haiti.In this study we will use this pan-species coronavirus laboratory test to study over 5 years, 16 Texas livestock farms (pigs, cattle, or poultry) for all coronaviruses. A biotech company, GeneCapture, Inc., will also develop and test a hand-held instrument which uses a similar approach but may be used by farm workers on the farm.In the study of the 16 farms, questionnaire data and samples will be collected every four months for one year from each farm's environment, the farm livestock and the livestock workers. In between the four farm visits to each farm, we will use postage-paid sample kits to collect and ship nasal/oral swabs from livestock or livestock workers with signs of respiratory illness to our University of Texas Medical Branch Laboratory. We will intensively study the viruses we detect with advanced laboratory techniques and compare them to other viruses to determine which viruses are most likely to cause future epidemics in animal or humans. Unusual viruses will be shared with the USDA for further assessment. No individual farm or farm worker will be identified.Overall, this study aims to develop effective and cost-efficient methods for the rapid detection of coronaviruses like that causing COVID-19 on livestock farms. Additionally, this project will offer practical virology training to up to 40 minority undergraduate students that is likely to help them gain scientific job opportunities. The program will be managed by Dr. Alex Peniche of Galveston College who will recruit and manage internship training of undergraduate students from the Honors program at Galveston College, a minority-serving 2-year degree institution. Each semester, up to 4 undergraduates from Biology, Chemistry or Life Science majors will be selected to work up to 10 hrs per week (for a semester) as paid virology interns in the UTMB One Health laboratory. Interns will receive instruction training in Laboratory Basic Biosafety, Chemical Safety, Institutional Animal Care and Use Training, Human Subjects Research Training, and Biomedical Responsible Conduct of Research Training. They will receive hands-on training in molecular biology, including: real-time and conventional PCR and RT-PCR, gel electrophoresis, cell culture, and Sanger sequencing techniques under close supervision by our team of viral laboratory professionals.Detecting new coronaviruses on farms at low cost is of great importance to US agriculture biosecurity, to international food security, in protecting the health of livestock and animal workers, as well in protecting the livestock industries' business models. Demonstrating that our coronavirus surveillance approach is effective and of relatively low cost, could influence the adoption of this surveillance approach throughout the world.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3113910117050%
3113910110140%
3113910109010%
Knowledge Area
311 - Animal Diseases;

Subject Of Investigation
3910 - Cross-commodity research--multiple animal species;

Field Of Science
1090 - Immunology; 1101 - Virology; 1170 - Epidemiology;
Goals / Objectives
Overall, this study aims to develop effective and cost-efficient methods for the rapid detection of SARS-CoV-2 and other coronaviruses on livestock farmsBackground: The SARS-CoV-2 pandemic markedly compromised national food security through explosive outbreaks among agriculture workers. Two years into the pandemic, sustained transmission of SARS-CoV-2 in humans, again threatens US livestock systems as the viruses are spilling over to new domestic animal and wildlife species. As of August 2022, human-adapted SARS-CoV-2 has infected at least 27 unique animals species in 39 countries. These spillbacks have occurred in at least 30 U.S. states with the greatest number (n=108) documented in Texas.3 Although evidence has been mixed, research findings suggest that some strains of SARS-CoV-2 may infect livestock including pigs and cattle. Adding to these threats, novel coronaviruses continue to circulate among livestock herds in Asia that may soon cause incursions in the United States. Even so, virtually no active surveillance for novel coronavirus is being conducted in US agriculture systems. Barriers include surveillance cost and the lack of broad diagnostics to detect novel coronavirus incursions on farms. In this proposal we will demonstrate that we can use a low-cost pan-species assay we developed and a similar commercial product as new biosecurity tools on livestock farms. We will also characterize novel coronaviruses we detect to understand how they may be spilling over to new species.Aim 1 - Over 5 years, we will conduct active, One-Health oriented, surveillance for SARS-CoV-2 and other coronaviruses on 16 livestock farms (pigs, cattle, poultry) in Texas using our pan-coronavirus assay. We will prospectively sample farm livestock, the farm environments, and a small cohort of animal workers for evidence of SARS-CoV-2 and other circulating coronaviruses. Each farm will be followed for 12 months. Upon enrollment and every four months, we will collect questionnaire data about the farm and animal workers, and these samples from each farm: 20 nasal/oral swabs from livestock (up to 75% with respiratory signs of illness), 10 nasopharyngeal (NP) swabs and 10 sera specimens (1 each from 10 animal workers), and 4 three-hour bioaerosol samples in areas where the duration and frequency of animal-human contact is the greatest. Between the four planned farm visits, farm employees will use postage-paid sample kits to collect and ship nasal/oral specimens from livestock with signs of respiratory illness. We will also ask workers who develop an influenza-like-illness to self-collect a deep nasal swab sample and mail it to our laboratory.Aim 2 -We will use next-generation sequencing to assemble the entire genome of the estimated 7 novel spillover viruses and phylogenetically compare their genomes with the genomes of similar viruses available in GenBank. We will study 3 of the most interesting 8 novel coronaviruses by developing clones of these viruses and further studying their pathogenicity using reverse genetics in cell line models. Per our working hypothesis, these phylogenetic studies of spillover viruses will yield important genetic markets for spillover events that are not limited to the genetic region coding for spike proteins.Aim 3 - Where we detect novel coronaviruses that have evidence of spilling over to animal workers, we will additionally develop a neutralization assay against the spillover viruses and conduct serological analyses of workers' serial sera. Our working hypothesis is that animal workers with the most animal-years of exposure to the animal species yielding the virus, will have the highest odds of elevated neutralization titer against that specific novel coronavirus.Aim 4 - Beginning in year 3 of the study, we will field-test a new, farm-deployable, RNA capture pan-species coronavirus diagnostic and compare results for 500 farm specimens with our pan-coronavirus assay. Our working hypothesis is that we will observe no statistically important differences in sensitivity or specificity between the two assays among all animal, human, and environmental samples.Spillback SARS-CoV-2 viruses, as well as novel emergent coronaviruses, may cause epizootics among their new animal hosts. Additionally, viruses may further change to threaten humans. Hence, this research is of great importance to US agriculture biosecurity, to international food security, in protecting the health of livestock and animal workers, as well in protecting the livestock industries' business models. Demonstrating that our pan-species coronavirus surveillance approach on these Texas farms is effective and of relatively low cost, could influence the adoption of this surveillance approach throughout the world.
Project Methods
Efforts:-A five year, prospective, One Health prospective research study of 16 Texas livestock farms (pigs, cattle, or poultry) for SARS-CoV-2 and other circulating coronaviruses using novel diagnostic tools.-Virological characterization of coronaviruses detected in the study-Field testing of a hand-held, commercial pan-coronavirus diagnostic device-Practical virology training to up to 40 minority undergraduate studentsEvaluation:-Research milestones for individual farm enrollment and follow-up, laboratory assessments are field diagnostic assessments are captured in the project timeline graphic -Overall, the scientific merit of the research will be judged by peer-reviewed scientific literature and via oral and poster presentations at scientific meetings.-Training will be assessed by the number of minority students who enroll and complete the training program.Detailed descriptions of the research methods are described in the proposal.

Progress 09/01/23 to 08/31/24

Outputs
Target Audience: Meat and dairy animal workers, veterinarians; students and researchers working on food security; Government agencies and academic virologists Changes/Problems:Initially, it was challenging to identify livestock farms willing to participate in this study. We have successfully enrolled dairy and beef cattle farms and now need to enroll swine and poultry farms. Having planned to conduct the study only in Texas but changing the study to include farms further away from our university has increased the study's cost which we are struggling to cover. What opportunities for training and professional development has the project provided?This last semester we trained four underprivileged undergraduate students from Galveston College in basic virology techniques. Three of these students and an additional new student will continue their laboratory training this fall. How have the results been disseminated to communities of interest?Scientific findings are being share via scientific journals and meetings. Journal reports: Shittu I, Silva D, Oguzie, JU, Marushchak LV, Olinger GG, Trujillo-Varga CM, Schneider N, Hao H, Gray GC. A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms medRxiv (preprint) https://medrxiv.org/cgi/content/short/2024.07.27.24310982v1 Clin Infect Dis resubmitted 11/3/24 This preprint journal article was covered by these two online reports: https://kffhealthnews.org/news/article/bird-flu-undetected-farmworkers-testing-contagious-mammals/ https://www.npr.org/sections/shots-health-news/2024/07/31/nx-s1-5059071/bird-flu-human-cases-farm-workers-testing These stories were repeated 87 news outlets including: Scientific America, Chicago Tribune, Medical News Today, KPBS, etc Abstracts: Hernandez G, Shittu I, Oguzie JU, Silva D, Moreno G, Marushchak LV, Trujillo-Vargas CM, Lednicky JA, Gray GC. Novel Rodent Coronavirus Detected in Beef Cattle, Mexico. Texas Branch ASM meeting, Nov 7-9 Galveston, TX. Poster presentation. Cummings DB, Groves JT, Hagan A, Oguzie JU, Marushchak LV, Nguyen-Tien, T, Shittu I, Trujillo-Vargas, CM, Rodriguez J, Gray GC A One-Health Approach in Surveilling for Emerging Respiratory Viruses on Cattle Farms in Kentucky and Indiana. Texas Branch ASM meeting, Nov 7-9 Galveston, TX. Poster presentation. News stories that mention our work or opinions: As Bird Flu Spreads, Additional Human Infection Is Reported in Missouri 10/24/24 by The New York Times Full Article: www.nytimes.com As Bird Flu Spreads, Two New Cases Diagnosed in California 10/04/24 by The New York Times Full Article: www.nytimes.com How U.S. Farms Could Start a Bird Flu Pandemic 08/21/24 by The New York Times Full Article: How U.S. Farms Could Start a Bird Flu Pandemic (pdf) Source: www.nytimes.com H5N1 avian flu found in Texas dairy cattle and milk, sparking concerns about underreported infections 08/04/24 by Medical.net Full Article: www.news-medical.net Bird flu on the rise among livestock workers 08/02/24 by UTMB Health Full Article: www.utmb.edu Cattle may become a permanent host for bird flu 05/13/24 by Earth.com Full Article: www.earth.com Safeguarding Against H5N1 Influenza Spillover: Protecting Human, Animal, and Environmental Health 05/10/24 by Infection Control Today Full Article: www.infectioncontroltoday.com How Poor Tracking of Bird Flu Leaves Dairy Workers at Risk 05/09/24 by The New York Times Full Article: www.nytimes.com Bird flu in US cows: where will it end? 05/09/24 by Nature.com Full Article: www.nature.com Human Bird Flu Cases May Be Going Unreported 05/05/24 by The Dallas Express Full Article: www.dallasexpress.com This Texas veterinarian helped crack the mystery of bird flu in cows 05/04/24 by CBS News Full Article: www.cbsnews.com The U.S. may be missing human cases of bird flu, scientists say 05/02/24 by NPR Full Article: www.npr.org This Texas veterinarian helped crack the mystery of bird flu in cows 05/01/24 by AP News Full Article:www.apnews.com What to Know About the Bird Flu Outbreak in Dairy Cows 04/09/24 by The New York Times Full Article: www.nytimes.com The U.S. government is taking action to stop 'cow flu.' Is it too little, too late? 04/25/24 by Science.org Full Article: www.science.org This Cow and Pig Influenza Virus Could Infect Humans: What We Know So Far 04/24/24 by Scientific American Full Article: www.scientificamerican.com Bird Flu & Dairy Cattle: Insights from Epidemiologist and Livestock Analyst 03/27/24 by Western Ag Network Full Interview: YouTube (video) Bird flu's outbreak in cattle spreads 03/25/24 by Science.org Full Article: www.science.org What do you plan to do during the next reporting period to accomplish the goals?We will continue to work with veterinarians from the US and Mexico to study currently enrolled and new farms. We will continue to work with GeneCapture in helping them develop their new diagnostics. We will continue to train undergraduate students from Galveston College in basic virological techniques.

Impacts
What was accomplished under these goals? Soon after we were notified that we had won this award, we sought and won UTMB IRB approval to conduct the study. UTMB's IACUC chair said the study did not require formal IACUC review as we were only collecting diagnostic samples from farm animals (no animal experimentation). With considerable effort, we next sought permission to conduct the study on multiple farms in Texas. Despite having many veterinary advocates for the study, we initially had difficulty enrolling Texas farms. Hence, we sought and won USDA permission and UTMB IRB permission to expand the study to farms in Mexico and the United States. Finding research colleagues in Mexico willing to recruit farms for the study, we next established a research collaboration with Faculty of Veterinary Medicine of Universidad Autonoma de Nuevo Leon (UANL) which is located near Monterrey, Mexico. After signing a research agreement and material transfer agreement with them, our collaborators identified a number of Mexican cattle farms which permitted us in February 2024 to collect swabs from sick and healthy beef cattle as well as to collect bioaerosol samples. In October, we have won Mexican IRB approval to enroll farm workers in the study. Thus far, none were positive for influenza A (FluA). However, 22/52 samples were positive for influenza D (FluD). 10/52 samples were positive for pan-coronavirus assay (pan-CoV). Four cattle nasal swab samples had evidence of bovine coronavirus. One bioaerosol sample and 5 cattle nasal swabs had evidence of a rodent coronavirus. The detection of this rodent coronavirus in sick beef cattle is quite novel. We are attempting to grow out and fully characterize the virus. An abstract for a poster presentation will be presented at the Texas Branch ASM meetings in Galveston in November and a manuscript is in development. After we studies farms in Mexico, veterinarians helped us engage two dairy farms in Texas, three beef cattle farms in Kentucky, and one beef cattle farm in Indianna. In April 2024, we employed the study in investigating a suspected outbreak of avian influenza in two dairy farms in Texas. Overall, we collected 81 samples including 39 cattle nasal swabs, 14 milk specimens,17 human nasopharyngeal swab samples; 8 farm bioaerosol samples; 1 fecal slurry waste sample and swab (oral and cloacal) specimens from a dead bird on one of the farms. We found only 1 (1.24%) out of the 81 samples positive for pan-CoV. This specimen from cattle nasal swab was positively confirmed for SARS-Cov-2. One (2.6%) of 39 nasal cattle swab specimens and 9 (64.2%) of 14 milk samples had molecular evidence of influenza A subtype H5. Six of these specimens were confirmed to be Highly Pathogenic Avian Influenza Virus (HPAIV H5N1). Similarly, the fecal slurry sample and oral and cloacal dead bird swab specimens also had evidence of as HPAIV by sequencing. Next, cell culture (MDCK and MDBK cell lines) and egg culture work were performed along with NGS to better characterize the viruses with 6 milk samples, dead bird's oral swab and 1 nasal swab from cattle which were positive for Inf A+ and H5+. The viruses were very similar to other HPAI H5N1 clade 2.3.4.4b isolated associated with a now nationwide epizootic of influenza A on US dairy farms. A manuscript titled "A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms"with these results is currently under journal review. In May 2024, we were privileged to enroll three cattle farms in Kentucky and one cattle farm in Indiana into the study. While these farm specimens (n=170) had no evidence of FluA in the cattle, human, or environmental samples, we did see considerable molecular evidence of FluD virus and bovine coronavirus (13/34 positive samples for pan-CoV). All samples were negative for influenza A, paramyxoviruses, and pneumoviruses. Influenza D genome was retrieved from one sample of Kentucky farm while bovine coronavirus genomes were retrieved from 3 samples of one farm in Indiana and two farms in Kentucky by NGS. In the last week of July, we visited the two Texas dairy farms for the second time. 95 samples were collected including milk (n=20); cattle nasal swab (n=40), human nasal swab (n=11); NIOSH bioaerosol (n=24). All samples were negative for FluA, FluD and pan-CoV. From 12-14 August, we again visited the three beef cattle farms in Kentucky and single beef cattle farm in Indiana.In total, we collected 145 samples including cattle nasal swabs, human nasal swabs, bioaerosol samples, wastewater samples, samples from a dead bird and a dead cow. All specimens were negative for FluA, 10 cattle nasal swabs were positive for FluD and 20 cattle nasal swabs were positive for pan-CoV. Sanger sequencing confirmed 15 out of 20 pan-CoV positive samples as bovine coronavirus. We are running workers sera with microneutralization against both recombinant H5N1 and FluD and continuing to characterize the viral detections with culture and NGS. Additionally, our team has shared RNA from numerous viruses with GeneCapture for their diagnostic development work to apply in the year 3 of this research project.

Publications

  • Type: Other Status: Published Year Published: 2024 Citation: UTMB One Health Newsletter project announcement in https://www.utmb.edu/one-health/research/projects/rapid-detection-of-incursions-SARS-CoV2-novel-corona-viruses and https://mailchi.mp/utmb/utmb-oh-newsletter-october-issue-13896822
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: Mitigating Future Pandemics: New Threats and Strategies to Consider Walter Reed Army Institute of Research One Health Webinar Sept 12th
  • Type: Other Journal Articles Status: Published Year Published: 2024 Citation: Shittu I, Silva D, Oguzie, JU, Marushchak LV, Olinger GG, Trujillo-Varga CM, Schneider N, Hao H, Gray GC. A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms medRxiv (preprint) https://medrxiv.org/cgi/content/short/2024.07.27.24310982v1 Under review at Clinical Infectious Diseases
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: One Health Research at UTMB. Food and Drug Administration One Health Webinar Sept 12th
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: Why One Health Action Is Critically Important to Our Future One Health Day Seminar, Texas Tech University, Amarillo, Texas, Nov 3rd
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: What is One Health and Why is it Important? Keynote virtual lecture, One Health Day, Duke Kunshan University, Kunshan, China, November 3rd.
  • Type: Other Status: Other Year Published: 2024 Citation: Interwoven Threads of Avian Influenza and One Health with Dr. Greg Gray Infectious Science Podcast November 15th
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: The One Health Approach to Mitigating Respiratory Virus Epidemics is Critically Important to Our Future Lecture to UTMBs Academy of Research Mentors (ARM) group, December 6
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: Mitigating Future Pandemics: New Threats and Strategies to Consider Virtual Grand Rounds, Texas Epidemic Public Health Institute, January 10
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: Using a One Health Approach to Search for the Next Pandemic Virus Lecture to students and faculy, Universidad Autonoma de Nuevo Leon Facultad de Medicina Veterinaria Y Zootecnia, Monterrey, Mexico, February 14th
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: Bird Flu & Dairy Cattle: Insights from Epidemiologist and Livestock Analyst Western Ag Network Radio (video and podcast) March 28 https://www.youtube.com/watch?v=1QLvSPLJhgg
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: A Practical One Health Strategy to Detect Pre-Pandemic Zoonotic Respiratory Virus Threats UTMB Conference Tropical and Emerging Infectious Diseases for Clinicians and Translational Scientists, Galveston, TX, April 9th
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: Mongolia GEOHealth Center Needs GEOHealth Center Meetings, Ulaanbaatar, Mongolia, July 2nd, 2024
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: A Practical One Health Strategy to Detect Pre-Pandemic Zoonotic Respiratory Virus Threats Division of Microbiology Seminar Series, U.S. Food and Drug Administration, Zoom lecture, July 10, 2024
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: OH Research Needs and Solutions North American One Health Network meetings, Ft. Collins, CO, Aug 8
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: Recent Emergence & Spread of Novel Avian Influenza H5N1 Strains Online SPECTRE HHS Region 6 meeting, Aug 22nd