Randomly primed, strand-switching, MinION-based sequencing for the detection and characterization of cultured RNA viruses.

RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.

Ranging patterns, spatial overlap, and association with dolphin morbillivirus exposure in common bottlenose dolphins (Tursiops truncatus) along the Georgia, USA coast.

During 2013-2015, an outbreak of dolphin morbillivirus (DMV) occurred in the western North Atlantic, which resulted in the stranding of over 1,600 common bottlenose dolphins (Tursiops truncatus). There are currently five coastal and 10 bay, sound, and estuary dolphin stocks along the U.S. Atlantic coast, yet there is very limited understanding of which stocks were exposed to DMV during the recent outbreak, or how DMV was transmitted across stocks. In order to address these questions, information is needed on spatial overlap and stock interactions. The goals of this project were to determine ranging patterns, prevalence of DMV, and spatial overlap of the South Carolina-Georgia (SC-GA) Coastal Stock, and adjacent Southern Georgia Estuarine System (SGES) Stock. During September 2015, a health assessment and telemetry study was conducted in which 19 dolphins were captured, tested for antibodies to DMV, and satellite tagged. Dolphins were classified into one of three ranging patterns (Coastal, Sound, or Estuary) based upon telemetry data. Coastal dolphins (likely members of the SC-GA Coastal Stock) had a significantly higher prevalence of positive DMV antibody titers (0.67; N = 2/3), than Sound and Estuary dolphins (likely members of the SGES Stock) (0.13; N = 2/16). These results suggest that the SC-GA Coastal Stock may have experienced greater exposure to DMV as compared to the SGES Stock. However, due to the small size of the SGES Stock and its exposure to high levels of persistent contaminants, this stock may be particularly vulnerable to DMV infection in the future.

Infectious disease and the decline of Steller sea lions (Eumetopias jubatus) in Alaska, USA: insights from serologic data.

Serologic data were examined to determine whether infectious disease may have played a role in the decline of Steller sea lions (Eumetopias jubatus) in the Gulf of Alaska and Aleutian Islands, USA. Available published data, unpublished data, and recent collections (1997-2000) were compared and reviewed. Data were stratified by geography to compare the declining western Alaskan population in the Aleutian Islands through eastern Prince William Sound to the increasing population in southeastern Alaska. Prevalences of antibodies from the 1970s to the early 1990s were noted for Leptospira interrogans, Chlamydophila psittaci, Brucella spp., phocid herpesvirus-1, and calciviruses. Serum samples collected from 1997-2000 were tested for antibodies to these agents as well as to marine mammal morbilliviruses, canine parvovirus, and canine adenovirus-1 and -2. Conclusions could not be drawn about changes in antibody prevalence to these agents during the decline of Steller sea lions, however, because data were incomplete or not comparable as a result of inconsistencies in testing techniques. Despite these shortcomings, results provided no convincing evidence of significant exposure of Steller sea lions to morbilliviruses, Brucella spp., canine parvovirus, or L. interrogans. Steller sea lions have been exposed to phocid herpesviruses, caliciviruses, canine adenovirus, and C. psittaci or to cross-reactive organisms in regions of both increasing and decreasing sea lion abundance. Based on similar antibody prevalence estimates from the increasing and decreasing populations, these agents are unlikely to have been the primary cause of the population decline. They may have contributed to the decline or impeded population recovery, however, because of undetected mortality and morbidity or reductions of fecundity and body condition in animals under other stresses. Systematic monitoring for disease agents and their effects is needed to determine whether infectious disease currently plays a role in the decline and lack of recovery of Steller sea lions.

Use of a polymerase chain reaction assay to detect bovine herpesvirus type 2 DNA in skin lesions from cattle suspected to have pseudo-lumpy skin disease.

Beef cattle from a herd in north Alabama were examined because of an outbreak of nonfatal skin disease characterized by discrete circumscribed areas of inflammation that developed on the skin from the neck to the hips. Areas of inflammation, which tended to be superficial, underwent necrosis and scabbed over. The scabs eventually dropped off leaving discrete, round, whitish, hairless lesions that were 1.2 to 2.5 cm diameter. Because clinical signs were consistent with those expected with pseudo-lumpy skin disease (PLSD) caused by bovine herpesvirus type 2 (BHV-2), samples from 16 representative animals were submitted for BHV-2 testing. All 16 animals were seropositive for BHV-2, but the virus could not be isolated from skin biopsy specimens or buffy coat samples. Results of a polymerase chain reaction assay incorporating primers designed to amplify 2 DNA sequences from BHV-2 were positive for 3 of the 10 cattle, suggesting that skin lesions in these cattle were a result of PLSD. Our findings suggest that PLSD may be more common and widespread in the United States than suggested by the frequency with which BHV-2 has been isolated from cattle with PLSD-like skin lesions.