Research Alliance for Veterinary Science and Biodefense BSL-3 Network (RAV3N): Report on network origin and phase I activities

Recent disease events have heightened awareness for the need for collaboration between the nation's public health and veterinary infectious disease communities to improve preparedness for current and future biological threats. To address this need, the U.S. Department of Agriculture's National Bio- and Agro-Defense Facility (USDA NBAF) has partnered with Texas A&M University through its Global Health Research Complex (TAMGHRC) to establish the Research Alliance for Veterinary Science and Biodefense BSL-3 Network (RAV3N). As a collaborative network of U.S. university and federal BSL-3Ag/BSL-3/BSL-4 laboratory research facilities, the objective of RAV3N is to establish strategic and coordinated approaches for harnessing collective large-animal biocontainment infrastructure and research capacity to improve bio-surveillance, diagnostics, and countermeasure development against high-consequence pathogens of veterinary and zoonotic importance. Here, we describe the origin and development of RAV3N, detail phase I activities, and summarize the proceedings of its first membership meeting held in August 2022.

Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants

To better understand the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant lineage distribution in a college campus population, we carried out viral genome surveillance over a 7-week period from January to March 2021. Among the sequences were three novel viral variants: BV-1 with a B.1.1.7/20I genetic background and an additional spike mutation Q493R, associated with a mild but longer-than-usual COVID-19 case in a college-age person, BV-2 with a T478K mutation on a 20B genetic background, and BV-3, an apparent recombinant lineage. This work highlights the potential of an undervaccinated younger population as a reservoir for the spread and generation of novel variants. This also demonstrates the value of whole genome sequencing as a routine disease surveillance tool.

A network approach for provisional assay recognition of a Hendra virus antibody ELISA: test validation with low sample numbers from infected horses

Obtaining statistically sound numbers of sera from Hendra virus (HeV)-infected horses is problematic because affected individuals usually die or are euthanized before developing a serum antibody response. As a consequence, test validation becomes a challenge. Our approach is an extension of OIE principles for provisional recognition and included 7 validation panels tested across multiple laboratories that provided estimates for test performance characteristics. At a 0.4 S/P cutoff, 16 of 19 sera from HeV-infected horses gave positive results in the HeV soluble G, indirect ELISA (HeVsG iELISA; DSe 84.2% [95% CI: 60.4-96.6%]); 463 of 477 non-infected horse sera tested negative (DSp 97.1% [95% CI: 95.1-98.4%]). The HeVsG iELISA eliminated almost all false-positive results from the previously used HeV iELISA, with marginally decreased relative sensitivity. Assay robustness was evaluated in inter-laboratory and proficiency testing panels. The HeVsG iELISA is considered to be fit for purpose for serosurveillance and international movement of horses when virus neutralization is used for follow-up testing of positive or inconclusive serum samples.

Dual-role FilmArray® diagnostics for high-impact viral diseases

In this study, we explored the potential utility of the human-focused FilmArray® Respiratory Panel for the diagnosis of a broad range of influenza viruses of veterinary concern as compared with the standard portfolio of recommended TaqMan®-based diagnostic tests. In addition, we discuss some potential operational advantages associated with the use of such integrated sample extraction, amplification and analysis devices in the context of a future long-term, dual-role strategy for the detection of emergency diseases of both human and veterinary concern.

Construction of a marsupial bacterial artificial chromosome library from the model Australian marsupial, the tammar wallaby (Macropus eugenii)

With the accelerating recognition of the power of comparative genomics, there is now enormous interest in sequencing the genomes of a broad range of species. Marsupials diverged at an important evolutionary time. The model Australian marsupial, the tammar wallaby (Macropus eugenii), has long been a resource for biological and genetic studies of marsupials, and the availability of a bacterial artificial chromosome (BAC) library will be a valuable resource in these studies. A tammar wallaby BAC library was constructed using pRazorBAC vector. It contains 55 296 clones with an average insert size of 108 kb, representing 2.2 times coverage of the wallaby genome (based on an estimated 2.7 × 109 bp haploid genome size). The library was arrayed in 384-well plates, and spotted in duplicate onto nylon membranes. Screening these membranes has yielded clones containing 34 single-copy genes distributed over the genome, while it failed for only one gene. Each probe isolated 1–12 BAC clones and, to date, no chimeric clones have been found. This BAC library will constitute an invaluable resource for creating physical maps, positional cloning of genes and other sequences in the tammar wallaby, as well as comparative mapping studies in mammals.

213 SAGE ANALYSIS OF TRANSITIONS IN THE PORCINE CONCEPTUS TRANSCRIPTOME DURING TROPHECTODERM ELONGATION

Rapid elongation of the pre-implantation conceptus trophectoderm between gestational days 11 and 12 represents a critical developmental period in swine. Serial analysis of gene expression (SAGE) in ovoid (Ovd; 7 mm diameter) and filamentous (Fil; 150 mm length) conceptuses has identified unique transcriptomes associated with these transitional states. The initial utility of SAGE prompted an investigation of the intermediate tubular conceptus (Tub; 15–20 mm length) as well as the development of micro-SAGE methodologies, small-amplified RNA-SAGE (SAR-SAGE) and PCR-amplified SAGE (m-SAGE), for future use with early pre-implantation conceptus stages. Total RNA from in vivo-derived Tub conceptuses was used to construct an unamplified SAGE library (Tub SAGE) and two micro-SAGE libraries (160X less template RNA) by SAR-SAGE and m-SAGE. Comparative analyses of the amplification proportionality between the Tub SAGE and amplified libraries, consisting of 12,000 tags each, demonstrated that SAR-SAGE was a more reliable amplification method. Seventy-five percent of the SAR-SAGE tags, in contrast to 43% of m-SAGE tags, had less than a 2-fold frequency difference when compared to Tub SAGE tags occurring at least 10 times in a library. The Tub SAGE library size was extended to a total of 42,415 tags representing 12,779 unique putative transcripts. Comparing the Tub SAGE tags with previously generated Ovd and Fil SAGE libraries (NCBI GEO Acc. Nos. GSM24470 and GSM24471, respectively) yielded a total of 33,191 unique tags, of which 3,575 tags (10.8%) were common to all three libraries. Chi-square-based analyses (SAGE2000 software; 1997 Gen. Res. 7, 986–995) of the tag frequencies revealed the differential expression of 479 tags between Ovd:Tub libraries and 362 tags between Tub:Fil libraries at a P < 0.05 significance. The Tub SAGE tags were annotated following batch BLASTS against the TIGR porcine index database and then classified according to function. Real-time RT-PCR was used to confirm the differential expression patterns identified between Ovd:Tub, Ovd:Fil, and Fil:Tub. For example, the relative quantity of mRNA for steroidogenic acute regulatory protein, 1.0:6.4:11.1 (Ovd:Tub:Fil), and cytokeratin 8, 1.1:0.6:0.4 (Ovd:Tub:Fil), demonstrated an increase and decrease (ANOVA; P < 0.05), respectively, throughout these three developmental stages. Based on their putative functional annotations, the differentially expressed genes revealed by SAGE are potentially involved in regulating embryo growth, cellular differentiation, apoptosis, steroidogenesis, and energy metabolism during embryo elongation. The present SAGE analyses have elucidated the tubular conceptus transcriptome and enabled the identification of genes that are differentially regulated during the 24-h period that encompasses pig embryo elongation. Furthermore, the decreased template requirement of SAR-SAGE makes this technique a suitable option for SAGE analyses of early stage embryos where the sample is small and limited.