{"title":"SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction–based assays in Addis Ababa, Ethiopia","authors":"Wodneh G/meskel , Kassu Desta , Regasa Diriba , Mahlet Belachew , Martin Evans , Vlademir Cantarelli , Maritza Urrego , Abay Sisay , Atsbeha Gebreegziabxier , Adugna Abera","doi":"10.1016/j.ijregi.2024.100363","DOIUrl":null,"url":null,"abstract":"<div><h3>Objectives</h3><p>This study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)–based variant detection in Addis Ababa, Ethiopia.</p></div><div><h3>Methods</h3><p>A cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 μl RNA and 20 μl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive.</p></div><div><h3>Results</h3><p>A total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30.</p></div><div><h3>Conclusions</h3><p>The study data demonstrated that reverse transcription-PCR–based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.</p></div>","PeriodicalId":73335,"journal":{"name":"IJID regions","volume":null,"pages":null},"PeriodicalIF":1.5000,"publicationDate":"2024-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772707624000341/pdfft?md5=ade831902fc7cd79a9a262e56bdad848&pid=1-s2.0-S2772707624000341-main.pdf","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"IJID regions","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2772707624000341","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
引用次数: 0
Abstract
Objectives
This study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)–based variant detection in Addis Ababa, Ethiopia.
Methods
A cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 μl RNA and 20 μl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive.
Results
A total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30.
Conclusions
The study data demonstrated that reverse transcription-PCR–based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.