tetano
Editor, Senior Moderator
J Med Virol
. 2022 Jan 7.
doi: 10.1002/jmv.27559. Online ahead of print.
COMPARISON OF COVID-19 LABORATORY DIAGNOSIS BY COMMERCIAL KITS: EFFECTIVITY OF RT-PCR TO THE RT-LAMP
Yakup Artik[SUP] 1 [/SUP], Alp Bahadır Coşğun[SUP] 2 [/SUP], Nevra Pelin Cesur[SUP] 1 [/SUP], Nedret Hızel[SUP] 2 3 [/SUP], Yavuz Uyar[SUP] 2 [/SUP], Haydar Sur[SUP] 4 [/SUP], Alp Ayan[SUP] 5 [/SUP]
Affiliations
Abstract
Coronavirus disease 2019 or COVID-19 caused by Novel Corona virus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 or 2019-nCoV) is an ongoing pandemic which has emerging global effects that requires a rapid and reliable diagnostic testing. Quantitative reverse transcription PCR (q-RT-PCR) is the gold standard method for SARS-CoV- 2 detection. On the other hand, new approaches facilitate the diagnosis difficulties gradually. Reverse Transcription Loop-Mediated Isothermal Amplification (RT- LAMP) as one of these novel approaches may also contribute to the faster and cheaper field-based testing on the field. The present study was designed to evaluate this rapid screening diagnostic test that can give results in 30-45 minutes and to compare the effectiveness of LAMP to the q-RT-PCR. The thirty randomly chosen patient samples were generated by nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. The sample of quantification cycle (Cq) values were tested using RT-LAMP as well as by conventional q-RT-PCR. The patient samples were tested with four different kits (SENSObiz COVID-19 (SARS-CoV-2) LAMP Assay, The QIAseq DIRECT SARS-CoV-2 Kit, Biospeedy SARS-CoV-2 Variant Plus Kit, and CoVirion-CV19-2 SARS-CoV-2 OneStep RT-PCR Kit) and two different PCR devices (GDS Rotor-Gene Q Thermocycler and Inovia Technologies GenX series). Based on 30 patient samples, the positive/negative ratio (P/N) was 30/0 as Biospeedy and Covirion (positivity 100%), 28/2 as Qiagen kit (pozitify 93.3%) for the samples studied on the Inovia device while the same samples on the Rotor-Gene device was 30/0 as Biospeedy and Covirion (positivity 100%), 29/1 as Qiagen kit at the first day (96.7%). In the fifth day, the samples were studied in the Inovia device and respective results were obtained: 27/3 as Biospeedy (positivity 90%), 16/14 as Qiagen (positivity 53.3%), 28/2 as Covirion kit (positivity 93.3%). When these samples were studied in the Rotor-Gene device, it was 29/1 in Biospeedy and Covirion (positivity 96.7%), 19/11 in Qiagen kit (positivity 63.3%). When these samples were compared with the LAMP method it was found to be 19/11 (positivity 63.3%) on the first day and 18/12 (positivity %60) on the fifth day. SARS-CoV-2 test studies will contribute to the proactive approach of development of rapid diagnosis systems. LAMP approach presents promising results to monitor exposed individuals and also improves screening efforts in potential ports of entry. This article is protected by copyright. All rights reserved.
Keywords: Coronavirus; Covid-19; LAMP-PCR; SARS-CoV-2; q-RT-PCR.
. 2022 Jan 7.
doi: 10.1002/jmv.27559. Online ahead of print.
COMPARISON OF COVID-19 LABORATORY DIAGNOSIS BY COMMERCIAL KITS: EFFECTIVITY OF RT-PCR TO THE RT-LAMP
Yakup Artik[SUP] 1 [/SUP], Alp Bahadır Coşğun[SUP] 2 [/SUP], Nevra Pelin Cesur[SUP] 1 [/SUP], Nedret Hızel[SUP] 2 3 [/SUP], Yavuz Uyar[SUP] 2 [/SUP], Haydar Sur[SUP] 4 [/SUP], Alp Ayan[SUP] 5 [/SUP]
Affiliations
- PMID: 34997587
- DOI: 10.1002/jmv.27559
Abstract
Coronavirus disease 2019 or COVID-19 caused by Novel Corona virus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 or 2019-nCoV) is an ongoing pandemic which has emerging global effects that requires a rapid and reliable diagnostic testing. Quantitative reverse transcription PCR (q-RT-PCR) is the gold standard method for SARS-CoV- 2 detection. On the other hand, new approaches facilitate the diagnosis difficulties gradually. Reverse Transcription Loop-Mediated Isothermal Amplification (RT- LAMP) as one of these novel approaches may also contribute to the faster and cheaper field-based testing on the field. The present study was designed to evaluate this rapid screening diagnostic test that can give results in 30-45 minutes and to compare the effectiveness of LAMP to the q-RT-PCR. The thirty randomly chosen patient samples were generated by nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. The sample of quantification cycle (Cq) values were tested using RT-LAMP as well as by conventional q-RT-PCR. The patient samples were tested with four different kits (SENSObiz COVID-19 (SARS-CoV-2) LAMP Assay, The QIAseq DIRECT SARS-CoV-2 Kit, Biospeedy SARS-CoV-2 Variant Plus Kit, and CoVirion-CV19-2 SARS-CoV-2 OneStep RT-PCR Kit) and two different PCR devices (GDS Rotor-Gene Q Thermocycler and Inovia Technologies GenX series). Based on 30 patient samples, the positive/negative ratio (P/N) was 30/0 as Biospeedy and Covirion (positivity 100%), 28/2 as Qiagen kit (pozitify 93.3%) for the samples studied on the Inovia device while the same samples on the Rotor-Gene device was 30/0 as Biospeedy and Covirion (positivity 100%), 29/1 as Qiagen kit at the first day (96.7%). In the fifth day, the samples were studied in the Inovia device and respective results were obtained: 27/3 as Biospeedy (positivity 90%), 16/14 as Qiagen (positivity 53.3%), 28/2 as Covirion kit (positivity 93.3%). When these samples were studied in the Rotor-Gene device, it was 29/1 in Biospeedy and Covirion (positivity 96.7%), 19/11 in Qiagen kit (positivity 63.3%). When these samples were compared with the LAMP method it was found to be 19/11 (positivity 63.3%) on the first day and 18/12 (positivity %60) on the fifth day. SARS-CoV-2 test studies will contribute to the proactive approach of development of rapid diagnosis systems. LAMP approach presents promising results to monitor exposed individuals and also improves screening efforts in potential ports of entry. This article is protected by copyright. All rights reserved.
Keywords: Coronavirus; Covid-19; LAMP-PCR; SARS-CoV-2; q-RT-PCR.