Ungulate bocaparvovirus 4 and rodent bocavirus are different genotypes of the same species of virus.

Bocaviruses are associated with many human infectious diseases, such as respiratory tract infections, gastroenteritis, and hepatitis. Rats are known to be reservoirs of bocaviruses, including rodent bocavirus and rat bocavirus. Recently, ungulate bocaparvovirus 4, a known porcine bocavirus, has also been found in rats. Thus, investigating bocaviruses in rats is important for determining the origin of the viruses and preventing and controlling their transmission. To the best of our knowledge, no study to date has investigated bocaviruses in the livers of rats. In this report, a total of 624 rats were trapped in southern China between 2014 and 2017. Liver and serum samples from rats were tested for the prevalence of bocaviruses using PCR. Sequences related to ungulate bocaparvovirus 4 and rodent bocavirus were detected in both liver and serum samples. Interestingly, the prevalence of ungulate bocaparvovirus 4 (reference strain: KJ622366.1) was higher than that of rodent bocavirus (reference strain: KY927868.1) in both liver (2.24% and 0.64%, respectively) and serum samples (2.19% and 0.44%, respectively). The NS1 regions of ungulate bocaparvovirus 4 and rodent bocavirus related sequences displayed over 84% and 88% identity at the nucleic acid and amino acid levels, respectively. Furthermore, these sequences had similar genomic structure, genomic features, and codon usage bias, and shared a common ancestor. These viruses also displayed greater adaptability to rats than pigs. Our results suggested that ungulate bocaparvovirus 4 and rodent bocavirus may originate from rats and may be different genotypes of the same bocavirus species.

Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

Hepatitis is a major global health concern. However, the etiology of 10-20% hepatitis cases remains unclear. Some hepatitis-associated viruses, like the hepatitis E virus, are zoonotic pathogens. Rats, shrews, and bats are reservoirs for many zoonotic pathogens. Therefore, understanding the virome in the liver of these animals is important for the investigation of the etiologies of hepatitis and monitoring the emerging zoonotic viruses. In this study, viral metagenomics and PCR methods were used to investigate viral communities in rats, mice, house shrews, and bats livers. Viral metagenomic analysis showed a diverse set of sequences in liver samples, comprising: sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses. Using PCR methods, we first detected hepatovirus sequences in Hipposideros larvatus (3.85%). We also reported the first detection of Zika virus-related sequences in rats and house shrews. Sequences related to influenza A virus and herpesviruses were detected in liver. Higher detection rates of pegivirus sequences were found in liver tissue and serum samples from rats (7.85% and 15.79%, respectively) than from house shrews. Torque teno virus sequences had higher detection rates in the serum samples of rats and house shrews (52.72% and 5.26%, respectively) than in the liver. Near-full length genomes of pegivirus and torque teno virus were amplified. This study is the first to compare the viral communities in the liver of bats, rats, mice, and house shrews. Its findings expand our understanding of the virome in the liver of these animals and provide an insight into hepatitis-related viruses.

Serological Prevalence Against Japanese Encephalitis Virus-Serocomplex Flaviviruses in Commensal and Field Rodents in South China.

BACKGROUND: Japanese encephalitis caused by Japanese encephalitis virus (JEV) is an endemic zoonotic disease of high public health importance in the Asian Pacific region. The aim of this study was to investigate the presence of JEV infection in commensal and field rodents in South China. MATERIALS AND METHODS: RNA copies of JEV were detected in brain samples of rodents using real-time RT-PCR. Detection of serum against JEV-reactive antibodies was performed using indirect enzyme-linked immunosorbent assay and microneutralization test. RESULTS: In total, 198 rodents were collected from Guangzhou City and Xiamen City between November 2013 and May 2014. JEV RNA was not detected in 188 brain samples. Forty-four in 96 serum samples (45.8%) were positive for JEV-reactive IgG antibodies. The prevalence of neutralizing antibodies to against JEV-reactive in these serum samples was 61.5% (24/39), with titers ranging from 1:10 to 1:56. CONCLUSION: Rodents are not known to play a role in transmission of JEV in Asia, nor is there an evidence to support a role for rodents in transmission of other related flaviviruses in China. However, in the current study, we detected evidence of JEV-reactive antibodies in large numbers of Rattus norvegicus and Rattus losea Swinhoe. Further studies of rodents as potential hosts of JEV or other related flaviviruses are warranted.

Molecular Detection and Phylogenetic Characteristics of Herpesviruses in Rectal Swab Samples from Rodents and Shrews in Southern China.

Herpesviruses (HVs) can cause asymptomatic, benign, or fatal infections in a variety of animal species. However, the prevalence and phylogenetic characteristics of HVs in rodents and shrews in China are poorly understood. We thus performed a molecular detection and phylogenetic analysis of rat and shrew HVs in southern China between 2012 and 2014. Seventeen (6.7%) of 255 rectal swab specimens from rats and six (6.7%) of 90 rectal swab specimens from shrews tested positive for HVs. Phylogenetic analysis revealed that rodent and shrew HVs detected in this study were species specific, clustering in the Betaherpesvirinae and Gammaherpesvirinae clade. Novel Macavirus was detected in Rattus norvegicus (RN/13YX52/24 and RN/14HC50) and gammaherpesviruses in Suncus murinus (SM/14BY7/16/20/97/99/106).These findings have contributed to our understanding of the taxonomy, phylogeny, and biology of HVs.

Detection of novel adenoviruses in fecal specimens from rodents and shrews in southern China.

The prevalence and phylogenetic characteristics of AdVs in rodents and shrews in China are still unknown. To explore the epidemiological characteristics of rodent and shrew AdVs in southern China, 255 fecal samples derived from four rodent species and 90 from shrews were collected in Xiamen and Guangzhou city of southern China. Amplification of a 314-324-bp fragment from the DNA polymerase gene of AdVs was attempted by using a nested PCR. Twenty-nine (11.4 %) specimens from rodents and one (1.1 %) specimen from shrews were tested positive for AdVs. Phylogenetic analysis revealed that nine samples from Rattus norvegicus in Guangzhou city between 2012 and 2013 might be the genuine AdV of R. norvegicus. The same putative AdV sequences were derived from samples of different host species from different/same places. A novel adenovirus was detected in Suncus murinus Linnaeus (SML/14GDGZ72) for the first time. Our findings provide new data on the prevalence and diversity of AdVs in rodents and shrews.

Comparison of genomic and amino acid sequences of eight Japanese encephalitis virus isolates from bats.

We compared nucleotide and deduced amino acid sequences of eight Japanese encephalitis virus (JEV) isolates derived from bats in China. We also compared the bat JEV isolates with other JEV isolates available from GenBank to determine their genetic similarity. We found a high genetic homogeneity among the bat JEVs isolated in different geographical areas from various bat species at different time periods. All eight bat JEV isolates belonged to genotype III. The mean evolutionary rate of bat JEV isolates was lower than those of isolates of other origin, but this difference was not statistically significant. Based on these results, we presume that the bat JEV isolates might be evolutionarily conserved. The eight bat JEV isolates were phylogenetically similar to mosquito BN19 and human Liyujie isolates of JEV. These results indicate that bats might be involved in natural cycle of JEV.

[Epidemiological characteristics of soil-borne nematodiasis in Xiamen City].

The infection rate of soil-borne nematodes was 6.37% in Xiamen City, 2008, and among which the infection rates of hookworm, Ascaris lumbricoides, Trichuris trichiura and pinworm were 5.97%, 0.29%, 0.09% and 20.13%, respectively. The infection rate of soil-borne nematodes outside the island and that of pinworm in children were still high.

Isolation and phylogenetic characterization of bat astroviruses in southern China.

Astroviruses are associated with acute gastroenteritis of human and many animal species. Recently, two studies have reported that novel astroviruses were found in bats. In order to extensively understand the genetic and phylogenetic characterization of bat astroviruses, we tested fecal samples of nine bat species that were collected at four natural habitats in three areas of southern China. The geographic distributions of the bats involved differed from previous reports. Three out of nine species of bats were observed to harbor astroviruses. These included Miniopterus schreibersii, Scotophilus kuhlii, and Rousettus leschenaultia. Phylogenetic analysis based on amino acid sequences of partial ORFs of astroviruses revealed that the bat astroviruses are not only divergent from previously described human and other animal astroviruses but also show remarkable diversity among themselves. However, five bat astroviruses were phylogenetically related to mink astrovirus, ovine astrovirus, and the recently discovered human astroviruses VA1, VA2, and VA3. The results indicate that astroviruses may have adapted to the Chiroptera, and bats may transmit astroviruses to humans and other animals, or vice versa.

Comparison of reverse transcription loop-mediated isothermal amplification, conventional PCR and real-time PCR assays for Japanese encephalitis virus.

We developed and evaluated a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detecting Japanese encephalitis virus (JEV). The sensitivity of the JEV RT-LAMP assay was in concordance with that of real-time RT-PCR and 10-fold more sensitive than that of conventional RT-PCR, which the detection limit was 24 copies/µl. The JEV RT-LAMP was highly specific, which no cross-reactivity was found with dengue-2 virus, rabies virus, norovirus, astrovirus and human enterovirus 71. The JEV RT-LAMP assay was more simple and less time-consuming compared to the conventional RT-PCR and real-time RT-PCR, which the amplification could be completed in a single tube within 1 h under isothermal conditions at temperature of 63°C. The results suggest that the RT-LAMP assay can be applied as a practical molecular diagnostic tool for JEV infection and surveillance.

[Establishment and application of a loop-mediated isothermal amplification method for rapid diagnosis of Vibrio cholerae].

OBJECTIVE: To establish a loop-mediated isothermal amplification (LAMP) method for rapid diagnosis of Vibrio cholerae. METHODS: Based on the ompW nucleic sequence of Vibrio cholerae, a pair of primers was designed for LAMP. The reaction conditions were optimized, and the specificity, sensitivity, and practicability of LAMP were tested using 47 bacterial strains and simulated contaminated sites. RESULTS: The results of viable bacterium count showed that LAMP was capable of detecting Vibrio cholerae at a level as low as 1.6x10(2) cfu/ml. The minimal detectable concentration was 1.6+10(3) cfu/ml for simulated contaminated samples such as feces and seawater, and 1.6+10(4) cfu/ml for contaminated milk. All the 21 strains of Vibrio cholerae yielded positive results in LAMP, and the 26 strains of other bacteria all showed negative results, with a detection specificity of 100%. CONCLUSION: The established LAMP method has high specificity and sensitivity for detecting Vibrio cholerae and is applicable in field monitoring and epidemiological study of Vibrio cholerae.

[Antimicrobial resistance of clinical isolates of Stenotrophomonas maltophilia].

OBJECTIVE: To investigate the antimicrobial resistance of clinical isolates of Stenotrophomonas matophilia (SMA) and the mechanisms of their drug resistance. METHODS: Disc diffusion method (NCCLS) was used to detect the resistant patterns of 88 initial SMA isolates resistant to 12 antibiotics isolated from a local hospital in the past 4 years. PCR was used to detect the 7 aminoglycosides modifying enzymes genes (AME) against amikacin and gentamicin. Metal-beta-lactamases (MBLs) were screened by synergic method, and extended-spectrum beta-lactamases (ESBLs) were detected by double-disk synergy test. RESULTS: The resistance rates of the SMA isolates were 0%-9.7% to minocycline, 12.5%-22.6% to ticarcillin-clavulanic acid, 12.5%-28.6% to levofloxacin, 18.8%-33.3% to doxycycline, 18.8%-40% to sulfamethoxazole compound, 50%-65.7% to ciprofloxacin, 50%-66.7% to cehazindme, 54.8%-66.7% to amikacin, 75%-100% to gentamicin, 81.3%-100% to piperacillin, 87.5%-100% to aztreonam and 93.5%-100% to imipenem. Aac(3)-I and ant(4')-II were not detected in these strains. The positive rates of the other 5 AME genes of aac(3)-II, ant(2'')-I, aac(6')-I, aac(3)-III, aac(3)-IV were 2.3%, 5.7%, 8%, 10%, and 10%, respectively. SMA strains producing ESBLs were found at the rate of 38.6%; 25% of the strains were MBL-producing, and 13.6% produced both ESBLs and MBLs. CONCLUSION: Most of the SMAs we isolated are multidrug-resistant through various mechanisms. The choice of antibiotics should be made according to the susceptibility results.

[An epidemiological investigation of bats carrying SARS-CoV in Guangzhou and its vicinity].

OBJECTIVE: To detect serve acute respiratory syndrome-associated coronavirus (SARS-CoV) and SARS-like-CoV in fruit bats captured in Guangzhou and its vicinity. METHODS: Totally 927 bats of 9 species (Cynopterus sphinx, Rousettus leschenaulti, Miniopterus schreibersi, Hipposideros pratti, Rhinolophusasinicus, Scotophilusakuhlii, Hipposideros Pomona, Rhinolophus affinis, and Rhinolophus pusillus) captured in Guangzhou and its vicinity from September 2004 to November 2005 were available for this investigation, from which 3,043 samples (813 throat swasb, 524 sera, 853 lung tissues and 853 colorectal tissue specimens) were obtained. SARS-Cov and SARS-like-CoV were detected in these specimens using diagnostic kit for novel coronavirus N protein (ELISA), SARS-CoV Virus RNA detection kit, fluorescence PCR, Genchip, RT-PCR and cell isolation culture methods. RESULTS AND CONCLUSION: No SARS-CoV and SARS-like-CoV were detected in the 3043 samples, indicating the current absence of SARS-CoV and SARS-like-CoV in the bats captured in Guangzhou and its vicinity.