First Detection and Genetic Characterization of Equus Caballus Papillomavirus 1, 2 and 7 in China

Abstract Background: Nine species of Equus caballus papillomavirus (EcPV) have been reported to infect horses, however, there are so far no reports of such infections in China. Results: In our pioneer study with Chinese horses, we found EcPV-1 in intranasal papilloma and nasal swabs, EcPV-2 in nasal swabs and semen, and EcPV-7 primarily in semen. This indicates that EcPVs are indeed hosted by horses in China, and that EcPV-2 and 7 may be getting transmitted though breeding. Sequence analyses for complete genomic sequences of EcPV-1 (G2), EcPV-2 (XJ-KS1391) and EcPV-7 (XJ-zs1) were performed which indicated that EcPV-1, 2 and 7, that infect horses in China, share 99.3% nt identity with the already published sequences for EcPV-1, 2 and 7. These observations indicate that three types of EcPVs identified in the current study are highly similar variants of previously known types of EcPV-1, 2 and 7. Phylogenetic analysis based on L1 genes in GenBank showed that EcPV-1, 2 and 7, found in Chinese horses, are closely related to and clustered together with already known EcPV-1, 2 and 7, respectively. Conclusion: Our study provides a novel evidence for EcPVs infection and circulation in Chinese horses and thus lays the foundation for a systematic and detailed epidemiological study of these infections in Chinese horses.

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Abortion storm of Yili Horses is Associated with Equus Caballus Papillomavirus 2 Variant Infection

10.21203/rs.3.rs-1039587/v1 ◽

2021 ◽

Author(s):

Panpan Tong ◽

Ruli Duan ◽

Xiaozhen Song ◽

Nuerlan Palidan ◽

Haifeng Deng ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Epidemiological Study ◽

Causative Agent ◽

Equus Caballus ◽

Equine Arteritis Virus ◽

Bovine Papillomavirus ◽

Sequence Analyses ◽

Equid Herpesvirus ◽

Thoroughbred Horses ◽

Nasal Swabs

Abstract Background: Nine different species of Equus caballus papillomavirus (EcPV) and three bovine papillomavirus (BPV) have been reported to infect horses, however, there are so far no describing such infections in China. In January 2021, an abortion storm occurred in Yili horses, as a result of which 50 out of 93 aborted fetus samples were found to be negative for equid herpesvirus (EHV) and equine arteritis virus (EAV).Results: In our pioneer study with Chinese horses, we first found EcPV-2 in the nasal swabs (4/230, 1.7%) of Yili horses, and semen (3/18, 16.7%) of the Thoroughbred horses. This indicated that EcPV can be indeed hosted by horses in China, and that EcPV-2 might be transmitted though breeding. Further detection of EcPVs in the lung tissues of aborted fetus in Yili horses, which were originally negative for equid herpesviruses, established that EcPV-2 was positive in 19 of 50 samples, thereby indicating that EcPV-2 might be a new pathogen causing of abortions. Thereafter, the sequence analyses for L1 genes sequences of 26 China’s EcPV-2 were performed which indicated that EcPV-2, that primarily infected the horses in China, shared 98.3%-99.9% nt identity with the already published sequences for EcPV-2. These observations indicated that EcPV-2 identified in the current study were highly similar variants of the previously identified strains of EcPV-2. Phylogenetic analysis based on L1 genes in GenBank showed that EcPV-2, found in the Chinese horses, was closely related to and clustered together with an already known EcPV-2a lineage. Conclusion: Our study provides the first evidence related to EcPV-2 infection in the Chinese horses, which can serve as a causative agent for Yili horse abortions, and thus can possibly lay the foundation for a systematic and detailed epidemiological study of this infection in the Chinese horses.

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Genetic characterization of Chinese measles vaccines by analysis of complete genomic sequences

Journal of Medical Virology ◽

10.1002/jmv.21535 ◽

2009 ◽

Vol 81 (8) ◽

pp. 1477-1483 ◽

Cited By ~ 12

Author(s):

Yan Zhang ◽

Jianhui Zhou ◽

William J. Bellini ◽

Wenbo Xu ◽

Paul A. Rota

Keyword(s):

Genetic Characterization ◽

Genomic Sequences ◽

Complete Genomic

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Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽

10.3390/pathogens10020089 ◽

2021 ◽

Vol 10 (2) ◽

pp. 89

Author(s):

Jiayu Li ◽

Fuxian Yang ◽

Ruobing Liang ◽

Sheng Guo ◽

Yaqiong Guo ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Genetic Characterization ◽

Zoonotic Potential ◽

Common Occurrence ◽

High Genetic Diversity ◽

Gp60 Gene ◽

The Common ◽

Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

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Genetic characterization of E2 gene of classical swine fever virus by restriction fragment length polymorphism and phylogenetic analysis

Virus Genes ◽

10.1007/s11262-010-0465-8 ◽

2010 ◽

Vol 40 (3) ◽

pp. 389-396 ◽

Cited By ~ 17

Author(s):

Ning Chen ◽

Dejiang Li ◽

Xuemei Yuan ◽

Xiaoliang Li ◽

Hongxia Hu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Restriction Fragment Length Polymorphism ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Genetic Characterization ◽

Classical Swine Fever ◽

E2 Gene ◽

Restriction Fragment Length

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Genetic characterization of Cryptosporidium spp. and Giardia duodenalis in dogs and cats in Guangdong, China

Parasites & Vectors ◽

10.1186/s13071-019-3822-z ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 3

Author(s):

Jiayu Li ◽

Xiaoyu Dan ◽

Kexin Zhu ◽

Na Li ◽

Yaqiong Guo ◽

...

Keyword(s):

Risk Factors ◽

Genetic Characterization ◽

Giardia Duodenalis ◽

Ratio Analysis ◽

Infection Rates ◽

Sequence Analyses ◽

Chi Square ◽

Significant Difference ◽

Chi Square Test

Abstract Background There are only limited number of reports on molecular epidemiology of Cryptosporidium spp. and Giardia duodenalis in dogs and cats in China. This study was conducted to assess the infection rates, genetic identity, and public health potential of these parasites in dogs and cats in Guangdong, China. Methods PCR and sequence analyses were used to identify and genotype Cryptosporidium spp. and G. duodenalis in fecal samples from 641 dogs and 418 cats in Guangdong. Chi-square test and odds ratio analysis were used to compare the occurrence rates of these pathogens and identify risk factors for infection. Results The overall infection rates of Cryptosporidium spp. and G. duodenalis were 6.9% (44/641) and 9.4% (60/641) in dogs, and 6.2% (26/418) and 3.6% (15/418) in cats. Purebred cats (12.4%; χ2 = 5.110, OR = 2.8, P = 0.024) and dogs (10.8%; χ2 = 5.597, OR = 4.8, P = 0.018) were more likely to be infected by Cryptosporidium spp. and G. duodenalis, respectively. Dogs (12.0%; χ2 = 7.589, OR = 2.6, P = 0.006) and cats (13.6%; χ2 = 8.235, OR = 3.5, P = 0.004) under 6 months had significantly higher infection rates of Cryptosporidium spp. than older animals. Household (13.9%; χ2 = 10.279, OR = 2.6, P = 0.008) and pet shop dogs (11.0%; χ2 = 7.182, OR = 2.0, P = 0.048) had higher occurrence of Cryptosporidium spp., as was the case for G. duodenalis occurrence in experimental dogs (13.4%; χ2 = 9.223, OR = 1.9, P = 0.017). Cryptosporidium canis (n = 42), C. muris (n = 1) and Cryptosporidium rat genotype IV (n = 1) were identified in dogs, while C. felis (n = 21), C. parvum (n = 3), C. muris (n = 1) and Cryptosporidium rat genotype IV (n = 1) were identified in cats. In contrast, the canine-specific assemblages C (n = 27) and D (n = 26) and the feline-specific assemblage F (n = 14) were almost exclusively the only genotypes of G. duodenalis in dogs and cats, respectively. There was no significant difference in infection rates of Cryptosporidium spp. and G. duodenalis between diarrheal and non-diarrheal pets. Conclusions While domestic pets in Guangdong are infected with zoonotic Cryptosporidium species, they are mainly infected with host-specific G. duodenalis genotypes. Risk factors for infections differ between Cryptosporidium spp. and G. duodenalis and between dogs and cats.

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Characterization of intronic structures and alternative splicing in Phytophthora sojae by comparative analysis of expressed sequence tags and genomic sequences

Canadian Journal of Microbiology ◽

10.1139/w10-103 ◽

2011 ◽

Vol 57 (2) ◽

pp. 84-90 ◽

Cited By ~ 17

Author(s):

Danyu Shen ◽

Wenwu Ye ◽

Suomeng Dong ◽

Yuanchao Wang ◽

Daolong Dou

Keyword(s):

Comparative Analysis ◽

Alternative Splicing ◽

Expressed Sequence Tags ◽

Phytophthora Sojae ◽

Genomic Sequences ◽

Splice Sites ◽

Distinct Phylogenetic Lineage ◽

Expressed Sequence ◽

Complete Genomic

The oomycetes, a distinct phylogenetic lineage of fungus-like microorganisms, are heterokonts (stramenopiles) belonging to the supergroup Chromalveolata. Although the complete genomic sequences of a number of oomycetes have been reported, little information regarding the introns therein is available. Here, we investigated the introns of Phytophthora sojae , a pathogen that causes soybean root and stem rot, by a comparative analysis of genomic sequences and expressed sequence tags. A total of 4013 introns were identified, of which 96.6% contained canonical splice sites. The P. sojae genome possessed features distinct from other organisms at 5′ splice sites, polypyrimidine tracts, branch sites, and 3′ splice sites. Diverse repeating sequences, ranging from 2 to 10 nucleotides in length, were found at more than half of the intron–exon boundaries. Furthermore, 122 genes underwent alternative splicing. These data indicate that P. sojae has unique splicing mechanisms, and recognition of those mechanisms may lead to more accurate predictions of the location of introns in P. sojae and even other oomycete species.

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Physical and genetic characterization of cloned enterobactin genomic sequences from Escherichia coli K-12

Gene ◽

10.1016/0378-1119(85)90293-8 ◽

1985 ◽

Vol 34 (1) ◽

pp. 47-54 ◽

Cited By ~ 13

Author(s):

Timothy P. Fleming ◽

Mary Schrodt Nahiik ◽

J.B. Neilands ◽

Mark A. McIntosh

Keyword(s):

Escherichia Coli ◽

Genetic Characterization ◽

Genomic Sequences ◽

K 12

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Characterization of the Full-Length Genome Sequences and Phylogenetic Analysis of HDV Strains Isolated from Patients with Chronic HBV and HDV Infection in Kyrgyz Republic

Problems of Particularly Dangerous Infections ◽

10.21055/0370-1069-2020-1-124-132 ◽

2020 ◽

pp. 124-132

Author(s):

Yu. V. Ostankova ◽

K. A. Nogoybaeva ◽

E. B. Zueva ◽

K. T. Kasymbekova ◽

S. T. Tobokalova ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genetic Characterization ◽

Molecular Genetic ◽

Kyrgyz Republic ◽

Genotype 1 ◽

Hepatitis D ◽

Hdv Infection ◽

Molecular Genetic Characterization ◽

Hdv Genotype

Objective. The purpose of our work was molecular genetic characterization of the hepatitis D virus isolates, circulating in the region with high prevalence of HBV + HDV super-infection. Materials and methods. The study material was 64 blood serum samples obtained from Kyrgyz Republic residents - patients with chronic viral hepatitis B+D. The hepatitis D virus complete genomes were sequenced, followed by phylogenetic analysis. Results and discussion. Based on the phylogenetic analysis of 64 HDV samples, it was shown that HDV genotype 1 (96.9 %) predominates in the examined group compared with HDV genotype 2 (3.1 %). Sequences were submitted to GenBank under access No MN984407 through MN984470. When assessing the genetic variability over the examined HDV genotype 1 samples, the maximum genetic distance was 12,49 %, and the minimum – 7,41 %. Within individual clusters, the genetic distance averaged from 2.6 % to 8.5 %. Among the sequences in GenBank, the closest resemblance to the HDV-2 Kyr41 and Kyr43 samples (nucleotide identity was 92.31 % and 89.57 %, respectively) was shown for the virus described earlier in Yakutia (AJ309880). To study the genetic relationships between the analyzed HDV genotype 1 strains in comparison with the HDV reference sequences, the predicted amino acid sequence was studied (111–214). Although hepatitis B preventive measures, including vaccination, have reduced the hepatitis D incidence, there is no effective way to prevent HDV infection in HBV carriers in endemic areas. The HDV sequence molecular-genetic characterization in this study, as well as the viral genomic sequence phylogenetic analysis, will help identify pathogen transmission pathways to control and / or prevent the spread of infection.

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Characterization of Vibrio parahaemolyticus strains isolated from clinically asymptomatic seafood workers

FEMS Microbiology Letters ◽

10.1093/femsle/fnaa209 ◽

2020 ◽

Author(s):

Kaknokrat Chonsin ◽

Neunghatai Supha ◽

Chie Nakajima ◽

Yasuhiko Suzuki ◽

Orasa Suthienkul

Keyword(s):

Phylogenetic Analysis ◽

Food Safety ◽

Vibrio Parahaemolyticus ◽

Environmental Samples ◽

Genetic Characterization ◽

Processing Plants ◽

Pandemic Strains ◽

Phenotypic And Genetic Characterization ◽

Seafood Processing

Abstract Vibrio parahaemolyticus (VP) is a major cause of gastroenteritis outbreaks in Thailand and other countries due to the consumption of contaminated and undercooked seafood. However, there have been few reports of the molecular epidemiology of VP isolates from asymptomatic seafood handlers. Here, we report the phenotypic and genetic characterization of 61 VP isolates obtained from asymptomatic workers in two seafood processing plants. We found 24 O:K serotypes of which O11:KUT, O1:KUT and O3:KUT were the dominant serotypes. Analysis by PCR showed 12 isolates harbored either tdh or trh genes with the potential to be pathogenic VP strains. The presence of T3SS2α and T3SS2β genes was correlated with the presence of tdh and trh, respectively. Four tdh+ isolates were positive for pandemic marker. In this study, VP isolates were commonly resistant to ampicillin, cephazolin, fosfomycin and novobiocin. Phylogenetic analysis of VP1680 loci in 35 isolates from 17 asymptomatic workers, six gastroenteritis patients, seven environmental samples and five genomes from a database showed 22 different alleles. Gene VP1680 was conserved in tdh+ isolates and pandemic strains, that of trh + isolates was diverse. Asymptomatic workers carrying VP were the most likely source of contamination, which raises concerns over food safety in seafood processing plants.

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