Detection of SARS-CoV-2 in Different Types of Clinical Specimens

Abstract

An epidemic of respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in China and has spread to other countries. 1 Real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) of nasopharyngeal swabs typically has been used to confirm the clinical diagnosis. 2 However, whether the virus can be detected in specimens from other sites, and therefore potentially transmitted in other ways than by respiratory droplets, is unknown.Methods | We investigated the biodistribution of SARS-CoV-2 among different tissues of inpatients with coronavirus disease 2019 (COVID-19) diagnosed based on symptoms and radiology and confirmed by SARS-CoV-2 detection. This study was approved by the ethics commissions of the participating hospitals, with a waiver of informed consent.Patients with specimens collected based on clinical indications from 3 hospitals in the Hubei and Shandong provinces and Beijing, China, from January 1 through February 17, 2020, were included. Pharyngeal swabs were collected from most patients 1 to 3 days after hospital admission. Blood, sputum, feces, urine, and nasal samples were collected throughout the illness. Bronchoalveolar lavage fluid and fibrobronchoscope brush biopsy were sampled from patients with severe illness or undergoing mechanical ventilation. RNA was extracted from clinical specimens and determined by rRT-PCR targeting the open reading frame 1ab gene of SARS-CoV-2 as previously described. 2 The cycle threshold values of rRT-PCR were used as indicators of the copy number of SARS-CoV-2 RNA in specimens with lower cycle threshold values corresponding to higher viral copy numbers. A cycle threshold value less than 40 is interpreted as positive for SARS-CoV-2 RNA. Four SARS-CoV-2 positive fecal specimens with high copy numbers were cultured, and then electron microscopy was performed to detect live virus. Patterns in a subgroup of patients with multiple specimens collected during hospitalization were explored.

Coronavirus Disease (COVID-19): A primer for emergency physicians

“…75 Serum samples are not necessary. 75,76 J o u r n a l P r e -p r o o f Data regarding sensitivity and specificity for the test have not been published, but false negatives may be seen in asymptomatic individuals or those early in the course of their disease who may not have high viral burden. 27 Patients who test negative for COVID-19…”

COVID-19: a meta-analysis of diagnostic test accuracy of commercial assays registered in Brazil

“…Our study reports that antigen testing and/or molecular assays using nasopharyngeal and oropharyngeal specimens had high accuracy for SARS-CoV-2 detection. In China, the rate of SARS-CoV-2 detection was higher in oropharyngeal compared to nasopharyngeal swabs during the COVID-19 outbreak 9. Naso/oropharyngeal tests might miss early infection leading to a strategy of repeated testing since the likelihood of the SARS-CoV-2 being present in the nasopharynx increases with time.8 In the present study, the pooled sensitivity of tests using the detection of COVID-19 IgM antibodies in blood was lower compared to antigen/molecularPage 7 of 12 J o u r n a l P r e -p r o o f 7 assay detection in nasopharyngeal/oropharyngeal swabs (82% [95%CI 76-87] vs 97% [95%CI 85-99]).…”

COVID-19 and Dialysis Units: What Do We Know Now and What Should We Do?

“…Interestingly, a recent study examining detection of SARS-CoV-2 in different types of clinical specimens indicated that positivity was as low as 32% in pharyngeal swabs, with lower respiratory tract samples most often testing positive for the virus (in up to 93%). 5 Currently, most patients are diagnosed by clinical criteria although significant efforts are being placed on rapid, high-throughput testing.…”