Use of Sequencing Technologies to Improve Swine Infectious Disease Management

University of Minnesota Ph.D. dissertation. 2020. Major: Veterinary Medicine. Advisors: Cheryl Dvorak, Mark Rutherford. 1 computer file (PDF); 156 pages.The swine industry is an indispensable part of the food production and agricultural system. However, infectious disease poses great threats to the industry. The current situation is that “old” infectious diseases are not totally under control and “new” pathogens keep emerging. In addition, via food chain and direct or indirect contact, some swine pathogens can infect humans and antimicrobial resistance arising from swine pathogens can also adversely impact public health. The threat of infectious disease to the swine population has been further magnified by globalization which increases the rate and breadth of disease transmission, thus having a more devastating impact. Fortunately, scientific advances have greatly bolstered our ability to develop effective disease control strategies. Sequencing technology has emerged as a powerful solution to deal with the challenging infectious disease situations we are facing today. The advantages of sequencing as a diagnostic tool are numerous. From our research, we confirmed that sequencing has improved the disease diagnostic resolution to the strain level, providing more precise and effective control strategies; it is able to generate additional genomic information for functional prediction of infectious agents, such as antimicrobial resistance profiling; and sequencing can facilitate a prompt response against emerging eventualities due to its ability to rapidly detect pathogens in a sample, including the novel or unexpected ones. Going forward, the more frequent use of sequencing in swine medicine can enhance our ability to predict and control the emergence and transmission of infectious disease within swine populations

Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools

Prompt detection and effective control of porcine reproductive and respiratory syndrome virus (PRRSV) during outbreaks is important given its immense adverse impact on the swine industry. However, the diagnostic process can be challenging due to the high genetic diversity and high mutation rate of PRRSV. A diagnostic method that can provide more detailed genetic information about pathogens is urgently needed. In this study, we evaluated the ability of Oxford Nanopore MinION direct RNA sequencing to generate a PRRSV whole genome sequence and detect and discriminate virus at the strain-level. A nearly full length PRRSV genome was successfully generated from raw sequence reads, achieving an accuracy of 96% after consensus genome generation. Direct RNA sequencing reliably detected the PRRSV strain present with an accuracy of 99.9% using as few as 5 raw sequencing reads and successfully differentiated multiple co-infecting strains present in a sample. In addition, PRRSV strain information was obtained from clinical samples containing 104 to 106 viral copies or more within 6 hours of sequencing. Overall, direct viral RNA sequencing followed by bioinformatic analysis proves to be a promising approach for identification of the viral strain or strains involved in clinical infections, allowing for more precise prevention and control strategies during PRRSV outbreaks

Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model

Emerging viral infectious diseases present a major threat to the global swine industry. Since 2015, Senecavirus A (SVA) has been identified as a cause of vesicular disease in different countries and is considered an emerging disease. Despite the growing concern about SVA, there is a lack of preventive and diagnostic strategies, which is also a problem for all emerging infectious diseases. Using SVA as a model, we demonstrated that Oxford Nanopore MinION sequencing could be used as a robust tool for the investigation and surveillance of emerging viral diseases. Our results identified that MinION sequencing allowed for rapid, unbiased pathogen detection at the species and strain level for clinical cases. SVA whole genome sequences were generated using both direct RNA sequencing and PCR-cDNA sequencing methods, with an optimized consensus accuracy of 94% and 99%, respectively. The advantages of direct RNA sequencing lie in its shorter turnaround time, higher analytical sensitivity and its quantitative relationship between input RNA and output sequencing reads, while PCR-cDNA sequencing excelled at creating highly accurate sequences. This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases

Electrically Tuning Interfacial Ion Redistribution for mica/WSe2 Memory Transistor

Abstract Memory device is an important part of electronic equipment. 2D transition metal dichalcogenides that exhibit novel electrical characteristics hold promise in developing new types of memory device. Here, the memory effect in 2D mica/WSe2 heterostructure is investigated. Under applying constant bias voltage and gate voltage, the K+ ions in mica will migrate in the direction of the electric field and be trapped to enable the memory function. The gradient K+ ions work as long‐range scatters to electrostatically dope the WSe2 channel. The shift of the threshold voltage indicates an electrostatic doping concentration up to 2.11 × 1012 cm−2. The operating voltage is as low as 10 V and the on/off ratio is estimated to be 104. To determine the mechanism, the dynamic behavior of the device is discussed and a model is proposed which reveals the correlation between the programming/erasing process and the device performance. Moreover, through defining and studying the effective charge trapping rate, θ, it is found that the trapped charge is proportional to the charge flowing through the channel which means that the device performance can be finely tuned by the programming process

Human Astroviruses: A Tale of Two Strains.

Since the 1970s, eight closely related serotypes of classical human astroviruses (HAstV) have been associated with gastrointestinal illness worldwide. In the late 2000s, three genetically unique human astrovirus clades, VA1-VA3, VA2-VA4, and MLB, were described. While the exact disease associated with these clades remains to be defined, VA1 has been associated with central nervous system infections. The discovery that VA1 could be grown in cell culture, supports exciting new studies aimed at understanding viral pathogenesis. Given the association of VA1 with often lethal CNS infections, we tested its susceptibility to the antimicrobial drug, nitazoxanide (NTZ), which we showed could inhibit classical HAstV infections. Our studies demonstrate that NTZ inhibited VA1 replication in Caco2 cells even when added at 12 h post-infection, which is later than in HAstV-1 infection. These data led us to further probe VA1 replication kinetics and cellular responses to infection in Caco-2 cells in comparison to the well-studied HAstV-1 strain. Overall, our studies highlight that VA1 replicates more slowly than HAstV-1 and elicits significantly different cellular responses, including the inability to disrupt cellular junctions and barrier permeability

Human Astroviruses: A Tale of Two Strains

Since the 1970s, eight closely related serotypes of classical human astroviruses (HAstV) have been associated with gastrointestinal illness worldwide. In the late 2000s, three genetically unique human astrovirus clades, VA1-VA3, VA2-VA4, and MLB, were described. While the exact disease associated with these clades remains to be defined, VA1 has been associated with central nervous system infections. The discovery that VA1 could be grown in cell culture, supports exciting new studies aimed at understanding viral pathogenesis. Given the association of VA1 with often lethal CNS infections, we tested its susceptibility to the antimicrobial drug, nitazoxanide (NTZ), which we showed could inhibit classical HAstV infections. Our studies demonstrate that NTZ inhibited VA1 replication in Caco2 cells even when added at 12 h post-infection, which is later than in HAstV-1 infection. These data led us to further probe VA1 replication kinetics and cellular responses to infection in Caco-2 cells in comparison to the well-studied HAstV-1 strain. Overall, our studies highlight that VA1 replicates more slowly than HAstV-1 and elicits significantly different cellular responses, including the inability to disrupt cellular junctions and barrier permeability

Strong Anisotropic Two-Dimensional In₂Se₃ for Light Intensity and Polarization Dual-Mode High-Performance Detection

Detecting the light from different freedom is of great significance to gain more information. Two-dimensional (2D) materials with low intrinsic carrier concentration and highly tunable electronic structure have been considered as the promising candidate for future room-temperature multi-functional photodetectors. However, current investigations mainly focus on intensity-sensitive detection; the multi-dimensional photodetection such as polarization-sensitive photodetection is still in its early stage. Herein, the intensity- and polarization-sensitive photodetection based on α-In2Se3 is studied. By using angle-resolved polarized Raman spectroscopy, it is demonstrated that α-In2Se3 shows an anisotropic phonon vibration property indicating its asymmetric structure. The α-In2Se3-based photodetector has a photoelectric performance with a responsivity of 1936 A/W and a specific detectivity of 2.1 × 1013 Jones under 0.2 mW/cm2 power density at 400 nm. Moreover, by studying the polarized angle-resolved photoelectrical effect, it is found that the ratio of maximum and minimum photocurrent (dichroic ratio) reaches 1.47 at 650 nm suggesting good polarization-sensitive detection. After post-annealing, α-In2Se3 in situ converts to β-In2Se3 which has similar in-plane anisotropic crystallinity and exhibits a dichroic ratio of 1.41. It is found that the responsivity of β-In2Se3 is 6 A/W, much lower than that of α-In2Se3. The high-performance light intensity- and polarization-detection of α-In2Se3 enlarges the 2D anisotropic materials family and provides new opportunities for future dual-mode photodetection

Novel Low Pathogenic Avian Influenza H6N1 in Backyard Chicken in Easter Island (Rapa Nui), Chilean Polynesia

Little is known about the prevalence of avian influenza viruses (AIV) in wildlife and domestic animals in Polynesia. Here, we present the results of active AIV surveillance performed during two sampling seasons in 2019 on Easter Island (Rapa Nui). Tracheal and cloacal swabs as well as sera samples were obtained from domestic backyard poultry, while fresh faeces were collected from wild birds. In addition to detecting antibodies against AIV in 46% of the domestic chickens in backyard production systems tested, we isolated a novel low pathogenic H6N1 virus from a chicken. Phylogenetic analysis of all genetic segments revealed that the virus was closely related to AIV’s circulating in South America. Our analysis showed different geographical origins of the genetic segments, with the PA, HA, NA, NP, and MP gene segments coming from central Chile and the PB2, PB1, and NS being closely related to viruses isolated in Argentina. While the route of introduction can only be speculated, our analysis shows the persistence and independent evolution of this strain in the island since its putative introduction between 2015 and 2016. The results of this research are the first evidence of AIV circulation in domestic birds on a Polynesian island and increase our understanding of AIV ecology in region, warranting further surveillance on Rapa Nui and beyond

Novel Low Pathogenic Avian Influenza H6N1 in Backyard Chicken in Easter Island (Rapa Nui), Chilean Polynesia

Little is known about the prevalence of avian influenza viruses (AIV) in wildlife and domestic animals in Polynesia. Here, we present the results of active AIV surveillance performed during two sampling seasons in 2019 on Easter Island (Rapa Nui). Tracheal and cloacal swabs as well as sera samples were obtained from domestic backyard poultry, while fresh faeces were collected from wild birds. In addition to detecting antibodies against AIV in 46% of the domestic chickens in backyard production systems tested, we isolated a novel low pathogenic H6N1 virus from a chicken. Phylogenetic analysis of all genetic segments revealed that the virus was closely related to AIV’s circulating in South America. Our analysis showed different geographical origins of the genetic segments, with the PA, HA, NA, NP, and MP gene segments coming from central Chile and the PB2, PB1, and NS being closely related to viruses isolated in Argentina. While the route of introduction can only be speculated, our analysis shows the persistence and independent evolution of this strain in the island since its putative introduction between 2015 and 2016. The results of this research are the first evidence of AIV circulation in domestic birds on a Polynesian island and increase our understanding of AIV ecology in region, warranting further surveillance on Rapa Nui and beyond