Genetic diversity of tilapia lake virus genome segment 1 from 2011 to 2019 and a newly validated semi-nested RT-PCR method

AbstractThe gene of RNA viruses, encoding RNA-directed RNA polymerase (RdRp) is relatively conserved due to its crucial function in viral genome replication and transcription making it a useful target for genetic diversity study and PCR detection. In this study, we investigated the genetic diversity of 21 tilapia lake virus (TiLV) genome segment 1 sequences predictively coding for RdRp subunit P1. Those sequences were obtained from infected fish samples collected in Ecuador, Israel, Peru, and Thailand between 2011 and 2019 (nine sequences from this study and 12 sequences from GenBank). Primers were then designed from the highly conserved regions among all 21 TiLV segment 1 sequences and used in semi-nested RT-PCR condition optimization. The result revealed that all 21 TiLV segment 1 sequences showed 95.00-99.94 and 99.00-100% nucleotide and amino acid sequence identity, respectively. These isolates were phylogenically clustered into three separate genetic clades, called i) Israeli-2011 clade (containing of TiLV isolates from Israel collected in 2011, Ecuador, and Peru isolates), ii) monophyletic Israel-2012 clade (containing only TiLV isolates collected from Israel in 2012), and iii) Thai clade (containing only sequences obtained from Thailand isolates). The newly established PCR protocol was 100 times more sensitive than our previous segment 3-based protocol when comparatively assayed with RNA extracted from infected fish. The assay was also shown to be specific when tested against negative control samples, i.e. RNA extracted from clinical healthy tilapia and from bacterial and viral pathogens (other than TiLV) commonly found in aquatic animals. Validation experiment with RNA extracted from naturally infected fish specimens collected in 2013-2019 yielded positive test results for all samples tested, confirming that our newly designed primers and detection protocol against TiLV segment 1, have a potential application for detection of all current genetic variants of TiLV.

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Genetic diversity of tilapia lake virus genome segment 1 from 2011 to 2019 and a newly validated semi-nested RT-PCR method

Aquaculture ◽

10.1016/j.aquaculture.2020.735423 ◽

2020 ◽

Vol 526 ◽

pp. 735423 ◽

Cited By ~ 4

Author(s):

Suwimon Taengphu ◽

Pakkakul Sangsuriya ◽

Kornsunee Phiwsaiya ◽

Partho Pratim Debnath ◽

Jerome Delamare-Deboutteville ◽

...

Keyword(s):

Genetic Diversity ◽

Virus Genome ◽

Genome Segment ◽

Rt Pcr ◽

Pcr Method

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Development and initial evaluation of a real-time RT-PCR assay to detect bluetongue virus genome segment 1

Journal of Virological Methods ◽

10.1016/j.jviromet.2007.05.014 ◽

2007 ◽

Vol 145 (2) ◽

pp. 115-126 ◽

Cited By ~ 105

Author(s):

A.E. Shaw ◽

P. Monaghan ◽

H.O. Alpar ◽

S. Anthony ◽

K.E. Darpel ◽

...

Keyword(s):

Real Time ◽

Bluetongue Virus ◽

Virus Genome ◽

Genome Segment ◽

Initial Evaluation ◽

Rt Pcr ◽

Pcr Assay

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Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

Phytopathology ◽

10.1094/phyto-07-19-0253-fi ◽

2020 ◽

Vol 110 (1) ◽

pp. 106-120 ◽

Cited By ~ 1

Author(s):

Avijit Roy ◽

Andrew L. Stone ◽

Gabriel Otero-Colina ◽

Gang Wei ◽

Ronald H. Brlansky ◽

...

Keyword(s):

High Throughput Sequencing ◽

Sensu Stricto ◽

Genome Segment ◽

Rt Pcr ◽

Sequence Comparisons ◽

Orchid Fleck Virus ◽

Reverse Transcription Pcr ◽

Sequencing Technologies ◽

Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

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Automated Western immunoblotting detection of anti-SARS-CoV-2 serum antibodies

European Journal of Clinical Microbiology & Infectious Diseases ◽

10.1007/s10096-021-04203-8 ◽

2021 ◽

Author(s):

Sophie Edouard ◽

Rita Jaafar ◽

Nicolas Orain ◽

Philippe Parola ◽

Philippe Colson ◽

...

Keyword(s):

Negative Control ◽

Cross Reactivity ◽

Spike Protein ◽

Rt Pcr ◽

Substantial Agreement ◽

Western Immunoblotting ◽

Elisa Kit ◽

Line Test ◽

Serologic Assay ◽

Control Samples

AbstractELISA and chemiluminescence serological assays for COVID-19 are currently incorporating only one or two SARS-CoV-2 antigens. We developed an automated Western immunoblotting as a complementary serologic assay for COVID-19. The JessTM Simple Western system, an automated capillary-based assay, was used, incorporating an inactivated SARS-CoV-2 lineage 20a strain as the source of antigen, and total immunoglobulins (IgG, IgM, IgA) detection. In total, 602 sera were tested including 223 from RT-PCR-confirmed COVID-19 patients, 76 from patients diagnosed with seasonal HCoVs and 303 from coronavirus-negative control sera. We also compared this assay with the EUROIMMUN® SARS-CoV-2 IgG ELISA kit. Among 223 sera obtained from RT-PCR-confirmed COVID-19 patients, 180/223 (81%) exhibited reactivity against the nucleocapsid and 70/223 (31%) against the spike protein. Nucleocapsid reactivity was further detected in 9/76 (14%) samples collected from patients diagnosed with seasonal HCoVs and in 15/303 (5%) coronavirus-negative control samples. In the subset of sera collected more than 2 weeks after the onset of symptoms, the sensitivity was 94% and the specificity 93%, the latter value probably reflecting cross-reactivity of SARS-CoV-2 with other coronaviruses. The automated Western immunoblotting presented a substantial agreement (90%) with the compared ELISA (Cohen’s Kappa=0.64). Automated Western immunoblotting may be used as a second line test to monitor exposure of people to HCoVs including SARS-CoV-2.

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Trueness and precision of the real-time RT-PCR method for quantifying the chronic bee paralysis virus genome in bee homogenates evaluated by a comparative inter-laboratory study

Journal of Virological Methods ◽

10.1016/j.jviromet.2017.07.013 ◽

2017 ◽

Vol 248 ◽

pp. 217-225 ◽

Cited By ~ 4

Author(s):

Frank Schurr ◽

Nicolas Cougoule ◽

Marie-Pierre Rivière ◽

Magali Ribière-Chabert ◽

Hamid Achour ◽

...

Keyword(s):

Real Time ◽

Laboratory Study ◽

Virus Genome ◽

Rt Pcr ◽

The Real ◽

Pcr Method ◽

Paralysis Virus

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Identification and Differentiation of the Twenty Six Bluetongue Virus Serotypes by RT–PCR Amplification of the Serotype-Specific Genome Segment 2

PLoS ONE ◽

10.1371/journal.pone.0032601 ◽

2012 ◽

Vol 7 (2) ◽

pp. e32601 ◽

Cited By ~ 97

Author(s):

Narender S. Maan ◽

Sushila Maan ◽

Manjunatha N. Belaganahalli ◽

Eileen N. Ostlund ◽

Donna J. Johnson ◽

...

Keyword(s):

Bluetongue Virus ◽

Pcr Amplification ◽

Genome Segment ◽

Rt Pcr

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Nucleotide Sequence of Rice Dwarf Virus Genome Segment 9

Journal of General Virology ◽

10.1099/0022-1317-70-5-1297 ◽

1989 ◽

Vol 70 (5) ◽

pp. 1297-1300 ◽

Cited By ~ 11

Author(s):

I. Uyeda ◽

H. Kudo ◽

T. Takahashi ◽

T. Sano ◽

K. Ohshima ◽

...

Keyword(s):

Nucleotide Sequence ◽

Virus Genome ◽

Genome Segment ◽

Dwarf Virus ◽

Rice Dwarf Virus

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Prevalence and Genetic Diversity of Group A Rotavirus Genotypes in Moscow (2019–2020)

Pathogens ◽

10.3390/pathogens10060674 ◽

2021 ◽

Vol 10 (6) ◽

pp. 674

Author(s):

Anton Yuzhakov ◽

Ksenia Yuzhakova ◽

Nadezhda Kulikova ◽

Lidia Kisteneva ◽

Stanislav Cherepushkin ◽

...

Keyword(s):

Infectious Disease ◽

Genetic Diversity ◽

Acute Gastroenteritis ◽

Rt Pcr ◽

Clinical Hospital ◽

Group A Rotavirus ◽

Group A ◽

First Time ◽

Common Combination ◽

Children Under 5

Group A rotavirus (RVA) infection is the leading cause of hospitalization of children under 5 years old, presenting with symptoms of acute gastroenteritis. The aim of our study was to explore the genetic diversity of RVA among patients admitted to Moscow Infectious Disease Clinical Hospital No. 1 with symptoms of acute gastroenteritis. A total of 653 samples were collected from May 2019 through March 2020. Out of them, 135 (20.67%) fecal samples were found to be positive for rotavirus antigen by ELISA. RT-PCR detected rotavirus RNA in 80 samples. Seven G-genotypes (G1, G2, G3, G4, G8, G9, and G12) and three P-genotypes (P[8], P[4], and P[6]) formed 9 different combinations. The most common combination was G9P[8]. However, for the first time in Moscow, the combination G3P[8] took second place. Moreover, all detected viruses of this combination belonged to Equine-like G3P[8] viruses that had never been detected in Russia before. The genotype G8P[8] and G9P[4] rotaviruses were also detected in Moscow for the first time. Among the studied rotaviruses, there were equal proportions of Wa and DS-1-like strains; previous studies showed that Wa-like strains accounted for the largest proportion of rotaviruses in Russia.

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