A pandemic guided by the SARS-CoV-2 PCR test: What should the clinician know?

Amidst an ever-evolving pandemic, the demand for timely and accurate diagnosis of coronavirus disease 2019 (COVID-19) continues to increase. Critically, managing and containing the spread of the disease requires expedient testing of infected individuals. Presently, the gold standard for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains the polymerase chain reaction (PCR) test. Potential vulnerabilities of this testing methodology can range from preanalytical variables to laboratory-related analytical factors and, ultimately, to the interpretation of results.

Laboratory Considerations for Reporting Cycle Threshold Value in COVID-19.

The Coronavirus Disease 2019 (COVID-19) pandemic is caused by the SARS-CoV-2 RNA virus. Nucleic acid amplification testing (NAAT) is the mainstay to confirm infection. A large number of reverse transcriptase polymerase chain reaction (RT-PCR) assays are currently available for qualitatively assessing SARS-CoV-2 infection. Although these assays show variation in cycle threshold values (Ct), advocacy for reporting Ct values (in addition to the qualitative result) is tabled to guide patient clinical management decisions. This article provides critical commentary on qualitative RT-PCR laboratory and clinical considerations for Ct value reporting. Factors contributing to Ct variation are discussed by considering relevant viral life-cycle factors, patient factors and the laboratory total testing processes that contribute to the Ct variation and mitigate against the reporting of Ct values by qualitative NAAT.

A pandemic guided by the SARS-CoV-2 PCR test: What should the clinician know?

Amidst an ever-evolving pandemic, the demand for timely and accurate diagnosis of coronavirus disease 2019 (COVID-19) continues to increase. Critically, managing and containing the spread of the disease requires expedient testing of infected individuals. Presently, the gold standard for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains the polymerase chain reaction (PCR) test. Potential vulnerabilities of this testing methodology can range from preanalytical variables to laboratory-related analytical factors and, ultimately, to the interpretation of results.

Evaluation of serological assays for the diagnosis of HIV infection in adults.

Serological tests based on the enzyme immunoassay (EIA) are the primary tool for the diagnosis of human immunodeficiency virus (HIV) in adults and have rapidly evolved to quicker, affordable and more accurate test formats to detect early HIV infection. Second- and third-generation HIV rapid tests detect the immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies to the HIV and are used at the point of care and in HIV self-testing. The tests are affordable and accessible in state and private diagnostic laboratories. The present-day fourth- and fifth-generation EIAs can detect both p24 antigen and IgG and IgM HIV antibodies and thereby diagnose early HIV infection at approximately 2 weeks. The fourth- and fifth-generation EIAs also report sensitivity and specificity of more than 99%. The correct interpretation of HIV diagnosis of false-positive and false-negative EIA test results requires collaborative scrutiny of patient factors and laboratory test methodologies.

Fake news and fallacies: Exploring vaccine hesitancy in South Africa.

Historically, vaccine hesitancy (VH) has been a thorn in the side of public health efforts to contain and eradicate infectious diseases. This phenomenon is magnified in light of the current coronavirus disease 2019 (COVID-19) pandemic. Surveys conducted across South Africa since the outbreak of COVID-19 demonstrate the complexity of factors that contribute towards VH in this population. Amidst the negative press that the COVID-19 vaccine has received, especially across social media, understanding and combatting VH remains important to achieve herd immunity. This article aims to shed light on key factors fuelling COVID-19 VH in South Africa and provides a framework from which to address this problem.

Feasibility and clinical relevance of HIV-1 drug resistance testing in patients with low-level viraemia in South Africa.

OBJECTIVES: To determine the feasibility of HIV genotyping at low-level viraemia (LLV) using an in-house assay in a South African population and the prevalence, as well as the clinical relevance, of drug resistance (HIVDR) in this population. METHODS: We conducted an observational, retrospective, cohort study on patient samples with LLV referred for routine HIVDR testing at a public sector Johannesburg laboratory from August 2017 to October 2018. Genotyping was performed using a nested RT-PCR assay and Sanger sequencing. The genotyping success rate was evaluated for different viraemia categories. Sequences were loaded onto the Stanford HIVdb genotypic resistance tool (version 8.7) for drug resistance interpretation. RESULTS: Plasma samples from 159 HIV-1-infected, treatment-experienced adults with LLV (5-999 copies/mL) were analysed. The in-house assay performed well with an overall success rate of 78.6% (125/159, 95% CI 71.6-84.3). The prevalence of drug resistance mutations in the LLV cohort was 79.2% (99/125, 95% CI 71.2-85.4) with most patients (n = 109, 68.6%) on a PI-based regimen at the time of genotyping. Of 125 sequences obtained, 73.6% (92/125) had ≥1 NRTI mutation while 70.4% (88/125) had ≥1 NNRTI mutation. Major PI mutations, including M46I and V82A, were detected in 7.2% (9/125) of patients. CONCLUSIONS: Current South African virological failure guidelines may keep patients on failing regimens for longer than necessary. Our data suggest that genotyping at LLV is feasible and implementation could result in earlier identification and referral of patients requiring third-line regimens.