Isolation and full-genome sequencing of porcine sapelovirus strain in piglets from Hainan province, China

2020 ◽  
Author(s):  
Hechao Zhu ◽  
Xinxin Li ◽  
Jingyi Xiong ◽  
Xiangmin Li ◽  
Huanchun Chen ◽  
...  
Keyword(s):  
Neurological Disorders ◽  
Genomic Sequence ◽  
Polyclonal Antibodies ◽  
Hainan Province ◽  
Rt Pcr ◽  
Full Genome Sequencing ◽  
The Family ◽  
Swine Population ◽  
Porcine Sapelovirus ◽  
Reference Strains

Abstract Background: Porcine sapelovirus (PSV) is a species of the genus Sapelovirus within the family Picornaviridae, which associated with facute diarrhoea, respiratory distress, reproductive failure, and severe neurological disorders in swine. The first isolate strian of PSV was reported in Hainan province, China in 2019. Results: We report the isolation, genomic sequence of PSV isolated from pig diarrhea samples. The PSV strain was correctly identified by RT-PCR, IFA, WB assays, which appeared spherical with a diameter of approximately 25 nm by TEM. We named the strain PSV HaN01-CH2019, and its full genomes were 7,551 bp nucleotides in length. Phylogenetic analysis revealed that PSV HaN01-CH2019 and Chinese HuN01 strain are related in comparing with other reference strains. Conclusions: We successfully isolated the first PSV strain in Hainan province and prepared polyclonal antibodies. It is evident that PSV infection has occurred in Hainan province, and therefore, active molecular and serological investigation is important to swine population. Moreover, veterinarians must pay attention to this diarrhoea and reinforce biosecurity measures to prevent PSV spread.

scholarly journals First Report of Coleus blumei viroid 2 from Commercial Coleus in China

Plant Disease ◽  
2011 ◽  
Vol 95 (4) ◽  
pp. 494-494 ◽  
Author(s):  
F. H. Fu ◽  
S. F. Li ◽  
D. M. Jiang ◽  
H. Q. Wang ◽  
A. Q. Liu ◽  
...  
Keyword(s):  
Ornamental Plant ◽  
Reference Sequence ◽  
Hainan Province ◽  
Rt Pcr ◽  
Specific Primers ◽  
First Report ◽  
Coleus Blumei ◽  
Blast Analysis ◽  
Pcr Product ◽  
The Family

Coleus (Coleus blumei) is an ornamental plant that is susceptible to infection by several viroids of the genus Coleviroid, which is a member of the family Pospiviroidae. Coleus blumei viroid (CbVd) -1 was first reported in commercial yellow coleus fields in Brazil in 1989 (1). In addition, CbVd-2, CbVd-3, and CbVd-4 have only been detected from coleus in Germany in 1996 (4). CbVd-5 and CbVd-6 were recently identified in China (2). In March 2010, leaves were collected from 50 symptomless coleus plants from a commercial nursery in Hainan Province, China. Total RNA was extracted from the leaves (3). Reverse transcription (RT)-PCR using CbVd-2 specific primers (forward: 5′-AGCTTACCTGGGTTCCCT-3′ and reverse: 5′-CTCTCCTCTATTTACTCTCTTCTC-3′) corresponding to positions 76 to 93 and 52 to 75 on the CbVd-2 reference sequence, respectively (GenBank Accession No. NC003682). Amplification of a 301-bp product was obtained from one sample. This PCR product was then cloned into pMD18-T (Takara, Dalian, China). Twelve positive clones were sequenced and the results were subjected to BLAST analysis. Sequence analysis showed that two sequences (GenBank Accessions Nos. HQ727542 and HQ727544) shared 99% identity with the reference sequence of CbVd-2 (NC003682), and four sequences (HQ727541, HQ727543, HQ727545 and HQ727547) had 99.34% identity with the reference sequence of CbVd-2 (NC003682). The proposed secondary structures of these variants have approximately 75% paired nucleotides. Results suggested the presence of CbVd-2, which is a member of the Coleviroid genus, Pospoviroidae family. To our knowledge, this is the first report of CbVd-2 from commercial coleus in China. References: (1) M. E. N. Fonseca et al. Fitopatol. Bras. 14:94, 1989. (2) W. Y. Hou et al. Arch. Virol. 154:993, 2009. (3) S. F. Li et al. Ann. Phytopathol. Soc. Jpn. 61:381, 1995. (4) R. L. Spieker et al. J. Gen. Virol. 77:2839, 1996.

scholarly journals First Report of Broad bean wilt virus 2 Infecting Bupleurum chinense in China

Plant Disease ◽  
2009 ◽  
Vol 93 (8) ◽  
pp. 844-844 ◽  
Author(s):  
C. Sui ◽  
J. H. Wei ◽  
Q. Q. Zhan ◽  
J. Zhang
Keyword(s):  
Medicinal Plant ◽  
Cdna Library ◽  
Genomic Sequence ◽  
Broad Bean ◽  
Rt Pcr ◽  
First Report ◽  
The Family ◽  
Local Lesions ◽  
Wilt Virus ◽  
Broad Bean Wilt Virus

Samples of the medicinal plant, Bupleurum chinense DC., were collected in October 2007 from the garden of the Institute of Medicinal Plant Development in Beijing. Partial fragments of the genomic RNA1 and RNA2 of Broad bean wilt virus 2 (BBWV-2) were obtained from the root cDNA library of these plants. Sequence analyses showed the 1,896-nt RNA1 fragment (GenBank No. FJ485684) encoding a portion of the RNA-dependent RNA polymerase (RdRp) and the 2,017-nt RNA2 fragment (No. FJ485685) encoding 612 amino acids of the complete large (LCP) and small coat protein (SCP), respectively. The amino acid identities of LCP and SCP were 90.8 to 96.7% compared with sequences of other BBWV-2 isolates deposited in the GenBank with the highest homology to Japanese IP (No. AB018698) and the lowest to Japanese 1-2 (No. AB018701). This strongly suggests that the B. chinense plants utilized for cDNA library construction were infected by what appears to be an isolate of BBWV-2. Seeds from the same batch were sown again in the same garden in May 2008. In August 2008, approximately 30% of these plants showed mosaic, distortion, and stunting. Reverse transcription (RT)-PCR amplicons were obtained from eight symptomatic plants using a pair of conserved primers for specific detection of viruses within the Fabavirus genus (2). A symptomless plant tested negative by RT-PCR. The same single 391-bp amplicon of RNA1 (No. FJ485686) obtained from five of those eight symptomatic plants were cloned and sequenced. Sequence comparison with the corresponding sequences of other BBWV-2 isolates showed that the sequenced isolate was most closely related to B935-a Chinese faba bean isolate (No. AF149425). Crude sap of one diseased B. chinense plant was used for mechanical inoculation to Chenopodium amaranticolor Coste & Reyn. Chlorotic local lesions were observed on inoculated leaves 5 days after inoculation, and subsequently, systemic mottle and malformed symptoms appeared on the upper leaves. Twelve plants were inoculated and all plants showed symptoms of virus infection. RT-PCR tests of inoculated indicator plants showing local lesions confirmed the presence of BBWV-2. To date, Clover yellow vein virus and Lettuce mosaic virus have been isolated from the genus Bupleurum (B. griffithii hort. and B. falcatum L. sensu lato) in Japan and Israel, respectively (1,3). Furthermore, to our knowledge, no genomic sequence of BBWV-2 naturally infecting plants in the family Umbelliferae/Apiaceae has been reported. Therefore, this is the first report of BBWV-2 on B. chinense (Umbelliferae/Apiaceae), which was designated as a BC isolate of BBWV-2. In China, BBWV-2 was reported to be infecting and causing heavy losses to many plant species mostly belonging to the family Leguminosae (4). B. chinense is a commonly used bulk medicinal plant mainly cultivated in Hebei, Sichuan, Gansu, and Shanxi provinces in China for decoction pieces and extracts of its dried roots, which are also exported to Japan, Korea, and Southeast Asia. These results demonstrate the need for further assessment of BBWV-2 incidence and the losses it may cause. References: (1) J. Cohen et al. Phytoparasitica 30:88, 2002. (2) R. M. Ferrer et al. J. Virol. Methods 144:156, 2007. (3) H. Yamamoto. Jpn. J. Phytopathol. 69:420, 2003. (4) X. P. Zhou et al. Acta Phytopathol. Sin. 26:347, 1996.

scholarly journals Detection and Characterization of Porcine Sapelovirus in Italian Pig Farms

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 966
Author(s):  
Eleonora Chelli ◽  
Luca De Sabato ◽  
Gabriele Vaccari ◽  
Fabio Ostanello ◽  
Ilaria Di Bartolo
Keyword(s):  
Phylogenetic Analyses ◽  
Whole Genome Sequence ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Genetic Characteristics ◽  
The Family ◽  
Polymerase Chain ◽  
Porcine Sapelovirus

Porcine sapelovirus (PSV) belongs to the genus Sapelovirus of the family Picornaviridae. PSV infects pigs asymptomatically, but it can also cause severe neurologic, enteric, and respiratory symptoms or reproductive failure. Sapelovirus infections have been reported worldwide in pigs. The objective of this study was to investigate the presence and the prevalence of PSV in Italian swine farms in animals of different ages to clarify the occurrence of the infection and the genetic characteristics of circulating strains. In the present study, 92 pools of fecal samples, collected from pigs across three farms, were analyzed by Reverse Transcriptase-polymerase Chain Reaction-PCR (RT-PCR). Fecal pools from young growers (63/64) were found positive for Sapelovirus in all farms while detection in sows (4/28) was observed in only one farm. Phylogenetic analyses of the 19 partial capsid protein nucleotide sequences (VP1) (6–7 each farm) enable the classification of the virus sequences into three distinct clades and highlighted the high heterogeneity within one farm. The whole genome sequence obtained from one strain showed the highest correlation with the Italian strain detected in 2015. The study adds novel information about the circulation and heterogeneity of PSV strains in Italy and considering the movement of pigs across Europe would also be informative for other countries.

scholarly journals Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 66
Author(s):  
Zoltán László ◽  
Péter Pankovics ◽  
Gábor Reuter ◽  
Attila Cságola ◽  
Ádám Bálint ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Background Information ◽  
Type Ii ◽  
Rt Pcr ◽  
Faecal Samples ◽  
The Family ◽  
Domestic Livestock

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

scholarly journals Chikungunya Manifestations and Viremia in Patients Who Presented to the Fever Clinic at Bangkok Hospital for Tropical Diseases during the 2019 Outbreak in Thailand

2021 ◽  
Vol 6 (1) ◽  
pp. 12
Author(s):  
Hisham A Imad ◽  
Juthamas Phadungsombat ◽  
Emi E Nakayama ◽  
Sajikapon Kludkleeb ◽  
Wasin Matsee ◽  
...  
Keyword(s):  
Chikungunya Virus ◽  
Clinical Manifestations ◽  
Clinical Findings ◽  
Acute Stage ◽  
Tropical Diseases ◽  
Healthy Individuals ◽  
Rt Pcr ◽  
Viral Loads ◽  
The Family ◽  
Systemic Symptoms

Chikungunya virus is an Alphavirus belonging to the family Togaviridae that is transmitted to humans by an infected Aedes mosquito. Patients develop fever, inflammatory arthritis, and rash during the acute stage of infection. Although the illness is self-limiting, atypical and severe cases are not uncommon, and 60% may develop chronic symptoms that persist for months or even for longer durations. Having a distinct periodical epidemiologic outbreak pattern, chikungunya virus reappeared in Thailand in December 2018. Here, we describe a cohort of acute chikungunya patients who had presented to the Bangkok Hospital for Tropical Diseases during October 2019. Infection was detected by a novel antigen kit and subsequently confirmed by real-time RT-PCR using serum collected at presentation to the Fever Clinic. Other possible acute febrile illnesses such as influenza, dengue, and malaria were excluded. We explored the sequence of clinical manifestations at presentation during the acute phase and associated the viral load with the clinical findings. Most of the patients were healthy individuals in their forties. Fever and arthralgia were the predominant clinical manifestations found in this patient cohort, with a small proportion of patients with systemic symptoms. Higher viral loads were associated with arthralgia, and arthralgia with the involvement of the large joints was more common in female patients.

scholarly journals Imunocompetent Mice Model for Dengue Virus Infection

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Denise Gonçalves ◽  
Rafael de Queiroz Prado ◽  
Eric Almeida Xavier ◽  
Natália Cristina de Oliveira ◽  
Paulo Marcos da Matta Guedes ◽  
...  
Keyword(s):  
Animal Model ◽  
Virus Infection ◽  
Dengue Virus ◽  
Viral Disease ◽  
Mice Model ◽  
Rt Pcr ◽  
Dengue Virus Infection ◽  
Dengue Disease ◽  
The Family ◽  
The World

Dengue fever is a noncontagious infectious disease caused by dengue virus (DENV). DENV belongs to the familyFlaviviridae, genusFlavivirus, and is classified into four antigenically distinct serotypes: DENV-1, DENV-2, DENV-3, and DENV-4. The number of nations and people affected has increased steadily and today is considered the most widely spread arbovirus (arthropod-borne viral disease) in the world. The absence of an appropriate animal model for studying the disease has hindered the understanding of dengue pathogenesis. In our study, we have found that immunocompetent C57BL/6 mice infected intraperitoneally with DENV-1 presented some signs of dengue disease such as thrombocytopenia, spleen hemorrhage, liver damage, and increase in production of IFNγand TNFαcytokines. Moreover, the animals became viremic and the virus was detected in several organs by real-time RT-PCR. Thus, this animal model could be used to study mechanism of dengue virus infection, to test antiviral drugs, as well as to evaluate candidate vaccines.

Expression of SSX-2 and SSX-4 Genes in Neuroblastoma

2002 ◽  
Vol 17 (4) ◽  
pp. 219-223 ◽  
Author(s):  
S.N. Chi ◽  
N.-K.V. Cheung ◽  
I.Y. Cheung
Keyword(s):  
Cytolytic T Lymphocytes ◽  
Rt Pcr ◽  
Normal Peripheral Blood ◽  
Normal Tissues ◽  
Cancer Testis Antigens ◽  
Stage 4 ◽  
The Family ◽  
Prognostic Utility ◽  
Stage 1 ◽  
Cancer Testis

The SSX genes are members of the family of cancer/testis antigens that encode tumor-associated antigens recognizable by autologous cytolytic T lymphocytes. Their expression is common in tumors of diverse lineages and absent in normal tissues except testis and thyroid. In this study, sixty-seven neuroblastomas (NB) (12 stage 1, 13 stage 2, 12 stage 3, 12 stage 4S and 13 stage 4) were examined by RT-PCR and a sensitive chemiluminescent detection method for SSX-2 and SSX-4 expression. Seventy-two percent (13/18) of stage 4 NB expressed SSX-2 and 67% (12/18) expressed SSX-4. SSX-2 and SSX-4 positivity correlated with metastatic NB stage 4 (p=0.02 and p=0.006, respectively). Sensitivity experiments showed SSX-2 detection was one tumor cell in 106 normal cells, and one in 104 for SSX-4. All normal tissues (n=6), with the exception of testis, normal bone marrow (BM, n=12) and normal peripheral blood (PBL, n=10) were negative for SSX-2 and SSX-4 expression. Thirty-two BM and 14 PBL obtained from 35 stage 4 NB patients at 24 months from their diagnosis were evaluated for SSX-2 expression. Unlike another cancer/testis antigen, GAGE, only one BM sample was positive, and no prognostic utility could be established. Further investigation of SSX expression at other relevant time points is warranted.

scholarly journals First Report of Cherry virus A in Sweet Cherry Trees in China

Plant Disease ◽  
2009 ◽  
Vol 93 (4) ◽  
pp. 425-425 ◽  
Author(s):  
W.-L. Rao ◽  
Z.-K. Zhang ◽  
R. Li
Keyword(s):  
Sweet Cherry ◽  
Community Gardens ◽  
Mottle Virus ◽  
Replicase Gene ◽  
Rt Pcr ◽  
First Report ◽  
Type Isolate ◽  
The Family ◽  
Flowering Cherry ◽  
Cherry Trees

Plants in the genus Prunus of the family Rosaceae are important fruit and ornamental trees in China. In June of 2007, sweet cherry (Prunus avium) trees with mottling and mosaic symptoms were observed in a private garden near Kunming, Yunnan Province. Twenty-four samples, six each from sweet cherry, sour cherry (P. cerasus), flowering cherry (P. serrulata), and peach (P. persica) were collected from trees in private and community gardens in the area. The peach and sour and flowering cherry trees did not show any symptoms. Total nucleic acids were extracted using a cetyltrimethylammoniumbromide (CTAB) extraction method, and the extracts were tested for the following eight viruses by reverse transcription (RT)-PCR: American plum line pattern virus, Apple chlorotic leaf spot virus, Cherry green ring mottle virus, Cherry necrotic rusty mottle virus, Cherry virus A (CVA), Little cherry virus 1, Prune dwarf virus, and Prunus necrotic ringspot virus. Only CVA was detected in two symptomatic sweet cherry trees by RT-PCR with forward (5′-GTGGCATTCAACTAGCACCTAT-3′) and reverse (5′-TCAGCTGCCTCAGCTTGGC-3′) primers specific to an 873-bp fragment of the CVA replicase gene (2). The CVA infection of the two trees was confirmed by RT-PCR using primers CVA-7097U and CVA-7383L that amplified a 287-bp fragment from the 3′-untranslated region (UTR) of the virus (1). Amplicons from both amplifications were cloned and sequenced. Analysis of the predicted amino acid sequences of the 873-bp fragments (GenBank Accession Nos. EU862278 and EU862279) showed that they were 98% identical with each other and 97 to 98% with the type isolate of CVA from Germany (GenBank Accession No. NC_003689). The 286-bp sequences of the 3′-UTR (GenBank Accession Nos. FJ608982 and FJ608983) were 93% identical with each other and 93 to 98% with the type isolate. The sequence indicated that the three isolates were very similar and should be considered to be the same strain. CVA is a member of the genus Capillovirus in the family Flexiviridae and has been previously reported in Europe, North America, and Japan. The contribution of CVA to the symptoms observed and its distribution in China remain to be evaluated. To our knowledge, this is the first report of CVA in sweet cherry in China. References: (1) M. Isogai et al. J. Gen. Plant Pathol. 70:288. (2) W. Jelkmann. J. Gen. Virol. 76:2015, 1995.

scholarly journals Rapid, sensitive, full genome sequencing of Severe Acute Respiratory Syndrome Virus Coronavirus 2 (SARS-CoV-2)

2020 ◽  
Author(s):  
Clinton R Paden ◽  
Ying Tao ◽  
Krista Queen ◽  
Jing Zhang ◽  
Yan Li ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Sanger Sequencing ◽  
Respiratory Syndrome Virus ◽  
Full Genome ◽  
Miseq Sequencing ◽  
Genomic Information ◽  
Rt Pcr ◽  
Full Genome Sequencing ◽  
High Quality ◽  
Global Pandemic

AbstractSARS-CoV-2 recently emerged, resulting a global pandemic. Rapid genomic information is critical to understanding transmission and pathogenesis. Here, we describe validated protocols for generating high-quality full-length genomes from primary samples. The first employs multiplex RT-PCR followed by MinION or MiSeq sequencing. The second uses singleplex, nested RT-PCR and Sanger sequencing.

scholarly journals Sequence variability ofChrysanthemum stunt viroidin different chrysanthemum cultivars

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2933 ◽  
Author(s):  
Hoseong Choi ◽  
Yeonhwa Jo ◽  
Ju-Yeon Yoon ◽  
Seung-Kook Choi ◽  
Won Kyong Cho
Keyword(s):  
Infectious Agents ◽  
Sequence Variability ◽  
Rt Pcr ◽  
Genome Sequences ◽  
Single Nucleotide ◽  
Genomic Variations ◽  
The Family ◽  
Chrysanthemum Plant ◽  
Single Nucleotide Variations ◽  
Polymerase Chain

Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein.Chrysanthemum stunt viroid(CSVd), a member of the familyPospiviroidae, causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity.

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