Effects of Patient Characteristics on Diagnostic Performance of Self-Collected Samples for SARS-CoV-2 Testing

Agnostic Sequencing for Detection of Viral Pathogens

The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.

An overview of the most important preanalytical factors influencing the clinical performance of SARS-CoV-2 antigen rapid diagnostic tests (Ag-RDTs)

Due to the many technical limitations of molecular biology, the possibility to sustain enormous volumes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic testing relies strongly on the use of antigen rapid diagnostic tests (Ag-RDTs). Besides a limited analytical sensitivity, the manually intensive test procedures needed for performing these tests, very often performed by unskilled personnel or by the patients themselves, may contribute to considerably impair their diagnostic accuracy. We provide here an updated overview on the leading preanalytical drawbacks that may impair SARS-CoV-2 Ag-RDT accuracy, and which encompass lower diagnostic sensitivity in certain age groups, in asymptomatic subjects and those with a longer time from symptoms onset, in vaccine recipients, in individuals not appropriately trained to their usage, in those recently using oral or nasal virucidal agents, in oropharyngeal swabs and saliva, as well as in circumstances when instructions provided by the manufacturers are unclear, incomplete or scarcely readable and intelligible. Acknowledging these important preanalytical limitations will lead the way to a better, more clinically efficient and even safer use of this important technology, which represents an extremely valuable resource for management of the ongoing pandemic.

Update of Guidelines for Laboratory Diagnosis of COVID-19 in Korea

Korean Society for Laboratory Medicine and the Korea Disease Prevention and Control Agency have announced guidelines for diagnosing coronavirus disease (COVID-19) in clinical laboratories in Korea. With the ongoing pandemic, we propose an update of the previous guidelines based on new scientific data. This update includes recommendations for tests that were not included in the previous guidelines, including the rapid molecular test, antigen test, antibody test, and self-collected specimens, and a revision of the previous recommendations. This update will aid clinical laboratories in performing laboratory tests for diagnosing COVID-19.

Saliva as a diagnostic specimen for SARS-CoV-2 detection: a scoping review

Objectives

This scoping review aims to summarize the diagnostic value of saliva assessed from current studies that (1) compare its performance in reverse transcriptase‐polymerase chain reaction testing to nasopharyngeal swabs, (2) evaluate its performance in rapid and point‐of‐care COVID‐19 diagnostic tests, and (3) explore its use as a specimen for detecting anti‐SARS‐CoV‐2 antibodies.

Materials and Methods

A systematic search was performed on the following databases: Medline and Embase (Ovid), World Health Organization, Centers for Disease Control and Prevention, and Global Health (Ovid) from January 2019 to September 2021. Of the 657 publications identified from the searches, n = 146 articles were included in the final scoping review.

Results

Our findings showcase that salivary samples exceed nasopharyngeal swabs in detecting SARS‐CoV‐2 using reverse transcriptase‐polymerase chain reaction testing in several studies. A select number of rapid antigen and point‐of‐care tests from the literature were also identified capable of high detection rates using saliva. Moreover, anti‐SARS‐CoV‐2 antibodies have been shown to be detectable in saliva through biochemical assays.

Conclusion

We highlight the potential of saliva as an all‐rounded specimen in detecting SARS‐CoV‐2. However, future large‐scale clinical studies will be needed to support its widespread use as a non‐invasive clinical specimen for COVID‐19 testing.

Risk-Factors for Exposure Associated With SARS-CoV-2 Detection After Recent Known or Potential COVID-19 Exposures Among Patients Seeking Medical Care at a Large Urban, Public Hospital in Fulton County, Georgia - A Cross-Sectional Investigation

We aimed to describe frequency of COVID-19 exposure risk factors among patients presenting for medical care at an urban, public hospital serving mostly uninsured/Medicare/Medicaid clients and risk factors associated with SARS-CoV-2 infection. Consenting, adult patients seeking care at a public hospital from August to November 2020 were enrolled in this cross-sectional investigation. Saliva, anterior nasal and nasopharyngeal swabs were collected and tested for SARS-CoV-2 using RT-PCR. Participant demographics, close contact, and activities ≤14 days prior to enrollment were collected through interview. Logistic regression was used to identify risk factors associated with testing positive for SARS-CoV-2. Among 1,078 participants, 51.8% were male, 57.0% were aged ≥50 years, 81.3% were non-Hispanic Black, and 7.6% had positive SARS-CoV-2 tests. Only 2.7% reported COVID-19 close contact ≤14 days before enrollment; this group had 6.79 adjusted odds of testing positive (95%CI = 2.78-16.62) than those without a reported exposure. Among participants who did not report COVID-19 close contact, working in proximity to ≥10 people (adjusted OR = 2.17; 95%CI = 1.03-4.55), choir practice (adjusted OR = 11.85; 95%CI = 1.44-97.91), traveling on a plane (adjusted OR = 5.78; 95%CI = 1.70-19.68), and not participating in an essential indoor activity (i.e., grocery shopping, public transit use, or visiting a healthcare facility; adjusted OR = 2.15; 95%CI = 1.07-4.30) were associated with increased odds of testing positive. Among this population of mostly Black, non-Hispanic participants seeking care at a public hospital, we found several activities associated with testing positive for SARS-CoV-2 infection in addition to close contact with a case. Understanding high-risk activities for SARS-CoV-2 infection among different communities is important for issuing awareness and prevention strategies.

Specimen self-collection for SARS-CoV-2 testing: Patient performance and preferences—Atlanta, Georgia, August-October 2020

Self-collected specimens can expand access to SARS-CoV-2 testing. At a large inner-city hospital 1,082 participants self-collected saliva and anterior nasal swab (ANS) samples before healthcare workers collected nasopharyngeal swab (NPS) samples on the same day. To characterize patient preferences for self-collection, this investigation explored ability, comfort, and ease of ANS and saliva self-collection for SARS-CoV-2 testing along with associated patient characteristics, including medical history and symptoms of COVID-19. With nearly all participants successfully submitting a specimen, favorable ratings from most participants (at least >79% in ease and comfort), and equivocal preference between saliva and ANS, self-collection is a viable SARS-CoV-2 testing option.