Evaluation of simple nucleic acid extraction methods for the detection of SARS-CoV-2 in nasopharyngeal and saliva specimens during global shortage of extraction kits

J Clin Virol. 2020 Aug:129:104519. doi: 10.1016/j.jcv.2020.104519. Epub 2020 Jun 23.

Abstract

Background: The severe shortage of nucleic acid extraction kits during the current COVID-19 pandemic represents a key limiting factor in testing capacity.

Objectives: This study compared the results of SARS-CoV-2 RT-PCR using different simple nucleic acid extraction methods on nasopharyngeal and saliva specimens.

Study design: Fifty nasopharyngeal swab and saliva specimens previously tested positive for SARS-CoV-2 were retrieved. Three different methods of nucleic acid extraction were compared. The first method involves incubating the specimen with proteinase K, and then heat treatment at 98 °C for 5 min (PKH); the second method involves heat treatment at 98 °C for 5 min without proteinase K pre-incubation (heat only); the third method involves no pre-processing steps (direct). The products from all 3 methods were tested by SARS-CoV-2 RT-PCR.

Results: PKH had significantly higher positive rate in SARS-CoV-2 RT-PCR (80 %) than those of heat only (58 %; P = 0.001) or direct (56 %; P = 0.002). The median Ct value was significantly earlier for PKH (median Ct: 37.0, IQR 31.7-40) than that of heat only (median Ct: 40, IQR 36.2-41; P < 0.0001) and direct (median Ct, 37.5; IQR 33.9-41.0; P = 0.0049). Subgroup analysis showed that PKH had higher detection rate, lower limit of detection and earlier Ct values than the other two groups for both NPS and saliva specimens.

Conclusions: PKH pre-processing resulted in the highest detection rate of SARS-CoV-2 by RT-PCR, and represents an alternative method for nucleic acid extraction when commercial extraction kits are not available.

Keywords: COVID-19; Detection; Nucleic acid extraction; Proteinase K; RT-PCR; SARS-CoV-2.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Betacoronavirus / genetics
  • Betacoronavirus / isolation & purification*
  • COVID-19
  • COVID-19 Testing
  • Clinical Laboratory Techniques / methods
  • Coronavirus Infections / diagnosis*
  • Coronavirus Infections / virology
  • Hot Temperature
  • Humans
  • Nasopharynx / virology*
  • Pandemics
  • Pneumonia, Viral / diagnosis*
  • Pneumonia, Viral / virology
  • RNA, Viral / isolation & purification*
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • SARS-CoV-2
  • Saliva / virology*
  • Specimen Handling / methods*

Substances

  • RNA, Viral