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- Publisher Website: 10.1016/j.jcv.2020.104519
- Scopus: eid_2-s2.0-85087309967
- PMID: 32629187
- WOS: WOS:000552973400012
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Article: 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
Title | 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 |
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Authors | |
Keywords | SARS-CoV-2 Proteinase K Detection RT-PCR COVID-19 |
Issue Date | 2020 |
Publisher | Elsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/jcv |
Citation | Journal of Clinical Virology, 2020, v. 129, p. article no. 104519 How to Cite? |
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. |
Persistent Identifier | http://hdl.handle.net/10722/285299 |
ISSN | 2021 Impact Factor: 14.481 2020 SCImago Journal Rankings: 1.430 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Chu, AWH | - |
dc.contributor.author | Chan, WM | - |
dc.contributor.author | Ip, JD | - |
dc.contributor.author | Yip, CCY | - |
dc.contributor.author | Chan, JFW | - |
dc.contributor.author | Yuen, KY | - |
dc.contributor.author | To, KKW | - |
dc.date.accessioned | 2020-08-18T03:52:10Z | - |
dc.date.available | 2020-08-18T03:52:10Z | - |
dc.date.issued | 2020 | - |
dc.identifier.citation | Journal of Clinical Virology, 2020, v. 129, p. article no. 104519 | - |
dc.identifier.issn | 1386-6532 | - |
dc.identifier.uri | http://hdl.handle.net/10722/285299 | - |
dc.description.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. | - |
dc.language | eng | - |
dc.publisher | Elsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/jcv | - |
dc.relation.ispartof | Journal of Clinical Virology | - |
dc.subject | SARS-CoV-2 | - |
dc.subject | Proteinase K | - |
dc.subject | Detection | - |
dc.subject | RT-PCR | - |
dc.subject | COVID-19 | - |
dc.title | 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 | - |
dc.type | Article | - |
dc.identifier.email | Chu, AWH: awhchu@hku.hk | - |
dc.identifier.email | Chan, WM: mbally@hku.hk | - |
dc.identifier.email | Ip, JD: jdip1007@connect.hku.hk | - |
dc.identifier.email | Yip, CCY: yipcyril@hku.hk | - |
dc.identifier.email | Chan, JFW: jfwchan@hku.hk | - |
dc.identifier.email | Yuen, KY: kyyuen@hkucc.hku.hk | - |
dc.identifier.email | To, KKW: kelvinto@hku.hk | - |
dc.identifier.authority | Yip, CCY=rp01721 | - |
dc.identifier.authority | Chan, JFW=rp01736 | - |
dc.identifier.authority | Yuen, KY=rp00366 | - |
dc.identifier.authority | To, KKW=rp01384 | - |
dc.description.nature | link_to_OA_fulltext | - |
dc.identifier.doi | 10.1016/j.jcv.2020.104519 | - |
dc.identifier.pmid | 32629187 | - |
dc.identifier.pmcid | PMC7309780 | - |
dc.identifier.scopus | eid_2-s2.0-85087309967 | - |
dc.identifier.hkuros | 312813 | - |
dc.identifier.volume | 129 | - |
dc.identifier.spage | article no. 104519 | - |
dc.identifier.epage | article no. 104519 | - |
dc.identifier.isi | WOS:000552973400012 | - |
dc.publisher.place | Netherlands | - |
dc.identifier.issnl | 1386-6532 | - |