Performance of Oropharyngeal Swab Testing Compared With Nasopharyngeal Swab Testing for Diagnosis of Coronavirus Disease 2019-United States, January 2020-February 2020

The Infectious Diseases Society of America Guidelines on the Diagnosis of Coronavirus Disease 2019 (COVID-19): Molecular Diagnostic Testing

Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19) and for identifying asymptomatic carriage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The number of available SARS-CoV-2 nucleic acid detection tests continues to increase as does the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) developed an evidence-based diagnostic guideline to assist clinicians, clinical laboratorians, patients, and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss nuances of test result interpretation in a variety of practice settings, and highlight important unmet research needs related to COVID-19 diagnostic testing. IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. The panel agreed on 12 diagnostic recommendations. Access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention, and the public health response to COVID-19 infection. Information on the clinical performance of available tests continues to grow, but the quality of evidence of the current literature to support this updated molecular diagnostic guideline remains moderate to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is suggested for asymptomatic individuals with known or suspected contact with a COVID-19 case when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions. Evidence in support of rapid testing and testing of upper respiratory specimens other than nasopharyngeal swabs, which offer logistical advantages, is sufficient to warrant conditional recommendations in favor of these approaches.

Higher SARS-CoV-2 detection of oropharyngeal compared with nasopharyngeal or saliva specimen for molecular testing: a multicentre randomised comparative accuracy study

BACKGROUND

Testing is critical for detecting SARS-CoV-2 infection, but the best sampling method remains unclear.

OBJECTIVES

To determine whether nasopharyngeal swab (NPS), oropharyngeal swab (OPS) or saliva specimen collection has the highest detection rate for SARS-CoV-2 molecular testing.

METHODS

We conducted a randomised clinical trial at two COVID-19 outpatient test centres where NPS, OPS and saliva specimens were collected by healthcare workers in different orders for reverse transcriptase PCR testing. The SARS-CoV-2 detection rate was calculated as the number positive by a specific sampling method divided by the number in which any of the three sampling methods was positive. As secondary outcomes, test-related discomfort was measured with an 11-point numeric scale and cost-effectiveness was calculated.

RESULTS

Among 23 102 adults completing the trial, 381 (1.65%) were SARS-CoV-2 positive. The SARS-CoV-2 detection rate was higher for OPSs, 78.7% (95% CI 74.3 to 82.7), compared with NPSs, 72.7% (95% CI 67.9 to 77.1) (p=0.049) and compared with saliva sampling, 61.9% (95% CI 56.9 to 66.8) (p<0.001). The discomfort score was highest for NPSs, at 5.76 (SD, 2.52), followed by OPSs, at 3.16 (SD 3.16) and saliva samples, at 1.03 (SD 18.8), p<0.001 between all measurements. Saliva specimens were associated with the lowest cost, and the incremental costs per detected SARS-CoV-2 infection for NPSs and OPSs were US$3258 and US$1832, respectively.

CONCLUSIONS

OPSs were associated with higher SARS-CoV-2 detection and lower test-related discomfort than NPSs for SARS-CoV-2 testing. Saliva sampling had the lowest SARS-CoV-2 detection but was the least costly strategy for mass testing.

TRIAL REGISTRATION NUMBER

NCT04715607.

Nasal Septal Abscess as a Complication of COVID-19 Nasal Swab Test: A Case Report

Nasal swab tests are widely used to screen for coronavirus disease 2019 (COVID-19). Pain, discomfort, and the urge to sneeze are the most common complications of this screening method. We report a case of a 55-year-old female patient with beta-thalassemia major suffering from a nasal septal abscess (NSA) as a complication of a COVID-19 nasal swab test. Following the test, the patient only had mild nasal congestion. However, three days later, her clinical condition deteriorated, and she developed fever, and her level of consciousness decreased to lethargy and drowsiness. Physical examinations revealed a bilateral nasal abscess. She underwent surgical intervention, and the abscess was removed. For the first time in Iran, a case of NSA after a COVID-19 nasal swab test is reported. It is strongly recommended to exercise caution while performing nasal swab tests, especially in the elderly and patients at risk of bleeding or hemoglobinopathy.

When to test for COVID-19 using real-time reverse transcriptase polymerase chain reaction: a systematic review

OBJECTIVES

The aim of this study was to evaluate the time in days between symptom onset and first positive real-time reverse transcriptase polymerase chain reaction (RT-PCR) result for COVID-19.

METHODS

This systematic review was conducted in the MEDLINE (PubMed), Embase, and Scopus databases using the following descriptors: "COVID-19", "SARS-CoV-2", "coronavirus", "RT-PCR", "real time PCR", and "diagnosis".

RESULTS

The included studies were conducted in 31 different countries and reported on a total of 6831 patients. The median age of the participants was 49.95 years. The three most common symptoms were fever, cough, and dyspnea, which affected 4012 (58.68%), 3192 (46.69%), and 2009 patients (29.38%), respectively. Among the 90 included studies, 13 were prospective cohorts, 15 were retrospective cohorts, 36 were case reports, 20 were case series, and six were cross-sectional studies. The overall mean time between symptom onset and positive test result was 6.72 days. Fourteen articles were analyzed separately for the temporal profile of RT-PCR test results; the best performance was on days 22-24, when 98% of test results were positive.

CONCLUSION

These findings corroborate the RT-PCR COVID-19 testing practices of some health units. In addition, the most frequently described symptoms of these patients can be considered the initial symptoms of infection and used in decision-making about RT-PCR testing.

Age and Sex Differences Among Mildly Symptomatic and Asymptomatic Patients with Omicron Infection in 2022 in Shanghai, China

Background

An epidemic of the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in March 2022, and over 600,000 cases were confirmed until early May 2022 in Shanghai, China. Data on Omicron infections are available in other countries, but the clinical features of patients in the Chinese population, especially in Shanghai, are still lacking. We collected data from a subset of asymptomatic and mildly ill patients to learn about the age and sex disparity of Omicron infection based on changes in cycle threshold values.

Methods

The basic information of 325 patients who were consecutively admitted to the Shanghai Geriatrics Center was collected through medical records, and patients were tested for viral nucleic acid carriage using nasal swab samples during hospitalization. SAS 9.4 was used for data analysis, and a p value < 0.05% was considered statistically significant.

Results

Among the 325 included patients, 58.8% were males, with a mean age of 47.2 years and 13.6 days of hospitalization on average. The average number of nucleic acid tests among female patients was 4.7, which was higher than that among male patients (4.1). The median value of the slope for cycle threshold (Ct) changes in the nucleic acid detection (NAD) test was 1.4. Logistic regression indicated that the proportion of slope for Ct changes >1.5 was slightly higher among male patients than among female patients (odds ratio (OR) = 1.06, 95% confidence interval (CI): 0.68–1.66), and patients aged <45 years and 45–59 years had a higher proportion of slope for Ct changes >1.5 than patients aged ≥60 years. Ct values were more variable in the early stages of infection and stabilized in the later stages of infection.

Conclusion

Among patients with mild illness or asymptomatic infection, the Ct value is a good, timely, and cost-effective method to reflect the recovery progress of patients. The slope of Ct changes was steeper among younger patients and male patients, which indicates faster disease recovery.

Molecular and antigen tests, and sample types for diagnosis of COVID-19: a review

Laboratory tests seeking to improve detection of COVID-19 have been widely developed by laboratories and commercial companies. This review provides an overview of molecular and antigen tests, presents the sensitivity and specificity for 329 assays that have received US FDA Emergency Use Authorization and evaluates six sample collection methods – nasal, nasopharyngeal, oropharyngeal swabs, saliva, blood and stool. Molecular testing is preferred for diagnosis of COVID-19, but negative results do not always rule out the presence of infection, especially when clinical suspicion is high. Sensitivity and specificity ranged from 88.1 to 100% and 88 to 100%, respectively. Antigen tests may be more easy to use and rapid. However, they have reported a wide range of detection sensitivities from 16.7 to 85%, which may potentially yield many false-negative results.

From SARS-CoV-2 infection to COVID-19 morbidity: an in silico projection of virion flow rates to the lower airway via nasopharyngeal fluid boluses

Background: While the nasopharynx is initially the dominant upper airway infection site for SARS-CoV-2, the physiologic mechanism launching the infection at the lower airway is still not well-understood. Based on the rapidity of infection progression to the lungs, it has been hypothesized that the nasopharynx may be acting as the primary seeding zone for subsequent contamination of the lower airway via aspiration of virus-laden boluses of nasopharyngeal fluids. Methodology: To examine the plausibility of the aspiration-driven mechanism, we have computationally tracked the inhalation process in three anatomic airway reconstructions and have quantified the nasopharyngeal liquid volume transmitted to the lower airspace during each aspiration. Results: Extending the numerical trends on aspiration volume to earlier records on aspiration frequencies indicates a total aspirated nasopharyngeal liquid volume of 0.3 – 0.76 ml/day. Subsequently, for mean sputum viral load, our modeling projects that the number of virions reaching the lower airway will range over 2.1×106 – 5.3×106 /day; for peak viral load, the corresponding number hovers between 7.1×108 – 1.8×109. Conclusions: The virion transmission findings fill in a key piece of the mechanistic puzzle on the systemic progression of SARS-CoV-2, and subjectively point to health conditions like dysphagia, with proclivity to increased aspiration, as some of the potential underlying risk factors for aggressive lung infections.

The challenges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing in low-middle income countries and possible cost-effective measures in resource-limited settings

Diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection remains a challenge around the world, especially in low-middle-income countries (LMICs) with poor socio-economic backgrounds. From the beginning of the pandemic in December 2019 to August 2021, a total of approximately 3.4 billion tests were performed globally. The majority of these tests were restricted to high income countries. Reagents for diagnostic testing became a premium, LMICs either cannot afford or find manufacturers unwilling to supply them with expensive analytical reagents and equipment. From March to December 2020 obtaining testing kits for SARS-CoV-2 testing was a challenge. As the number of SARS-CoV-2 infection cases increases globally, large-scale testing still remains a challenge in LMICs. The aim of this review paper is to compare the total number and frequencies of SARS-CoV-2 testing in LMICs and high-income countries (HICs) using publicly available data from Worldometer COVID-19, as well as discussing possible interventions and cost-effective measures to increase testing capability in LMICs. In summary, HICs conducted more SARS-CoV-2 testing (USA: 192%, Australia: 146%, Switzerland: 124% and Canada: 113%) compared to middle-income countries (MICs) (Vietnam: 43%, South Africa: 29%, Brazil: 27% and Venezuela: 12%) and low-income countries (LICs) (Bangladesh: 6%, Uganda: 4% and Nigeria: 1%). Some of the cost-effective solutions to counteract the aforementioned problems includes using saliva instead of oropharyngeal or nasopharyngeal swabs, sample pooling, and testing high-priority groups to increase the number of mass testing in LMICs.

Clinical evaluation of nasopharyngeal, midturbinate nasal and oropharyngeal swabs for the detection of SARS-CoV-2

In the setting of supply chain shortages of nasopharyngeal (NP) swabs, we sought to compare the ability of nasopharyngeal, midturbinate nasal, and oropharyngeal swabs (NPS, MTS, and OPS) to detect SARS-CoV-2. Community and hospitalized participants post-COVID-19 diagnosis were swabbed and tested for SARS-CoV-2 by PCR. Thirty-six participants had all 3 swabs collected. Using detection at any site as the standard, the percent positive agreements were 90% (95% CI 74.4−96.5), 80% (70.3−94.7) and 87% (62.7−90.5) for NPS, MTS, and OPS, respectively. Subsequently, 43 participants had OPS and NPS collected. Thirty-nine were positive with a percent positive agreement of 82.1% (95% CI 67.3−91.0) for OPS and 87.2% (73.3−94.4) for NPS. Combining all 79 patients tested, 67 were positive at either site with a positive agreement was 86.5% (76.4−92.7) for OPS and 91.1% (81.8−95.8) for NPS. OPS are an acceptable alternative to NPS for the detection of SARS-CoV-2 infections.

Different Respiratory Samples for COVID-19 Detection by Standard and Direct Quantitative RT-PCR: A Literature Review

The most common diagnostic method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR). Upper respiratory tract samples, including nasopharyngeal swab (NPS), oropharyngeal swab (OPS), saliva and lower respiratory tract samples such as sputum, are the most widely used specimens for diagnosis of SARS-CoV-2 using RT-qPCR. This study aimed to compare the diagnostic performance of different samples for Coronavirus disease 2019 (COVID-19) detection. It was found that NPS, the reference respiratory specimen for COVID-19 detection, is more sensitive than OPS. However, the application of NPS has many drawbacks, including challenging sampling process and increased risk of transmission to healthcare workers (HCWs). Saliva samples can be collected less invasively and quickly by HCWs with less contact or by own patients, and they can be considered as an alternative to NPS for COVID-19 detection by RT-qPCR. Additionally, sputum, which demonstrates higher viral load can be applied in patients with productive coughs and negative results from NPS. Commonly, after viral RNA purification from patient samples, which is time-consuming and costly, RT-qPCR is performed to diagnose SARS-CoV-2. Herein, different approaches including physical (heat inactivation) and chemical (proteinase K treatment) methods, used in RNA extraction free- direct RT-qPCR, were reviewed. The results of direct RT-qPCR assays were comparable to the results of standard RT-qPCR, while cost and time were saved. However, optimal protocol to decrease cost and processing time, proper transport medium and detection kit should be determined.

Accuracy of anterior nasal swab rapid antigen tests compared with RT-PCR for massive SARS-CoV-2 screening in low prevalence population

The aim was to determine the accuracy of anterior nasal swab in rapid antigen (Ag) tests in a low SARS‐CoV‐2 prevalence and massive screened community. Individuals, aged 18 years or older, who self‐booked an appointment for real‐time reverse transcriptase‐polymerase chain reaction (RT‐PCR) test in March 2021 at a public test center in Copenhagen, Denmark were included. An oropharyngeal swab was collected for RT‐PCR testing, followed by a swab from the anterior parts of the nose examined by Ag test (SD Biosensor). Accuracy of the Ag test was calculated with RT‐PCR as reference. We included 7074 paired conclusive tests (n = 3461, female: 50.7%). The median age was 48 years (IQR: 36–57 years). The prevalence was 0.9%, that is, 66 tests were positive on RT‐PCR. Thirty‐two had a paired positive Ag test. The sensitivity was 48.5% and the specificity was 100%. This study conducted in a low prevalence setting in a massive screening set‐up showed that the Ag test had a sensitivity of 48.5% and a specificity of 100%, that is, no false positive tests. The lower sensitivity is a challenge especially if Ag testing is not repeated frequently allowing this scalable test to be a robust supplement to RT‐PCR testing in an ambitious public SARS‐CoV‐2 screening.

High Seroprevalence of SARS-CoV-2 (COVID-19)-Specific Antibodies among Healthcare Workers: A Cross-Sectional Study in Guilan, Iran

Background

This study was conducted to evaluate the anti‐SARS‐CoV‐2 IgM and IgG antibodies among healthcare workers in Guilan.

Methods

This cross-sectional study was conducted on 503 healthcare workers. Between April and May 2020, blood samples were collected from the healthcare workers of Razi Hospital in Rasht, Guilan, Iran. Enzyme-linked immunosorbent assay (ELISA) was used for the detection and quantitation of anti‐SARS‐CoV‐2 IgM/IgG antibodies by using kits made by Pishtaz Teb Company, Tehran, Iran.

Results

From a total of 503 participants, the result of the anti‐SARS‐CoV‐2 IgM antibody test was positive in 28 subjects (5.6%) and the anti‐SARS‐CoV‐2 IgG antibody test was positive in171 subjects (34%). Participants in the age group of 35–54 years were significantly more likely to have a positive anti‐SARS‐CoV‐2 antibody test than the age group of 20–34 years (odds ratio = 1.53, 95% CI: 1.04–2.25, P=0.029). Also, physicians were significantly more likely to have a positive antibody test than office workers (odds ratio = 1.92, 95% CI: 1.04–3.54, P=0.037). The wide range of symptoms was significantly associated with the positive anti‐SARS‐CoV‐2 antibody test. The most significant association was observed between fever and a positive anti‐SARS‐CoV‐2 antibody test (odds ratio = 3.03, 95% CI: 2.06–4.44, P < 0.001).

Conclusion

The results of the current study indicated that the seroprevalence of COVID-19 was high among healthcare workers of Guilan Province. It seems that this finding was due to the earlier exposure to COVID-19 and the lack of awareness and preparedness to deal with the pandemic in Iran, compared to other countries.

Natural spring water gargle and direct RT-PCR for the diagnosis of COVID-19 (COVID-SPRING study)

Background

Nasopharyngeal swab has long been considered the specimen of choice for the diagnosis of respiratory viral infections, including SARS-CoV-2 infection, but it suffers from several drawbacks: its discomfort limits screening acceptability, and it is vulnerable to shortages in both specialized materials and trained healthcare workers in the context of a pandemic.

Methods

We prospectively compared natural spring water gargle to combined oro-nasopharyngeal swab (ONPS) for the diagnosis of coronavirus disease 2019 (COVID-19) in paired clinical specimens (1005 ONPS and 1005 gargles) collected from 987 unique early symptomatic as well as asymptomatic individuals from the community.

Results

Using a direct RT-PCR method with the Allplex™ 2019-nCoV Assay (Seegene), the clinical sensitivity of the gargle was 95.3% (95% confidence interval [CI], 90.2 – 98.3%), similar to the sensitivity of the ONPS (93.8%; 95% CI, 88.2 – 97.3%), despite significantly lower viral RNA concentration in gargles, as reflected by higher cycle threshold values. No single specimen type detected all COVID-19 cases. SARS-CoV-2 RNA was stable in gargles at room temperature for at least 7 days.

Conclusion

The simplicity of this sampling method coupled with the accessibility of spring water are clear advantages in a pandemic situation where testing frequency, turnaround time and shortage of consumables and trained staff are critical elements.

Salivary detection of COVID-19: clinical performance of oral sponge sampling for SARS-CoV-2 testing

BACKGROUND

The current diagnostic standard for coronavirus disease 2019 (COVID-19) is reverse transcriptase-polymerase chain reaction (RT-PCR) testing with nasopharyngeal (NP) swabs. The invasiveness and need for trained personnel make the NP technique unsuited for repeated community-based mass screening. We developed a technique to collect saliva in a simple and easy way with the sponges that are usually used for tamponade of epistaxis. This study was carried out to validate the clinical performance of oral sponge (OS) sampling for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing.

METHODS

Over a period of 22 weeks, we collected prospectively 409 paired NP and OS samples from consecutive subjects presenting to a public community-based free screening centre. Subjects were referred by their attending physician because of recent COVID-19 symptoms (n = 147) or by the contact tracing staff of the French public health insurance because they were considered as close contacts of a laboratory-confirmed COVID-19 case (n = 262).

RESULTS

In symptomatic subjects, RT-PCR SARS-CoV-2 testing with OS showed a 96.5% (95% CI: 89.6-94.8) concordance with NP testing, and a 93.2% (95% CI: 89.1-97.3) sensitivity when using the IdyllaTM platform and a sensitivity of 76.3% (95% CI: 69.4-83.2) on the Synlab Barla laboratory platform. In close contacts the NP-OS concordance (93.8%, 95% CI: 90.9-96.7) and OS sensitivity (71.9%, 95% CI: 66.5-77.3) were slightly lower.

CONCLUSION

These results strongly suggest that OS testing is a straightforward, low-cost and high-throughput sampling method that can be used for frequent RT-PCR testing of COVID-19 patients and mass screening of populations.

Chest computed tomography versus RT-PCR in early diagnostics of COVID-19 - a systematic review with meta-analysis

The purpose of this study was to compare the sensitivity and specificity of computed tomography (CT) scans of the chests of patients with the reference reverse-transcription real-time polymerase chain reaction (RT-PCR) in early diagnosis of COVID-19. A systematic review with meta-analysis for numerical outcomes was performed, including 10 studies (6528 patients). High risk of systematic bias (spectrum bias) was demonstrated in all studies, while in several studies research information bias was found to be possible. The sensitivity of CT examination ranged from 72% to 98%, and the specificity from 22% to 96%. The overall sensitivity of the CT scan was 91% and the specificity 87% (95% CI). Overall sensitivity of the RT-PCR reference test was lower (87%) than its specificity (99%) (95% CI). No clear conclusion could be drawn on the rationale of using CT scanning in the early diagnosis of COVID-19 in situations when specific clinical symptoms and epidemiological history would indicate coronavirus infection. The sensitivity of the CT test seems to be higher than that of the RT-PCR reference test, but this may be related to the mode of analysis and type of material analysed in genetic tests. CT scanning could be performed in symptomatic patients, with a defined time interval from symptom onset to performing CT or RT-PCR, and it should be explicitly included as an additional procedure when initial coronavirus genetic test results are negative, while clinical symptoms and epidemiological history indicate possible infection. However, a reference test showing the presence of coronavirus genetic material is essential throughout the diagnostic and treatment process.

Clinical performance and accuracy of a qPCR-based SARS-CoV-2 mass-screening workflow for healthcare-worker surveillance using pooled self-sampled gargling solutions: A cross-sectional study

Introduction

The large number of asymptomatic SARS-CoV-2 infections necessitates general screening of employees. We evaluate the performance of a SARS-CoV-2 screening program in asymptomatic healthcare-workers (HCW), utilizing self-sampled gargling-solution and sample pooling for RT-qPCR.

Methods

We conducted a cross-sectional retrospective study to collect real-life data on the performance of a screening-workflow based on automated-pooling and high-throughput qPCR testing over a 3-month-period at the University Hospital Hamburg.

Results

Matrix validation reveals that lower limit of detection for SARS-CoV-2 RNA in gargling-solution was 180 copies/mL (5-sample-pool). A total of 55,122 self-collected gargle samples (= 7513 HCWs) was analyzed. The median time to result was 8.5 hours (IQR 7.2–10.8). Of 11,192 pools analyzed, 11,041 (98.7%) were negative, 69 (0.6%) were positive and 82 (0.7%) were invalid. Individual testing of pool participants revealed 57 SARS-CoV-2 previously unrecognized infections. All 57 HCWs were either pre-symptomatic or asymptomatic (prevalence 0.76%,CI95%0.58–0.98%). Accuracy based on HCWs with gargle-solution and NP-swab available within 3-day-interval (N = 521) was 99.5% (CI95%98.3–99.9%), sensitivity 88.9% (CI95%65.3–98.6%) while specificity 99.8% (CI95%98.9–99.9).

Conclusion

This workflow was highly effective in identifying SARS-CoV-2 positive HCWs, thereby lowering the potential of inter-HCW and HCW-patient transmissions. Automated-sample-pooling helped to conserve qPCR reagents and represents a promising alternative strategy to antigen testing in mass-screening programs.

Diagnostic performance of different sampling approaches for SARS-CoV-2 RT-PCR testing: a systematic review and meta-analysis

BACKGROUND

The comparative performance of different clinical sampling methods for diagnosis of SARS-CoV-2 infection by RT-PCR among populations with suspected infection remains unclear. This meta-analysis aims to systematically compare the diagnostic performance of different clinical specimen collection methods.

METHODS

In this systematic review and meta-analysis, we systematically searched PubMed, Embase, MEDLINE, Web of Science, medRxiv, bioRxiv, SSRN, and Research Square from Jan 1, 2000, to Nov 16, 2020. We included original clinical studies that examined the performance of nasopharyngeal swabs and any additional respiratory specimens for the diagnosis of SARS-CoV-2 infection among individuals presenting in ambulatory care. Studies without data on paired samples, or those that only examined different samples from confirmed SARS-CoV-2 cases were not useful for examining diagnostic performance of a test and were excluded. Diagnostic performance, including sensitivity, specificity, positive predictive value, and negative predictive value, was examined using random effects models and double arcsine transformation.

FINDINGS

Of the 5577 studies identified in our search, 23 studies including 7973 participants with 16 762 respiratory samples were included. Respiratory specimens examined in these studies included 7973 nasopharyngeal swabs, 1622 nasal swabs, 6110 saliva samples, 338 throat swabs, and 719 pooled nasal and throat swabs. Using nasopharyngeal swabs as the gold standard, pooled nasal and throat swabs gave the highest sensitivity of 97% (95% CI 93-100), whereas lower sensitivities were achieved by saliva (85%, 75-93) and nasal swabs (86%, 77-93) and a much lower sensitivity by throat swabs (68%, 35-94). A comparably high positive predictive value was obtained by pooled nasal and throat (97%, 90-100) and nasal swabs (96%, 87-100) and a slightly lower positive predictive value by saliva (93%, 88-97). Throat swabs have the lowest positive predictive value of 75% (95% CI 45-96). Comparably high specificities (range 97-99%) and negative predictive value (range 95-99%) were observed among different clinical specimens. Comparison between health-care-worker collection and self-collection for pooled nasal and throat swabs and nasal swabs showed comparable diagnostic performance. No significant heterogeneity was observed in the analysis of pooled nasal and throat swabs and throat swabs, whereas moderate to substantial heterogeneity (I2 ≥30%) was observed in studies on saliva and nasal swabs.

INTERPRETATION

Our review suggests that, compared with the gold standard of nasopharyngeal swabs, pooled nasal and throat swabs offered the best diagnostic performance of the alternative sampling approaches for diagnosis of SARS-CoV-2 infection in ambulatory care. Saliva and nasal swabs gave comparable and very good diagnostic performance and are clinically acceptable alternative specimen collection methods. Throat swabs gave a much lower sensitivity and positive predictive value and should not be recommended. Self-collection for pooled nasal and throat swabs and nasal swabs was not associated with any significant impairment of diagnostic accuracy. Our results also provide a useful reference framework for the proper interpretation of SARS-CoV-2 testing results using different clinical specimens.

FUNDING

Hong Kong Research Grants Council.

Diagnostic performance of different sampling approaches for SARS-CoV-2 RT-PCR testing: a systematic review and meta-analysis

BACKGROUND

The comparative performance of different clinical sampling methods for diagnosis of SARS-CoV-2 infection by RT-PCR among populations with suspected infection remains unclear. This meta-analysis aims to systematically compare the diagnostic performance of different clinical specimen collection methods.

METHODS

In this systematic review and meta-analysis, we systematically searched PubMed, Embase, MEDLINE, Web of Science, medRxiv, bioRxiv, SSRN, and Research Square from Jan 1, 2000, to Nov 16, 2020. We included original clinical studies that examined the performance of nasopharyngeal swabs and any additional respiratory specimens for the diagnosis of SARS-CoV-2 infection among individuals presenting in ambulatory care. Studies without data on paired samples, or those that only examined different samples from confirmed SARS-CoV-2 cases were not useful for examining diagnostic performance of a test and were excluded. Diagnostic performance, including sensitivity, specificity, positive predictive value, and negative predictive value, was examined using random effects models and double arcsine transformation.

FINDINGS

Of the 5577 studies identified in our search, 23 studies including 7973 participants with 16 762 respiratory samples were included. Respiratory specimens examined in these studies included 7973 nasopharyngeal swabs, 1622 nasal swabs, 6110 saliva samples, 338 throat swabs, and 719 pooled nasal and throat swabs. Using nasopharyngeal swabs as the gold standard, pooled nasal and throat swabs gave the highest sensitivity of 97% (95% CI 93-100), whereas lower sensitivities were achieved by saliva (85%, 75-93) and nasal swabs (86%, 77-93) and a much lower sensitivity by throat swabs (68%, 35-94). A comparably high positive predictive value was obtained by pooled nasal and throat (97%, 90-100) and nasal swabs (96%, 87-100) and a slightly lower positive predictive value by saliva (93%, 88-97). Throat swabs have the lowest positive predictive value of 75% (95% CI 45-96). Comparably high specificities (range 97-99%) and negative predictive value (range 95-99%) were observed among different clinical specimens. Comparison between health-care-worker collection and self-collection for pooled nasal and throat swabs and nasal swabs showed comparable diagnostic performance. No significant heterogeneity was observed in the analysis of pooled nasal and throat swabs and throat swabs, whereas moderate to substantial heterogeneity (I² ≥30%) was observed in studies on saliva and nasal swabs.

INTERPRETATION

Our review suggests that, compared with the gold standard of nasopharyngeal swabs, pooled nasal and throat swabs offered the best diagnostic performance of the alternative sampling approaches for diagnosis of SARS-CoV-2 infection in ambulatory care. Saliva and nasal swabs gave comparable and very good diagnostic performance and are clinically acceptable alternative specimen collection methods. Throat swabs gave a much lower sensitivity and positive predictive value and should not be recommended. Self-collection for pooled nasal and throat swabs and nasal swabs was not associated with any significant impairment of diagnostic accuracy. Our results also provide a useful reference framework for the proper interpretation of SARS-CoV-2 testing results using different clinical specimens.

FUNDING

Hong Kong Research Grants Council.

A Comparison of Less Invasive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Diagnostic Specimens in Nursing Home Residents-Arkansas, June-August 2020

Background

SARS-CoV-2 testing remains essential for early identification and clinical management of cases. We compared the diagnostic performance of three specimen types for characterizing SARS-CoV-2 in infected nursing home residents.

Methods

A convenience sample of 17 residents were enrolled within 15 days of first positive SARS-CoV-2 result by real-time reverse transcription polymerase chain reaction (RT-PCR) and prospectively followed for 42 days. Anterior nasal swabs (AN), oropharyngeal swabs (OP), and saliva specimens (SA) were collected on the day of enrollment, every 3 days for the first 21 days, then weekly for 21 days. Specimens were tested for presence of SARS-CoV-2 RNA using RT-PCR and replication-competent virus by viral culture.

Results

Comparing the three specimen types collected from each participant at each time point, the concordance of paired RT-PCR results ranged from 80–88%. After the first positive result, SA and OP were RT-PCR–positive for ≤48 days; AN were RT-PCR–positive for ≤33 days. AN had the highest percentage of RT-PCR–positive results (81%; 21/26) when collected ≤10 days of participants’ first positive result. Eleven specimens were positive by viral culture: nine AN collected ≤19 days following first positive result and two OP collected ≤5 days following first positive result.

Conclusions

AN, OP, and SA were effective methods for repeated testing in this population. More AN than OP were positive by viral culture. SA and OP remained RT-PCR–positive longer than AN, which could lead to unnecessary interventions if RT-PCR detection occurred after viral shedding has likely ceased.

Saliva Testing Is Accurate for Early-Stage and Presymptomatic COVID-19

Although nasopharyngeal samples have been considered the gold standard for COVID-19 testing, variability in viral load across different anatomical sites could cause nasopharyngeal samples to be less sensitive than saliva or nasal samples in certain cases. Self-collected samples have logistical advantages over nasopharyngeal samples, making them amenable to population-scale screening. To evaluate sampling alternatives for population screening, we collected nasopharyngeal, saliva, and nasal samples from two cohorts with varied levels and types of symptoms. In a mixed cohort of 60 symptomatic and asymptomatic participants, we found that saliva had 88% concordance with nasopharyngeal samples when tested in the same testing lab (n = 41) and 68% concordance when tested in different testing labs (n = 19). In a second cohort of 20 participants hospitalized for COVID-19, saliva had 74% concordance with nasopharyngeal samples tested in the same testing lab but detected virus in two participants that tested negative with nasopharyngeal samples on the same day. Medical record review showed that the saliva-based testing sensitivity was related to the timing of symptom onset and disease stage. We find that no sample site will be perfectly sensitive for COVID-19 testing in all situations, and the significance of negative results will always need to be determined in the context of clinical signs and symptoms. Saliva retained high clinical sensitivity for early-stage and presymptomatic COVID-19 while allowing easier collection, minimizing the exposure of health care workers, and need for personal protective equipment and making it a viable option for population-scale testing.

IMPORTANCE Methods for COVID-19 detection are necessary for public health efforts to monitor the spread of disease. Nasopharyngeal samples have been considered the best approach for COVID-19 testing. However, alternative samples like self-collected saliva offer advantages for population-scale screening. Meta-analyses of recent studies suggest that saliva is useful for detecting SARS-CoV-2; however, differences in disease prevalence, sample collection, and analysis methods still confound strong conclusions on the utility of saliva compared to nasopharyngeal samples. Here, we find that the sensitivity of saliva testing is related to both the timing of the sample collection relative to symptom onset and the disease stage. Importantly, several clinical vignettes in our cohorts highlight the challenges of medical decision making with limited knowledge of the associations between laboratory test data and the natural biology of infection.

Characteristics of SARS-CoV-2 testing for rapid diagnosis of COVID-19 during the initial stages of a global pandemic

Accurate SARS-CoV-2 diagnosis is essential to guide prevention and control of COVID-19. Here we examine SARS-CoV-2 molecular-based test performance characteristics and summarize case-level data related to COVID-19 diagnosis. From January 11 through April 22, 2020, Public Health Ontario conducted SARS-CoV-2 testing of 86,942 specimens collected from 80,354 individuals, primarily using real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods. We analyzed test results across specimen types and for individuals with multiple same-day and multi-day collected specimens. Nasopharyngeal compared to throat swabs had a higher positivity (8.8% vs. 4.8%) and an adjusted estimate 2.9 C_t lower (SE = 0.5, p<0.001). Same-day specimens showed high concordance (98.8%), and the median C_t of multi-day specimens increased over time. Symptomatic cases had rRT-PCR results with an adjusted estimate 3.0 C_t (SE = 0.5, p<0.001) lower than asymptomatic/pre-symptomatic cases. Overall test sensitivity was 84.6%, with a negative predictive value of 95.5%. Molecular testing is the mainstay of SARS-CoV-2 diagnosis and testing protocols will continue to be dynamic and iteratively modified as more is learned about this emerging pathogen.

Epidemiology of SARS-CoV-2 Infection Evaluated by Immunochromatographic Rapid Testing for the Determination of IgM and IgG Against SARS-CoV-2 in a Cohort of Mask Wearing Workers in the Metal-Mechanical Sector in an Area With a High Incidence of COVID-19

Background: Although the diagnosis of new coronavirus 2019 (COVID-19) is made through the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory secretions by means of molecular methods, a more accurate estimation of SARS-CoV-2 circulation can be obtained by seroprevalence studies. The main aim of this study was to evaluate the true epidemiology of SARS-CoV-2 infection among workers in the metal-mechanical sector who never stopped working during the pandemic period in an area with a high incidence of COVID-19 and to define whether and how they could continue the work without appreciable risks during a second wave.

Methods: A total of 815 metal-mechanical workers who had never stopped working even during the pandemic period in three different factories in the Emilia-Romagna Region, Italy, and who had always used face masks during working hours, underwent a capillary blood rapid test for the determination of IgM and IgG against SARS-CoV-2 (COVID-19 IgG/IgM Rapid test, PrimaLab, Modena, Italy). In the event of a positive test, a nasopharyngeal was performed and tested for the presence of SARS-CoV-2.

Results: The detection of serum IgG/IgM against SARS-CoV-2 was significantly more common among workers employed in Parma (21/345, 6.1%) than among those employed in Calerno (7/242, 2.9%) or in Spilamberto (3/228, 1.3%) (p <0.001). The analysis of the role of the different variables as predictors of seropositivity for IgG/IgM against SARS-CoV-2 revealed that the presence of specific antibodies was strictly associated with a previous history of COVID-19-like symptoms (odds ratio [OR] 3.95, 95% confidence interval [CI] 1.9–8.2) and household members with COVID-19-like symptoms (OR 2.20, 95% CI 1.04–4.82).

Conclusion: This study shows that seropositivity to SARS-CoV-2 is low even among employees who did not interrupt their work during the lockdown phase in a region with a high incidence of COVID-19. The use of face masks appears effective in the avoidance of the transmission of SARS-CoV-2 in factories even in the presence of asymptomatic or mildly symptomatic workers, suggesting that work activities can continue if adequate infection control measures are used during a second wave.

Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Diagnostic testing plays a critical role in addressing the coronavirus disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Rapid and accurate diagnostic tests are imperative for identifying and managing infected individuals, contact tracing, epidemiologic characterization, and public health decision making. Laboratory testing may be performed based on symptomatic presentation or for screening of asymptomatic people. Confirmation of SARS-CoV-2 infection is typically by nucleic acid amplification tests (NAAT), which requires specialized equipment and training and may be particularly challenging in resource-limited settings. NAAT may give false-negative results due to timing of sample collection relative to infection, improper sampling of respiratory specimens, inadequate preservation of samples, and technical limitations; false-positives may occur due to technical errors, particularly contamination during the manual real-time polymerase chain reaction (RT-PCR) process. Thus, clinical presentation, contact history and contemporary phyloepidemiology must be considered when interpreting results. Several sample-to-answer platforms, including high-throughput systems and Point of Care (PoC) assays, have been developed to increase testing capacity and decrease technical errors. Alternatives to RT-PCR assay, such as other RNA detection methods and antigen tests may be appropriate for certain situations, such as resource-limited settings. While sequencing is important to monitor on-going evolution of the SARS-CoV-2 genome, antibody assays are useful for epidemiologic purposes. The ever-expanding assortment of tests, with varying clinical utility, performance requirements, and limitations, merits comparative evaluation. We herein provide a comprehensive review of currently available COVID-19 diagnostics, exploring their pros and cons as well as appropriate indications. Strategies to further optimize safety, speed, and ease of SARS-CoV-2 testing without compromising accuracy are suggested. Access to scalable diagnostic tools and continued technologic advances, including machine learning and smartphone integration, will facilitate control of the current pandemic as well as preparedness for the next one.

Point-of-Care PCR Assays for COVID-19 Detection

Molecular diagnostics has been the front runner in the world's response to the COVID-19 pandemic. Particularly, reverse transcriptase-polymerase chain reaction (RT-PCR) and the quantitative variant (qRT-PCR) have been the gold standard for COVID-19 diagnosis. However, faster antigen tests and other point-of-care (POC) devices have also played a significant role in containing the spread of SARS-CoV-2 by facilitating mass screening and delivering results in less time. Thus, despite the higher sensitivity and specificity of the RT-PCR assays, the impact of POC tests cannot be ignored. As a consequence, there has been an increased interest in the development of miniaturized, high-throughput, and automated PCR systems, many of which can be used at point-of-care. This review summarizes the recent advances in the development of miniaturized PCR systems with an emphasis on COVID-19 detection. The distinct features of digital PCR and electrochemical PCR are detailed along with the challenges. The potential of CRISPR/Cas technology for POC diagnostics is also highlighted. Commercial RT-PCR POC systems approved by various agencies for COVID-19 detection are discussed.

Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis

Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.

Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis

Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.

Computational characterization of inhaled droplet transport to the nasopharynx

How human respiratory physiology and the transport phenomena associated with inhaled airflow in the upper airway proceed to impact transmission of SARS-CoV-2, leading to the initial infection, stays an open question. An answer can help determine the susceptibility of an individual on exposure to a COVID-2019 carrier and can also provide a preliminary projection of the still-unknown infectious dose for the disease. Computational fluid mechanics enabled tracking of respiratory transport in medical imaging-based anatomic domains shows that the regional deposition of virus-laden inhaled droplets at the initial nasopharyngeal infection site peaks for the droplet size range of approximately 2.5-19 [Formula: see text]. Through integrating the numerical findings on inhaled transmission with sputum assessment data from hospitalized COVID-19 patients and earlier measurements of ejecta size distribution generated during regular speech, this study further reveals that the number of virions that may go on to establish the SARS-CoV-2 infection in a subject could merely be in the order of hundreds.

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

Rising demands for repetitive SARS-CoV-2 screens and mass testing necessitate additional test strategies. Saliva may serve as an alternative to nasopharyngeal swab (NPS) as its collection is simple, non-invasive and amenable for mass- and home testing, but its rigorous validation, particularly in children, is missing. We conducted a large-scale head-to-head comparison of SARS-CoV-2 detection by RT-PCR in saliva and NPS of 1270 adults and children reporting to outpatient test centers and an emergency unit. In total, 273 individuals were tested positive for SARS-CoV-2 in either NPS or saliva. SARS-CoV-2 RT-PCR results in the two specimens showed a high agreement (overall percent agreement = 97.8%). Despite lower viral loads in the saliva of both adults and children, detection of SARS-CoV-2 in saliva fared well compared to NPS (positive percent agreement = 92.5%). Importantly, in children, SARS-CoV-2 infections were more often detected in saliva than NPS (positive predictive value = 84.8%), underlining that NPS sampling in children can be challenging. The comprehensive parallel analysis reported here establishes saliva as a generally reliable specimen for the detection of SARS-CoV-2, with particular advantages for testing children, that is readily applicable to increase and facilitate repetitive and mass testing in adults and children.

SARS-CoV-2 early infection signature identified potential key infection mechanisms and drug targets

Background

The ongoing COVID-19 outbreak has caused devastating mortality and posed a significant threat to public health worldwide. Despite the severity of this illness and 2.3 million worldwide deaths, the disease mechanism is mostly unknown. Previous studies that characterized differential gene expression due to SARS-CoV-2 infection lacked robust validation. Although vaccines are  now available, effective treatment options are still out of reach.

Results

To characterize the transcriptional activity of SARS-CoV-2 infection, a gene signature consisting of 25 genes was generated using a publicly available RNA-Sequencing (RNA-Seq) dataset of cultured cells infected with SARS-CoV-2. The signature estimated infection level accurately in bronchoalveolar lavage fluid (BALF) cells and peripheral blood mononuclear cells (PBMCs) from healthy and infected patients (mean 0.001 vs. 0.958; P < 0.0001). These signature genes were investigated in their ability to distinguish the severity of SARS-CoV-2 infection in a single-cell RNA-Sequencing dataset. TNFAIP3, PPP1R15A, NFKBIA, and IFIT2 had shown bimodal gene expression in various immune cells from severely infected patients compared to healthy or moderate infection cases. Finally, this signature was assessed using the publicly available ConnectivityMap database to identify potential disease mechanisms and drug repurposing candidates. Pharmacological classes of tricyclic antidepressants, SRC-inhibitors, HDAC inhibitors, MEK inhibitors, and drugs such as atorvastatin, ibuprofen, and ketoconazole showed strong negative associations (connectivity score < − 90), highlighting the need for further evaluation of these candidates for their efficacy in treating SARS-CoV-2 infection.

Conclusions

Thus, using the 25-gene SARS-CoV-2 infection signature, the SARS-CoV-2 infection status was captured in BALF cells, PBMCs and postmortem lung biopsies. In addition, candidate SARS-CoV-2 therapies with known safety profiles were identified. The signature genes could potentially also be used to characterize the COVID-19 disease severity in patients’ expression profiles of BALF cells.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07433-4.

The Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19: Molecular Diagnostic Testing

BACKGROUND

Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19). Direct detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acids in respiratory tract specimens informs patient, healthcare institution and public health level decision-making. The numbers of available SARS-CoV-2 nucleic acid detection tests are rapidly increasing, as is the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) recognized a significant need for frequently updated systematic reviews of the literature to inform evidence-based best practice guidance.

OBJECTIVE

The IDSA's goal was to develop an evidence-based diagnostic guideline to assist clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss the nuance of test result interpretation in a variety of practice settings and highlight important unmet research needs in the COVID-19 diagnostic testing space.

METHODS

IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations.

RESULTS

The panel agreed on 17 diagnostic recommendations.

CONCLUSIONS

Universal access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention and the public response to the COVID-19 pandemic. Information on the clinical performance of available tests is rapidly emerging, but the quality of evidence of the current literature is considered moderate to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is recommended for asymptomatic individuals with known or suspected contact with a COVID-19 case. Testing asymptomatic individuals without known exposure is suggested when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions, dictate eligibility for surgery, or inform solid organ or hematopoietic stem cell transplantation timing. Ultimately, prioritization of testing will depend on institutional-specific resources and the needs of different patient populations.

COVID-19: Test, Test and Test

A new virus was identified in late December 2019 when China reported the first cases of pneumonia in Wuhan, and a global COVID-19 pandemic followed. The world was not late to respond, with a number of sweeping measures ranging from social distancing protocols, stringent hygienic practices, and nation-wide lockdowns, as well as COVID-19 testing campaigns in an attempt to prevent the transmission of the disease and contain the pandemic. Currently, different types of diagnostic testing have been adopted globally, such as nucleic acid detection tests, immunological tests and imaging approaches; however, real-time reverse transcriptase–polymerase chain reaction (RT-PCR) remains the “gold standard” for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pre-analytical factors, such as specimen selection and collection, are crucial for RT-PCR, and any suboptimal collection may contribute to false-negative results. Herein, we address some of the specimen types that have been used in molecular detection methods for COVID-19. However, the pandemic is still evolving, and information might change as more studies are conducted.

3D printing of nasopharyngeal swabs for COVID-19 diagnose: Past and current trends

The current technological advancements in emerging 3D printing technologies are indeed propitious. To date, ground-breaking 3D printing technologies are used in automobile, aerospace, clothing, pharma, and biomedical industries by creating pre-requisite engineered and tailored end-user products reaching standard sets. 3D printing is also becoming a crucial technology in support of enhanced health care and general emergency response since the beginning of the COVID-19 pandemic. As the world is facing a significant lack of medicinal supplies, manufactures are struggling to fulfill demands due to the ongoing COVID-19 pandemic. The decline in the diagnostic testing kits supply chained to increased interest in 3D printed Nasopharyngeal (NP) swabs. This article has reviewed and studied the sensitivity of the NP swabs and various NP swab designs. The process of different 3D printing technologies that are employed to address the swab shortages during COVID-19 is explained in detail. The paper ends with the conclusions drawn from the literature review.

Assessing the dilution effect of specimen pooling on the sensitivity of SARS-CoV-2 PCR tests

The SARS-CoV-2 pandemic has led to an unprecedented demand for diagnostic tests. Many studies have modeled the efficiency gains of specimen pooling, but few have systematically evaluated the dilution effect of pooling on the sensitivity of tests. Using the frequency distribution of cycle threshold (C_t ) values of our first 838 SARS-CoV-2 positive specimens, we modeled 100 specimens on the same frequency distribution. Given this distribution, we then tested dilutions of 1:5, 1:10, and 1:50 to find the percentage of specimens positive at each C_t value with each pool size. Using the frequency distribution and the percentage of specimens positive at each C_t value, we estimate that pools of 5 lead to 93% sensitivity, pools of 10 lead to 91% sensitivity, and pools of 50 lead to 81% sensitivity. Pools of 5 and 10 lead to some specimens with C_t values of ≥32 becoming negative, while pools of 50 lead to some specimens with C_t values of ≥28 becoming negative. These sensitivity estimates can inform laboratories seeking to implement pooling approaches as they seek to balance test efficiency with sensitivity.

Using the COVID-19 to influenza ratio to estimate early pandemic spread in Wuhan, China and Seattle, US

BACKGROUND

Pandemic SARS-CoV-2 was first reported in Wuhan, China on December 31, 2019. Twenty-one days later, the US identified its first case--a man who had traveled from Wuhan to the state of Washington. Recent studies in the Wuhan and Seattle metropolitan areas retrospectively tested samples taken from patients with COVID-like symptoms. In the Wuhan study, there were 4 SARS-CoV-2 positives and 7 influenza positives out of 26 adults outpatients who sought care for influenza-like-illness at two central hospitals prior to January 12, 2020. The Seattle study reported 25 SARS-CoV-2 positives and 442 influenza positives out of 2353 children and adults who reported acute respiratory illness prior to March 9, 2020. Here, we use these findings to extrapolate the early prevalence of symptomatic COVID-19 in Wuhan and Seattle.

METHODS

For each city, we estimate the ratio of COVID-19 to influenza infections from the retrospective testing data and estimate the age-specific prevalence of influenza from surveillance reports during the same time period. Combining these, we approximate the total number of symptomatic COVID-19 infections.

FINDINGS

In Wuhan, there were an estimated 1386 [95% CrI: 420-3793] symptomatic cases over 30 of COVID-19 between December 30, 2019 and January 12, 2020. In Seattle, we estimate that 2268 [95% CrI: 498, 6069] children under 18 and 4367 [95% CrI: 2776, 6526] adults were symptomatically infected between February 24 and March 9, 2020. We also find that the initial pandemic wave in Wuhan likely originated with a single infected case who developed symptoms sometime between October 26 and December 13, 2019; in Seattle, the seeding likely occurred between December 25, 2019 and January 15, 2020.

INTERPRETATION

The spread of COVID-19 in Wuhan and Seattle was far more extensive than initially reported. The virus likely spread for months in Wuhan before the lockdown. Given that COVID-19 appears to be overwhelmingly mild in children, our high estimate for symptomatic pediatric cases in Seattle suggests that there may have been thousands more mild cases at the time.

Combined throat/nasal swab sampling for SARS-CoV-2 is equivalent to nasopharyngeal sampling

PURPOSE

PCR on a nasopharyngeal sample is the reference method for the detection of SARS-nCoV-2. However, combined throat/nasal sampling as a testing method has several advantages. We compared the combined throat/nasal sampling with nasopharyngeal sampling for detection of SARS-CoV-2 in healthcare workers suspected of COVID-19.

METHODS

In 107 healthcare workers with symptoms of COVID-19, combined throat/nasal sampling and nasopharyngeal sampling was performed. Detection of SARS-CoV-2 was performed by RT-PCR targeting.

RESULTS

A total of 80 healthcare workers (74.8%) tested negative with both sampling methods, and 25 healthcare workers (23.4%) tested positive with both sampling methods. There were two discrepant results with positive PCR in combined throat/nasal swabs and negative PCR in nasopharyngeal swabs (1.9%). The κ index for concordance between the 2 sampling methods was high (0.95). The median cycle threshold (Ct) value of PCR on nasopharyngeal samples was significantly lower than the Ct value of PCR on combined throat/nasal samples (19 (IQR 17-20) versus 21 (IQR 18-29) cycles, p value 0.01).

CONCLUSION

Combined throat/nasal swabs yield a similar sensitivity to detect SARS-CoV-2 as nasopharyngeal swabs and are a good alternative sampling method, despite a lower Ct value for the nasopharyngeal samples.