Detection of human food-borne and zoonotic viruses on irrigated, field-grown strawberries

This study evaluated the presence of pathogenic human and zoonotic viruses on irrigated, field-grown strawberries. Norovirus genogroup I, rotavirus, and swine hepatitis E virus genogroup 3 were detected on strawberries, and irrigation water is suspected as the contamination origin.     

野生中缅鼩病毒携带情况的初步调查

病毒学检测和监测是树鼩实验动物化和质量控制的重要标准和依据,而野生中缅树鼩是否携带人兽共患病毒鲜见报道。本研究采用酶联免疫吸附(ELISA)方法,对来源于云南昆明市城郊青龙峡地区的野生树鼩是否携带单纯疱疹病毒、轮状病毒、流感病毒、柯萨奇病毒、甲肝病毒、乙肝病毒、丙肝病毒、丁肝病毒、登革热病毒、出血热病毒和麻疹病毒等11种常见病毒进行筛查。结果表明,在已筛查的60只野生中缅树鼩中,可检测到单纯疱疹病毒和柯萨奇病毒,其血清抗体阳性比例分别为36.7%(22/60)和1.67%(1/60),而在粪便中仅检测到轮状病毒,其抗原阳性为6.7%(4/60),未检测到其他病毒,初步显示了野生树鼩自然状态下携带病毒的状况。为此,建议将单纯疱疹病毒、柯萨奇病毒和轮状病毒列为普通级树鼩病毒质量控制的首检项目,进一步大样本筛查将显示是否将其他病毒列为必检项目。     

The prevalence and genomic characteristics of hepatitis E virus in murine rodents and house shrews from several regions in China

Background

Urban rodents and house shrews are closely correlated in terms of location with humans and can transmit many pathogens to them. Hepatitis E has been confirmed to be a zoonotic disease. However, the zoonotic potential of rat HEV is still unclear. The aim of this study was to determine the prevalence and genomic characteristics of hepatitis E virus (HEV) in rodents and house shrews.

Results

We collected a total of 788 animals from four provinces in China. From the 614 collected murine rodents, 20.19% of the liver tissue samples and 45.76% of the fecal samples were positive for HEV. From the 174 house shrews (Suncus murinus), 5.17% fecal samples and 0.57% liver tissue samples were positive for HEV. All of the HEV sequences obtained in this study belonged to Orthohepevirus C1. However, we observed a lower percentage of identity in the ORF3 region upon comparing the amino acid sequences between Rattus norvegicus and Rattus losea. HEV derived from house shrews shared a high percentage of identity with rat HEV. Notably, the first near full-length of the HEV genome from Rattus losea is described in our study, and we also report the first near full-length rat HEV genomes in Rattus norvegicus from China.

Conclusion

HEV is prevalent among the three common species of murine rodents (Rattus. norvegicus, Rattus. tanezumi, and Rattus. losea) in China. HEV sequences detected from house shrews were similar to rat HEV sequences. The high identity of HEV from murine rodents and house shrews suggested that HEV can spread among different animal species.

     

Dietary niche separation of rodents and shrews in an African savanna

While niche separation and relationships with environmental conditions of large mammals of the African savanna have been studied intensively, less conspicuous components have not received similar attention. This is the case of Kafue National Park (KNP), Zambia, where mechanisms supporting coexistence among rodent and shrew species remain unclear, much less the influence of fire on their dietary resource use. Here, we use stable carbon and nitrogen isotopes to assess dietary resource use and partitioning among rodents and shrews found in three vegetation formations of KNP. According to the nitrogen isotope signatures, rodents are one to two trophic levels above primary production, save for Mus triton that is above by two to three. Shrews are two trophic levels above primary production. Among shrews, factors allowing coexistence of similar sized species could not be resolved. Rodent species of the same assemblage either differ in body mass by a factor of two (following Hutchinson's rule) or similar sized species occupy different trophic levels or dietary guilds based on their isotopic nitrogen or carbon signatures. At sites with frequent fires, rodents have broader dietary niches than at sites with low fire frequencies. This could either indicate relaxed competition under high fire frequencies as rodent populations do not reach the carrying capacity of the habitat, or it could reflect reduced competition due to lower species numbers under high versus low fire recurrence regimes. The results indicate competition as an important component structuring rodent communities in Zambian savannas, thus suggesting limited resources.     

Detection and genetical characterization of Shiga toxin-producing Escherichia coli from wild deer

Shiga toxin (Stx)-producing Escherichia coli (STEC) strains isolated from wild deer in Japan were examined. A total of 43 fecal samples were collected 4 times from 4 different sites around Obihiro City, Hokkaido, Japan, in June and July 1997. Seven STEC strains were isolated by PCR screening, all of them were confirmed by ELISA and Vero cell cytotoxicity assay to be producing only active Stx type 2 (Stx2). Moreover, they seemed to carry the hemolysin and eaeA genes of STEC O157:H7, and some isolates harbored large plasmids which were similar to the 90-kilobase virulence plasmid of STEC O157:H7. Based on their plasmid profiles, antibiotic resistance patterns, PCR-based DNA fingerprinting data obtained by using random amplified polymorphic DNA (RAPD) and the stx2 gene sequences, all isolates were divergent from each other except for 3 isolates from the first and second samplings. A DNA sequence analysis of representative isolates revealed that deer originating STEC strains were closely related to each other, but not to the Stx2-producing STEC strains isolated from a mass outbreak in Obihiro at the same time. A phylogenic analysis of the deduced Stx2 amino acid sequences demonstrated that three distinct clusters existed in the deer originating STEC strains and that the Stx of deer originating STEC was closely associated with that originating from humans, but not those of STEC originating from other animals. These results suggest that STEC contamination of deer carcasses should be considered as a potential source of human infection and adequate sanitary inspection of meat for human consumption is also essential for wild animals.     

Prevalence of Ife virus infection in wild rodents and birds from Zaria, Nigeria

One hundred eighty-three wild rodents and 38 wild birds trapped near Zaria were screened for virus and complement fixing (CF) antibody to Ife virus. Virus was not isolated but CF antibody was detected in 8% Cricetomys gambianus and 31% Arvicanthis niloticus tested. The presence of Ife virus has been documented now in three ecological zones of Nigeria.     

Interrelationship between ectoparasites and wild rodents from northeastern Buenos Aires Province,Argentina

Infestation parameters and indices of mites, ticks and fleas associated with wild rodents from northeastern Buenos Aires Province, Argentina, were studied. Host species similarity was also analyzed in relation to their ectoparasites. Fifty-five rodents were captured from January 2000 to March 2001. In total, 1,022 ectoparasites were collected and three ectoparasite-host associations were new records. However, this is the first study on Craneopsylla minerva wolffhuegeli infesting parameters. Ectoparasite total mean abundance and total prevalence were higher in Holochilus brasiliensis (MA = 47.7; P = 100%) and Scapteromys aquaticus (MA = 25.4; P = 95.4%), meanwhile specific richness and diversity were higher in Oligoryzomys flavescens (S = 6; H = 1.3) and Akodon azarae (S = 4; H = 1.0). On the other hand, the only individual of Calomys laucha was not parasited. S. aquaticus-H. brasiliensis, which preferred similar microhabitats, shared the same ectoparasite species (Css = 100). Whereas, A. azarae, which was mostly associated with grassland, showed the highest difference with the other hosts (Css < 0.4). Considering every ectoparasite species, H. brasiliensis showed the highest mean abundance, prevalence and preference. The results suggest that the particular characteristics of this rodent would give it better possibilities not only of being infested by ectoparasites, but also of transmitting them to its progeny.     

Colonization of post-mining landscapes by shrews and rodents (Mammalia: Rodentia,Soricomorpha)

The presence and relative abundance of shrews and rodents have been studied in four different former brown coal mining areas in Lower Lusatia between 1995 and 1997 as well as 2001 and 2002. Several sites of undisturbed, i.e. non-mined, areas were included for comparison. Four species of shrews and four species of rodents have been found. Generally only few shrews were recorded in the Lower Lusatian area. Sorex araneus and S. minutus are the most abundant species, while Crocidura leucodon and C. suaveolens are rare. In the brown coal mining area shrews mainly occur in older sites with higher vegetation. The analysis of the distribution of rodent species revealed that Microtus arvalis having a comparably small spread potential, colonizes sites preferably with dense vegetation, while Apodemus sylvaticus was also found in sites with sparse vegetation. The relative abundance of all species is significantly higher in undisturbed sites. The colonization of the dumped openland areas is difficult for small mammals.     

Detection of resistance mutations to antivirals oseltamivir and zanamivir in avian influenza A viruses isolated from wild birds

The neuraminidase (NA) inhibitors oseltamivir and zanamivir are the first-line of defense against potentially fatal variants of influenza A pandemic strains. However, if resistant virus strains start to arise easily or at a high frequency, a new anti-influenza strategy will be necessary. This study aimed to investigate if and to what extent NA inhibitor–resistant mutants exist in the wild population of influenza A viruses that inhabit wild birds. NA sequences of all NA subtypes available from 5490 avian, 379 swine and 122 environmental isolates were extracted from NCBI databases. In addition, a dataset containing 230 virus isolates from mallard collected at Ottenby Bird Observatory (Öland, Sweden) was analyzed. Isolated NA RNA fragments from Ottenby were transformed to cDNA by RT-PCR, which was followed by sequencing. The analysis of genotypic profiles for NAs from both data sets in regard to antiviral resistance mutations was performed using bioinformatics tools. All 6221 sequences were scanned for oseltamivir- (I117V, E119V, D198N, I222V, H274Y, R292K, N294S and I314V) and zanamivir-related mutations (V116A, R118K, E119G/A/D, Q136K, D151E, R152K, R224K, E276D, R292K and R371K). Of the sequences from the avian NCBI dataset, 132 (2.4%) carried at least one, or in two cases even two and three, NA inhibitor resistance mutations. Swine and environmental isolates from the same data set had 18 (4.75%) and one (0.82%) mutant, respectively, with at least one mutation. The Ottenby sequences carried at least one mutation in 15 cases (6.52%). Therefore, resistant strains were more frequently found in Ottenby samples than in NCBI data sets. However, it is still uncertain if these mutations are the result of natural variations in the viruses or if they are induced by the selective pressure of xenobiotics (e.g., oseltamivir, zanamivir).     

Seroprevalence of Angiostrongylus cantonensis in wild rodents from the Canary Islands

Background

Angiostrongylus cantonensis is a lungworm of rats (Muridae) that is the causative agent of human cerebral angiostrongyliasis. The life cycle of A. cantonensis involves rats and mollusks as the definitive and intermediate hosts, respectively. This study was designed to increase the knowledge about the occurrence and distribution of A. cantonensis in its definitive host in the Canary Islands, using parasitological and serological analysis in different areas and age groups.

Methodology/Principal Findings

Between 2009 and 2010, 54 black rats (Rattus rattus) from Tenerife were captured from six human-inhabited areas and sera samples were obtained. The lung nematodes were identified by morphological and molecular tools as A. cantonensis. The 31-kDa glycoprotein antigen was purified from A. cantonensis adult worms by electrophoresis and electroelution. Of the 54 tested rodents, 30 showed IgG antibodies against A. cantonensis 31-kDa antigen by ELISA. Therefore, the overall seroprevalence was 55.6% (95% CI: 42.4–68). Seroprevalent rodents were found in all the 6 areas. This 31-kDa antigen was not recognized by some sera of rats infected by other helminth species (but not A. cantonensis). Seroprevalence of IgG antibodies against A. cantonensis and prevalence based on the presence of adult worms showed significant correlation (R² = 0.954, p<0.05).

Conclusions/Significance

The present results could indicate a high prevalence of A. cantonensis in Tenerife and suggest the inclusion of two new zones in the distribution area of the parasite. The commonness and wide distribution of A. cantonensis in rats implies the presence of intermediate hosts, indicating that humans may be at risk of getting infected.     

Emmonsiosis of wild rodents and insectivores in Czechland

Adiaspores of the fungus Emmonsia crescens were detected microscopically in the lung tissue of 13% of 10.081 small mammals belonging to 24 species examined in 14 areas of the Czech Republic between 1986 and 1997; 441/1.934 (23%) Clethrionomys glareolus, 1/6 (17%) Arvicola terrestris, 357/2.172 (16%) Apodemus flavicollis, 220/1.981 (11%). A sylvaticus, 23/265 (9%) A. microps, 11/81 (14%) Microtus subterraneus, 93/1.275 (7%) M. arvalis, 98/1.439 (7%) M. agrestis, 1/3 (33%) Ondatra zibethicus, 1/1 Cricetus cricetus, 1/20 (5%) Crocidura suaveolens, 2/40 (5%) Neomys fodiens, and 13/529 (2%) Sorex araneus were infected. Emmonsiosis was not recorded among the species of rodents that do not build their nests in the soil (Muscardinus avellanarius, Micromys minutus, Mus musculus, Rattus norvegicus). The overall prevalence of emmonsiosis was significantly higher in adult (19%) than in juvenile (7%) mammals, and in rodents (13%, and 20% in adults) than in insectivores (2%, and 4% in adults). The frequency of infected mammals also varied according to geographic area, altitude, habitat, and season.     

Diversity of rodents and shrews along an elevational gradient in Bwindi Impenetrable National Park, south-western Uganda

Small mammal species diversity in the major vegetation zones of Bwindi Impenetrable National Park is discussed in relation to altitude. Species richness of the small mammals was found to decrease with an increase in altitude. The main factors accounting for the observed diversity are the wide altitudinal variation and a complex array of vegetation types. Sixty‐seven species of rodents and shrews were found to exist in the Park; 47 of which were rodents and 20 shrews. Of these, 26 species are new to the Bwindi Park list. Three species have probably not been described before. The study found 10 species of small mammals to be Albertine Rift endemics. Three genera are recorded in Uganda for the first time: Rwenzorisorex, Suncus and Paracrocidura. Five species are new records for East Africa. These are Crocidura stenocephala, Lophuromys rahmi, L. medicaudatus, Paracrocidura maxima and Hylomyscus aeta. Because of the high endemism of plants, butterflies, birds and now of small mammal species, Bwindi forest is a unique biodiversity hotspot and is among the highest conservation priorities in the Albertine Rift.     

Systematic relationships of hymenolepidid cestodes of rodents and shrews inferred from sequences of 28S ribosomal RNA

Haukisalmi, V., Hardman, L. M., Foronda, P., Feliu, C., Laakkonen, J., Niemimaa, J., Lehtonen, J. T. & Henttonen, H. (2010). Systematic relationships of hymenolepidid cestodes of rodents and shrews inferred from sequences of 28S ribosomal RNA. —Zoologica Scripta, 39, 631–641. This study attempts to elucidate systematic relationships of hymenolepidid cestodes of rodents (18 species), shrews (13 species) and bats (one species) using sequences of partial 28S ribosomal RNA, with special reference to the genus Rodentolepis. The main finding is the presence of four multispecies clades of hymenolepidid cestodes showing pronounced morphological variation and frequent colonizations between unrelated hosts. Neither the hymenolepidid cestodes of shrews nor rodents were monophyletic. Also, the genus Rodentolepis sensu Vaucher in Czaplinski & Vaucher (1994, Keys to the Cestode Parasites of Vertebrates. Commonwealth Agricultural Bureaux International, Cambridge) is clearly non‐monophyletic. Although rostellar morphology is obviously a key feature on specific and generic levels, on higher systematic levels it seems to be a rather poor indicator of phylogenetic affinity in hymenolepidid cestodes. The presence of clades with more than one rostellar type (armed rostellum present, rudimentary unarmed rostellum present and rostellum absent) also conflicts with the proposed subfamilial and tribal classifications of hymenolepidid cestodes. The overall evidence suggests that the recent trend of splitting hymenolepidid cestodes into multiple genera will produce a more stable and practical classification than the earlier practice of favouring a few, morphologically variable genera. New classifications of hymenolepidid cestodes should, however, consider both morphological and molecular evidence.     

Genetic characterization of wild and captive rhesus macaques in China

The genetic structures of wild and captive rhesus macaque populations within China were compared by analyzing the mtDNA sequences of 203 captive-bred Chinese rhesus macaques with 77 GenBank sequences from wild-caught animals trapped throughout China. The genotypes of 22 microsatellites of captive Chinese rhesus macaques were also compared with those of captive Indian animals. The Chinese population is significantly differentiated from the Indian population and is more heterogeneous. Thus, compared with Indian rhesus macaques the phenotypic variance of traits with high heritability will be inflated in Chinese animals. Our data suggest that the western Chinese provinces have more subdivided populations than the eastern and southern Chinese provinces. The southern Chinese populations are the least structured and might have been more recently established. Human-mediated interbreeding among captive Chinese populations has occurred, implying that Chinese breeding strategies can influence the interpretation of biomedical research in the USA.     

Detection and characterization of diverse alpha- and betacoronaviruses from bats in China

Bats have been implicated as important reservoir hosts of alpha- and betacoronaviruses. In this study, diverse coronaviruses (CoVs) were detected in 50 of 951 (positive rate 5.3%) intestinal specimens of eight bat species collected in four provinces and the Tibet Autonomous Region of China by pan-coronavirus RT-PCR screening. Based on 400-nt RNA-dependent RNA polymerase (RdRP) sequence analysis, eight belonged to genus Alphacoronavirus and 42 to Betacoronavirus. Among the 50 positive specimens, thirteen gave rise to CoV full-length RdRP gene amplification for further sequence comparison, of which three divergent sequences (two from a unreported province) were subjected to full genome sequencing. Two complete genomes of betacoronaviruses (JTMC15 and JPDB144) and one nearly-complete genome of alphacoronavirus (JTAC2) were sequenced and their genomic organization predicted. The present study has identified additional numbers of genetically diverse bat-borne coronaviruses with a wide distribution in China. Two new species of bat CoV, identified through sequence comparison and phylogenetic analysis, are proposed.

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Detection of low pathogenic avian influenza viruses in wild ducks from Canada: comparison of two sampling methods

Surveillance for avian influenza viruses in wild birds was initiated in Canada in 2005. In 2006, in order to maximize detection of highly pathogenic avian influenza viruses, the sampling protocol used in Canada's Inter-agency Wild Bird Influenza Survey was changed. Instead of collecting a single cloacal swab, as previously done in 2005, cloacal and oropharyngeal swabs were combined in a single vial at collection. In order to compare the two sampling methods, duplicate samples were collected from 798 wild dabbling ducks (tribe Anatini) in Canada between 24 July and 7 September 2006. Low pathogenic avian influenza viruses were detected significantly more often (P<0.0001) in combined oropharyngeal and cloacal samples (261/798, 33%) than in cloacal swabs alone (205/798, 26%). Compared to traditional single cloacal samples, combined samples improved virus detection at minimal additional cost.