scholarly journals Molecular Epidemiological Study of Porcine Epidemic Diarrhea from Winter 2020 to Spring 2021 in Jiangsu Province

2021 ◽  
Author(s):  
Tingfan Zhu ◽  
Jinhan Qian ◽  
Zijun Shen ◽  
Hongxia Shao ◽  
Kun qian ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Epidemiological Study ◽  
Amino Acid Identity ◽  
Jiangsu Province ◽  
Nucleotide Identity ◽  
Acid Identity ◽  
Molecular Epidemiological Study ◽  
Pig Farms ◽  
Porcine Epidemic Diarrhea

Abstract Background: Porcine epidemic diarrhea (PED) is an acute and highly contagious infectious disease caused by the porcine epidemic diarrhea virus (PEDV) that occurs most frequently from winter to spring. It is associated with high morbidity and mortality rates, especially among piglets, and causes huge losses in the pig industry. The aim of this molecular epidemiological study was to identify the current strains of PEDV that are prevalent in Jiangsu Province, China.Methods: From winter 2020 to spring 2021, 793 small intestine tissue, fecal, and anal swab samples were collected from 72 pig farms in 11 counties in the jurisdiction of 5 regions of Jiangsu Province (Yancheng, Suqian, Changzhou, Xuzhou, and Yangzhou). A highly variable region of the S gene was amplified and sequenced, and phylogenetic analysis was conducted to compare this sequence with corresponding sequences from reference strains deposited in GenBank. Results: A total of 457 samples from 57 pig farms were positive for PEDV: this implies a positivity rate of 79% (57/72) for pig farms and a sample positivity rate of 57.6% (457/793). The positivity rates were 78% (107/137) in Yancheng, 53% (218/409) in Suqian, 48% (94/195) in Changzhou, 80% (16/20) in Xuzhou, and 88% (14/16) in Yangzhou. Seven representative samples were selected for sequencing, and phylogenetic analysis showed that the seven isolated strains exhibited 88.0%–100% nucleotide identity and 87.3%–99% amino acid identity. Additionally, our isolates exhibited 88.3%–99.7% nucleotide identity and 88%–98.5% amino acid identity with the reference PEDV strains. Phylogenetic tree analysis indicated that there were considerable difference in the sources of the variants.Conclusions: PEDV had a high infection rate among pigs and is possibly the main pathogenic agent of pig diarrhea in Jiangsu province. Importantly, vaccines must be screened for their efficacy against the newly identified variants.

scholarly journals Molecular Characterization of the Porcine Group A Rotavirus NSP2 and NSP5/6 Genes from São Paulo State, Brazil, in 2011/12

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Bruna Rocha Passos Barbosa ◽  
Nara Thiers Cacciatori Galleti Bernardes ◽  
Laila Andreia Rodrigues Beserra ◽  
Fábio Gregori
Keyword(s):  
Amino Acid ◽  
Amino Acid Identity ◽  
Sao Paulo ◽  
Nucleotide Identity ◽  
Nucleotide Sequencing ◽  
São Paulo ◽  
Acid Identity ◽  
Paulo State ◽  
Pig Farms ◽  
São Paulo State

Rotaviruses are responsible for the acute diarrhea in various mammalian and avian species. The nonstructural proteins NSP2 and NSP5 are involved in the rotavirus replication and the formation of viroplasm, cytoplasmic inclusion bodies within which new viral particles morphogenesis and viral RNA replication occur. There are few studies on the genetic diversity of those proteins; thus this study aims at characterizing the diversity of rotavirus based on NSP2 and NSP5 genes in rotaviruses circulating in Brazilian pig farms. For this purpose, 63 fecal samples from pig farms located in six different cities in the São Paulo State, Brazil, were screened by nested RT-PCR. Seven strains had the partial nucleotide sequencing for NSP2, whereas in six, the total sequencing for NSP5. All were characterized as genotype H1 and N1. The nucleotide identity of NSP2 genes ranged from 100% to 86.4% and the amino acid identity from 100% to 91.5%. For NSP5, the nucleotide identity was from 100% to 95.1% and the amino acid identity from 100% to 97.4%. It is concluded that the genotypes of the strains circulating in the region of study are in agreement with those reported in the literature for swine and that there is the possibility of interaction between human and animal rotaviruses.

Variation analysis of the ORF5 gene of Porcine reproductive and respiratory syndrome virus

2004 ◽  
Vol 1 (3) ◽  
pp. 173-179
Author(s):  
Gao Zhi-Qiang ◽  
Guo Xin ◽  
Cha Zhen-Lin ◽  
Chen Yan-Hong ◽  
Yang Han-Chun
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Amino Acid Identity ◽  
Respiratory Syndrome Virus ◽  
Variation Analysis ◽  
Rt Pcr ◽  
Acid Identity ◽  
Pig Farms ◽  
Orf5 Gene

AbstractThree Porcine reproductive and respiratory syndrome virus (PRRSV) isolates (HB-1(sh)/2002, HB-2(sh)/2002 and JX-1/2002) were obtained from pig farms in Hebei and Jiangxi provinces, China. The complete ORF5 gene of the isolates was amplified using RT-PCR and sequenced. It was shown that ORF5 genes of all isolates encoded 200 amino acids. Comparing ORF5 genes of the three isolates and published sequences for five other PRRSV isolates in China, variation analysis showed that all of the isolates were of the American genotype, with 88.2–99.0% amino acid identity. ORF5 genes among BJ-4, S1 and J1 had higher similarity, sharing 98–99% identity of the deduced amino acids. HB-1(sh)/2002, HB-2(sh)/2002 and JX-1/2002 and CH-1a presented 92–96% identity among their ORF5 genes. Phylogenetic analysis revealed that these isolates could be divided into two subgroups based on the genetic distance of their ORF5 gene: the first subgroup comprised BJ-4, S1 and J1 and was closer to VR2332 and vaccine strains; the second included HB-1(sh)/2002, HB-2(sh)/2002, JX-1/2002 and CH-1a.

scholarly journals Phylogenetic relationships among haloalkaliphilic archaea of the family Natrialbaceae

2020 ◽  
Author(s):  
Shivakumara Siddaramappa
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Novel Species ◽  
Single Species ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Acid Identity ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Clade 1

ABSTRACTThe family Natrialbaceae is a member of the class Halobacteria of the archaeal phylum Euryarchaeota. Seventeen genera with validly or effectively published names are currently included within this family. In this study, using pairwise average nucleotide identity and average amino acid identity comparisons in conjunction with phylogenetic analysis, it has been shown that the family Natrialbaceae is highly diverse and contains several potentially novel species and genera that are yet to be fully characterized. The deduced proteome sequence-based phylogenetic tree, constructed using the alignment- and parameter-free method CVTree3, contained six major clades, with Salinarchaeum sp. Harcht-Bsk1 being the only representative within clade 1. Furthermore, Haloterrigena daqingensis was found to be closely related to Natronorubrum sediminis, and it is proposed that these archaea together represent a novel genus. Interestingly, Haloterrigena jeotgali, Haloterrigena thermotolerans, and Natrinema pellirubrum were found to be very closely related to each other, and it is proposed that they be merged into a single species. Notably, the type genus Natrialba itself appeared to be heterogenous and contains species that could be broadly classified among two genera. Likewise, the genus Natrinema is also heterogenous and contains species that could be classified among six genera. Altogether, 19 novel genera have been proposed to be created, and four haloalkaliphilic archaea hitherto recognized only using genus names are confirmed to represent novel species.

scholarly journals Identification of cytochrome P-450 1A (CYP1A) genes from two teleost fish, toadfish (Opsanus tau) and scup (Stenotomus chrysops), and phylogenetic analysis of CYP1A genes

1995 ◽  
Vol 308 (1) ◽  
pp. 97-104 ◽  
Author(s):  
H G Morrison ◽  
M F Oleksiak ◽  
N W Cornell ◽  
M L Sogin ◽  
J J Stegeman
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Teleost Fish ◽  
Amino Acid Identity ◽  
Coding Region ◽  
Acid Identity ◽  
Opsanus Tau ◽  
Pcr Product ◽  
Cytochrome P 450 ◽  
Stenotomus Chrysops

Cytochrome P-450-mediated responses to environmental challenges are well known in diverse animal taxa, but the evolution of the complex gene superfamily coding for these enzymes is poorly understood. Here we report a phylogenetic analysis of the cytochrome P-450 1A (CYP1A) genes including two new sequences determined from teleost fish, toadfish (Opsanus tau) and scup (Stenotomus chrysops). Degenerate PCR primers were used to amplify a 1.2 kbp fragment from liver cDNA. The toadfish PCR product was used as a probe to identify a full-length CYP1A clone from a toadfish liver cDNA library. The entire coding region of the scup CYP1A was obtained by rapid amplification of cDNA ends (RACE) using specific primers based on the sequence of the partial PCR product. The predicted protein sequences for toadfish and scup CYP1A shared 78% and 83% amino acid identity with rainbow trout CYP1A1 respectively. Amino acid identity with mammalian CYP1A proteins ranged from 51 to 60% for 505 aligned positions. Phylogenetic analysis of four teleost fish CYP1A genes (trout, toadfish, scup and plaice) and 12 mammalian CYP1A genes suggests a monophyletic origin of the teleost genes, with the trout gene being most divergent, and indicates three distinct groupings: mammalian 1A1, mammalian 1A2, and fish 1A. This supports the idea that the gene duplication event which gave rise to CYP1A1 and CYP1A2 occurred after the divergence of the lines leading to mammals and fish. These results establish a molecular phylogeny within the CYP1A subfamily, the first such detailed phylogenetic analysis within a cytochrome P-450 family.

scholarly journals Characterization of the Complete Genome and P0 Protein for a Previously Unreported Genotype of Cotton Leafroll Dwarf Virus, an Introduced Polerovirus in the United States

Plant Disease ◽  
2020 ◽  
Vol 104 (3) ◽  
pp. 780-786 ◽  
Author(s):  
Sofia Avelar ◽  
Roberto Ramos-Sobrinho ◽  
Kassie Conner ◽  
Robert L. Nichols ◽  
Kathy Lawrence ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome ◽  
The United States ◽  
Amino Acid Identity ◽  
Full Length ◽  
Dwarf Virus ◽  
Nucleotide Identity ◽  
Acid Identity ◽  
Cotton Leafroll Dwarf Virus

Virus-like disease symptoms consisting of leaf cupping, shortened internodes, and overall stunting were observed in commercial cotton fields in Alabama in 2017 to 2018. To determine the complete genome sequence of the suspected causal polerovirus, symptomatic leaf samples were collected in Macon County, Alabama, and subjected to Illumina RNA sequencing. Based on BLASTn analysis, the Illumina contig of 5,771 nt shared the highest nucleotide identity (approximately 95%) with members of the species Cotton leafroll dwarf virus (CLRDV) (genus Polerovirus; family Luteoviridae) from Argentina and Brazil. The full-length viral genome sequence was verified by reverse transcription (RT)-PCR amplification, cloning, and Sanger sequencing. The complete CLRDV genome of 5,865 nt in length shared 94.8 to 95.2% nucleotide identity with six previously reported CLRDV isolates. The genome of the CLRDV isolate amplified from Alabama samples (CLRDV-AL) has seven predicted open reading frames (ORFs). Viral proteins 1 to 5 (P1 to P5) shared 91.9 to 99.5% amino acid identity with the six CLRDV isolates from Argentina and Brazil. However, P0, the suppressor of host gene silencing, shared 82.4 to 88.5% pairwise amino acid identity with the latter CLRDV isolates. Phylogenetic analysis of the seven full-length CLRDV genomes resolved three sister clades: CLRDV-AL, CLRDV-typical, and CLRDV-atypical, respectively. Three recombination events were detected by the recombination detection program among the seven CLRDV isolates with breakpoints occurring along the genome. Pairwise nucleotide identity comparisons of ORF0 sequences for the three CLRDV-AL field isolates indicated that they were >99% identical, suggesting that this previously unknown CLRDV genotype represents a single introduction to Alabama.

scholarly journals Identification of a Progenitor of the CTX-M-9 Group of Extended-Spectrum β-Lactamases from Kluyvera georgiana Isolated in Guyana

2005 ◽  
Vol 49 (5) ◽  
pp. 2112-2115 ◽  
Author(s):  
Adam B. Olson ◽  
M. Silverman ◽  
David A. Boyd ◽  
Allison McGeer ◽  
Barbara M. Willey ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Chromosomal Region ◽  
Amino Acid Identity ◽  
Nucleotide Identity ◽  
Acid Identity ◽  
Extended Spectrum ◽  
M 14

ABSTRACT Chromosomal β-lactamase genes (bla KLUY) from six Kluyvera georgiana strains isolated in Guyana were cloned and expressed in Escherichia coli. KLUY-1 exhibited 100% amino acid identity with the extended-spectrum β-lactamase CTX-M-14. We also show that a 2.7-kb Kluyvera chromosomal region exhibits 99% nucleotide identity to a portion of In60 that includes bla CTX-M-9.

scholarly journals Identification of Tomato mosaic virus Infection in Lisianthus in Taiwan

Plant Disease ◽  
2003 ◽  
Vol 87 (12) ◽  
pp. 1537-1537 ◽  
Author(s):  
F.-J. Jan ◽  
C.-C. Chen ◽  
H. T. Hsu
Keyword(s):  
Amino Acid ◽  
Mosaic Virus ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Systemic Infection ◽  
Amino Acid Identity ◽  
Tomato Mosaic Virus ◽  
Nucleotide Identity ◽  
Acid Identity ◽  
Cp Gene

In recent years, Lisianthus (Eustoma russellianum (Don.) Griseb) has become popular as potted plants and cut flowers in Taiwan. They are grown in the central and southern regions of the island. Since 1998, diseased plants with mosaic symptoms, followed by necrosis of leaf tissues, were observed in commercial greenhouses and field-grown lisianthus. Newly emergent leaves were curled and smaller compared with those on healthy plants. These symptoms greatly decreased the commercial value of the crop. Rigid rods similar to tobamoviruses that measured 300 × 18 nm were found consistently associated with symptomatic plants. In July 2002, a virus culture was isolated from diseased lisianthus from Chiayi County, Taiwan and established and maintained in systemic hosts Nicotiana tabacum L. and N. benthamiana Domin. Chlorotic and necrotic spots developed on lisianthus leaves 1 to 2 weeks after inoculation with the virus; symptoms eventually became systemic. Virions were purified from inoculated N. tabacum. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed that the virus contained one 18-kDa (Mr) polypeptide. The virus reacted positively in agar gel double diffusion tests and enzyme-linked immunosorbent assays with antisera prepared to Tobacco mosaic virus (TMV) or Tomato mosaic virus (ToMV) (gifts of S. D. Yeh, National Chung Hsing University, Taichung, Taiwan). A viral coat protein (CP) gene approximately 0.5 kb was amplified by reverse transcription-polymerase chain reaction from total RNA prepared from infected N. benthamiana using 5′-GCGAGCCATGGATTCTTACTCAATTACT as a forward primer and 5′-ACTCTCGGATCCTTAAGATGCAGGTGCAGA as a reverse primer. Comparison of the 480-nt CP gene region with that of ToMV-OM (GenBank Accession No. X02144) (3) revealed 99.2% nucleotide identity and 99.4% amino acid identity. It shares, however, 74.4% nucleotide identity and 83.9% amino acid identity with CP genes of TMV-U1 (GenBank Accession No. AX040174) and TMV-vulgare (GenBank Accession No. J02415) (1). The virus induced local lesion responses similar to ToMV on inoculated N. tabacum cv. White Burley, N. sylvestris Speg. & Comes, and Datura stramonium L. Inoculation of TMV, however, resulted in a systemic infection in these plants. Results from sequence analysis and diagnosis based on host reaction to the virus inoculation indicated that the tobamovirus infecting lisianthus in Taiwan is an isolate of ToMV. The virus is economically important to lisianthus and tomato in Taiwan. To our knowledge, this is the first report of ToMV causing disease on lisianthus in Taiwan. The disease was previously observed on lisianthus in Italy (2). References: (1) P. Goelet et al. Proc. Natl. Acad. Sci. USA 79:5818, 1982. (2) V. Lisa and A. Gera. Lisianthus. Pages 443–448 in: Virus and Virus-like Diseases of Bulb and Flower Crops. G. Loebenstein et al. eds. John Wiley and Sons, West Sussex, U.K., 1995. (3) T. Ohno et al. J. Biochem. 96:1915, 1984.

scholarly journals Genetic Heterogeneity and Recombination in Canine Noroviruses

2009 ◽  
Vol 83 (21) ◽  
pp. 11391-11396 ◽  
Author(s):  
Vito Martella ◽  
Nicola Decaro ◽  
Eleonora Lorusso ◽  
Arianna Radogna ◽  
Paschalina Moschidou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Heterogeneity ◽  
Environmental Contaminants ◽  
Amino Acid Identity ◽  
Human Strain ◽  
Capsid Gene ◽  
Nucleotide Identity ◽  
Fecal Samples ◽  
Acid Identity ◽  
Unique Strain

ABSTRACT Alphatronlike (genogroup IV [GIV]) noroviruses (NoVs) have been recently identified in carnivores. By screening a collection of 183 fecal samples collected during 2007 from dogs with enteric signs, the overall NoV prevalence was found to be 2.2% (4/183). A unique strain, Bari/91/07/ITA, resembled GIV.2 NoVs in its ORF1 (polymerase complex), while it was genetically unrelated in its full-length ORF2 (capsid gene) to GIV animal and human NoVs (54.0 to 54.4% amino acid identity) and to any other NoV genogroup (<54.7% amino acid identity). It displayed the highest identity (58.1% amino acid identity) to unclassified human strain Chiba/040502/04/Jp. Interestingly, the very 5′ end of ORF2 of the canine virus matched short noroviral sequences (88.9% nucleotide identity and 98.9% amino acid identity) identified from oysters in Japan, indicating that similar viruses may be common environmental contaminants.

Identification and characterization of Boone Cardiovirus, a novel virus of laboratory rats

2012 ◽  
Author(s):  
◽  
Judith Diane Gohndrone
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Western Blot ◽  
Amino Acid Identity ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Acid Identity ◽  
Laboratory Rats ◽  
Persistent Infections ◽  
Qrt Pcr

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Cardioviruses are members of the Picornaviridae family capable of causing several forms of disease including myocarditis, encephalitis, diabetes, fetal death, and neuron degeneration. A wide range of hosts are susceptible to cardioviruses with rodents frequently being suspected as the viral reservoir following outbreaks of infection. In this study we discovered a novel Cardiovirus, provisionally designated Boone Cardiovirus (BCV). BCV was identified in the feces of laboratory rats using a pan picornavirus-PCR assay. Phylogenetic analysis revealed that BCV is a new species within the Cardiovirus genus distinct from both Encephalomyelitis Virus (EMCV) and Theilovirus. With these two species, BCV shares [less-than]45% amino acid identity in the polyprotein region and [less-than]50% amino acid identity in the capsid proteins. To assess the prevalence of BCV in laboratory rodents a sensitive hemi-nested RT-PCR assay was developed to screen fecal samples. Screening revealed that 20% of rat samples and 30% of research institutions tested positive for BCV. During the screening process a second isolate of BCV was also identified. Phylogenetic analysis of the second isolate determined it shared 91% amino acid identity with the original strain in the polyprotein region. Identification of additional BCV strains aids in the understanding of BCV variability and provides additional information for the development of comprehensive PCR and serologic screening assays. As no definitive clinical disease has been observed with BCV, a quantitative RT-PCR (qRT-PCR) assay was developed to screen rat tissues for sites of replication. BCV was found predominately localized to the gastrointestinal tract with the highest titers in the duodenum. Screening animals of various ages also revealed that BCV causes persistent infections in laboratory rats. In addition, to the RT-PCR and qRT-PCR assays the VP2 protein was expressed and purified for use in Western blot analysis of rat serum for preliminary serologic data on BCV. Collectively, the RT-PCR and Western blot assays provide a foundation for BCV detection and will enable researchers to screen animals prior to experiments. These assays will also make it possible to establish BCV-free rat colonies as virally infected research animals can confound and invalidate research findings. Preliminary data from infections of nude rats suggest that BCV is capable of replication and the immune system of immunocompetent animals plays a role in modulating infections as once T-cell are eliminated viral titers are approximately 4 logs higher. Furthermore, the discovery of BCV may lead to the establishment of research models that can provide valuable information including host-viral interactions during persistent infections.

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