A fully-integrated microfluidic chip for RNA-virus detection

RNA viruses are distributed in various environments, and most RNA viruses have been recently identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify their sequences. Therefore, this study generated a dataset of RNA-dependent RNA polymerase (RdRp) domains essential for all RNA viruses belonging to Orthornavirae. Also, the collected genes with RdRp domains from various RNA viruses were clustered by amino acid sequence similarity. For each cluster, a multiple sequence alignment was generated, and a hidden Markov model (HMM) profile was created if the number of sequences was greater than five. Using the 1,467 HMM profiles, we detected RdRp domains in the RefSeq RNA virus sequences, combined the hit sequences with the RdRp domains, and reconstructed the HMM profiles. As a result, 2,234 HMM profiles were generated from 12,316 RdRp domain sequences, and the dataset was named NeoRdRp. Additionally, using the UniProt dataset, we confirmed that almost all NeoRdRp HMM profiles could specifically detect RdRps in Orthornavirae. Furthermore, we compared the NeoRdRp dataset with two previously reported RNA virus detection methods to detect RNA virus sequences from metatranscriptome sequencing data. Our methods can identify most of the RNA viruses in the datasets; however, some RNA viruses were not detected, similar to the other two methods. The NeoRdRp can be improved by repeatedly adding new RdRp sequences and can be expected to be widely applied as a system for detecting various RNA viruses from metatranscriptome data.

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Using RT-PCR for plant RNA virus detection.

CAB Reviews Perspectives in Agriculture Veterinary Science Nutrition and Natural Resources ◽

10.1079/pavsnnr20094053 ◽

2009 ◽

Vol 4 (053) ◽

Author(s):

N Capote

Keyword(s):

Rna Virus ◽

Virus Detection ◽

Rt Pcr

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MRPrimerV: a database of PCR primers for RNA virus detection

Nucleic Acids Research ◽

10.1093/nar/gkw1095 ◽

2016 ◽

Vol 45 (D1) ◽

pp. D475-D481 ◽

Cited By ~ 6

Author(s):

Hyerin Kim ◽

NaNa Kang ◽

KyuHyeon An ◽

Doyun Kim ◽

JaeHyung Koo ◽

...

Keyword(s):

Rna Virus ◽

Virus Detection ◽

Pcr Primers

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RNA polymerization actuating nucleic acid membrane (RANAM)-based biosensing for universal RNA virus detection

Biosensors and Bioelectronics ◽

10.1016/j.bios.2021.113880 ◽

2021 ◽

pp. 113880

Author(s):

Dajeong Kim ◽

Sangwoo Han ◽

Yoonbin Ji ◽

Heejeong Youn ◽

Hyejin Kim ◽

...

Keyword(s):

Nucleic Acid ◽

Rna Virus ◽

Virus Detection ◽

Rna Polymerization

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No evidence of Zika, dengue, or chikungunya virus infection in field-caught mosquitoes from the Recife Metropolitan Region, Brazil, 2015

Wellcome Open Research ◽

10.12688/wellcomeopenres.15295.1 ◽

2019 ◽

Vol 4 ◽

pp. 93 ◽

Cited By ~ 2

Author(s):

Anita Ramesh ◽

Claire L. Jeffries ◽

Priscila Castanha ◽

Paula A. S. Oliveira ◽

Neal Alexander ◽

...

Keyword(s):

Adult Female ◽

Chikungunya Virus ◽

Rna Virus ◽

Virus Detection ◽

Geographic Area ◽

Metropolitan Region ◽

Physiological Status ◽

Mosquito Abundance ◽

Time Period ◽

Short Time

Background: The Recife Metropolitan Region (RMR), north-eastern Brazil, was the epicentre of the 2015 Zika virus (ZIKV) epidemic, which was followed by a 2016 chikungunya virus (CHIKV) epidemic. It historically has amongst the highest incidence of dengue virus (DENV) infections and is the only remaining focus of lymphatic filariasis (LF) in Brazil. In early 2015, a molecular xenomonitoring surveillance project focused on Culex (Cx.) quinquefasciatus commenced to inform LF elimination activities. Aedes (Ae.) aegypti mosquitoes were also collected, concurrent with the first microcephaly cases detected in the RMR. In terms of the 2015 ZIKV epidemic, these are the earliest known field-collected mosquitoes, preserved for potential RNA virus detection, when ZIKV was known to be circulating locally. Methods: Adult mosquitoes were collected in two sites (0.4 km2) of Sítio Novo, Olinda, RMR, from July 22 to August 21, 2015. Mosquitoes were morphologically identified, sorted by physiological status, and pooled (up to 10 mosquitoes per house per day or week). RNA was extracted, reverse transcribed and the cDNA tested by real-time PCR. Results: A total of 10,139 adult female Cx. quinquefasciatus and 939 adult female Ae. aegypti were captured. All female Ae. aegypti specimens were included within 156 pools and screened for ZIKV, DENV and CHIKV. In addition, a sub-set of 1,556 Cx. quinquefasciatus adult females in 182 pools were screened for ZIKV. No evidence of infection with any of the three arboviruses was found. Conclusions: The absence of arbovirus detection may have been expected given the extremely restricted geographic area and collection of mosquitoes during a very short time period of peak mosquito abundance (July–September), but low arbovirus circulation (November–March). However, this study demonstrates the potential to retrospectively screen for additional unexpected pathogens in situations of rapid emergence, such as occurred during the outbreak of ZIKV in the RMR.

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P–794 Prevalence of positivity for SARS-CoV–2 RNA in follicular fluid in infertile patients

Human Reproduction ◽

10.1093/humrep/deab130.793 ◽

2021 ◽

Vol 36 (Supplement_1) ◽

Author(s):

E Porcu ◽

L Cipriani ◽

M Dirodi ◽

N Calza ◽

P M Ciotti ◽

...

Keyword(s):

Follicular Fluid ◽

Rna Virus ◽

Transvaginal Ultrasound ◽

Virus Detection ◽

Oocyte Retrieval ◽

Viral Rna ◽

University Hospital ◽

Real Time Analysis ◽

Registration Number ◽

Infertile Patients

Abstract Study question Is Sars-Cov–2 present in the follicular fluid of infertile patients? Summary answer In the experience of the Infertility and IVF Unit, University Of Bologna, Italy, RNA of SARS-Cov–2 was not detected in the follicular fluid. What is known already Data on the risk of virus presence in reproductive cells and transmissibility in IVF procedures are very limited. In literature only one study reports the detection of SARS-Cov–2 viral RNA in oocytes of PCR positive women. Research of RNA in follicular fluid could be a marker able to indicate whether to continue IVF treatments in the case of swab-positive patients. Study design, size, duration Prospective study performed at Infertility and IVF Unit, Sant’Orsola University Hospital, University of Bologna, Italy, from March 2020 to January 2021. 451 IVF cycles were performed on 902 patients. In addition 59 cycles of oocyte cryopreservation were also performed to fertility preservation in oncological patients. In all positive swab patients was analyzed the follicular fluid for RNA virus detection. Participants/materials, setting, methods 961 patients underwent telephone triage before going to the IVF Center to identify subjects with suspected or confirmed infection. Body temperature was measured on all patients before entering the IVF Center. All patients were subjected to real-time analysis (RT PCR) of pharyngeal swab samples 48 hours before transvaginal ultrasound-guided oocyte retrieval. In case of positive swab, PCR was performed on follicular fluid. Main results and the role of chance In our population of infertile patients the incidence of SARS COV–2 infection positivity was 0.4% (4/961). No IVF treatments were suspended. The oocytes of the 4 women with positive swab were cryopreserved using closed devices stored in a special dedicated cryogenic container. No viral RNA was detected in the follicular fluid. Limitations, reasons for caution there are no limitations to the study. Wider implications of the findings: The absence of SARS-COV–2 RNA in the follicular fluid is a reassuring result in the storage and future use of oocytes. Trial registration number Not applicable

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