High detection rates of picobirnaviruses in free roaming rats (Rattus spp.): Molecular characterization of complete gene segment-2

132 Background: Numerous resistance mechanisms have been postulated in progressive mCRPC. Determining the presence of putative predictive biomarkers in patients requires a real-time tumor assessment because the biology changes under the influence of the specific therapy(ies) that a patient (Pt) has received. We examined CTC and CTC subpopulation incidence and molecular characterization of tumors from Pts with progressive mCRPC to assess if determinants of resistance can be assessed through a CTC test. Methods: 48 samples from 21 unique progressive mCRPC pts treated with androgen receptor targeted (AR tx) therapies, 9 (43%) on Abiraterone plus Prednisone (AA+P) and 12 (57%) on Enzalutamide (E). Samples were collected and shipped to Epic Sciences, where cells were stained and CTC identified by fluorescent scanners and algorithmic analysis. CTCs, defined as classic (CK+ CD45- w/intact DAPI nuclei and distinct), apopotic (CK+, CD45-, non-intact nuclei) and CK- (CK-, CD45-, intact and distinct) were identified. CTCs reported per mL of blood and were examined for AR, PTEN & ERG. CTC data were analyzed in context of PSA, Veridex CTC (reported per 7.5mL of blood), and clinical history. Results: With Epic, all 21 pts had detectable CTCs (mdn 23 cells/ml, range 2 to 249), whereas with Veridex, 14 (67%) pts had > 5 CTC/7.5 ml (mdn 5 cells/7.5 ml, range 0 to >200). 0/7 (0%) with high AR responded to AA+P or E, 8/14 (53%) with low AR had a PSA decline and stable radiographic disease (median follow-up 12 wks). Variations in AR protein expression and localization heterogeneity was seen in all pts to varying degrees. 6/21 (29%) Pts demonstrated CK- CTC/CTC ratio >50% (mdn 9 cells/ml, range 5-38). ERG rearrangement and PTEN loss were correlated. Conclusions: Epic CTC analysis provides higher detection rates, while enabling individual cell analyses for predictive biomarkers of sensitivity to AR directed therapies. Notable was the marked heterogeneity of detection of AR, ERG, and PTEN of individual CTCs. Studies are ongoing to further explore associations with outcomes. [Table: see text]

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Detection and Molecular Characterization of Picobirnaviruses (PBVs) in the Mongoose: Identification of a Novel PBV Using an Alternative Genetic Code

Viruses ◽

10.3390/v12010099 ◽

2020 ◽

Vol 12 (1) ◽

pp. 99 ◽

Cited By ~ 1

Author(s):

Alyssa Kleymann ◽

Anne A. M. J. Becker ◽

Yashpal S. Malik ◽

Nobumichi Kobayashi ◽

Souvik Ghosh

Keyword(s):

Genetic Code ◽

Molecular Characterization ◽

Gene Sequence ◽

Gene Segment ◽

Host Cells ◽

Rdrp Gene ◽

The Novel ◽

High Genetic Diversity ◽

Mitochondrial Genetic Code

We report high rates of detection (35.36%, 29/82) of genogroup-I (GI) picobirnaviruses (PBVs) in non-diarrheic fecal samples from the small Indian mongoose (Urva auropunctata). In addition, we identified a novel PBV-like RNA-dependent RNA polymerase (RdRp) gene sequence that uses an alternative mitochondrial genetic code (that of mold or invertebrate) for translation. The complete/nearly complete gene segment-2/RdRp gene sequences of seven mongoose PBV GI strains and the novel PBV-like strain were obtained by combining a modified non-specific primer-based amplification method with conventional RT-PCRs, facilitated by the inclusion of a new primer targeting the 3′-untranslated region (UTR) of PBV gene segment-2. The mongoose PBV and PBV-like strains retained the various features that are conserved in gene segment-2/RdRps of other PBVs. However, high genetic diversity was observed among the mongoose PBVs within and between host species. This is the first report on detection of PBVs in the mongoose. Molecular characterization of the PBV and PBV-like strains from a new animal species provided important insights into the various features and complex diversity of PBV gene segment-2/putative RdRps. The presence of the prokaryotic ribosomal binding site in the mongoose PBV genomes, and analysis of the novel PBV-like RdRp gene sequence that uses an alternative mitochondrial genetic code (especially that of mold) for translation corroborated recent speculations that PBVs may actually infect prokaryotic or fungal host cells.

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Molecular characterization of a major outer capsid protein encoded by the Threadfin aquareovirus (TFV) gene segment 10 (S10)

Archives of Virology ◽

10.1007/s00705-005-0550-9 ◽

2005 ◽

Vol 150 (10) ◽

pp. 2021-2036 ◽

Cited By ~ 4

Author(s):

E. K. Seng ◽

Q. Fang ◽

Y. M. Sin ◽

T. J. Lam

Keyword(s):

Molecular Characterization ◽

Capsid Protein ◽

Gene Segment ◽

Outer Capsid Protein ◽

Outer Capsid

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Molecular characterization of full-length genomic segment 2 of a bovine picobirnavirus (PBV) strain: evidence for high genetic diversity with genogroup I PBVs

Journal of General Virology ◽

10.1099/vir.0.013987-0 ◽

2009 ◽

Vol 90 (10) ◽

pp. 2519-2524 ◽

Cited By ~ 29

Author(s):

S. Ghosh ◽

N. Kobayashi ◽

S. Nagashima ◽

T. N. Naik

Keyword(s):

Molecular Characterization ◽

Genetic Relatedness ◽

Gene Segment ◽

Sequence Comparisons ◽

High Genetic Diversity ◽

Double Stranded Rna ◽

Amplification Method ◽

Bovine Strain ◽

Single Primer

We report here the molecular characterization of a bovine genogroup I picobirnavirus strain RUBV-P detected from a 1-month-old diarrhoeic calf in eastern India. Sequence comparisons and phylogenetic analysis of a short stretch of gene segment 2 of RUBV-P revealed low nucleotide identities (51.2–64.9 %) with and distant genetic relatedness to other genogroup I picobirnaviruses. The complete gene segment 2 sequence of RUBV-P was obtained by the single primer amplification method with modifications. Gene segment 2 of RUBV-P was 1758 bp long, encoded a predicted protein of 554 aa and exhibited low nucleotide (58.1–58.8 %) and amino acid (51.3–55.4 %) identities with genogroup I human strains Hy005102 and 1-CHN-97. The 5′- and 3′-end nucleotide sequences, and the three motifs of RNA-dependent RNA polymerases of double-stranded RNA viruses, were conserved among these strains. Our findings suggested that bovine strain RUBV-P might be distinct from genogroup I picobirnaviruses of humans and other animals.

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Comparative molecular characterization of gene segment 11-derived NSP6 from lamb rotavirus LLR strain used as a human vaccine in China

Biologicals ◽

10.1016/j.biologicals.2005.11.005 ◽

2006 ◽

Vol 34 (4) ◽

pp. 265-272 ◽

Cited By ~ 7

Author(s):

K.V.K. Mohan ◽

R.I. Glass ◽

C.D. Atreya

Keyword(s):

Molecular Characterization ◽

Gene Segment ◽

Human Vaccine

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Detection and Molecular Characterization of Human Adenovirus Infections among Hospitalized Children with Acute Diarrhea in Shanghai, China, 2006–2011

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2017/9304830 ◽

2017 ◽

Vol 2017 ◽

pp. 1-6 ◽

Cited By ~ 5

Author(s):

Lijuan Lu ◽

Huaqing Zhong ◽

Liyun Su ◽

Lingfeng Cao ◽

Menghua Xu ◽

...

Keyword(s):

Molecular Characterization ◽

Acute Diarrhea ◽

Human Adenovirus ◽

Hospitalized Children ◽

Limited Data ◽

Rt Pcr ◽

Detection Rates ◽

Fecal Samples ◽

Viral Diarrhea

Background: Human adenovirus (HAdV) is considered a significant enteropathogen associated with sporadic diarrhea in children. However, limited data are available regarding the epidemiology of HAdV in hospitalized children with viral diarrhea in Shanghai. The aim of this study was to characterize the epidemiology of HAdVs and describe their association with acute diarrhea in hospitalized children.Methods: A total of 674 fecal samples were subjected to PCR or RT-PCR to detect RVA, HuCV, HAstV, and HAdV.Results: HAdV infections were detected in 4.7% (32/674) of specimens, with detection rates of 13.4% (11/82), 4.6% (8/174), 3.2% (4/124), 4.1% (3/74), 2.0% (2/100), and 3.3% (4/120) from 2006 to 2011, respectively. Comprehensive detection of the four viruses revealed the presence of a high percentage (90.6%) of coinfections among HAdV-positive samples, where HAdV+RVA was the most prevalent coinfection. Of the 32 HAdV-positive samples, 50.0% (16/32) were classified as HAdV-41, and 18.8% (6/32) were classified as HAdV-3. Almost 94.0% of children infected with HAdV were less than 24 months of age.Conclusions: These results clearly indicated diversity across the HAdV genotypes detected in inpatient children with acute diarrhea in Shanghai and suggested that HAdVs play a role in children with acute diarrhea.

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