Molecular Epidemiology of Seal Parvovirus, 1988–2014

A novel parvovirus was discovered recently in the brain of a harbor seal (Phoca vitulina) with chronic meningo-encephalitis. Phylogenetic analysis of this virus indicated that it belongs to the genus Erythroparvovirus, to which also human parvovirus B19 belongs. In the present study, the prevalence, genetic diversity and clinical relevance of seal parvovirus (SePV) infections was evaluated in both harbor and grey seals (Halichoerus grypus) that lived in Northwestern European coastal waters from 1988 to 2014. To this end, serum and tissue samples collected from seals were tested for the presence of seal parvovirus DNA by real-time PCR and the sequences of the partial NS gene and the complete VP2 gene of positive samples were determined. Seal parvovirus DNA was detected in nine (8%) of the spleen tissues tested and in one (0.5%) of the serum samples tested, including samples collected from seals that died in 1988. Sequence analysis of the partial NS and complete VP2 genes of nine SePV revealed multiple sites with nucleotide substitutions but only one amino acid change in the VP2 gene. Estimated nucleotide substitution rates per year were 2.00×10⁻⁴ for the partial NS gene and 1.15×10⁻⁴ for the complete VP2 gene. Most samples containing SePV DNA were co-infected with phocine herpesvirus 1 or PDV, so no conclusions could be drawn about the clinical impact of SePV infection alone. The present study is one of the few in which the mutation rates of parvoviruses were evaluated over a period of more than 20 years, especially in a wildlife population, providing additional insights into the genetic diversity of parvoviruses.     

Simian parvovirus

Parvovirus B19 is currently the only member of theErythrovirusgenus. Recently a second parvovirus, simian parvovirus, was identified in cynomolgus monkeys which also appeared to be highly tropic for erythroid progenitor cells. This review describes the identification of this new arrival parvovirus and summarizes current knowledge of its clinical, molecular and epidemiological features. The virus has many biological similarities to the parvovirus B19 and close homology to the B19 genome at the molecular level, both of which justify the inclusion of this novel virus as a new member of theErythrovirusgenus.     

Postrelease movement of rehabilitated harbor seal (Phoca vitulina richardii) pups compared with cohort‐matched wild seal pups

Harbor seal (Phoca vitulina richardii) populations in the inland waters of Washington and British Columbia are at or near carrying capacity. Stranded pups often are collected and admitted to rehabilitation centers, and then released when they reach a weight of 22 kg and meet a variety of preestablished health and release conditions. While rehabilitation is common practice, it is unclear if rehabilitated seal pups behave like wild weaned pups. Using satellite transmitters, we compared movement patterns of 10 rehabilitated pups with 10 wild weaned pups. When released, rehabilitated seals were longer and heavier than wild pups, while wild pups had a larger mean axillary girth. No clinically different blood parameters were detected. On average, rehabilitated harbor seal pups traveled nearly twice as far cumulatively, almost three times as far daily, and dispersed over three times as far from the release site compared to wild weaned seals. Additionally, wild harbor seals transmitted nearly twice as long as did rehabilitated seals. These patterns suggest that learned behavior during the brief 3–4 wk nursing period likely enables wild harbor seal pups to move less daily and remain closer to their weaning site than rehabilitated pups.     

Interannual differences in postrelease movements of rehabilitated harbor seal pups (Phoca vitulina richardii) in the Salish Sea

Despite the large number of harbor seals (Phoca vitulina richardii) rehabilitated worldwide, few studies have been conducted on postrelease movement and behavior of rehabilitated harbor seal pups. We compared interannual differences in movements and survival of 24 rehabilitated seal pups released in the Salish Sea in 2010 (n = 10), 2012 (n = 5), 2013 (n = 5), and 2014 (n = 4). We also compared the postrelease movement of these seals to the movement of 10 wild seal pups tracked in the same ecosystem in 2010. Transmission duration, total cumulative distance, and average daily distance varied annually. Maximum linear distance traveled from the release site was similar for the rehabilitated seal groups. Compared to wild seals (n = 10), and consistent with prior studies, rehabilitated pups (n = 24) traveled significantly farther daily and cumulatively than wild weaned pups. Unlike in a prior study in this ecosystem, we found no significant difference between transmission duration in wild and rehabilitated pups.     

Postrelease dive ability in rehabilitated harbor seals

The efficacy of seal rehabilitation is examined in a postrelease study of dive ability in harbor seal pups (Phoca vitulina) in the Wash, United Kingdom. Six rehabilitated seals were fitted with Sea Mammal Research Unit (SMRU) Argos Satellite Relay Data Logger tags and their individual dive behavior was monitored for an average of 122 d. The upper 90 percentile edge of dive behavior (dive duration [DD₉₀] and percentage of time at‐sea spent in a dive [PD₉₀]), in 7 d bins, was used as a proxy for physiological dive ability. The results are compared with data from five wild adult harbor seals. There was no statistically significant difference between (1) the mean track duration of rehabilitated seals (126.20 ± 27.48 [SD] d) and adult seals (150.2 ± 24.62 d) (P= 0.108), indicating no evidence that short‐term survival was less in the rehabilitated group; (2) the mean mass‐scaled DD₉₀ of rehabilitated seals (3.95 ± 0.37 min) and adult seals (4.09 ± 0.55 min) (P= 0.632); and (3) the mean PD₉₀ of rehabilitated seals (81.62 ± 1.21%) and adult seals (81.48 ± 3.93%) (P= 0.943). These three results all suggest the success of the rehabilitation program in terms of short‐term survival and dive ability.     

Seroprevalence of Antibodies against Seal Influenza A(H10N7) Virus in Harbor Seals and Gray Seals from the Netherlands

In the spring and summer 2014, an outbreak of seal influenza A(H10N7) virus infection occurred among harbor seals (Phoca vitulina) off the coasts of Sweden and Denmark. This virus subsequently spread to harbor seals off the coasts of Germany and the Netherlands. While thousands of seals were reported dead in Sweden, Denmark and Germany, only a limited number of seals were found dead in the Netherlands. To determine the extent of exposure of seals in the Netherlands to influenza A/H10N7 virus, we measured specific antibody titers in serum samples from live-captured seals and seals admitted for rehabilitation in the Netherlands by use of a hemagglutination inhibition assay and an ELISA. In harbor seals in 2015, antibodies against seal influenza A(H10N7) virus were detected in 41% (32 out of 78) pups, 10% (5 out of 52) weaners, and 58% (7 out of 12) subadults or adults. In gray seals (Halichoerus grypus) in 2015, specific antibodies were not found in the pups (n = 26), but in 26% (5 out of 19) of the older animals. These findings indicate that, despite apparent low mortality, infection with seal influenza A(H10N7) virus was geographically widespread and also occurred in grey seals.     

ADRENAL FUNCTION IN WILD AND REHABILITATED PACIFIC HARBOR SEALS (PHOCA VITULINA RICHARDII) AND IN SEALS WITH PHOCINE HERPESVIRUS-ASSOCIATED ADRENAL NECROSIS

Adrenal function in harbor seals (Phoca vitulina richardii) was evaluated using adrenocorticotrophic hormone (ACTH) stimulation tests and fecal cortisol levels. The effect of ACTH administration on plasma cortisol and aldosterone levels in five free-living and 14 rehabilitated harbor seal pups was determined using enzyme immunoassay and radioimmunoassay, respectively. In free-living seals, injection of ACTH caused a significant increase in mean plasma cortisol but not of mean aldosterone levels 60 min postinjection. In these seals, mean initial plasma aldosterone was significantly higher than initial levels in rehabilitated seals, while initial cortisol levels were similar. Of the rehabilitated seals, eight died with adrenal cortical necrosis associated with herpesvirus inclusions, while six lived to be released. In the seals that were released, both mean initial cortisol levels and response to ACTH decreased through rehabilitation. In the seals that died, mean initial cortisol and response to ACTH increased through rehabilitation. The differences between initial cortisol levels in seals that lived and those that died were significant at weeks two and four of rehabilitation but not at the week of admission. There was considerable individual variation in initial plasma aldosterone levels and responses to ACTH, although initial aldosterone levels were significantly higher in rehabilitated seals that died than in seals that lived. Seals with adrenal necrosis associated with herpesvirus infection did not have decreased adrenal hormone responses to ACTH. Differences between initial hormone levels and responses to ACTH in different groups of seals may be associated with differing stress levels. Fecal cortisol assays were not a useful method of assessing adrenal function in these seals, as measured levels did not correlate with plasma cortisol levels.     

Phocanema decipiens: Pathology in seals

Infective larvae of the anisakine nematode, Phocanema decipiens from cod (Gadus morhua), were fed to harbor seals (Phoca vitulina) and gray seals (Halichoerus grypus). At termination of the experimental infections, 6 of 8 harbor seals were infected with 34(6–64) P. decipiens, while the remaining 2 seals had relatively heavy infections of 250 and 547 nematodes, respectively; 10 of 11 gray seals were infected with 128 (68–229) P. decipiens, but only 2 nematodes were recovered from the 11th seal. Larvae and adults of P. decipiens occurred throughout the gastrointestinal tract, but mainly in the fundic portion of the stomach; the anterior extremities of the nematodes were embedded in mucosa and submucosa. Clusters of adult P. decipiens were associated with ulcerous gastric lesions in harbor seals and raised inflammatory areas in stomachs of gray seals. Singly occurring larvae from challenge transmissions were associated with raised inflammatory areas in the stomachs of both host species. Histological examinations revealed that the lesions and inflammatory areas were eosinophilic granulomata. Anisakis sp. larvae from the viscera of cod were also fed to 1 of the gray seals. Eighty of these larvae were subsequently found in association with a general inflammation in the cardiac area of the stomach in this seal. Natural anisakine infection were surveyed in 16 harbor and 53 gray seals from the Nova Scotia mainland. The natural incidence of P. decipiens was 62(5–177) in harbor seals and 577(11–1694) in gray seals. Clusters of adult P. decipiens were found in association with gastric lesions in 2 juvenile harbor seals; however, in gray seals, the nematodes neither occurred in clusters nor in association with gastric lesions.     

Metagenomic Survey of Viral Diversity Obtained from Feces of Subantarctic and South American Fur Seals

The Brazilian South coast seasonally hosts numerous marine species, observed particularly during winter months. Some animals, including fur seals, are found dead or debilitated along the shore and may harbor potential pathogens within their microbiota. In the present study, a metagenomic approach was performed to evaluate the viral diversity in feces of fur seals found deceased along the coast of the state of Rio Grande do Sul. The fecal virome of two fur seal species was characterized: the South American fur seal (Arctocephalus australis) and the Subantarctic fur seal (Arctocephalus tropicalis). Fecal samples from 10 specimens (A. australis, n = 5; A. tropicalis, n = 5) were collected and viral particles were purified, extracted and amplified with a random PCR. The products were sequenced through Ion Torrent and Illumina platforms and assembled reads were submitted to BLASTx searches. Both viromes were dominated by bacteriophages and included a number of potentially novel virus genomes. Sequences of picobirnaviruses, picornaviruses and a hepevirus-like were identified in A. australis. A rotavirus related to group C, a novel member of the Sakobuvirus and a sapovirus very similar to California sea lion sapovirus 1 were found in A. tropicalis. Additionally, sequences of members of the Anelloviridae and Parvoviridae families were detected in both fur seal species. This is the first metagenomic study to screen the fecal virome of fur seals, contributing to a better understanding of the complexity of the viral community present in the intestinal microbiota of these animals.     

Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism

Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals’ classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores.     

A Novel Tool to Mitigate By-Catch Mortality of Baltic Seals in Coastal Fyke Net Fishery

Developing methods to reduce the incidental catch of non-target species is important, as by-catch mortality poses threats especially to large aquatic predators. We examined the effectiveness of a novel device, a “seal sock”, in mitigating the by-catch mortality of seals in coastal fyke net fisheries in the Baltic Sea. The seal sock developed and tested in this study was a cylindrical net attached to the fyke net, allowing the seals access to the surface to breathe while trapped inside fishing gear. The number of dead and live seals caught in fyke nets without a seal sock (years 2008–2010) and with a sock (years 2011–2013) was recorded. The seals caught in fyke nets were mainly juveniles. Of ringed seals (Phoca hispida botnica) both sexes were equally represented, while of grey seals (Halichoerus grypus) the ratio was biased (71%) towards males. All the by-caught seals were dead in the fyke nets without a seal sock, whereas 70% of ringed seals and 11% of grey seals survived when the seal sock was used. The seal sock proved to be effective in reducing the by-catch mortality of ringed seals, but did not perform as well with grey seals.     

Domoic acid exposure and associated clinical signs and histopathology in Pacific harbor seals (Phoca vitulina richardii)

Domoic acid (DA) is a potent neurotoxin that has caused strandings and mortality of seabirds and marine mammals off the California coast. Pacific harbor seals (Phoca vitulina richardii) are an abundant, nearshore species in California; however, DA exposure and toxicosis have not been documented for harbor seals in this region. To investigate DA exposure in harbor seals, samples were collected from free-ranging and stranded seals off California to assess exposure, clinical signs of toxicosis, and brain lesions in harbor seals exposed to DA. Domoic acid was detected in 65% (17/26) of urine samples collected from apparently healthy free-ranging seals, with concentrations of 0.4–11.7 ng/ml. Domoic acid also was detected in feces (2.4–2887 ng/g), stomach contents (1.4 ng/g; stranded only), milk (2.2 ng/ml; stranded only), amniotic fluid (9.7 ng/ml; free-ranging only), fetal meconium (14.6–39.8 ng/g), and fetal urine (2.0–10.2 ng/ml). Clinical signs indicative of DA toxicosis were observed in two live-stranded seals, and included disorientation, seizures, and uncoordinated movements. Histopathology revealed the presence of brain lesions consistent with DA toxicosis in two live-stranded seals, and one free-ranging seal that died during capture. Results indicated that harbor seals were exposed to DA, exhibited clinical signs and histological lesions associated with DA exposure, and that pups were exposed to DA in utero and during lactation via milk. Future investigation is required to determine the magnitude of impact that DA has on the health and mortality of harbor seals.     

Food habits of harbor seals (Phoca vitulina richardii) as an indicator of invasive species in San Francisco Bay,California

The diet of harbor seals (Phoca vitulina richardii) in San Francisco Bay (SFB), California, was determined from July 2007 to July 2008 using prey hard parts recovered from 442 scats collected at five haul‐out sites. Twenty‐two species of fish and one species of crustacean were identified, but harbor seals primarily ate a nonnative invasive species, yellowfin goby (Acanthogobius flavimanus), which increased in dietary importance since the diet was last studied in 1991/1992. Additionally, another nonnative invasive fish species, chameleon goby (Tridentiger trigonocephalus), was found for the first time in the diet of harbor seals in SFB. Harbor seal diet was statistically different between years (1991/1992 and 2007/2008), between the pupping and nonpupping seasons, and between North SFB and South SFB haul‐out locations. The diet of harbor seals was significantly correlated with fish species caught in trawl surveys conducted by the California Department of Fish and Wildlife (CDFW) during the same time periods as this study (2007/2008). Harbor seals currently are influencing the health of the SFB ecosystem in a positive manner by consuming large quantities of nonnative invasive fish species.     

Natural and human effects on harbor seal abundance and spatial distribution in an Alaskan glacial fjord

Tidewater glacial fjords support the largest populations of harbor seals (Phoca vitulina richardii) in Alaska and are a prime destination for tour ships. Chronic disturbance from ships, however subtle, could impact long‐term population stability. We examined variation in abundance and distribution of harbor seals on floating ice in Disenchantment Bay, Alaska, a tour ship destination for over a century with near daily visitation by ships in the spring/summer over the last decade. Counts of seals by aerial transect showed a sharp decline in May, prior to pupping and the first ships arriving; counts rebounded by the end of June remaining high until August. Seal distribution and abundance peaked in 5–7 tenths ice cover; total area of ice cover showed no effect. Despite regular flushing of seals by ships, we found no broad‐scale patterns in seal abundance and distribution that could be explained by ship presence. We cannot rule out mechanisms of long‐term disturbance, difficult to detect and that might explain notable differences with other, similar sites. Population declines at disturbed glacial sites and the still rising popularity of vessel‐based tourism indicate a need for individual‐based studies on how seals respond to the dynamics of glacial ice environments and human‐caused stresses.     

Temporal variation in distribution and density of ice-obligated seals in western Hudson Bay, Canada

Recent unidirectional climatic trends and changes in top predator population ecology suggest that long-term modifications may be happening in Hudson Bay, Canada. Effects of such changes on ice-obligated seal populations are expected but long-term studies are required to differentiate climate-induced changes from natural variation. We conducted strip-transect surveys in late spring in 1995–1997, 1999–2000 and 2007–2008 to estimate distribution, density and abundance of ice-obligated ringed (Phoca hispida) and bearded (Erignathus barbatus) seals in western Hudson Bay. When hauled out, ringed seals preferred land-fast and consolidated pack ice, whereas bearded seals preferred unconsolidated pack ice. Bearded and ringed seal density estimates varied from 0.0036 to 0.0229 seals/km² of ice and from 0.46 to 1.60 seals/km² of ice, respectively. Strong inter-annual variations were recorded in the abundance estimates of both species, with the largest abundance estimates in 1995 (104,162 and 1,494 ringed and bearded seals, respectively) and the lowest in 2008 for ringed seals (33,701) and 1997 for bearded seals (278). A sine function best described seal density estimates in western Hudson Bay and suggested a decadal cycle. Previous studies that reported low ringed seal demographic parameters in the 1990s and a recovery in the 2000s supported our interpretation of the survey results. We discuss our results in the context of climate warming and suggest that a long-term decline in ice-obligated seal density estimates may overlay a possible natural decadal cycle.     

Behavior of Cape fur seals (Arctocephalus pusillus pusillus) in relation to temporal variation in predation risk by white sharks (Carcharodon carcharias) around a seal rookery in False Bay,South Africa

The marked differences in predation risk posed by white sharks (Carcarodon carcarias) at island rookeries of Cape fur seals (Arctocephalus pusillus pusillus) offer a quasi‐experimental design within a natural system for exploring how prey adjust their behavior in response to temporal variation in predation risk. Here we compare movement of juvenile and adult Cape fur seals at a high risk (Seal Island) and low risk (Egg Island) rookery. We further compare juveniles and adults at Seal Island in low and high risk seasons and at low and high risk times of day within those seasons. Adult fur seals at Seal Island avoided traversing the zone of high white shark predation risk during the high risk period (0700–0959) in the season of high risk (winter), but not during the low risk season (summer). By contrast, adult fur seals at Egg Island showed no temporal discretion in either season. Unlike juvenile fur seals at Egg Island, juveniles at Seal Island adjusted their temporal movement patterns to more closely mimic adult seal movement patterns. This suggests that exposure to predators is the primary driver of temporal adjustments to movement by prey species commuting from a central place.     

SEALNET: Facial recognition software for ecological studies of harbor seals

Methods for long‐term monitoring of coastal species such as harbor seals (Phoca vitulina) are often costly, time‐consuming, and highly invasive, underscoring the need for improved techniques for data collection and analysis. Here, we propose the use of automated facial recognition technology for identification of individual seals and demonstrate its utility in ecological and population studies. We created a software package, SealNet, that automates photo identification of seals, using a graphical user interface (GUI) software to detect, align, and chip seal faces from photographs and a deep convolutional neural network (CNN) suitable for small datasets (e.g., 100 seals with five photos per seal) to classify individual seals. We piloted the SealNet technology with a population of harbor seals located within Casco Bay on the coast of Maine, USA. Across two years of sampling, 2019 and 2020, at seven haul‐out sites in Middle Bay, we obtained a dataset optimized for the development and testing of SealNet. We processed 1752 images representing 408 individual seals and achieved 88% Rank‐1 and 96% Rank‐5 accuracy in closed set seal identification. In identifying individual seals, SealNet software outperformed a similar face recognition method, PrimNet, developed for primates but retrained on seals. The ease and wealth of image data that can be processed using SealNet software contributes a vital tool for ecological and behavioral studies of marine mammals in the developing field of conservation technology.

In this paper, we describe the successful application of our newly developed automated facial recognition software as a tool for ecological analysis of harbor seals (Phoca vitulina). We outline an emerging method of data collection and analysis that facilitates rapid interpretation of large photo datasets over wide temporal and geographic scales. In addition, we use this machine learning‐based technology in a preliminary ecological study in a wild population of seals in the Casco Bay region of Maine to demonstrate the effectiveness of this non‐invasive method for use in mark‐recapture and site fidelity studies in the field.     

Harbor seal population decline in the Aleutian Archipelago

Populations of Steller sea lions, northern fur seals, and northern sea otters declined substantially during recent decades in the Bering Sea and Aleutian Islands region, yet the population status of harbor seals has not been assessed adequately. We determined that counts obtained during skiff‐based surveys conducted in 1977–1982 represent the earliest estimate of harbor seal abundance throughout the Aleutian Islands. By comparing counts from 106 islands surveyed in 1977–1982 (8,601 seals) with counts from the same islands during a 1999 aerial survey (2,859 seals), we observed a 67% decline over the ～20‐yr period. Regionally, the largest decline of 86% was in the western Aleutians (n= 7 islands), followed by 66% in the central Aleutians (n= 64 islands), and 45% in the eastern Aleutians (n= 35 islands). Harbor seal counts decreased at the majority of islands in each region, the number of islands with >100 seals decreased ～70%, and the number of islands with no seals counted increased ～80%, indicating that harbor seal abundance throughout the Aleutian Islands was substantially lower in the late 1990s than in the 1970s and 1980s.