A recombinase polymerase amplification-based lateral flow strip assay for rapid detection of genogroup II noroviruses in the field

Jia, Tianhui; Yu, Yongxin; Wang, Yongjie

doi:10.1007/s00705-020-04798-x

Cited by 11 publications

(11 citation statements)

References 33 publications

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“…NoVs are genetically diverse RNA viruses, and thousands of NoV sequences have emerged in recent years (Chhabra et al, 2019 ; de Graaf et al, 2016 ; Jia et al, 2020 ). In 2013, 8951 NoV sequences were available from the NCBI database.…”

Section: Discussionmentioning

confidence: 99%

“…All NoV sequences available online were downloaded from NCBI nucleotide database ( https://www.ncbi.nlm.nih.gov/nucleotide/ ) on December 14, 2020 and then genotyped by using the Norovirus Typing Tool v.2.0 ( https://www.rivm.nl/mpf/typingtool/norovirus ). Sequences containing ORF1 only or having fewer than 1000 nucleotides (nt) were removed from analysis (Guo et al, 2018 ; Jia et al, 2020 ). The most abundant genotype was GII.4, with a sequence abundance of 52.7%.…”

Section: Methodsmentioning

confidence: 99%

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Updating a New Semi-nested PCR Primer Pair for the Specific Detection of GII Norovirus in Oysters

Liu

Jia

et al. 2022

Food Environ Virol

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Oysters are major transmission vectors of noroviruses (NoVs) in the environment. Outbreaks of NoVs are often associated with the consumption of NoV-contaminated oysters. Laboratory confirmation of suspected oyster samples is a critical step in the surveillance and control of NoVs. Because of non-specific amplification, false-positive results are frequently obtained by semi-nested RT-PCR with the presently widely used primer set (G2SKF/G2SKR). Here, a novel universal PCR primer set N (NG2OF/NG2OR) specific for genogroup II (GII) NoVs was designed based on all GII NoV sequences available in public databases. Specific products were obtained with the primer set N when the NoV-positive oysters, spiked with each of five representative genotypes of GII NoVs (GII.17, GII.13, GII.4, GII.3, and GII.12), were subjected to analyzing. No products were detected with the primer set N for the NoV-negative oysters, while the primer set C gave various non-specific bands. Twenty-three out of 156 fresh oyster samples were NoV-positive with both the primer set N and the classic primer set, while eight were NoV-positive solely with the primer set N. Compared with the classic primer set, the newly designed primer set N had a higher detection rate and improved specificity for GII NoVs in oyster samples. These results show that the novel PCR primer pair is specific and applicable for the detection of GII NoVs in oysters. Supplementary Information The online version contains supplementary material available at 10.1007/s12560-022-09511-6.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Updating a New Semi-nested PCR Primer Pair for the Specific Detection of GII Norovirus in Oysters

Liu

Jia

et al. 2022

Food Environ Virol

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“…Although RPA is thought to be one of the more advantageous tests than PCR in terms of time‐saving, it still creates confusion in terms of sensitivity and reliability. However, RT‐RPA has also been shown to be more sensitive than RT‐PCR, using lateral flow and real‐time detection (Amer et al., 2013; Jia et al.,2020). Thus, it allows to perform the reaction in mobile suitcases (Faye et al., 2015; Patel et al., 2016).…”

Section: Discussionmentioning

confidence: 99%

“…It is widely accepted that due to their specificity nucleic acid detection of viruses offers advantages over traditional methods such as cell culture and immunohistochemistry, especially with regard to time to result (Faye et al., 2015; Patel et al., 2016). RPA amplificates can be detected in an agarose gel after purification or by real‐time detection or lateral flow strip depending on the probe design (Abd El Wahed et al., 2013; Davi et al., 2019; Jia et al., 2020; Weili et al., 2021). RPA operates best at 37–42°C; therefore, the reaction can be carried out without using a thermal cycler and even by incubating the reaction tubes with body heat in your hands (Piepenburg et al., 2006; Wang et al., 2017).…”

Section: Introductionmentioning

confidence: 99%

Development of a recombinase polymerase amplification assay for viral haemorrhagic septicemia virus

Tamer

Benkaroun

Kuruçay

et al. 2022

Journal of Fish Diseases

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Viral diseases of fish cause significant economic losses in the aquaculture industry.Viral haemorrhagic septicemia virus (VHSV) is one of the most important viral diseases that affects more than 80 fish species. Detection of the disease, especially in the field, is critical to managing disease prevention and control programmes. Recombinase polymerase amplification (RPA) is an isothermal method with a very short amplification period and a single incubation temperature ranging from 37 to 42°C, which is a good alternative to the polymerase chain reaction (PCR). This study aimed to develop an RPA assay as sensitive as a real-time RT-PCR to detect VHSV. For this purpose, primers and probes are designed for the same targeted region of gG of VHSV. The ssRNA standards were prepared to find the detection limits of the assay. Detection limits were found ten-fold differences between real-time RT-PCR and real-time RT-RPA.While the detection limit of the RT-PCR was found as 95.5 viral RNA molecules/reaction in 95% probit value, the detection limit of RT-RPA was found as 943.75 viral RNA molecules/reaction in 95% probit value using ssRNA standards. These results show that RPA is a suitable test for VHSV Ie detection.

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“…However, it requires expensive and sophisticated thermal cyclers to complete the assay, which is not feasible for smaller, more basic laboratories. As alternatives, methods involving isothermal amplification technology have also been applied for the detection of norovirus, such as nuclear acid sequence-based amplification ( Patterson et al, 2006 ), loop-mediated isothermal amplification ( Luo et al, 2014 ), and recombinase polymerase amplification (RPA; Han et al, 2020 ; Jia et al, 2020 ). Unlike qPCR, isothermal amplification techniques do not require the use of sophisticated thermal cyclers, as in qPCR, which allows for simplification of the procedure and improved accessibility.…”

Section: Introductionmentioning

confidence: 99%

Development of a rapid and accurate CRISPR/Cas13-based diagnostic test for GII.4 norovirus infection

et al. 2022

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Genogroup II genotype 4 (GII.4) norovirus causes acute gastroenteritis in children, and its infection is more severe than that of other genotypes. Early and precise detection and treatment are critical for controlling its spread and reducing the severity of infection. In this study, a rapid and efficient isothermal assay for the GII.4 norovirus detection (GII.4-CRISPR detection) was developed based on the CRISPR/Cas13a system. The assay can be applied without expensive instrumentation, and the results can be read via both fluorescence and lateral flow strip (LFS). The analytical sensitivity of this assay was 5 copies/reaction, and there was no cross-reaction with other genotypes of norovirus or other clinically common pathogens. There was a coincidence rate of 100% between our assay and commercial quantitative polymerase chain reaction. GII.4-CRISPR detection improves upon the shortcomings of some previously established molecular methods of detection, particularly with regard to accessibility. It provides an alternative tool for outbreak control and early diagnosis of GII.4 norovirus infection.

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A recombinase polymerase amplification-based lateral flow strip assay for rapid detection of genogroup II noroviruses in the field

Cited by 11 publications

References 33 publications

Updating a New Semi-nested PCR Primer Pair for the Specific Detection of GII Norovirus in Oysters

Updating a New Semi-nested PCR Primer Pair for the Specific Detection of GII Norovirus in Oysters

Development of a recombinase polymerase amplification assay for viral haemorrhagic septicemia virus

Development of a rapid and accurate CRISPR/Cas13-based diagnostic test for GII.4 norovirus infection

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