Use of strips of rapid diagnostic tests as a source of ribonucleic acid for genomic surveillance of viruses: an example of SARS-CoV-2.

IF 4 3区医学 Q2 VIROLOGY

Virology Journal Pub Date : 2024-08-01 DOI:10.1186/s12985-024-02442-7

Alpha Kabiné Keita, Aminata Mbaye, Abdoul Karim Soumah, Kadio Jean Jacques Olivier Kadio, Haby Diallo, Thibaut Armel Chérif Gnimadi, Joel Balla Koivogui, Moriba Kowa Povogui, Jean Louis Monemou, Baba Traore, Nicole Vidal, Emilande Guichet, Ahidjo Ayouba, Eric Delaporte, Martine Peeters, Abdoulaye Toure, Alpha Kabinet Keita

{"title":"Use of strips of rapid diagnostic tests as a source of ribonucleic acid for genomic surveillance of viruses: an example of SARS-CoV-2.","authors":"Alpha Kabiné Keita, Aminata Mbaye, Abdoul Karim Soumah, Kadio Jean Jacques Olivier Kadio, Haby Diallo, Thibaut Armel Chérif Gnimadi, Joel Balla Koivogui, Moriba Kowa Povogui, Jean Louis Monemou, Baba Traore, Nicole Vidal, Emilande Guichet, Ahidjo Ayouba, Eric Delaporte, Martine Peeters, Abdoulaye Toure, Alpha Kabinet Keita","doi":"10.1186/s12985-024-02442-7","DOIUrl":null,"url":null,"abstract":"Background: This study aimed to demonstrate that the genomic material of SARS-CoV-2 can be isolated from strips of COVID-19 rapid diagnostic test cassettes.Method: It was a prospective cross-sectional study involving patients admitted to treatment centers and sampling sites in the city of Conakry, Guinea. A total of 121 patients were double sampled, and 9 more patients were tested only for RDT. PCR was conducted according to the protocol of the RunMei kit. Sequencing was performed by using the illumina COVIDSeq protocol. Nine COVID-19 RDTs without nasopharyngeal swabs were in addition tested.Result: Among the 130 COVID-19 RDTs, forty-seven were macroscopically positive, whereas seventy-two were positive according to PCR using RDT strip, while among the 121 VTM swabs, sixty-four were positive. Among eighty-three negative COVID-19 RDTs, twenty-seven were positive by PCR using RDT strip with a geometric mean Ct value of 32.49 cycles. Compared to those of PCR using VTM, the sensitivity and specificity of PCR using RDT strip were estimated to be 100% and 85.96%, respectively, with 93.39% test accuracy. Among the fifteen COVID-19 RDT extracts eligible for sequencing, eleven had sequences identical to those obtained via the standard method, with coverage between 75 and 99.6%.Conclusion: These results show that COVID-19 RDTs can be used as biological material for the genomic surveillance of SARS-CoV-2.","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":null,"pages":null},"PeriodicalIF":4.0000,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11295317/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Virology Journal","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1186/s12985-024-02442-7","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"VIROLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Background: This study aimed to demonstrate that the genomic material of SARS-CoV-2 can be isolated from strips of COVID-19 rapid diagnostic test cassettes.

Method: It was a prospective cross-sectional study involving patients admitted to treatment centers and sampling sites in the city of Conakry, Guinea. A total of 121 patients were double sampled, and 9 more patients were tested only for RDT. PCR was conducted according to the protocol of the RunMei kit. Sequencing was performed by using the illumina COVIDSeq protocol. Nine COVID-19 RDTs without nasopharyngeal swabs were in addition tested.

Result: Among the 130 COVID-19 RDTs, forty-seven were macroscopically positive, whereas seventy-two were positive according to PCR using RDT strip, while among the 121 VTM swabs, sixty-four were positive. Among eighty-three negative COVID-19 RDTs, twenty-seven were positive by PCR using RDT strip with a geometric mean Ct value of 32.49 cycles. Compared to those of PCR using VTM, the sensitivity and specificity of PCR using RDT strip were estimated to be 100% and 85.96%, respectively, with 93.39% test accuracy. Among the fifteen COVID-19 RDT extracts eligible for sequencing, eleven had sequences identical to those obtained via the standard method, with coverage between 75 and 99.6%.

Conclusion: These results show that COVID-19 RDTs can be used as biological material for the genomic surveillance of SARS-CoV-2.

查看原文本刊更多论文

使用快速诊断检测条作为病毒基因组监测的核糖核酸来源：以 SARS-CoV-2 为例。

背景：本研究旨在证明从COVID-19快速诊断试剂盒条中可以分离出SARS-CoV-2的基因组物质：本研究旨在证明可以从 COVID-19 快速诊断试剂盒的条带中分离出 SARS-CoV-2 的基因组物质：这是一项前瞻性横断面研究，涉及几内亚科纳克里市治疗中心和采样点的住院病人。共有 121 名患者接受了双重采样，另有 9 名患者仅接受了 RDT 检测。PCR 按照 RunMei 试剂盒的方案进行。采用 illumina COVIDSeq 方案进行测序。此外，还检测了 9 例没有鼻咽拭子的 COVID-19 RDT 患者：结果：在 130 份 COVID-19 RDT 中，47 份呈宏观阳性，72 份呈 RDT 条带 PCR 阳性，而在 121 份 VTM 拭子中，64 份呈阳性。在 83 份 COVID-19 RDT 阴性样本中，有 27 份在使用 RDT 条进行 PCR 检测时呈阳性，其几何平均 Ct 值为 32.49 个周期。与使用 VTM 进行 PCR 检测相比，使用 RDT 条形检测进行 PCR 检测的灵敏度和特异性分别为 100%和 85.96%，检测准确率为 93.39%。在符合测序条件的 15 份 COVID-19 RDT 提取物中，有 11 份的序列与标准方法获得的序列相同，覆盖率在 75% 到 99.6% 之间：这些结果表明，COVID-19 RDT 可用作监测 SARS-CoV-2 基因组的生物材料。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Virology Journal 医学-病毒学

CiteScore

7.40

自引率

2.10%

发文量

186

审稿时长

1 months

期刊介绍： Virology Journal is an open access, peer reviewed journal that considers articles on all aspects of virology, including research on the viruses of animals, plants and microbes. The journal welcomes basic research as well as pre-clinical and clinical studies of novel diagnostic tools, vaccines and anti-viral therapies. The Editorial policy of Virology Journal is to publish all research which is assessed by peer reviewers to be a coherent and sound addition to the scientific literature, and puts less emphasis on interest levels or perceived impact.