Identification of a third human polyomavirus

We have previously reported on a system for large-scale molecular virus screening of clinical samples. As part of an effort to systematically search for unrecognized human pathogens, the technology was applied for virus screening of human respiratory tract samples. This resulted in the identification of a previously unknown polyomavirus provisionally named KI polyomavirus. The virus is phylogenetically related to other primate polyomaviruses in the early region of the genome but has very little homology (<30% amino acid identity) to known polyomaviruses in the late region. The virus was found by PCR in 6 (1%) of 637 nasopharyngeal aspirates and in 1 (0.5%) of 192 fecal samples but was not detected in sets of urine and blood samples. Since polyomaviruses have oncogenic potential and may produce severe disease in immunosuppressed individuals, continued searching for the virus in different medical contexts is important. This finding further illustrates how unbiased screening of respiratory tract samples can be used for the discovery of diverse virus types.     

Lack of detection of host associated differences in Newcastle disease viruses of genotype VIId isolated from chickens and geese

ABSTRACT: BACKGROUND: The goose is usually considered to be resistant even to strains of Newcastle disease virus (NDV) that are markedly virulent for chickens. However, ND outbreaks have been frequently reported in goose flocks in China since the late 1990s with the concurrent emergence of genotype VIId NDV in chickens. Although the NDVs isolated from both chickens and geese in the past 15 years have been predominantly VIId viruses, published data comparing goose- and chicken-originated ND viruses are scarce and controversial. RESULTS: In this paper, we compared genotype VIId NDVs originated from geese and chickens genetically and pathologically. Ten entire genomic sequences and 329 complete coding sequences of individual genes from genotype VIId NDVs of both goose- and chicken-origin were analyzed. We then randomly selected two goose-originated and two chicken-originated VIId NDVs and compared their pathobiology in both geese and chickens in vivo and in vitro with genotype IV virus Herts/33 as a reference. The results showed that all the VIId NDVs either from geese or from chickens shared high sequence homology and characteristic amino acid substitutions and clustered together in phylogenetic trees. In addition, geese and chickens infected by goose or chicken VIId viruses manifested very similar pathological features distinct from those of birds infected with Herts/33. CONCLUSIONS: There is no genetic or phenotypic difference between genotype VIId NDVs originated from geese and chickens. Therefore, no species-preference exists for either goose or chicken viruses and more attention should be paid to the trans-species transmission of VIId NDVs between geese and chickens for the control and eradication of ND.     

Identification and characterization of the virus causing rabbit hemorrhagic disease.

Liver tissue from animals that died of rabbit hemorrhagic disease (RHD) was used to identify the causative agent. After extraction of liver homogenates and sucrose density gradient ultracentrifugation, distinct bands were obtained. The respective gradient fractions reacted positively in an enzyme-linked immunosorbent assay as well as in hemagglutination assays and were infective for rabbits. These fractions contained virions which had a diameter of 40 nm and resembled morphologically those of the family Caliciviridae. By immunoblotting, a major structural protein with a molecular weight of 60,000 was identified. Highly pure RNA of about 8 kilobases was isolated from virions. Labeled cDNA synthesized from virion RNA detected two RNAs of 8 and 2 kilobases in Northern (RNA) blots of liver RNA from animals infected with RHD virus. Finally, isolated virion RNA injected into the liver of rabbits produced a disease with clinical symptoms and pathological findings typical of RHD. We conclude that a calicivirus represents the causative agent of RHD.     

Comparing phylogenetic codivergence between polyomaviruses and their hosts

Seventy-two full genomes corresponding to nine mammalian (67 strains) and two avian (5 strains) polyomavirus species were analyzed using maximum likelihood and Bayesian methods of phylogenetic inference. Our fully resolved and well-supported (bootstrap proportions > 90%; posterior probabilities = 1.0) trees separate the bird polyomaviruses (avian polyomavirus and goose hemorrhagic polyomavirus) from the mammalian polyomaviruses, which supports the idea of spitting the genus into two subgenera. Such a split is also consistent with the different viral life strategies of each group. Simian (simian virus 40, simian agent 12 [Sa12], and lymphotropic polyomavirus) and rodent (hamster polyomavirus, mouse polyomavirus, and murine pneumotropic polyomavirus [MPtV]) polyomaviruses did not form monophyletic groups. Using our best hypothesis of polyomavirus evolutionary relationships and established host phylogenies, we performed a cophylogenetic reconciliation analysis of codivergence. Our analyses generated six optimal cophylogenetic scenarios of coevolution, including 12 codivergence events (P < 0.01), suggesting that Polyomaviridae coevolved with their avian and mammal hosts. As individual lineages, our analyses showed evidence of host switching in four terminal branches leading to MPtV, bovine polyomavirus, Sa12, and BK virus, suggesting a combination of vertical and horizontal transfer in the evolutionary history of the polyomaviruses.     

Isolation of virus causing hemorrhagic fever with renal syndrome (HFRS) through a cell culture system

Twenty-three rat lung specimens collected in outbreaks of hemorrhagic fever with renal syndrome (HFRS) in three medical institutions were inoculated onto the VERO-E6 cell monolayers. After several blind passages, an agent growing serially in the cell cultures and reacting specifically with known HFRS-positive sera was isolated from two of these specimens. The two isolates were antigenically identical each other. The agent, named strain SR-11, was identified as the causative virus of HFRS by its antigenic identity with E6 cell-adapted HFRS virus, Hantaan 76-118 strain, and the specific reactions with sera from various HFRS cases.     

Complete nucleotide sequence of polyomavirus SA12

The Polyomaviridae have small icosahedral virions that contain a genome of approximately 5,000 bp of circular double-stranded DNA. Polyomaviruses infect hosts ranging from humans to birds, and some members of this family induce tumors in test animals or in their natural hosts. We report the complete nucleotide sequence of simian agent 12 (SA12), whose natural host is thought to be Papio ursinus, the chacma baboon. The 5,230-bp genome has a genetic organization typical of polyomaviruses. Sequences encoding large T antigen, small t antigen, agnoprotein, and the viral capsid proteins VP1, VP2, and VP3 are present in the expected locations. We show that, like its close relative simian virus 40 (SV40), SA12 expresses microRNAs that are encoded by the late DNA strand overlapping the 3' end of large T antigen coding sequences. Based on sequence comparisons, SA12 is most closely related to BK virus (BKV), a human polyomavirus. We have developed a real-time PCR test that distinguishes SA12 from BKV and the other closely related polyomaviruses JC virus and SV40. The close relationship between SA12 and BKV raises the possibility that these viruses circulate between human and baboon hosts.     

Human MxA protein inhibits the replication of Crimean-Congo hemorrhagic fever virus

Crimean-Congo hemorrhagic fever virus (CCHFV) belongs to the genus Nairovirus within the family Bunyaviridae and is the causative agent of severe hemorrhagic fever. Despite increasing knowledge about hemorrhagic fever viruses, the factors determining their pathogenicity are still poorly understood. The interferon-induced MxA protein has been shown to have an inhibitory effect on several members of the Bunyaviridae family, but the effect of MxA against CCHFV has not previously been studied. Here, we report that human MxA has antiviral activity against CCHFV. The yield of progeny virus in cells constitutively expressing MxA was reduced up to 1,000-fold compared with control cells, and accumulation of viral genomes was blocked. Confocal microscopy revealed that MxA colocalizes with the nucleocapsid protein (NP) of CCHFV in the perinuclear regions of infected cells. Furthermore, we found that MxA interacted with NP by using a coimmunoprecipitation assay. We also found that an amino acid substitution (E645R) within the C-terminal domain of MxA resulted in a loss of MxA antiviral activity and, concomitantly, in the capacity to interact with CCHFV NP. These results suggest that MxA, by interacting with a component of the nucleocapsid, prevents replication of CCHFV viral RNA and thereby inhibits the production of new infectious virus particles.     

Field preference of Greylag geese <Emphasis Type="Italic">Anser anser</Emphasis> during the breeding season

Few studies address food preference of geese on agricultural land (utilization related to availability) and only a handful so for the breeding season. We studied Greylag geese Anser anser during the breeding season in an intensively farmed area in southern Sweden. Few of 22 available field types were truly preferred. Pastureland was the most consistently preferred, by goslings (with parents) as well as by non-breeders. In some sampling periods, goslings also preferred grazed hay, ley, and carrot fields. Non-breeders exploited a greater variety of crops/fields, feeding also on barley, fallow, grazed hay, lettuce, oats, potatoes, and carrots. Most of these crops were preferred on at least one sampling occasion, except for fallow, grazed hay, and wheat, which were always used less than expected from availability. GLMs revealed that goslings rested more than they fed and preferred shorter vegetation before higher. Moreover, goslings occurred in higher densities in younger age classes than in older and preferred nearshore areas. In contrast, density of non-breeders was only related to field type and sampling occasion (higher densities as the season progressed). The maximum number of broods observed (106) implies a breeding success of 34% based on 311 active nests earlier in the season. Brood size decreased from 3.5 to 2.1 during the study period. Our study shows that goose management during the breeding season should consider goslings and their parents separately from non-breeders, and it implies little potential conflict between Greylag geese and agriculture during the breeding period.     

Characterization of two novel polyomaviruses of birds by using multiply primed rolling-circle amplification of their genomes

Polyomaviruses are small nonenveloped particles with a circular double-stranded genome, approximately 5 kbp in size. The mammalian polyomaviruses mainly cause persistent subclinical infections in their natural nonimmunocompromised hosts. In contrast, the polyomaviruses of birds--avian polyomavirus (APV) and goose hemorrhagic polyomavirus (GHPV)--are the primary agents of acute and chronic disease with high mortality rates in young birds. Screening of field samples of diseased birds by consensus PCR revealed the presence of two novel polyomaviruses in the liver of an Eurasian bullfinch (Pyrrhula pyrrhula griseiventris) and in the spleen of a Eurasian jackdaw (Corvus monedula), tentatively designated as finch polyomavirus (FPyV) and crow polyomavirus (CPyV), respectively. The genomes of the viruses were amplified by using multiply primed rolling-circle amplification and cloned. Analysis of the FPyV and CPyV genome sequences revealed a close relationship to APV and GHPV, indicating the existence of a distinct avian group among the polyomaviruses. The main characteristics of this group are (i) involvement in fatal disease, (ii) the existence of an additional open reading frame in the 5' region of the late mRNAs, and (iii) a different manner of DNA binding of the large tumor antigen compared to that of the mammalian polyomaviruses.     

The role of sialic acid in human polyomavirus infections

JC virus (JCV) and BK virus (BKV) are human polyomaviruses that infect approximately 85% of the population worldwide [1,2]. JCV is the underlying cause of the fatal demyelinating disease, progressive multifocal leukoencephalopathy (PML), a condition resulting from JCV induced lytic destruction of myelin producing oligodendrocytes in the brain [3]. BKV infection of kidneys in renal transplant recipients results in a gradual loss of graft function known as polyomavirus associated nephropathy (PVN) [4]. Following the identification of these viruses as the etiological agents of disease, there has been greater interest in understanding the basic biology of these human pathogens [5,6]. Recent advances in the field have shown that viral entry of both JCV and BKV is dependent on the ability to interact with sialic acid. This review focuses on what is known about the human polyomaviruses and the role that sialic acid plays in determining viral tropism.     

Immune response of heterologous recombinant antigenic protein of viral hemorrhagic septicemia virus (VHSV) in mice

Viral hemorrhagic septicemia (VHS) is an important infectious disease in fish worldwide caused by viral hemorrhagic septicemia virus (VHSV). VHSV is the causative agent of serious systemic diseases in fish, affecting a number of teleost fish species. In this study, VHSV glycoprotein (G), including its epitope, as a subunit vaccine candidate, was expressed in tobacco plant (Nicotiana tabacum). The recombinant gene, VHSVG, was fused to the immunoglobulin Fc fragment and extended with the endoplasmic reticulum (ER) retention signal (KDEL) to generate VHSVG-FcK. The recombinant expression vector for VHSVG-FcK was transferred into Agrobacterium tumefaciens (LBA4404), and plant transformation was conducted N. tabacum. Polymerase chain reaction (PCR) was performed to confirm gene insertion and VHSVG-FcK protein expression was confirmed by immunoblot analysis. VHSVG-FcK protein was successfully purified from tobacco plant leaves. Furthermore, ELISA analysis showed that mice serum immunized with the plant-derived VHSVG-FcK (VHSVGP-FcK) had a high absorbance against VHSVG-FcK, indicating that the plant-derived recombinant subunit vaccine protein VHSVG-FcK can induce immune response. Taken together, this recombinant vaccine protein can be expressed in plant expression systems and can be appropriately assembled to be functional in immunogenicity.     

Growth of Greater White-Fronted Goose Goslings Relates to Population Dynamics at Multiple Scales

The abundance of greater white-fronted geese (Anser albifrons frontalis) on the Arctic Coastal Plain (ACP) of northern Alaska, USA, has more than tripled since the late 1990s; however, recent rate of annual population growth has declined as population size increased, which may indicate white-fronted geese on the ACP are approaching carrying capacity. We examined rates of gosling growth in greater white-fronted geese at 3 sites on the ACP during 2012–2014 to assist with predictions of future population trends and assess evidence for density-dependent constraints on recruitment. We marked goslings at hatch with individually coded webtags and conducted brood drives during early August to capture, measure, and weigh goslings. Annual estimates of gosling mass at 32 days old (range = 1,190–1,685) indicate that goslings had obtained >60% of asymptotic size. This rate of growth corresponds with that of other goose species and populations with access to high-quality forage and no limitations on forage availability, and is consistent with the overall increase in abundance of white-fronted geese at the ACP scale. Contrary to most previous investigations, age-adjusted mass of goslings did not decline with hatch date. Goslings grew faster in coastal areas than at inland freshwater sites. Taken together, these findings suggest forage was not limiting gosling growth rates in either ecosystem, but forage was of greater quality in coastal areas where goose foraging habitat is expanding because of permafrost subsidence. Spatial patterns of gosling growth corresponded with local-scale patterns of population density and population change; the areas with greatest rates of gosling growth were those with the greatest population density and rates of population increase. We found little evidence to suggest forage during brood rearing was limiting population increase of white-fronted geese on the ACP. Factors responsible for the apparent slowing of ACP-wide population growth are likely those that occur in stages of the annual cycle outside of the breeding grounds. Published 2021. This article is a U.S. Government work and is in the public domain in the USA.     

Complete Genome Sequence of an Amur Virus Isolated from Apodemus peninsulae in Northeastern China

Amur virus was recently identified as the causative agent of hemorrhagic fever with renal syndrome. Here we report the complete genome sequence of an Amur virus isolated from Apodemus peninsulae in Northeastern China. The sequence information provided here is critical for the molecular epidemiology and evolution of Amur virus in China.     

Dark-bellied brent geese Branta b. bernicla breeding near snowy owl Nyctea scandiaca nests lay more and larger eggs

Several studies have demonstrated that snowy owls Nyctea scandiaca defend an area around their nests against predators, hereby inadvertently creating safe havens for breeding dark-bellied brent geese Branta b. bernicla . However, studies investigating brent goose breeding ecology within the predator-exclusion zones of the snowy owls are absent. In 1999 and 2005, years of high lemming abundance Lemmus sibiricus and Dicrostonyx torquatus , brent geese were primarily breeding in association with snowy owls in the Medusa river catchment on western Taimyr, Russia. Goose nest failure, either as a result of nest abandonment by the adult birds or of nest depredation, increased with increasing distance from the owl nests. Within the brent goose colonies, clutch size as well as egg size increased with decreasing distance from the snowy owl nest, indicating an increasing adult quality closer to owl nests. However, as a result of the abandonment of eggs and goslings, the increasing clutch size did not result in a higher nest success during this study. Apparently brent geese compete for breeding sites close to owl nests, but details of this process remain unknown.     

The Origin of the White Roman Goose

In order to avoid interference from nuclear copies of mitochondrial DNA (numts), mtDNA of the white Roman goose (domestic goose) was extracted from liver mitochondria. The mtDNA control region was amplified using a long PCR strategy and then sequenced. Neighbor-joining, maximum parsimony, and maximum-likelihood approaches were implemented using the 1,177 bp mtDNA control region sequences to compute the phylogenetic relationships of the domestic goose with other geese. The resulting identity values for the white Roman geese were 99.1% (1,166/1,177) with western graylag geese and 98.8% (1,163/1,177) with eastern graylag geese. In molecular phylogenetic trees, the white Roman goose was grouped in the graylag lineage, indicating that the white Roman goose came from the graylag goose (Anser anser). Thus, the scientific name of the white Roman goose should be Anser anser ‘White Roman.’     

Nicarbazin OvoControl G Bait Reduces Hatchability of Eggs Laid by Resident Canada Geese in Oregon

Abstract: Expanding populations of resident Canada geese (Branta canadensis) are resulting in increased conflicts with humans. Nonlethal and humane means are needed for managing Canada goose flocks at a variety of sites, including golf courses, industrial parks, government sites, and city parks. Decreased egg production and hatching are side effects of nicarbazin, a veterinary drug used to treat coccidiosis in chickens. Capitalizing on these effects, we developed nicarbazin as a reproductive inhibitor for Canada geese and conducted a field efficacy study. We recruited study sites in 2002 and 2003. Following laboratory testing, we conducted a field efficacy trial of nicarbazin for reducing the hatchability of Canada goose eggs in spring 2004 in Oregon, USA. The study began in February 2004 at 10 sites in Oregon, with 2 control and 3 treated sites on each side of the Cascades. We fed bait daily to resident Canada geese for approximately 6 weeks. We located and monitored nests until hatching or ≥5 days beyond the expected hatching date to determine hatchability. We completed data collection in May 2004. Geese consumed 8,000 kg of bait, with 5,100 kg of OvoControl G® (Innolytics, LLC, Rancho Santa Fe, CA) 2,500-ppm nicarbazin bait consumed among 6 treated sites and 2,900 kg of untreated bait consumed among 4 control sites. We monitored 63 nests at treated sites and 46 nests at control sites to determine hatching success of eggs. There was a 62% reduction in the percentage of nests with 100% hatchability at treated sites as compared to controls. There was a 93% increase in the percentage of nests at treated sites with 0% hatchability as compared to nests with no eggs hatching at control sites. Hatchability from treated sites versus control sites was reduced 36% (F = 5.72, P = 0.0622). We submitted results from this study to support Environmental Protection Agency registration of nicarbazin as a reproductive inhibitor for use in Canada geese. We have shown that treatment of resident Canada geese with OvoControl G 2,500-ppm nicarbazin bait by licensed, trained applicators immediately prior to and during the breeding season can reduce hatchability of eggs laid by treated geese, thereby reducing recruitment of goslings into problem resident Canada goose populations.     

Climate change,phenology, and habitat degradation: drivers of gosling body condition and juvenile survival in lesser snow geese

Nesting migratory geese are among the dominant herbivores in (sub) arctic environments, which have undergone unprecedented increases in temperatures and plant growing days over the last three decades. Within these regions, the Hudson Bay Lowlands are home to an overabundant breeding population of lesser snow geese that has dramatically damaged the ecosystem, with cascading effects at multiple trophic levels. In some areas the overabundance of geese has led to a drastic reduction in available forage. In addition, warming of this region has widened the gap between goose migration timing and plant green‐up, and this ‘mismatch’ between goose and plant phenologies could in turn affect gosling development. The dual effects of climate change and habitat quality on gosling body condition and juvenile survival are not known, but are critical for predicting population growth and related degradation of (sub) arctic ecosystems. To address these issues, we used information on female goslings marked and measured between 1978 and 2005 (4125 individuals). Goslings that developed within and near the traditional center of the breeding colony experienced the effects of long‐term habitat degradation: body condition and juvenile survival declined over time. In newly colonized areas, however, we observed the opposite pattern (increase in body condition and juvenile survival). In addition, warmer than average winters and summers resulted in lower gosling body condition and first‐year survival. Too few plant ‘growing days’ in the spring relative to hatch led to similar results. Our assessment indicates that geese are recovering from habitat degradation by moving to newly colonized locales. However, a warmer climate could negatively affect snow goose populations in the long‐run, but it will depend on which seasons warm the fastest. These antagonistic mechanisms will require further study to help predict snow goose population dynamics and manage the trophic cascade they induce.     

Etiological relation between Korean hemorrhagic fever and epidemic hemorrhagic fever in Japan.

The first case of epidemic hemorrhagic fever in Japan was seen in Osaka in 1960. The etiologic agent of this disease has not yet been isolated, but a close etiologic relation between Korean hemorrhagic fever and epidemic hemorrhagic fever in Japan has been suspected because of similarities in the clinical and pathological pictures of the two diseases. This relation has now been confirmed serologically by demonstrating specific immunofluorescent antibodies to Korean hemorrhagic fever virus in 19 of 20 sera obtained from subjects 7 to 17 years after an acute attack of epidemic hemorrhagic fever.     

Novel Polyomaviruses of Nonhuman Primates: Genetic and Serological Predictors for the Existence of Multiple Unknown Polyomaviruses within the Human Population

Polyomaviruses are a family of small non-enveloped DNA viruses that encode oncogenes and have been associated, to greater or lesser extent, with human disease and cancer. Currently, twelve polyomaviruses are known to circulate within the human population. To further examine the diversity of human polyomaviruses, we have utilized a combinatorial approach comprised of initial degenerate primer-based PCR identification and phylogenetic analysis of nonhuman primate (NHP) polyomavirus species, followed by polyomavirus-specific serological analysis of human sera. Using this approach we identified twenty novel NHP polyomaviruses: nine in great apes (six in chimpanzees, two in gorillas and one in orangutan), five in Old World monkeys and six in New World monkeys. Phylogenetic analysis indicated that only four of the nine chimpanzee polyomaviruses (six novel and three previously identified) had known close human counterparts. To determine whether the remaining chimpanzee polyomaviruses had potential human counterparts, the major viral capsid proteins (VP1) of four chimpanzee polyomaviruses were expressed in E. coli for use as antigens in enzyme-linked immunoassay (ELISA). Human serum/plasma samples from both Côte d''Ivoire and Germany showed frequent seropositivity for the four viruses. Antibody pre-adsorption-based ELISA excluded the possibility that reactivities resulted from binding to known human polyomaviruses. Together, these results support the existence of additional polyomaviruses circulating within the human population that are genetically and serologically related to existing chimpanzee polyomaviruses.