scholarly journals Analyzing genetic mutations of porcine reproductive and respiratory syndrome virus strains by serial passages in cell line from field wild strain

2020 ◽  
Vol 4 (4) ◽  
pp. 857-867
Author(s):  
Bui Anh Thy ◽  
Lê Thanh Hòa ◽  
Trần Xuân Hạnh ◽  
Trần Linh Thước
Keyword(s):  
Amino Acid ◽  
Clinical Symptoms ◽  
Virulent Strain ◽  
Wild Strain ◽  
Variable Region ◽  
Molecular Data ◽  
Genetic Mutation ◽  
Respiratory Syndrome Virus ◽  
Structural Protein ◽  
Nucleotide Substitutions

In this study, we compared the genetic mutation and virulence of the attenuated PRRSV strains obtained by 95 serial passages in Marc-145 cells with the parental virulent strain (designated as BG81) isolated in Vietnam. Results showed that there were marked changes in virulence: pigs inoculated with BG81 exhibited high fever ( 41◦C), which lasted for 12 days, and presented typical clinical symptoms of PRRSV; otherwise, pigs inoculated with BG895 (from passage 95), maintained mean rectal temperature from 39,5oC to 39,9oC, did not develop any significant clinical symptoms. Whole genomes of the attenuated strains were significantly different, but their sequence lengths were conserved, i.e., 15,321 nucleotides. The attenuated strain from passage 95 (BG895) contained 38 nucleotide substitutions that resulted in 14 amino acid changes. Most of these changes (about 65%) occurred before passage 50. The 14 amino acid changes were distributed in Nsp1, Nsp4, Nsp9, Nsp10, GP2, E, GP3, GP4, GP5 and N. Specially, there were two single substitutes within a codon in ORF3, corresponding to parallel mutation at position F143L. However, structural protein (M) and eight non-structural proteins (Nsp2, Nsp3, Nsp5, Nsp6, Nsp7, Nsp8, Nsp11 and Nsp12) among the 19 PRRSV proteins, remained conserved, without any mutations and supposed for consideration as irrelative to the attenuation process. It is interesting that in the gene coding for the smallest structural protein (E protein), there was the highest mutation rate among all of the structural genes analyzed, and genetically, seemed to be a highly variable region. These changes may provide the molecular bases for the observation of the attenuated phenotype in pigs. Thus, our variation results obtained between the attenuated BG895 and the parental virulent BG81 strains provide appropriate molecular data for potential use to test and control the masterseed strain in production of a PRRSV vaccine in Vietnam.

scholarly journals Emerging Novel GII.P16 Noroviruses Associated with Multiple Capsid Genotypes

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 535 ◽  
Author(s):  
Leslie Barclay ◽  
Jennifer L. Cannon ◽  
Mary E. Wikswo ◽  
Annie R. Phillips ◽  
Hannah Browne ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Case ◽  
Molecular Data ◽  
Antigenic Drift ◽  
The Novel ◽  
Structural Protein ◽  
Protein Coding ◽  
Recombinant Viruses ◽  
The Us ◽  
Genomic Regions

Noroviruses evolve by antigenic drift and recombination, which occurs most frequently at the junction between the non-structural and structural protein coding genomic regions. In 2015, a novel GII.P16-GII.4 Sydney recombinant strain emerged, replacing the predominance of GII.Pe-GII.4 Sydney among US outbreaks. Distinct from GII.P16 polymerases detected since 2010, this novel GII.P16 was subsequently detected among GII.1, GII.2, GII.3, GII.10 and GII.12 viruses, prompting an investigation on the unique characteristics of these viruses. Norovirus positive samples (n = 1807) were dual-typed, of which a subset (n = 124) was sequenced to yield near-complete genomes. CaliciNet and National Outbreak Reporting System (NORS) records were matched to link outbreak characteristics and case outcomes to molecular data and GenBank was mined for contextualization. Recombination with the novel GII.P16 polymerase extended GII.4 Sydney predominance and increased the number of GII.2 outbreaks in the US. Introduction of the novel GII.P16 noroviruses occurred without unique amino acid changes in VP1, more severe case outcomes, or differences in affected population. However, unique changes were found among NS1/2, NS4 and VP2 proteins, which have immune antagonistic functions, and the RdRp. Multiple polymerase-capsid combinations were detected among GII viruses including 11 involving GII.P16. Molecular surveillance of protein sequences from norovirus genomes can inform the functional importance of amino acid changes in emerging recombinant viruses and aid in vaccine and antiviral formulation.

scholarly journals Identification of amino acid residues important for anti-IFN activity of porcine reproductive and respiratory syndrome virus non-structural protein 1

Virology ◽  
2012 ◽  
Vol 433 (2) ◽  
pp. 431-439 ◽  
Author(s):  
Lalit K. Beura ◽  
Sakthivel Subramaniam ◽  
Hiep L.X. Vu ◽  
Byungjoon Kwon ◽  
Asit K. Pattnaik ◽  
...  
Keyword(s):  
Amino Acid ◽  
Respiratory Syndrome Virus ◽  
Amino Acid Residues ◽  
Structural Protein

scholarly journals Molecular and Antigenic Characterization of a Highly Evolved Derivative of the Type 2 Oral Poliovaccine Strain Isolated from Sewage in Israel

2000 ◽  
Vol 38 (10) ◽  
pp. 3729-3734 ◽  
Author(s):  
Lester M. Shulman ◽  
Yosef Manor ◽  
Rachel Handsher ◽  
Francis Delpeyroux ◽  
Michael J. McDonough ◽  
...  
Keyword(s):  
Amino Acid ◽  
Geometric Mean ◽  
Wild Strain ◽  
Polio Eradication ◽  
Reproductive Capacity ◽  
Nucleotide Substitutions ◽  
Poliovirus Receptor ◽  
Antigenic Characterization ◽  
Highly Evolved

An unusual, highly diverged derivative of the Sabin type 2 oral poliovaccine (OPV) strain was recovered from environmental samples during routine screening for wild polioviruses. Virus was cultivated in L20B cells and then passaged on BGM cells at 40°C (RCT [reproductive capacity at supraoptimal temperature]-positive marker) to select against most OPV strains. All but 1 of 25 RCT-positive OPV-derived environmental isolates were antigenically and genetically (>99.5% VP1 sequence match) similar to the respective Sabin strains. However, isolate PV2/4568-1/ISR98 (referred to below as 4568-1) escaped neutralization with Sabin 2-specific monoclonal antibodies and cross-adsorbed sera, and had multiple nucleotide substitutions (220 of 2,646; 8.3%) in the P1 capsid region. Fourteen of the 44 associated amino acid substitutions in the capsid mapped to neutralizing antigenic sites. Neutralizing titers in the sera of 50 Israeli children 15 years old were significantly lower to 4568-1 (geometric mean titer [GMT], 47) than to Sabin 2 (GMT, 162) or to the prototype wild strain, PV2/MEF-1/EGY42 (GMT, 108). Two key attenuating sites had also reverted in 4568-1 (A481 to G in the 5′ untranslated region and the VP1 amino acid I143 to T), and the isolate was highly neurovirulent for transgenic mice expressing the poliovirus receptor (PVR-Tg21 mice). The extensive genetic divergence of 4568-1 from the parental Sabin 2 strain suggested that the virus had replicated in one or more people for ∼6 years. The presence in the environment of a highly evolved, neurovirulent OPV-derived poliovirus in the absence of polio cases has important implications for strategies for the cessation of immunization with OPV following global polio eradication.

scholarly journals Proposed Standardization of Neisseria meningitidis PorA Variable-Region Typing Nomenclature

1998 ◽  
Vol 5 (6) ◽  
pp. 845-855 ◽  
Author(s):  
Claudio T. Sacchi ◽  
Ana P. S. Lemos ◽  
Mary E. Brandt ◽  
Anne M. Whitney ◽  
Carmo E. A. Melles ◽  
...  
Keyword(s):  
Amino Acid ◽  
Neisseria Meningitidis ◽  
Dna Sequences ◽  
Vaccine Coverage ◽  
Variable Region ◽  
Molecular Data ◽  
Epidemiologic Studies ◽  
Amino Acid Sequences ◽  
Vaccine Candidates ◽  
Classification Schemes

ABSTRACT Neisseria meningitidis isolates are conventionally classified by serosubtyping, which characterizes the reactivities of the PorA outer membrane protein variable-region (VR) epitopes with monoclonal antibodies (MAbs). A newer method (PorA VR typing) uses predicted amino acid sequences derived from DNA sequence analysis. The resulting classification schemes are not standardized, offering conflicting and sometimes irreconcilable data from the two methods. In this paper, we propose a standardization of the PorA VR typing nomenclature that incorporates serologic information from traditional PorA serosubtyping with molecular data from predicted VR sequences. We performed a comprehensive literature and database search, generating a collection of strains and DNA sequences that reflects the diversity within PorA that exists to date. We have arranged this information in a comprehensive logical model that includes both serosubtype and PorA VR type assignments. Our data demonstrate that the current panel of serosubtype-defining MAbs underestimates PorA VR variability by at least 50%. Our proposal for VR typing is informative because amino acid sequence and serologic information, when serosubtype-defining MAbs are available, can be deduced simultaneously from the PorA VR designation. This scheme will be useful in future classification and applied epidemiologic studies of N. meningitidis, being a systematic way of selecting PorA vaccine candidates and analyzing vaccine coverage and failure.

Structural protein reorganization and fold emergence investigated through amino acid sequence permutations

Amino Acids ◽  
2014 ◽  
Vol 47 (1) ◽  
pp. 147-152
Author(s):  
Giovanni Minervini ◽  
Alessandro Masiero ◽  
Emilio Potenza ◽  
Silvio C. E. Tosatto
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Structural Protein

scholarly journals Diversity of 3′ variable region of cagA gene in Helicobacter pylori strains isolated from Chinese population

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Zhijing Xue ◽  
Yuanhai You ◽  
Lihua He ◽  
Yanan Gong ◽  
Lu Sun ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Helicobacter Pylori ◽  
Amino Acid ◽  
Chinese Population ◽  
Statistical Difference ◽  
Variable Region ◽  
Repeat Region ◽  
Geographical Regions ◽  
H Pylori ◽  
Epiya Motifs

Abstract Background The cytotoxin-associated gene A (cagA) is one of the most important virulence factors of Helicobacter pylori (H. pylori). There is a highly polymorphic Glu-Pro-Ile-Tyr-Ala (EPIYA) repeat region in the C-terminal of CagA protein. This repeat region is thought to play an important role in the pathogenesis of gastrointestinal diseases. The aim of this study was to investigate the diversity of cagA 3′ variable region and the amino acid polymorphisms in the EPIYA segments of the CagA C-terminal region of H. pylori, and their association with gastroduodenal diseases. Methods A total of 515 H. pylori strains from patients in 14 different geographical regions of China were collected. The genomic DNA from each strain was extracted and the cagA 3′ variable region was amplified by polymerase chain reaction (PCR). The PCR products were sequenced and analyzed using MEGA 7.0 software. Results A total of 503 (97.7%) H. pylori strains were cagA-positive and 1,587 EPIYA motifs were identified, including 12 types of EPIYA or EPIYA-like sequences. In addition to the four reported major segments, several rare segments (e.g., B′, B″ and D′) were defined and 20 different sequence types (e.g., ABD, ABC) were found in our study. A total of 481 (95.6%) strains carried the East Asian type CagA, and the ABD subtypes were most prevalent (82.1%). Only 22 strains carried the Western type CagA, which included AC, ABC, ABCC and ABCCCC subtypes. The CagA-ABD subtype had statistical difference in different geographical regions (P = 0.006). There were seven amino acid polymorphisms in the sequences surrounding the EPIYA motifs, among which amino acids 893 and 894 had a statistical difference with gastric cancer (P = 0.004). Conclusions In this study, 503 CagA sequences were studied and analyzed in depth. In Chinese population, most H. pylori strains were of the CagA-ABD subtype and its presence was associated with gastroduodenal diseases. Amino acid polymorphisms at residues 893 and 894 flanking the EPIYA motifs had a statistically significant association with gastric cancer.

scholarly journals The strength of selection is consistent across both domains of the MHC class I peptide-binding groove in birds

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Piotr Minias ◽  
Ke He ◽  
Peter O. Dunn
Keyword(s):  
Mhc Class I ◽  
Peptide Binding ◽  
Variable Region ◽  
Molecular Data ◽  
Class I ◽  
Amino Acid Polymorphism ◽  
Exon 2 ◽  
Peptide Binding Groove ◽  
Binding Groove ◽  
Avian Mhc

Abstract Background The Major Histocompatibility Complex (MHC) codes for the key vertebrate immune receptors responsible for pathogen recognition. Foreign antigens are recognized via their compatibility to hyper-variable region of the peptide-binding groove (PBR), which consists of two separate protein domains. Specifically, the PBR of the MHC class I receptors, which recognize intra-cellular pathogens, has two α domains encoded by exon 2 (α1) and exon 3 (α2) of the same gene. Most research on avian MHC class I polymorphism has traditionally focused exclusively on exon 3 and comparisons of selection between the two domains have been hampered by the scarcity of molecular data for exon 2. Thus, it is not clear whether the two domains vary in their specificity towards different antigens and whether they are subject to different selective pressure. Results Here, we took advantage of rapidly accumulating genomic resources to test for the differences in selection patterns between both MHC class I domains of the peptide-binding groove in birds. For this purpose, we compiled a dataset of MHC class I exon 2 and 3 sequences for 120 avian species from 46 families. Our phylogenetically-robust approach provided strong evidence for highly consistent levels of selection on the α1 and α2 domains. There were strong correlations in all selection measures (number of positively/negatively selected residues and dN/dS ratios) between both PBR exons. Similar positive associations were found for the level of amino acid polymorphism across the two domains. Conclusions We conclude that the strength of selection and the level of polymorphism are highly consistent between both peptide-binding domains (α1 and α2) of the avian MHC class I.

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