Insight into PCR testing for surgeons.

The most commonly used molecular diagnostic technique is the polymerase chain reaction (PCR). PCR detects a short section of genetic code of interest, a cancer gene, human mRNA or a pathogen's genome. It is used by every specialty in medicine and surgery, with increasing frequency and importance. In this article, the history, steps of the cycle, uses, forms, advantages and disadvantages of PCR are discussed. With the SARS coronavirus-2 pandemic having such an enormous impact on the delivery of elective surgery, decisions to proceed or defer are made by surgeons on a daily basis, based on PCR results. An understanding of these results is provided, what they tell us, what they do not and what other information is required to make these decisions. It is imperative to also look beyond PCR results, seeing the patient within the context of their symptoms, other pathology and imaging results, with the assistance of a medical virologist or microbiologist, in complex cases.

Can a quantitative assessment of SARS-CoV-2 PCR predict degree of severity and outcomes in critical care patients with COVID-19?

Real-Time polymerase chain reaction (qPCR) is the gold standard diagnostic method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Cycle threshold (Ct) is defined as the number of heating and cooling cycles required during the PCR process. Ct-values are inversely proportional to the amount of target nucleic acid in a sample. Our aim, in this retrospective study, was to determine the impact of serial SARS-CoV-2 qPCR Ct-values on: mortality, need for mechanical ventilation (MV) and development of acute kidney injury (AKI) in patients admitted to the intensive care unit (ICU) with COVID-19. Ct values were evaluated during the time points from pre-ICU admission to week 1, week 2 and week 3 during ICU stay; impact on mortality, need for MV and AKI was determined. There was a continuous increment in Ct-values over the ICU stay from 1st week through to 3rd week. Although not significant, lower ICU 1st week Ct-values were associated with Black ethnicity, increased need for MV and mortality. However, patients who had developed AKI at any stage of their illness had significantly lower Ct-values compared to those with normal renal function. When ICU 1st-week Ct-values are subcategorised as <20, 20-30 and >30 the 28-day survival probability was less for patients with Ct-values of <20. This report shows that the impact of Ct-values and outcomes, especially AKI, among patients at different time points prior to and during ICU stay, larger studies are required to confirm out findings.

The laboratory investigation of a measles outbreak in the eve of its elimination in Sri Lanka.

BACKGROUND: Measles is highly contagious and cause significant morbidity and mortality. Sri-Lanka has the goal to eliminate endogenous measles by 2020 in par with WHO. OBJECTIVE: To describe laboratory confirmation and genotype distribution of measles cases during the outbreak occurred from mid-March to May 2019, Sri-Lanka STUDY DESIGN: This retrospective study was conducted at National Measles Reference Laboratory (NMRL), Sri-Lanka. All samples received were tested according to the testing flow chart at NMRL with WHO recommended kits. Blood samples were tested for anti-measles IgM and IgG with IgG avidity for IgG positives. Samples within 5days post-onset rash were tested with measles real-time RT-PCR. Products of genotyping PCR were sent to Regional Reference Laboratory, Thailand for sequencing. Subsequent phylogenetic analysis was done at NMRL. Data were analyzed by descriptive statistics. RESULTS: A total of 182 blood and 46 throat/nasopharyngeal swabs were received from 195 suspected cases and 37(19 %) were positive for measles by anti-measles IgM, rRT-PCR or both. Majority was females, with mean age of 20 years. Cases represented three main geographical areas; Western-35 %, Central-32 % and Southern-27 %. High avidity IgG was detected in 27/37(73 %). Sequencing data of six cases (4 from Western and 2 from Central province) revealed genotype D8. CONCLUSION: Nineteen percent of the suspected patients were measles positive with 73 % having re-infections. Majority were 22 years or over. Measles genotype was D8 in two provinces, suggesting the spread of virus within the country. Laboratory confirmation with measles PCR; IgG avidity and sequencing/genetic analysis is critical in the verge of measles elimination.