Clinical Performance of SARS-CoV-2 Molecular Tests

The effect of sample site and collection procedure on identification of SARS-CoV-2 infection

BACKGROUND

Sample collection is a key driver of accuracy in the diagnosis of SARS-CoV-2 infection. Viral load may vary at different anatomical sampling sites and accuracy may be compromised by difficulties obtaining specimens and the expertise of the person taking the sample. It is important to optimise sampling accuracy within cost, safety and accessibility constraints.

OBJECTIVES

To compare the sensitivity of different sampling collection sites and methods for the detection of current SARS-CoV-2 infection with any molecular or antigen-based test.

SEARCH METHODS

Electronic searches of the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on 22 February 2022. We included independent evaluations from national reference laboratories, FIND and the Diagnostics Global Health website. We did not apply language restrictions.

SELECTION CRITERIA

We included studies of symptomatic or asymptomatic people with suspected SARS-CoV-2 infection undergoing testing. We included studies of any design that compared results from different sample types (anatomical location, operator, collection device) collected from the same participant within a 24-hour period.

DATA COLLECTION AND ANALYSIS

Within a sample pair, we defined a reference sample and an index sample collected from the same participant within the same clinical encounter (within 24 hours). Where the sample comparison was different anatomical sites, the reference standard was defined as a nasopharyngeal or combined naso/oropharyngeal sample collected into the same sample container and the index sample as the alternative anatomical site. Where the sample comparison was concerned with differences in the sample collection method from the same site, we defined the reference sample as that closest to standard practice for that sample type. Where the sample pair comparison was concerned with differences in personnel collecting the sample, the more skilled or experienced operator was considered the reference sample. Two review authors independently assessed the risk of bias and applicability concerns using the QUADAS-2 and QUADAS-C checklists, tailored to this review. We present estimates of the difference in the sensitivity (reference sample (%) minus index sample sensitivity (%)) in a pair and as an average across studies for each index sampling method using forest plots and tables. We examined heterogeneity between studies according to population (age, symptom status) and index sample (time post-symptom onset, operator expertise, use of transport medium) characteristics.

MAIN RESULTS

This review includes 106 studies reporting 154 evaluations and 60,523 sample pair comparisons, of which 11,045 had SARS-CoV-2 infection. Ninety evaluations were of saliva samples, 37 nasal, seven oropharyngeal, six gargle, six oral and four combined nasal/oropharyngeal samples. Four evaluations were of the effect of operator expertise on the accuracy of three different sample types. The majority of included evaluations (146) used molecular tests, of which 140 used RT-PCR (reverse transcription polymerase chain reaction). Eight evaluations were of nasal samples used with Ag-RDTs (rapid antigen tests). The majority of studies were conducted in Europe (35/106, 33%) or the USA (27%) and conducted in dedicated COVID-19 testing clinics or in ambulatory hospital settings (53%). Targeted screening or contact tracing accounted for only 4% of evaluations. Where reported, the majority of evaluations were of adults (91/154, 59%), 28 (18%) were in mixed populations with only seven (4%) in children. The median prevalence of confirmed SARS-CoV-2 was 23% (interquartile (IQR) 13%-40%). Risk of bias and applicability assessment were hampered by poor reporting in 77% and 65% of included studies, respectively. Risk of bias was low across all domains in only 3% of evaluations due to inappropriate inclusion or exclusion criteria, unclear recruitment, lack of blinding, nonrandomised sampling order or differences in testing kit within a sample pair. Sixty-eight percent of evaluation cohorts were judged as being at high or unclear applicability concern either due to inflation of the prevalence of SARS-CoV-2 infection in study populations by selectively including individuals with confirmed PCR-positive samples or because there was insufficient detail to allow replication of sample collection. When used with RT-PCR • There was no evidence of a difference in sensitivity between gargle and nasopharyngeal samples (on average -1 percentage points, 95% CI -5 to +2, based on 6 evaluations, 2138 sample pairs, of which 389 had SARS-CoV-2). • There was no evidence of a difference in sensitivity between saliva collection from the deep throat and nasopharyngeal samples (on average +10 percentage points, 95% CI -1 to +21, based on 2192 sample pairs, of which 730 had SARS-CoV-2). • There was evidence that saliva collection using spitting, drooling or salivating was on average -12 percentage points less sensitive (95% CI -16 to -8, based on 27,253 sample pairs, of which 4636 had SARS-CoV-2) compared to nasopharyngeal samples. We did not find any evidence of a difference in the sensitivity of saliva collected using spitting, drooling or salivating (sensitivity difference: range from -13 percentage points (spit) to -21 percentage points (salivate)). • Nasal samples (anterior and mid-turbinate collection combined) were, on average, 12 percentage points less sensitive compared to nasopharyngeal samples (95% CI -17 to -7), based on 9291 sample pairs, of which 1485 had SARS-CoV-2. We did not find any evidence of a difference in sensitivity between nasal samples collected from the mid-turbinates (3942 sample pairs) or from the anterior nares (8272 sample pairs). • There was evidence that oropharyngeal samples were, on average, 17 percentage points less sensitive than nasopharyngeal samples (95% CI -29 to -5), based on seven evaluations, 2522 sample pairs, of which 511 had SARS-CoV-2. A much smaller volume of evidence was available for combined nasal/oropharyngeal samples and oral samples. Age, symptom status and use of transport media do not appear to affect the sensitivity of saliva samples and nasal samples. When used with Ag-RDTs • There was no evidence of a difference in sensitivity between nasal samples compared to nasopharyngeal samples (sensitivity, on average, 0 percentage points -0.2 to +0.2, based on 3688 sample pairs, of which 535 had SARS-CoV-2).

AUTHORS' CONCLUSIONS

When used with RT-PCR, there is no evidence for a difference in sensitivity of self-collected gargle or deep-throat saliva samples compared to nasopharyngeal samples collected by healthcare workers when used with RT-PCR. Use of these alternative, self-collected sample types has the potential to reduce cost and discomfort and improve the safety of sampling by reducing risk of transmission from aerosol spread which occurs as a result of coughing and gagging during the nasopharyngeal or oropharyngeal sample collection procedure. This may, in turn, improve access to and uptake of testing. Other types of saliva, nasal, oral and oropharyngeal samples are, on average, less sensitive compared to healthcare worker-collected nasopharyngeal samples, and it is unlikely that sensitivities of this magnitude would be acceptable for confirmation of SARS-CoV-2 infection with RT-PCR. When used with Ag-RDTs, there is no evidence of a difference in sensitivity between nasal samples and healthcare worker-collected nasopharyngeal samples for detecting SARS-CoV-2. The implications of this for self-testing are unclear as evaluations did not report whether nasal samples were self-collected or collected by healthcare workers. Further research is needed in asymptomatic individuals, children and in Ag-RDTs, and to investigate the effect of operator expertise on accuracy. Quality assessment of the evidence base underpinning these conclusions was restricted by poor reporting. There is a need for further high-quality studies, adhering to reporting standards for test accuracy studies.

Single-tube protocol for culture-independent spoligotyping of Mycobacterium tuberculosis based on MeltArray

IMPORTANCE

Spacer oligonucleotide typing (spoligotyping), the first-line genotyping assay for Mycobacterium tuberculosis (MTB), plays a fundamental role in the investigation of its epidemiology and evolution. In this study, we established a single-tube spoligotyping assay using MeltArray, a highly multiplex polymerase chain reaction (PCR) approach that runs on a real-time PCR thermocycler. The MeltArray protocol included an internal positive control, gyrB, to indicate the abundance of MTB via the quantification cycle and 43 spacers to identify the spoligotype via melting curve analysis. The entire protocol was completed in a single step within 2.5 hours. The lowest detectable copy number for the tested strains was 20 copies/reaction and thus sufficient for analyzing both culture and sputum samples. We conclude that MeltArray-based spoligotyping could be used immediately in low- and middle-income countries with a high tuberculosis burden, given its easy access, improved throughput, and potential applicability to clinical samples.

Quality of the sample-based RNA determines the real-time RT-PCR results in the laboratory diagnosis of COVID-19

Effect of the quality of sample-based RNA on COVID-19 real-time RT-PCR results was investigated. The purity of the extracts was dependent on the extraction method (P<0.0001) and affected the test interpretations (P = 0.002). Gross RNA concentration negatively correlated with Ct values (P < 0.0001). The presence of impurities contributed to inconclusive test results.

Efficiency evaluation of a SARS-CoV-2 diagnostic strategy combining high throughput quantitative antigen immunoassay and real time PCR

OBJECTIVES

Laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has played an important role in the effort to prevent and contain local outbreaks. The aim of this study was to assess the diagnostic accuracy of a new fully automated SARS-CoV-2 laboratory-based antigen assay (CoV2Ag) and to explore the efficiency of a diagnostic algorithm combining antigen and conventional high-throughput molecular assays to address potential future challenges of the SARS-CoV-2 pandemic.

METHODS

One thousand two hundred and twenty four consecutive nasopharyngeal swabs were tested using RT-PCR and CoV2Ag assay.

RESULTS

The overall sensitivity and specificity of CoV2Ag were 79.1 and 97.8%, respectively. When the analysis was restricted to cases with Ct values ≤30, the sensitivity of the assay improved to 98.1%. Acceptable sensitivity was found when the analysis was limited to patients presenting within one or two to four days of symptom onset (80.5 and 84.8%, respectively). A retrospective analysis of the use of a two-step diagnostic approach combining the CoV2Ag assay and RT-PCR during an acute pandemic phase of 97 days showed a potential reduction in the number of RT-PCR tests by 36.1%, corresponding to savings in reagent costs and technician workload of approximately €8,000 and 10.5 h per day, respectively.

CONCLUSIONS

Our data show that the proposed algorithm represents a valid alternative diagnostic approach to increase testing efficiency during future pandemic phases with high positivity rates (>20%) and elevated numbers of RT-PCR test requests.

Digital Microfluidic Multiplex RT-qPCR for SARS-CoV-2 Detection and Variants Discrimination

Continuous mutations have occurred in the genome of the SARS-CoV-2 virus since the onset of the COVID-19 pandemic. The increased transmissibility of the mutated viruses has not only imposed medical burdens but also prolonged the duration of the pandemic. A point-of-care (POC) platform that provides multitarget detection will help to track and reduce disease transmissions. Here we detected and discriminated three genotypes of SARS-CoV-2, including the wildtype and two variants of concern (VOCs), the Delta variant and Omicron variant, through reverse transcription quantitative polymerase chain reaction (RT-qPCR) on a digital microfluidics (DMF)-based cartridge. Upon evaluating with the RNA samples of Omicron variant, the DMF RT-qPCR presented a sensitivity of 10 copies/μL and an amplification efficiency of 96.1%, capable for clinical diagnosis. When spiking with SARS-CoV-2 RNA (wildtype, Delta variant, or Omicron variant) and 18S rDNA, the clinical analog samples demonstrated accurate detection and discrimination of different SARS-CoV-2 strains in 49 min.

Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples

OBJECTIVE

Validate the performance characteristics of two analyte specific, laboratory developed tests (LDTs) for the quantification of SARS-CoV-2 subgenomic RNA (sgRNA) and viral load on the Hologic Panther Fusion® using the Open Access functionality.

METHODS

Custom-designed primers/probe sets targeting the SARS-CoV-2 Envelope gene (E) and subgenomic E were optimized. A 20-day performance validation following laboratory developed test requirements was conducted to assess assay precision, accuracy, analytical sensitivity/specificity, lower limit of detection and reportable range.

RESULTS

Quantitative SARS-CoV-2 sgRNA (LDT-Quant sgRNA) assay, which measures intermediates of replication, and viral load (LDT-Quant VLCoV) assay demonstrated acceptable performance. Both assays were linear with an R2 and slope equal to 0.99 and 1.00, respectively. Assay precision was evaluated between 4-6 Log10 with a maximum CV of 2.6% and 2.5% for LDT-Quant sgRNA and LDT-Quant VLCoV respectively. Using negative or positive SARS-CoV-2 human nasopharyngeal swab samples, both assays were accurate (kappa coefficient of 1.00 and 0.92). Common respiratory flora and other viral pathogens were not detected and did not interfere with the detection or quantification by either assay. Based on 95% detection, the assay LLODs were 729 and 1206 Copies/mL for the sgRNA and VL load LDTs, respectively.

CONCLUSION

The LDT-Quant sgRNA and LDT-Quant VLCoV demonstrated good analytical performance. These assays could be further investigated as alternative monitoring assays for viral replication; and thus, medical management in clinical settings which could inform isolation/quarantine requirements.

Operational analysis for COVID-19 testing: Determining the risk from asymptomatic infections

Testing remains a key tool for managing health care and making health policy during the coronavirus pandemic, and it will probably be important in future pandemics. Because of false negative and false positive tests, the observed fraction of positive tests-the surface positivity-is generally different from the fraction of infected individuals (the incidence rate of the disease). In this paper a previous method for translating surface positivity to a point estimate for incidence rate, then to an appropriate range of values for the incidence rate consistent with the model and data (the test range), and finally to the risk (the probability of including one infected individual) associated with groups of different sizes is illustrated. The method is then extended to include asymptomatic infections. To do so, the process of testing is modeled using both analysis and Monte Carlo simulation. Doing so shows that it is possible to determine point estimates for the fraction of infected and symptomatic individuals, the fraction of uninfected and symptomatic individuals, and the ratio of infected asymptomatic individuals to infected symptomatic individuals. Inclusion of symptom status generalizes the test range from an interval to a region in the plane determined by the incidence rate and the ratio of asymptomatic to symptomatic infections; likelihood methods can be used to determine the contour of the rest region. Points on this contour can be used to compute the risk (defined as the probability of including one asymptomatic infected individual) in groups of different sizes. These results have operational implications that include: positivity rate is not incidence rate; symptom status at testing can provide valuable information about asymptomatic infections; collecting information on time since putative virus exposure at testing is valuable for determining point estimates and test ranges; risk is a graded (rather than binary) function of group size; and because the information provided by testing becomes more accurate with more tests but at a decreasing rate, it is possible to over-test fixed spatial regions. The paper concludes with limitations of the method and directions for future work.

Sensitivity and Diagnostic Yield of the First SARS-CoV-2 Nucleic Acid Amplification Test Performed for Patients Presenting to the Hospital

IMPORTANCE

Early and accurate diagnostic testing for SARS-CoV-2 is essential to initiate appropriate treatment and infection control and prevention measures among patients presenting to the hospital.

OBJECTIVE

To evaluate the diagnostic sensitivity of the SARS-CoV-2 nucleic acid amplification test (NAAT) performed within 24 hours of arrival to the emergency department among a nationally representative sample of patients.

DESIGN, SETTING, AND PARTICIPANTS

This diagnostic study was conducted at 47 hospitals across 7 provinces in Canada participating in the Canadian COVID-19 Rapid Response Emergency Department Network among consecutive eligible patients presenting to a participating emergency department who were tested for SARS-CoV-2 from March 1, 2020, to December 31, 2021. Patients not tested within 24 hours of arrival and those presenting with a positive result from a test performed in the community were excluded.

MAIN OUTCOMES AND MEASURES

The primary outcome was a positive result from the SARS-CoV-2 NAAT. Outcome measures were the diagnostic sensitivity and yield of the SARS-CoV-2 NAAT.

RESULTS

Of 132 760 eligible patients (66 433 women [50.0%]; median age, 57 years [IQR, 37-74 years]), 17 174 (12.9%) tested positive for SARS-CoV-2 within 14 days of their first NAAT. The diagnostic sensitivity of the SARS-CoV-2 NAAT was 96.2% (17 070 of 17 740 [95% CI, 95.9%-96.4%]) among all of the tests performed. Estimates ranged from a high of 97.7% (1710 of 1751 [95% CI, 96.8%-98.3%]) on day 2 of symptoms to a low of 90.4% (170 of 188 [95% CI, 85.3%-94.2%]) on day 11 of symptoms among patients presenting with COVID-19 symptoms. Among patients reporting COVID-19 symptoms, the sensitivity of the SARS-CoV-2 NAAT was 97.1% (11 870 of 12 225 [95% CI, 96.7%-97.3%]) compared with 87.6% (812 of 927 [95% CI, 85.2%-89.6%]) among patients without COVID-19 symptoms. The diagnostic yield of the SARS-CoV-2 NAAT was 12.0% (18 985 of 158 004 [95% CI, 11.8%-12.2%]) and varied from a high of 20.0% (445 of 2229 [95% CI, 18.3%-21.6%]) among patients tested on day 10 after symptom onset to a low of 8.1% (1686 of 20 719 [95% CI, 7.7%-8.5%]) among patients presenting within the first 24 hours of symptom onset.

CONCLUSIONS AND RELEVANCE

This study suggests that the diagnostic sensitivity was high for the first SARS-CoV-2 NAAT performed in the hospital and did not vary significantly by symptom duration. Repeated testing of patients with negative test results should be avoided unless their pretest probability of disease is high.

Patient characteristics associated with conversion from negative to positive severe acute respiratory syndrome coronavirus-2 polymerase chain reaction test results: Implications for clinical false-negativity from a single-center: A case-control study

BACKGROUND

Accurate diagnosis of coronavirus disease 2019 is essential to limiting transmission within healthcare settings. The aim of this study was to identify patient demographic and clinical characteristics that could impact the clinical sensitivity of the nasopharyngeal severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) reverse transcription polymerase chain reaction (RT-PCR) test.

METHODS

We conducted a retrospective, matched case-control study of patients who underwent repeated nasopharyngeal SARS-CoV2 RT-PCR testing at a tertiary care academic medical center between March 1 and July 23, 2020. The primary endpoint was conversion from negative to positive PCR status within 14 days. We conducted conditional logistic regression modeling to assess the associations between demographic and clinical features and conversion to test positivity.

RESULTS

Of 51,116 patients with conclusive SARS-CoV2 nasopharyngeal RT-PCR results, 97 patients converted from negative to positive within 14 days. We matched those patients 1:2 to 194 controls by initial test date. In multivariate analysis, clinical suspicion for a respiratory infection (adjusted odds ratio [aOR] 20.9, 95% confidence interval [CI]: 3.1-141.2) and lack of pulmonary imaging (aOR 4.7, 95% CI: 1.03-21.8) were associated with conversion, while a lower burden of comorbidities trended toward an increased odds of conversion (aOR 2.2, 95% CI: 0.9-5.3).

CONCLUSIONS

Symptoms consistent with a respiratory infection, especially in relatively healthy individuals, should raise concerns about a clinical false-negative result. We have identified several characteristics that should be considered when creating institutional infection prevention guidelines in the absence of more definitive data and should be included in future studies.

Potential Use of Exhaled Breath Condensate for Diagnosis of SARS-CoV-2 Infections: A Systematic Review and Meta-Analysis

Background. Reverse-transcriptase polymerase chain reaction (RT-qPCR) assays performed on respiratory samples collected through nasal swabs still represent the gold standard for COVID-19 diagnosis. Alternative methods to this invasive and time-consuming options are still being inquired, including the collection of airways lining fluids through exhaled breath condensate (EBC). Materials and Methods. We performed a systematic review and meta-analysis in order to explore the reliability of EBC as a way to collect respiratory specimens for RT-qPCR for diagnosis of COVID-19. Results. A total of 4 studies (205 specimens), were ultimately collected, with a pooled sensitivity of 69.5% (95%CI 26.8–93.4), and a pooled specificity of 98.3% (95%CI 87.8–99.8), associated with high heterogeneity and scarce diagnostic agreement with the gold standard represented by nasal swabs (Cohen’s kappa = 0.585). Discussion. Even though non-invasive options for diagnosis of COVID-19 are still necessary, EBC-based RT-qPCR showed scarce diagnostic performances, ultimately impairing its implementation in real-world settings. However, as few studies have been carried out to date, and the studies included in the present review are characterized by low numbers and low sample power, further research are requested to fully characterize the actual reliability of EBC-based RT-qPCR in the diagnosis of COVID-19.

SARS-CoV-2 in children and their accompanying caregivers: Implications for testing strategies in resource limited hospitals

Background

Identification of SARS-CoV-2 infected individuals is imperative to prevent hospital transmission, but symptom-based screening may fail to identify asymptomatic/mildly symptomatic infectious children and their caregivers.

Methods

A COVID-19 period prevalence study was conducted between 13 and 26 August 2020 at Tygerberg Hospital, testing all children and their accompanying asymptomatic caregivers after initial symptom screening. One nasopharyngeal swab was submitted for SARS-CoV-2 using real-time reverse-transcription polymerase chain reaction (rRT-PCR). An additional Respiratory Viral 16-multiplex rRT-PCR test was simultaneously done in children presenting with symptoms compatible with possible SARS-CoV-2 infection.

Results

SARS-Co-V 2 RT-PCR tests from 196 children and 116 caregivers were included in the analysis. The SARS-CoV-2 period prevalence in children was 5.6% (11/196) versus 15.5% (18/116) in asymptomatic caregivers (p<0.01). Presenting symptoms did not correlate with SARS-CoV-2 test positivity; children without typical symptoms of SARS-CoV-2 were more likely to be positive than those with typical symptoms (10.2% [10/99] vs 1% [1/97]; p<0.01). Children with typical symptoms (97/196; 49.5%) mainly presented with acute respiratory (68/97; 70.1%), fever (17/97; 17.5%), or gastro-intestinal complaints (12/97; 12.4%); Human Rhinovirus (23/81; 28.4%) and Respiratory Syncytial Virus (18/81; 22.2%) were frequently identified in this group. Children-caregiver pairs' SARS-CoV-2 tests were discordant in 83.3%; 15/18 infected caregivers' children tested negative. Symptom-based COVID-19 screening alone would have missed 90% of the positive children and 100% of asymptomatic but positive caregivers.

Conclusion

Given the poor correlation between SARS-CoV-2 symptoms and RT-PCR test positivity, universal testing of children and their accompanying caregivers should be considered for emergency and inpatient paediatric admissions during high COVID-19 community transmission periods. Universal PPE and optimising ventilation is likely the most effective way to control transmission of respiratory viral infections, including SARS-CoV-2, where universal testing is not feasible. In these settings, repeated point prevalence studies may be useful to inform local testing and cohorting strategies.

SARS-CoV-2 Seroprevalence among Healthcare Workers after the First and Second Pandemic Waves

Background: The Grand Hôpital de Charleroi is a large non-academic Belgian hospital that treated a large number of COVID-19 inpatients. In the context of this pandemic, all professions-combined healthcare workers (HCWs), and not only direct caregivers, are a frontline workforce in contact with suspected and confirmed COVID-19 cases and seem to be a high-risk group for exposure. The aim of our study was to estimate the prevalence of anti-SARS-CoV-2 antibodies in HCWs in our hospital after the first and second pandemic waves and to characterize the distribution of this seroprevalence in relation to various criteria. Methods: At the end of the two recruitment periods, a total of 4008 serological tests were performed in this single-center cross-sectional study. After completing a questionnaire including demographic and personal data, possible previous COVID-19 diagnostic test results and/or the presence of symptoms potentially related to COVID-19, the study participants underwent blood sampling and serological testing using DiaSorin's LIAISON® SARS-CoV-2 S1/S2 IgG test for the first phase and LIAISON® SARS-CoV-2 TrimericS IgG test for the second phase of this study. Results: In total, 302 study participants (10.72%) in the first round of the study and 404 (33.92%) in the second round were positive for SARS-CoV-2-IgG antibodies. The prevalence of seropositivity observed after the second wave was 3.16 times higher than after the first wave. We confirmed that direct, prolonged, and repeated contact with patients or their environment was a predominant seroconversion factor, but more unexpectedly, that this was the case for all HCWs and not only caregivers. Finally, the notion of high-risk contact seemed more readily identifiable in one's workplace than in one's private life. Conclusions: Our study confirmed that HCWs are at a significantly higher risk of contracting COVID-19 than the general population, and suggests that repeated contacts with at-risk patients, regardless of the HCWs' professions, represents the most important risk factor for seroconversion (Clinicaltrials.gov number, NCT04723290).

A 14+7 day quarantine period and a dual nucleic acid testing reagent strategy detect potentially indiscoverable Coronavirus disease 2019 infections in Xiamen, China

Background

Determining what quarantine period and detection strategy are more effective and sustainable remains a challenge for further prevention and social stability.

Methods

From October 2020 to December 2021, 290,547 inbound overseas travelers were subject to government quarantine in Xiamen, China. The detection rate of COVID-19 during different quarantine periods using dual or single nucleic acid testing reagents.

Results

The COVID-19 positive rate was 1.79% (519/290,547). The detection rates during the 7-day, 14-day and 14+7-day quarantine periods using the dual reagents were 78.4%, 91.7%, and 100%, respectively. The detection rate of the 7-day, 14-day and 14+7-day quarantine periods were 73.99%, 86.51%, and 94.22%, respectively, using the Liferiver reagent and 72.25%, 84.59%, and 91.91%, respectively, using the Daan reagent. Based on the 14+7 day strategy, dual nucleic acid testing reagent strategy detected all imported cases, but 30 cases (5.78%) were not detected via Liferiver reagent and 42 (8.09%) cases not detected via Daan reagent.

Conclusion

A 14+7-day quarantine period and dual nucleic acid testing reagent strategy are effective screening methods for COVID-19 among inbound overseas travelers. The superior detection rate of these strategies reduce the risk of secondary transmission of the SARS-CoV-2 virus.

Advancements in Testing Strategies for COVID-19

The SARS-CoV-2 coronavirus, also known as the disease-causing agent for COVID-19, is a virulent pathogen that may infect people and certain animals. The global spread of COVID-19 and its emerging variation necessitates the development of rapid, reliable, simple, and low-cost diagnostic tools. Many methodologies and devices have been developed for the highly sensitive, selective, cost-effective, and rapid diagnosis of COVID-19. This review organizes the diagnosis platforms into four groups: imaging, molecular-based detection, serological testing, and biosensors. Each platform's principle, advancement, utilization, and challenges for monitoring SARS-CoV-2 are discussed in detail. In addition, an overview of the impact of variants on detection, commercially available kits, and readout signal analysis has been presented. This review will expand our understanding of developing advanced diagnostic approaches to evolve into susceptible, precise, and reproducible technologies to combat any future outbreak.

Development and validation of a PCR-free nucleic acid testing method for RNA viruses based on linear molecular beacon probes

Background

RNA viruses periodically trigger pandemics of severe human diseases, frequently causing enormous economic losses. Here, a nucleic acid extraction-free and amplification-free RNA virus testing probe was proposed for the sensitive and simple detection of classical swine fever virus (CSFV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), based on a double-stranded molecular beacon method. This RNA virus probe contains two base sequences—a recognition strand that binds to the specific domain of CSFV N2 or SARS-CoV-2 N, with a fluorophore (FAM) labeled at the 5′ end, and a complementary strand (CSFV-Probe B or SARS-CoV-2-Probe B), combined with a quencher (BHQ2) labeled at the 3′ end.

Results

Using linear molecular beacon probe technology, the detection limit of the RNA virus probe corresponding to CSFV and SARS-CoV-2 were as low as 0.28 nM and 0.24 nM, respectively. After CSFV E2 and SARS-CoV-2 N genes were transfected into corresponding host cells, the monitoring of RNA virus probes showed that fluorescence signals were dramatically enhanced in a concentration- and time-dependent manner. These results were supported by those of quantitative (qRT-PCR) and visualization (confocal microscopy) analyses. Furthermore, CSF-positive swine samples and simulated SARS-CoV-2 infected mouse samples were used to demonstrate their applicability for different distributions of viral nucleic acids in series tissues.

Conclusions

The proposed RNA virus probe could be used as a PCR-free, cost-effective, and rapid point-of-care (POC) diagnostic platform for target RNA virus detection, holding great potential for the convenient monitoring of different RNA viruses for early mass virus screening.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-022-01470-1.

SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection

Being in the epicenter of the COVID-19 pandemic, our lab tested 193,054 specimens for SARS-CoV-2 RNA by diagnostic multiplex reverse transcription polymerase chain reaction (mRT-PCR) starting in March 2020, of which 17,196 specimens resulted positive. To investigate the dynamics of virus molecular evolution and epidemiology, whole genome amplification (WGA) and Next Generation Sequencing (NGS) were performed on 9516 isolates. 7586 isolates with a high quality were further analyzed for the mutation frequency and spectrum. Lastly, we evaluated the utility of the mRT-PCR detection pattern among 26 reinfected patients with repeat positive testing three months after testing negative from the initial infection. Our results show a continuation of the genetic divergence in viral genomes. Furthermore, our results indicate that independent mutations in the primer and probe regions of the nucleocapsid gene amplicon and envelope gene amplicon accumulate over time. Some of these mutations correlate with the changes of detection pattern of viral targets of mRT-PCR. Our data highlight the significance of a continuous genetic divergence on a gene amplification-based assay, the value of the mRT-PCR detection pattern for complementing the clinical diagnosis of reinfection, and the potential for WGA and NGS to identify mutation hotspots throughout the entire viral genome to optimize the design of the PCR-based gene amplification assay.

Acute kidney injury in critically Ill children and young adults with suspected SARS-CoV2 infection

BACKGROUND

We aimed to study the association of suspected versus confirmed infection with the novel SARS-CoV2 virus with the prevalence of acute kidney injury (AKI) in critically ill children.

METHODS

Sequential point-prevalence study of children and young adults aged 7 days to 25 years admitted to intensive care units under investigation for SARS-CoV2 infection. AKI was staged in the first 14 days of enrollment using KDIGO creatinine-based staging. SARS-CoV2 positive (CONFIRMED) were compared to SUSPECTED (negative or unknown). Outcome data was censored at 28-days.

RESULTS

In 331 patients of both sexes, 179 (54.1%) were CONFIRMED, 4.2% (14) died. AKI occurred in 124 (37.5%) and severe AKI occurred in 63 (19.0%). Incidence of AKI in CONFIRMED was 74/179 (41.3%) versus 50/152 (32.9%) for SUSPECTED; severe AKI occurred in 35 (19.6%) of CONFIRMED and 28 (18.4%) of SUSPECTED. Mortality was 6.2% (n = 11) in CONFIRMED, but 9.5% (n = 7) in those CONFIRMED with AKI. On multivariable analysis, only Hispanic ethnicity (relative risk 0.5, 95% CI 0.3-0.9) was associated with less AKI development among those CONFIRMED.

CONCLUSIONS

AKI and severe AKI occur commonly in critically ill children with SARS-CoV2 infection, more than double the historical standard. Further investigation is needed during this continuing pandemic to describe and refine the understanding of pediatric AKI epidemiology and outcomes.

TRIAL REGISTRATION

NCT01987921.

IMPACT

What is the key message of the article? AKI occurs in children exposed to the novel SARS-CoV2 virus at high prevalence (~40% with some form of AKI and 20% with severe AKI). What does it add to the existing literature? Acute kidney injury (AKI) occurs commonly in adult patients with SARS-CoV2 (COVID), very little data describes the epidemiology of AKI in children exposed to the virus. What is the impact? A pediatric vaccine is not available; thus, the pandemic is not over for children. Pediatricians will need to manage significant end-organ ramifications of the novel SARS-CoV2 virus including AKI.

Comparison of Abbott ID NOW COVID-19 Rapid Molecular Assay to Allplex 2019-nCoV and VIASURE SARS-CoV-2 Detection in Nasal Swabs

BACKGROUND: Readily available, accurate, and rapid diagnostic technologies are of high priority to contain emerging and re-emerging pandemics and to properly allocate personal protective equipment usage and preventing nosocomial spread with subsequent community transmission. Detection of positive 2019-nCoV nucleic acids by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR)-based assays remains the gold standard for COVID-19 diagnostics. However, these assays take an average over 3–5 h to generate results and the PCR tests require certified laboratories, expensive equipment, and trained technicians to operate. Therefore, there is an urgent need for rapid point of care molecular tests that can be readily used in a healthcare setting that generates reliable results within few hours. Those tests should provide reliable results in the setting to facilitate the diagnosis and rapid decision-making. AIM: The present study aimed to evaluate the diagnostic performance of Abbott ID NOW SARS-CoV-2 compared to two gold standard assays (Allplex 2019- nCoV and VIASURE SARS-CoV-2) and to detect the relation between viral load and the sensitivity of ID NOW SARS-CoV-2 assay. METHODS: A total of 86 and 42 nasopharyngeal swabs collected from patients attending the Reference Laboratory of Egyptian University Hospitals during the period from January 2022 to May 2022, were tested by our reference methods of RT-PCR for COVID-19 detection; VIASURE kit and Allplex kits, respectively. Corresponding dry nasal swabs were collected from the same patients for ID NOW SARS-CoV-2 ribonucleic acid (RNA) detection assay. RESULTS: As regards the results of the 86 nasopharyngeal swabs tested by both VIASURE kit and ID NOW, there was a good agreement between both methods (95%) (kappa = 0.924), where the ID NOW method was not able to detect three COVID-19-positive samples (3/86, 5.1%). ID NOW exhibited specificity and sensitivity of 100% and 94.9%, respectively. As for comparing results of ID NOW with Allplex kit, the results of the 42 nasopharyngeal swabs tested by both tests revealed good agreement between both methods (kappa = 0.908). In comparison with Allplex kit, ID NOW exhibited specificity and sensitivity of 90% and 100%, respectively. Regarding the relation between the viral load detected by VIASURE kit and results of the ID NOW test, we found that ID NOW showed a sensitivity of 82.35% in samples with low viral load (CT > 30), while for samples with intermediate (CT: 20–30) and high (CT < 20) viral loads, sensitivity was 100%. CONCLUSION: ID NOW assay in our study exhibited a high diagnostic performance when evaluated with the gold standard RT-PCR methods. Our study further substantiates the high sensitivity of ID NOW in the presence of intermediate and high viral loads detected by molecular RT-PCR SARS-CoV-2 testing. Its analytical performances, combined with the very short 13 min reactional time and the friendly device-guided handling procedure, constitute an additional advantage of ID NOW COVID-19 for setting up a rapid diagnosis within the clinical laboratories and for timely identification of outbreaks allowing for aggressive contact tracing and containment.

Multiplatform Assessment of Saliva for SARS-CoV-2 Molecular Detection in Symptomatic Healthcare Personnel and Patients Presenting to the Emergency Department

BACKGROUND

Saliva has garnered great interest as an alternative specimen type for molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Data are limited on the relative performance of different molecular methods using saliva specimens and the relative sensitivity of saliva to nasopharyngeal (NP) swabs.

METHODS

To address the gap in knowledge, we enrolled symptomatic healthcare personnel (n = 250) from Barnes-Jewish Hospital/Washington University Medical Center and patients presenting to the Emergency Department with clinical symptoms compatible with coronavirus disease 2019 (COVID-19; n = 292). We collected paired saliva specimens and NP swabs. The Lyra SARS-CoV-2 assay (Quidel) was evaluated on paired saliva and NP samples. Subsequently we compared the Simplexa COVID-19 Direct Kit (Diasorin) and a modified SalivaDirect (Yale) assay on a subset of positive and negative saliva specimens.

RESULTS

The positive percent agreement (PPA) between saliva and NP samples using the Lyra SARS-CoV-2 assay was 63.2%. Saliva samples had higher SARS-CoV-2 cycle threshold values compared to NP swabs (P < 0.0001). We found a 76.47% (26/34) PPA for Simplexa COVID-19 Direct Kit on saliva and a 67.6% (23/34) PPA for SalivaDirect compared to NP swab results.

CONCLUSION

These data demonstrate molecular assays have variability in performance for detection of SARS-CoV-2 in saliva.

Clinical characteristics of hospitalized patients with false-negative severe acute respiratory coronavirus virus 2 (SARS-CoV-2) test results

OBJECTIVE

To determine clinical characteristics associated with false-negative severe acute respiratory coronavirus virus 2 (SARS-CoV-2) test results to help inform coronavirus disease 2019 (COVID-19) testing practices in the inpatient setting.

DESIGN

A retrospective observational cohort study.

SETTING

Tertiary-care facility.

PATIENTS

All patients 2 years of age and older tested for SARS-CoV-2 between March 14, 2020, and April 30, 2020, who had at least 2 SARS-CoV-2 reverse-transcriptase polymerase chain reaction tests within 7 days.

METHODS

The primary outcome measure was a false-negative testing episode, which we defined as an initial negative test followed by a positive test within the subsequent 7 days. Data collected included symptoms, demographics, comorbidities, vital signs, labs, and imaging studies. Logistic regression was used to model associations between clinical variables and false-negative SARS-CoV-2 test results.

RESULTS

Of the 1,009 SARS-CoV-2 test results included in the analysis, 4.0% were false-negative results. In multivariable regression analysis, compared with true-negative test results, false-negative test results were associated with anosmia or ageusia (adjusted odds ratio [aOR], 8.4; 95% confidence interval [CI], 1.4-50.5; P = .02), having had a COVID-19-positive contact (aOR, 10.5; 95% CI, 4.3-25.4; P < .0001), and having an elevated lactate dehydrogenase level (aOR, 3.3; 95% CI, 1.2-9.3; P = .03). Demographics, symptom duration, other laboratory values, and abnormal chest imaging were not significantly associated with false-negative test results in our multivariable analysis.

CONCLUSIONS

Clinical features can help predict which patients are more likely to have false-negative SARS-CoV-2 test results.

Review of non-invasive detection of SARS-CoV-2 and other respiratory pathogens in exhaled breath condensate

In 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged to cause high viral infectivity and severe respiratory illness in humans (COVID-19). Worldwide, limited pandemic mitigation strategies, including lack of diagnostic test availability, resulted in COVID-19 overrunning health systems and spreading throughout the global population. Currently, proximal respiratory tract (PRT) specimens such as nasopharyngeal swabs are used to diagnose COVID-19 because of their relative ease of collection and applicability in large scale screening. However, localization of SARS-CoV-2 in the distal respiratory tract (DRT) is associated with more severe infection and symptoms. Exhaled breath condensate (EBC) is a sample matrix comprising aerosolized droplets originating from alveolar lining fluid that are further diluted in the DRT and then PRT and collected via condensation during tidal breathing. The COVID-19 pandemic has resulted in recent resurgence of interest in EBC collection as an alternative, non-invasive sampling method for the staging and accurate detection of SARS-CoV-2 infections. Herein, we review the potential utility of EBC collection for detection of SARS-CoV-2 and other respiratory infections. While much remains to be discovered in fundamental EBC physiology, pathogen-airway interactions, and optimal sampling protocols, EBC, combined with emerging detection methods, presents a promising non-invasive sample matrix for detection of SARS-CoV-2.

Recent advances of functional nucleic acid-based sensors for point-of-care detection of SARS-CoV-2

This review focuses on critical scientific barriers that the field of point-of-care (POC) testing of SARS-CoV-2 is facing and possible solutions to overcome these barriers using functional nucleic acid (FNA)-based technology. Beyond the summary of recent advances in FNA-based sensors for COVID-19 diagnostics, our goal is to outline how FNA might serve to overcome the scientific barriers that currently available diagnostic approaches are suffering. The first introductory section on the operationalization of the COVID-19 pandemic in historical view and its clinical features contextualizes essential SARS-CoV-2-specific biomarkers. The second part highlights three major scientific barriers for POC COVID-19 diagnosis, that is, the lack of a general method for (1) designing receptors of SARS-CoV-2 variants; (2) improving sensitivity to overcome false negatives; and (3) signal readout in resource-limited settings. The subsequent part provides fundamental insights into FNA and technical tricks to successfully achieve effective COVID-19 diagnosis by using in vitro selection of FNA to overcome receptor design barriers, combining FNA with multiple DNA signal amplification strategies to improve sensitivity, and interfacing FNA with portable analyzers to overcome signal readout barriers. This review concludes with an overview of further opportunities and emerging applications for FNA-based sensors against COVID-19.

A Comparison of Pharyngeal Swabs and Tracheal Secretions for the Diagnosing of COVID-19

The aim of this study was to compare the test results from patients who, within a short timescale, have been tested for COVID-19 using both a pharyngeal swab and tracheal secretion. Data were collected from the database of AUH, from patients hospitalized between 1 March 2020 and 1 March 2021 who, due to symptoms of COVID-19, were tested by a pharyngeal swab and by tracheal secretion. We found great agreement between oropharyngeal swab and tracheal secretion RT-PCR testing for the diagnosis of COVID-19, with 98.5% of double tests being concordant and only 1.5% being discordant. This finding may advocate a single-test strategy being either an oropharyngeal swab RT-PCR testing or tracheal secretion, although this study revealed 15.9% false negative oropharyngeal swabs.

A case-control evaluation of pulmonary and extrapulmonary findings of incidental asymptomatic COVID-19 infection on FDG PET-CT

OBJECTIVES

To describe the findings of incidental asymptomatic COVID-19 infection on FDG PET-CT using a case-control design.

METHODS

Incidental pulmonary findings suspicious of asymptomatic COVID-19 infection on FDG PET-CT were classified as a confirmed (positive RT-PCR test) or suspected case (no/negative RT-PCR test). Control cases were identified using a 4:1 control:case ratio. Pulmonary findings were re-categorised by two reporters using the BSTI classification. SUV metrics in ground glass opacification (GGO)/consolidation (where present), background lung, intrathoracic nodes, liver, spleen and bone marrow were measured.

RESULTS

7/9 confirmed and 11/15 suspected cases (COVID-19 group) were re-categorised as BSTI 1 (classic/probable COVID-19) or BSTI 2 (indeterminate COVID-19); 0/96 control cases were categorised as BSTI 1. Agreement between two reporters using the BSTI classification was almost perfect (weighted κ = 0.94). SUVmax GGO/consolidation (5.1 vs 2.2; p < 0.0001) and target-to-background ratio, normalised to liver SUVmean (2.4 vs 1.0; p < 0.0001) were higher in the BSTI 1 & 2 group vs BSTI 3 (non-COVID-19) cases. SUVmax GGO/consolidation discriminated between the BSTI 1 & 2 group vs BSTI 3 (non-COVID-19) cases with high accuracy (AUC = 0.93). SUV metrics were higher (p < 0.05) in the COVID-19 group vs control cases in the lungs, intrathoracic nodes and spleen.

CONCLUSION

Asymptomatic COVID-19 infection on FDG PET-CT is characterised by bilateral areas of FDG avid (intensity > x2 liver SUVmean) GGO/consolidation and can be identified with high interobserver agreement using the BSTI classification. There is generalised background inflammation within the lungs, intrathoracic nodes and spleen.

ADVANCES IN KNOWLEDGE

Incidental asymptomatic COVID-19 infection on FDG PET-CT, characterised by bilateral areas of ground glass opacification and consolidation, can be identified with high reproducibility using the BSTI classification. The intensity of associated FDG uptake (>x2 liver SUVmean) provides high discriminative ability in differentiating such cases from pulmonary findings in a non-COVID-19 pattern. Asymptomatic COVID-19 infection causes a generalised background inflammation within the mid-lower zones of the lungs, hilar and central mediastinal nodal stations, and spleen on FDG PET-CT.

Clinical Comparative Evaluation of the LabTurboTM AIO® Reverse Transcription-Polymerase Chain Reaction and World Health Organization-Recommended Assays for the Detection of Emerging SARS-CoV-2 Variants of Concern

PURPOSE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent behind coronavirus disease-2019 (COVID-19). Single-plex reverse transcription-polymerase chain reaction (RT-PCR)-based assays are widely used for COVID-19 detection but exhibit decreased sensitivity and specificity in detecting the rapidly spreading SARS-CoV-2 variants; in contrast, multiplex RT-PCR reportedly yields better results. Here, we aimed at comparatively analyzing the clinical performance of the LabTurbo^TM AIO COVID-19 RNA testing kit, a multiplex quantitative RT-PCR kit, including a three-target (E, N1, and RNase P), single-reaction, triplex assay used for SARS-CoV-2 detection, with that of the WHO-recommended RT-PCR assay.

MATERIALS AND METHODS

Residual, natural, nasopharyngeal swabs obtained from universal transport medium specimens at SARS-CoV-2 testing centers (n = 414) were collected from May to October 2021. For SARS-CoV-2 qRT-PCR, total viral nucleic acid was extracted. The limit of detection (LOD) and the comparative clinical performances of the LabTurbo^TM AIO COVID-19 RNA kit and the WHO-recommended RT-PCR assay were assessed. Statistical analysis of the correlation was performed and results with R² values >0.9 were considered to be highly correlated.

RESULTS

The LOD of the LabTurbo^TM AIO COVID-19 RNA kit was 9.4 copies/reaction for the target genes N1 and E. The results obtained from 102 SARS-CoV-2-positive and 312 SARS-CoV-2-negative samples showed 100% correlation with previous WHO-recommended RT-PCR assay results.

CONCLUSION

Multiplex qRT-PCR is a critical tool for detecting unknown pathogens and employs multiple target genes. The LabTurbo^TM AIO COVID-19 RNA testing kit provides an effective and efficient assay for SARS-CoV-2 detection and is highly compatible with SARS-CoV-2 variants.

Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens

Viral pathogens can rapidly evolve, adapt to novel hosts, and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire group of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.

Recent findings and applications of biomedical engineering for COVID-19 diagnosis: a critical review

COVID-19 is one of the most severe global health crises that humanity has ever faced. Researchers have restlessly focused on developing solutions for monitoring and tracing the viral culprit, SARS-CoV-2, as vital steps to break the chain of infection. Even though biomedical engineering (BME) is considered a rising field of medical sciences, it has demonstrated its pivotal role in nurturing the maturation of COVID-19 diagnostic technologies. Within a very short period of time, BME research applied to COVID-19 diagnosis has advanced with ever-increasing knowledge and inventions, especially in adapting available virus detection technologies into clinical practice and exploiting the power of interdisciplinary research to design novel diagnostic tools or improve the detection efficiency. To assist the development of BME in COVID-19 diagnosis, this review highlights the most recent diagnostic approaches and evaluates the potential of each research direction in the context of the pandemic.

Demographics and clinical characteristics of hospitalised patients under investigation for COVID-19 with an initial negative SARS-CoV-2 PCR test result

Background

The COVID-19 pandemic is placing abnormally high and ongoing demands on healthcare systems. Little is known about the full effect of the COVID-19 pandemic on diseases other than COVID-19 in the South African setting.

Objective

To describe a cohort of hospitalised patients under investigation for SARS-CoV-2 that initially tested negative.

Methods

Consecutive patients hospitalised at Khayelitsha Hospital from April to June 2020, whose initial polymerase chain reaction test for SARS-CoV-2 was negative were included. Patient demographics, clinical characteristics, ICD-10 (International Statistical Classification of Diseases and Related Health Problems 10th Revision) diagnosis, referral to tertiary level facilities and ICU, and all-cause in-hospital mortality were collected. The 90-day re-test rate was determined and comparisons were made using the χ²-test and the independent samples median test.

Results

Overall, 261 patients were included: median age 39.8 years, 55.6% female (n = 145). Frequent comorbidities included HIV (41.4%), hypertension (26.4%), and previous or current tuberculosis (24.1%). Nine (3.7%) patients were admitted to ICU and 38 (15.6%) patients died. Ninety-three patients (35.6%) were re-tested and 21 (22.6%) were positive for SARS-CoV-2. The top primary diagnoses related to respiratory diseases (n = 82, 33.6%), and infectious and parasitic diseases (n = 62, 25.4%). Thirty-five (14.3%) had a COVID-19 diagnostic code assigned (26 without microbiological confirmation) and 43 (16.5%) had tuberculosis. Older age (p = 0.001), chronic renal impairment (p = 0.03) and referral to higher level of care (all p < 0.001; ICU p = 0.03) were more frequent in those that died.

Conclusion

Patients with tuberculosis and other diseases are still presenting to emergency centres with symptoms that may be attributable to SARS-CoV-2 and requiring admission. Extreme vigilance will be necessary to diagnosis and treat tuberculosis and other diseases as we emerge from the COVID-19 pandemic.

Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid and antibody tests up to 22 August 2020

BackgroundReliable testing for SARS-CoV-2 is key for the management of the COVID-19 pandemic.AimWe estimate diagnostic accuracy for nucleic acid and antibody tests 5 months into the COVID-19 pandemic, and compare with manufacturer-reported accuracy.MethodsWe reviewed the clinical performance of SARS-CoV-2 nucleic acid and antibody tests based on 93,757 test results from 151 published studies and 20,205 new test results from 12 countries in the European Union and European Economic Area (EU/EEA).ResultsPooling the results and considering only results with 95% confidence interval width ≤ 5%, we found four nucleic acid tests, including one point-of-care test and three antibody tests, with a clinical sensitivity ≥ 95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Nine nucleic acid tests and 25 antibody tests, 12 of them point-of-care tests, had a clinical specificity of ≥ 98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid point-of-care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for eight of 14 sensitivity and 68 of 84 specificity results with confidence interval width ≤ 5%, and lower for nucleic acid tests than antibody tests. Manufacturer-reported clinical performance was significantly higher than independently assessed in 11 of 32 and four of 34 cases, respectively, for sensitivity and specificity, indicating a need for improvement in this area.ConclusionContinuous monitoring of clinical performance within more clearly defined target populations is needed.

Risk factors for prolonged virus shedding of respiratory tract and fecal in adults with severe acute respiratory syndrome coronavirus-2 infection

BACKGROUND

The dynamic alteration and comparative study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA shedding pattern during treatment are limited. This study explores the potential risk factors influencing prolonged viral shedding in COVID-19.

METHODS

A total of 126 COVID-19 patients were enrolled in this retrospective longitudinal study. A multivariate logistic regression analysis was carried out to estimate the potential risk factors.

RESULTS

38.1% (48/126) cases presented prolonged respiratory tract viral shedding, and 30 (23.8%) cases presented prolonged rectal swab viral shedding. Obesity (OR, 3.31; 95% CI, 1.08-10.09), positive rectal swab (OR, 3.43; 95% CI, 1.53-7.7), treatment by lopinavir/ritonavir with chloroquine phosphate (OR, 2.5; 95% CI, 1.04-6.03), the interval from onset to antiviral treatment more than 7 days (OR, 2.26; 95% CI, 1.04-4.93), lower CD4+ T cell (OR, 0.92; 95% CI, 0.86-0.99) and higher NK cells (OR, 1.11; 95% CI, 1.02-1.20) were significantly associated with prolonged respiratory tract viral shedding. CD3-CD56+ NK cells (OR, 0.87; 95% CI, 0.76-0.99) were related with prolonged fecal shedding.

CONCLUSIONS

Obesity, delayed antiviral treatment, and positive SARS-CoV-2 for stool were independent risk factors for prolonged SARS-CoV-2 RNA shedding of the respiratory tract. A combination of LPV/r and abidol as the initial antiviral regimen was effective in shortening the duration of viral shedding compared with LPV/r combined with chloroquine phosphate. CD4+ T cell and NK cells were significantly associated with prolonged viral shedding, and further studies are to be warranted to determine the mechanism of immunomodulatory response in virus clearance.

Comparison of analytical sensitivity of SARS-CoV-2 molecular detection kits

Objectives

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has had a significant impact on global public health systems, making nucleic acid detection an important tool in epidemic prevention and control. Detection kits based on real-time reverse transcriptase PCR (rRT-PCR) have been used widely in clinics, but their analytical sensitivity (limit of detection, LOD) remains controversial. Moreover, there is limited research evaluating the analytical sensitivity of other molecular detection kits.

Methods

In this study, armored ribonucleic acid reference materials developed in-house were used to evaluate the analytical sensitivity of SARS-CoV-2 detection kits approved by the National Medical Products Administration. These were based on rRT-PCR and other molecular detection assays.

Results

The percentage retesting required with rRT-PCR kits was as follows: 0%, 7.69%, 15.38%, and 23.08% for samples with concentrations ranging from 50 000 to 781 copies/ml. In total, 93% of rRT-PCR kits had a LOD <1000 copies/ml. Only one kit had an LOD >1000 copies/ml. The LOD of other molecular detection kits ranged from 68 to 2264 copies/ml.

Conclusions

The study findings can help pharmaceutical companies optimize and improve detection kits, guide laboratories in selecting kits, and assist medical workers in their daily work.

Clinical and epidemiologic characteristics of inconclusive results in SARS-CoV-2 RT-PCR assays

Background

Inconclusive results in SARS-CoV-2 molecular assays cause confusion among clinicians and delay appropriate infection prevention and control. In this study, we aimed to characterize the respiratory specimens associated with inconclusive SARS-CoV-2 molecular assay results.

Methods

We re-evaluated inconclusive specimens by 3 additional RT-PCR assays and attempted to detect subgenomic RNA (sgRNA) in these specimens.

Results

Among follow-up tests from confirmed SARS-CoV-2 cases, 36.3% of the inconclusive results were classified as presumptive positive results (45/124). However, none of the specimens from 36 screening cases was classified as a presumptive positive result. Among 160 inconclusive specimens, sgRNAs were detected in 78 samples (48.8%): 58 were confirmed cases (58/124, 46.8%) and 20 were screening cases (20/36, 55.6%).

Conclusions

The results of our study suggest the recommendation of considering inconclusive results as positive results for confirmed SARS-CoV-2 cases. In screening cases, viral remnants could be partially amplified in PCR assays, and these inconclusive results could be related to previous infections. In addition, sgRNAs were detected in about half of the inconclusive specimens; however, the clinical significance of sgRNA is not yet clear.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06534-5.

Variation in SARS-CoV-2 molecular test sensitivity by specimen types in a large sample of emergency department patients

BACKGROUND

Provider-collected nasopharyngeal specimens for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular testing are the standard of care in many clinical settings, but patient-collected saliva and anterior nares specimens are less invasive and more flexible alternatives. Prior studies comparing specimen types for SARS-CoV-2 molecular testing have been limited by small sample sizes and low pretest probability. We conducted a large observational study among symptomatic adults at 7 emergency departments of Kaiser Permanente Southern California to examine sensitivity of SARS-CoV-2 molecular tests by specimen type and patient characteristics.

METHODS

Provider-collected nasopharyngeal/oropharyngeal (NP/OP) specimens and patient-collected saliva and anterior nares specimens were collected at the same visit and analyzed with the Roche cobas® SARS-CoV-2 assay. Patients were considered truly positive for SARS-CoV-2 if any of the three specimens was positive and negative if all three specimens were negative. Factors associated with discordant and missed positive results were examined with multivariable logistic regression.

RESULTS

Of 2112 patients, 350 (16.6%) were positive for SARS-CoV-2. Sensitivity of NP/OP was 93.7% (95% confidence interval [CI] 90.6%-96.0%), sensitivity of saliva was 87.7% (83.8%-91.0%), and sensitivity of anterior nares was 85.4% (81.3%-89.0%). Patients ages 18-39 years versus ≥40 years were more likely to have discordant results [adjusted odds ratio (aOR) 1.97 (1.12-3.45)], as were patients with <4 symptoms versus ≥4 [aOR 2.43 (1.39-4.25)]. Cycle threshold values were higher for saliva and anterior nares than NP/OP specimens, as well as for specimens in discordant versus concordant sets and patients with fewer symptoms.

CONCLUSION

This study provides robust evidence that patient-collected saliva and anterior nares are sensitive for SARS-CoV-2 molecular testing in emergency department settings, particularly among adults ages ≥40 years and those with multiple symptoms. Higher sensitivity of provider-collected NP/OP specimens must be weighed against the benefits of patient-collected specimens in tailored strategies for SARS-CoV-2 testing.

Supervised Machine Learning Approach to Identify Early Predictors of Poor Outcome in Patients with COVID-19 Presenting to a Large Quaternary Care Hospital in New York City

Background: The progression of clinical manifestations in patients with coronavirus disease 2019 (COVID-19) highlights the need to account for symptom duration at the time of hospital presentation in decision-making algorithms. Methods: We performed a nested case–control analysis of 4103 adult patients with COVID-19 and at least 28 days of follow-up who presented to a New York City medical center. Multivariable logistic regression and classification and regression tree (CART) analysis were used to identify predictors of poor outcome. Results: Patients presenting to the hospital earlier in their disease course were older, had more comorbidities, and a greater proportion decompensated (<4 days, 41%; 4–8 days, 31%; >8 days, 26%). The first recorded oxygen delivery method was the most important predictor of decompensation overall in CART analysis. In patients with symptoms for <4, 4–8, and >8 days, requiring at least non-rebreather, age ≥ 63 years, and neutrophil/lymphocyte ratio ≥ 5.1; requiring at least non-rebreather, IL-6 ≥ 24.7 pg/mL, and D-dimer ≥ 2.4 µg/mL; and IL-6 ≥ 64.3 pg/mL, requiring non-rebreather, and CRP ≥ 152.5 mg/mL in predictive models were independently associated with poor outcome, respectively. Conclusion: Symptom duration in tandem with initial clinical and laboratory markers can be used to identify patients with COVID-19 at increased risk for poor outcomes.

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.

Study of Thoracic CT in COVID-19: The STOIC Project

Background There are conflicting data regarding the diagnostic performance of Chest computed tomography (CT) for COVID-19 pneumonia. Disease extent on CT has been reported to influence prognosis. Purpose To create a large publicly available dataset and assess the diagnostic and prognostic value of CT in COVID-19 pneumonia. Materials and Methods This multicenter observational retrospective cohort study (ClinicalTrials.gov: NCT04355507) involved 20 French university hospitals. Eligible subjects presented at the emergency departments of the hospitals involved between March 1st and April 30th, 2020 and underwent both thoracic CT and RT-PCR for suspected COVID-19 pneumonia. CT images were read blinded to initial reports, RT-PCR, demographic characteristics, clinical symptoms, and outcome. Readers classified CT scans as positive or negative for COVID-19, based on criteria published by the French Society of Radiology. Multivariable logistic regression was used to develop a model predicting severe outcome (intubation or death) at 1-month follow-up in subjects positive for both RT-PCR and CT, using clinical and radiological features. Results Of 10,930 subjects screened for eligibility, 10,735 (median age 65 years, interquartile range, 51-77 years; 6,147 men) were included and 6,448 (60.0%) had a positive RT-PCR result. With RT-PCR as reference, the sensitivity and specificity and CT were 80.2% (95%CI: 79.3, 81.2) and 79.7% (95%CI: 78.5, 80.9), respectively with strong agreement between junior and senior radiologists (Gwet's AC1 coefficient: 0.79) Of all the variables analysed, the extent of pneumonia on CT (OR 3.25, 95%CI: 2.71, 3.89) was the best predictor of severe outcome at one month. A score based solely on clinical variables predicted a severe outcome with an AUC of 0.64 (95%CI: 0.62, 0.66), improving to 0.69 (95%CI: 0.6, 0.71) when it also included the extent of pneumonia and coronary calcium score on CT. Conclusion Using pre-defined criteria, CT reading is not influenced by reader's experience and helps predict the outcome at one month. Published under a CC BY 4.0 license. See also the editorial by Rubin.

Machine Learning Highlights Downtrending of COVID-19 Patients with a Distinct Laboratory Profile

BACKGROUND

New York City (NYC) experienced an initial surge and gradual decline in the number of SARS-CoV-2-confirmed cases in 2020. A change in the pattern of laboratory test results in COVID-19 patients over this time has not been reported or correlated with patient outcome.

METHODS

We performed a retrospective study of routine laboratory and SARS-CoV-2 RT-PCR test results from 5,785 patients evaluated in a NYC hospital emergency department from March to June employing machine learning analysis.

RESULTS

A COVID-19 high-risk laboratory test result profile (COVID19-HRP), consisting of 21 routine blood tests, was identified to characterize the SARS-CoV-2 patients. Approximately half of the SARS-CoV-2 positive patients had the distinct COVID19-HRP that separated them from SARS-CoV-2 negative patients. SARS-CoV-2 patients with the COVID19-HRP had higher SARS-CoV-2 viral loads, determined by cycle threshold values from the RT-PCR, and poorer clinical outcome compared to other positive patients without the COVID12-HRP. Furthermore, the percentage of SARS-CoV-2 patients with the COVID19-HRP has significantly decreased from March/April to May/June. Notably, viral load in the SARS-CoV-2 patients declined, and their laboratory profile became less distinguishable from SARS-CoV-2 negative patients in the later phase.

CONCLUSIONS

Our longitudinal analysis illustrates the temporal change of laboratory test result profile in SARS-CoV-2 patients and the COVID-19 evolvement in a US epicenter. This analysis could become an important tool in COVID-19 population disease severity tracking and prediction. In addition, this analysis may play an important role in prioritizing high-risk patients, assisting in patient triaging and optimizing the usage of resources.

Optimizing Safe Dental Practice During the COVID-19 Pandemic: Recommendations Based on a Guide Developed for Dental Practices in China

The current global coronavirus disease 2019 (COVID-19) outbreak is still exerting severe global implications, and its development in various regions is complex and variable. The high risk of cross-infection poses a great challenge to the dental practice environment; it is therefore urgent to develop a set of pandemic prevention measures to ensure dental practice safety during the COVID-19 outbreak. Therefore, we combined the epidemiological characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), public emergency measures for COVID-19, characteristics of dental practice, and relevant literature reports to develop a set of dynamic practice measures for dental practices in high-, medium-, and low-risk areas affected by COVID-19. This will help dental practices to achieve standard prevention and ensure their safe and smooth operation during the pandemic. It is hoped that these measures will provide a reference basis for dental hospitals and dental clinics in their care and pandemic prevention work.

Real-life clinical sensitivity of SARS-CoV-2 RT-PCR test in symptomatic patients

BACKGROUND

Understanding the false negative rates of SARS-CoV-2 RT-PCR testing is pivotal for the management of the COVID-19 pandemic and it has implications for patient management. Our aim was to determine the real-life clinical sensitivity of SARS-CoV-2 RT-PCR.

METHODS

This population-based retrospective study was conducted in March-April 2020 in the Helsinki Capital Region, Finland. Adults who were clinically suspected of SARS-CoV-2 infection and underwent SARS-CoV-2 RT-PCR testing, with sufficient data in their medical records for grading of clinical suspicion were eligible. In addition to examining the first RT-PCR test of repeat-tested individuals, we also used high clinical suspicion for COVID-19 as the reference standard for calculating the sensitivity of SARS-CoV-2 RT-PCR.

RESULTS

All 1,194 inpatients (mean [SD] age, 63.2 [18.3] years; 45.2% women) admitted to COVID-19 cohort wards during the study period were included. The outpatient cohort of 1,814 individuals (mean [SD] age, 45.4 [17.2] years; 69.1% women) was sampled from epidemiological line lists by systematic quasi-random sampling. The sensitivity (95% CI) for laboratory confirmed cases (repeat-tested patients) was 85.7% (81.5-89.1%) inpatients; 95.5% (92.2-97.5%) outpatients, 89.9% (88.2-92.1%) all. When also patients that were graded as high suspicion but never tested positive were included in the denominator, the sensitivity (95% CI) was: 67.5% (62.9-71.9%) inpatients; 34.9% (31.4-38.5%) outpatients; 47.3% (44.4-50.3%) all.

CONCLUSIONS

The clinical sensitivity of SARS-CoV-2 RT-PCR testing was only moderate at best. The relatively high false negative rates of SARS-CoV-2 RT-PCR testing need to be accounted for in clinical decision making, epidemiological interpretations, and when using RT-PCR as a reference for other tests.

Real-world assessment of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) nasopharyngeal swab testing in a region with a high burden of coronavirus disease 2019 (COVID-19)

Concerns persist regarding possible false-negative results that may compromise COVID-19 containment. Although obtaining a true false-negative rate is infeasible, using real-life observations, the data suggest a possible false-negative rate of ˜2.3%. Use of a sensitive, amplified RNA platform should reassure healthcare systems.

Cardiac Corrected QT Interval Changes Among Patients Treated for COVID-19 Infection During the Early Phase of the Pandemic

IMPORTANCE

Critical illness, a marked inflammatory response, and viruses such as SARS-CoV-2 may prolong corrected QT interval (QTc).

OBJECTIVE

To evaluate baseline QTc interval on 12-lead electrocardiograms (ECGs) and ensuing changes among patients with and without COVID-19.

DESIGN, SETTING, AND PARTICIPANTS

This cohort study included 3050 patients aged 18 years and older who underwent SARS-CoV-2 testing and had ECGs at Columbia University Irving Medical Center from March 1 through May 1, 2020. Patients were analyzed by treatment group over 5 days, as follows: hydroxychloroquine with azithromycin, hydroxychloroquine alone, azithromycin alone, and neither hydroxychloroquine nor azithromycin. ECGs were manually analyzed by electrophysiologists masked to COVID-19 status. Multivariable modeling evaluated clinical associations with QTc prolongation from baseline.

EXPOSURES

COVID-19, hydroxychloroquine, azithromycin.

MAIN OUTCOMES AND MEASURES

Mean QTc prolongation, percentage of patients with QTc of 500 milliseconds or greater.

RESULTS

A total of 965 patients had more than 2 ECGs and were included in the study, with 561 (58.1%) men, 198 (26.2%) Black patients, and 191 (19.8%) aged 80 years and older. There were 733 patients (76.0%) with COVID-19 and 232 patients (24.0%) without COVID-19. COVID-19 infection was associated with significant mean QTc prolongation from baseline by both 5-day and 2-day multivariable models (5-day, patients with COVID-19: 20.81 [95% CI, 15.29 to 26.33] milliseconds; P < .001; patients without COVID-19: -2.01 [95% CI, -17.31 to 21.32] milliseconds; P = .93; 2-day, patients with COVID-19: 17.40 [95% CI, 12.65 to 22.16] milliseconds; P < .001; patients without COVID-19: 0.11 [95% CI, -12.60 to 12.81] milliseconds; P = .99). COVID-19 infection was independently associated with a modeled mean 27.32 (95% CI, 4.63-43.21) millisecond increase in QTc at 5 days compared with COVID-19-negative status (mean QTc, with COVID-19: 450.45 [95% CI, 441.6 to 459.3] milliseconds; without COVID-19: 423.13 [95% CI, 403.25 to 443.01] milliseconds; P = .01). More patients with COVID-19 not receiving hydroxychloroquine and azithromycin had QTc of 500 milliseconds or greater compared with patients without COVID-19 (34 of 136 [25.0%] vs 17 of 158 [10.8%], P = .002). Multivariable analysis revealed that age 80 years and older compared with those younger than 50 years (mean difference in QTc, 11.91 [SE, 4.69; 95% CI, 2.73 to 21.09]; P = .01), severe chronic kidney disease compared with no chronic kidney disease (mean difference in QTc, 12.20 [SE, 5.26; 95% CI, 1.89 to 22.51; P = .02]), elevated high-sensitivity troponin levels (mean difference in QTc, 5.05 [SE, 1.19; 95% CI, 2.72 to 7.38]; P < .001), and elevated lactate dehydrogenase levels (mean difference in QTc, 5.31 [SE, 2.68; 95% CI, 0.06 to 10.57]; P = .04) were associated with QTc prolongation. Torsades de pointes occurred in 1 patient (0.1%) with COVID-19.

CONCLUSIONS AND RELEVANCE

In this cohort study, COVID-19 infection was independently associated with significant mean QTc prolongation at days 5 and 2 of hospitalization compared with day 0. More patients with COVID-19 had QTc of 500 milliseconds or greater compared with patients without COVID-19.

Approaching the Interpretation of Discordances in SARS-CoV-2 Testing

The coronavirus disease 2019 pandemic has upended life throughout the globe. Appropriate emphasis has been placed on developing effective therapies and vaccines to curb the pandemic. While awaiting such countermeasures, mitigation efforts coupled with robust testing remain essential to controlling spread of the disease. In particular, serological testing plays a critical role in providing important diagnostic, prognostic, and therapeutic information. However, this information is only useful if the results can be accurately interpreted. This pandemic placed clinical testing laboratories and requesting physicians in a precarious position because we are actively learning about the disease and how to interpret serological results. Having developed robust assays to detect antibodies generated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and serving the hardest-hit areas within the New York City epicenter, we found 3 types of discordances in SARS-CoV-2 test results that challenge interpretation. Using representative clinical vignettes, these interpretation dilemmas are highlighted, along with suggested approaches to resolve such cases.

Molecular (real-time reverse transcription polymerase chain reaction) diagnosis of SARS-CoV-2 infections: complexity and challenges

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first recorded in Wuhan, China. The World Health Organization initially classified COVID-19 as a public health emergency and subsequently declared the disease a global pandemic. COVID-19 can take at least three distinct forms: severe acute distress syndrome with a potentially fatal outcome, mild respiratory illness (pneumonia with eventual recovery) and asymptomatic infection. All three disease forms have the potential to transmit the infection to healthy contacts. At present, real-time reverse transcription polymerase chain reaction (RT-PCR) is the only available laboratory tool to confirm the presence of viral RNA in patient specimens. These assays are designed to detect one or more (at least 2) SARS-CoV-2 RNA gene targets allowing the detection of the virus. Commercially available RT-PCR assays employ various gene targets of the viral genome in their assay systems. Additionally, there are differences in primer selection for the same gene region of SARS-CoV-2. At present, it is unclear whether the results from different RT-PCR assays are comparable in detecting the spectrum of COVID-19 manifestations. The purpose of the present article is twofold: first, to briefly focus on the findings of these reports; and second, to emphasize the various challenges and flaws that can potentially impact the diagnostic accuracy of RT-PCR testing for SARS-CoV-2.

A multicenter analysis of the clinical microbiology and antimicrobial usage in hospitalized patients in the US with or without COVID-19

BACKGROUND

Past respiratory viral epidemics suggest that bacterial infections impact clinical outcomes. There is minimal information on potential co-pathogens in patients with coronavirus disease-2019 (COVID-19) in the US. We analyzed pathogens, antimicrobial use, and healthcare utilization in hospitalized US patients with and without severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2).

METHODS

This multicenter retrospective study included patients with > 1 day of inpatient admission and discharge/death between March 1 and May 31, 2020 at 241 US acute care hospitals in the BD Insights Research Database. We assessed microbiological testing data, antimicrobial utilization in admitted patients with ≥24 h of antimicrobial therapy, and length of stay (LOS).

RESULTS

A total of 141,621 patients were tested for SARS-CoV-2 (17,003 [12.0%] positive) and 449,339 patients were not tested. Most (> 90%) patients tested for SARS-CoV-2 had additional microbiologic testing performed compared with 41.9% of SARS-CoV-2-untested patients. Non-SARS-CoV-2 pathogen rates were 20.9% for SARS-CoV-2-positive patients compared with 21.3 and 27.9% for SARS-CoV-2-negative and -untested patients, respectively. Gram-negative bacteria were the most common pathogens (45.5, 44.1, and 43.5% for SARS-CoV-2-positive, -negative, and -untested patients). SARS-CoV-2-positive patients had higher rates of hospital-onset (versus admission-onset) non-SARS-CoV-2 pathogens compared with SARS-CoV-2-negative or -untested patients (42.4, 22.2, and 19.5%, respectively), more antimicrobial usage (68.0, 45.2, and 25.1% of patients), and longer hospital LOS (mean [standard deviation (SD)] of 8.6 [11.4], 5.1 [8.9], and 4.2 [8.0] days) and intensive care unit (ICU) LOS (mean [SD] of 7.8 [8.5], 3.6 [6.2], and 3.6 [5.9] days). For all groups, the presence of a non-SARS-CoV-2 pathogen was associated with increased hospital LOS (mean [SD] days for patients with versus without a non-SARS-CoV-2 pathogen: 13.7 [15.7] vs 7.3 [9.6] days for SARS-CoV-2-positive patients, 8.2 [11.5] vs 4.3 [7.9] days for SARS-CoV-2-negative patients, and 7.1 [11.0] vs 3.9 [7.4] days for SARS-CoV-2-untested patients).

CONCLUSIONS

Despite similar rates of non-SARS-CoV-2 pathogens in SARS-CoV-2-positive, -negative, and -untested patients, SARS-CoV-2 was associated with higher rates of hospital-onset infections, greater antimicrobial usage, and extended hospital and ICU LOS. This finding highlights the heavy burden of the COVID-19 pandemic on healthcare systems and suggests possible opportunities for diagnostic and antimicrobial stewardship.

The effect of anticancer treatment on cancer patients with COVID-19: A systematic review and meta-analysis

BACKGROUND

The relationship between cancer and COVID-19 has been revealed during the pandemic. Some anticancer treatments have been reported to have negative influences on COVID-19-infected patients while other studies did not support this hypothesis.

METHODS

A literature search was conducted in WOS, PubMed, Embase, Cochrane Library, CNKI and VIP between Dec 1, 2019 and Sept 23, 2020 for studies on anticancer treatments in patients with COVID-19. Cohort studies involving over 20 patients with cancer were included. The characteristics of the patients and studies, treatment types, mortality, and other additional outcomes were extracted and pooled for synthesis. RRs and forest plots were adopted to present the results. The literature quality and publication bias were assessed using NOS and Egger's test, respectively.

RESULTS

We analyzed the data from 29 studies, with 5121 cancer patients with COVID-19 meeting the inclusion criteria. There were no significant differences in mortality between patients receiving anticancer treatment and those not (RR 1.17, 95%CI: 0.96-1.43, I2 =66%, p = 0.12). Importantly, in patients with hematological malignancies, chemotherapy could markedly increase the mortality (RR 2.68, 95% CI: 1.90-3.78, I2 =0%, p < 0.00001). In patients with solid tumors, no significant differences in mortality were observed (RR 1.16, 95% CI: 0.57-2.36, I2 =72%, p = 0.67). In addition, our analysis revealed that anticancer therapies had no effects on the ICU admission rate (RR 0.87, 95% CI: 0.70-1.09, I2 =25%, p = 0.23), the severe rate (RR 1.04, 95% CI: 0.95-1.13, I2 =31%, p = 0.42), or respiratory support rate (RR 0.92, 95% CI: 0.70-1.21, I2 =32%, p = 0.55) in COVID-19-infected patients with cancer. Notably, patients receiving surgery had a higher rate of respiratory support than those without any antitumor treatment (RR 1.87, 95%CI: 1.02-3.46, I2 =0%, p = 0.04).

CONCLUSIONS

No significant difference was seen in any anticancer treatments in the solid tumor subgroup. Chemotherapy, however, will lead to higher mortality in patients with hematological malignancies. Multicenter, prospective studies are needed to re-evaluate the results.