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. 2020 Dec:286:113974.
doi: 10.1016/j.jviromet.2020.113974. Epub 2020 Sep 16.

Value of swab types and collection time on SARS-COV-2 detection using RT-PCR assay

Min Liu  1 , Qianyuan Li  1 , Jun Zhou  1 , Wen Ai  1 , Xiaoling Zheng  1 , Jingjing Zeng  1 , Yuwen Liu  1 , Xiying Xiang  1 , Rong Guo  1 , Xiaoyin Li  1 , Xiandi Wu  1 , Haiying Xu  1 , Ling Jiang  1 , Huaqin Zhang  1 , Jing Chen  1 , Lili Tian  1 , Jun Luo  2 , Chunhua Luo  3
Affiliations

Value of swab types and collection time on SARS-COV-2 detection using RT-PCR assay

Min Liu et al. J Virol Methods. 2020 Dec.

Abstract

Objective: Low viral load from patients infected with SARS-CoV-2 during infection late stage easily lead to false negative nucleic acid testing results, thus having great challenges to the prevention and control of the current pandemic. In present study, we mainly aimed to evaluate specimen types and specimen collection timepoint on the positive detection of 2019 novel coronavirus from patients at infection late stage based on RT-PCR testing.

Methods: Paired nasopharyngeal swabs, nasal swabs, oropharyngeal swabs and anal swabs were collected from patients infected with SARS-CoV-2 during infection late stage before washing in the morning and afternoon on the same day. Then virus RNA was extracted and tested for 2019-nCoV identification by RT-PCR within 24 h.

Results: Viral load was low at late infection stage. Specimens collected before washing in the morning would increase the detection ratio of 2019-nCoV. Detection ratio of nasopharyngeal swab [65 (95 % CI: 49.51-77.87) vs 42.5(95 % CI: 28.51-57.8)] or nasal swab [57.5 (95 % CI: 42.2-71.49) vs 35 (95 % CI: 22.13-50.49)] is higher not only than oropharyngeal swab[22.5 (95 % CI: 12.32-37.5) vs 7.5 (95 % CI: 2.58-19.86)], but also anal swab[2.5 (95 % CI: 0.44-12.88) vs 5 (95 % CI: 1.38-16.5)].

Conclusions: In summary, our research discovers that nasopharyngeal or nasal swab collected before washing in the morning might be more suitable for detecting of large-scale specimens from patients infected with low SARS-CoV-2 load during infection late stage. Those results could facilitate other laboratories in collecting appropriate specimens for improving detection of SARS-CoV-2 from patients during infection late stage as well as initially screening.

Keywords: Collection timepoint; Positive detection rate; RT-PCR; SARS-Cov-2; Specimen types.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Recovery index of patients in this study. Note: The recovery index = The patient's hospitalization time on the day of testing /the patient's whole hospitalization time.
Fig. 2
Fig. 2
Ct value for different swab specimens collected before washing in the morning and afternoon. Note: Morning and afternoon show swab specimen were collected before washing in the morning and afternoon.
See this image and copyright information in PMC

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