Comparison between the molecular diagnostic test and chest X-ray combined with multi-slice spiral CT in the diagnosis of lobar pneumonia

Lobar pneumonia is an inflammatory condition of the lung that mainly affects the lobes of the lungs and the alveoli, and it is usually caused by a bacterial infection. There are many ways to diagnosis this disease. But an early and accurate method for lobar pneumonia diagnosis has an important role in its treatment. Therefore, in this study, a comparison between the molecular diagnostic test and chest x-ray combined with multi-slice spiral CT was done to find out better diagnosis of lobar pneumonia. For this purpose, 122 individuals suspected of lobar pneumonia were studied by clinical examination, chest X-ray, and multi-slice spiral CT. For the molecular diagnosis test, the multiplex PCR was used for two main causes of the disease, Streptococcus pneumoniae and Klebsiella pneumoniae. Results showed that the specificity for Chest X-ray + Multi-slice Spiral CT had the highest amount (82.8%), but high sensitivity (100%) belonged to a molecular diagnostic test for both bacteria. On the other hand, the sensitivity and specificity of Streptococcus pneumoniae were better than Klebsiella pneumoniae and the possibility of error in Streptococcus pneumoniae was lower than Klebsiella pneumoniae. In general, although the Chest X-ray + Multi-slice Spiral CT method was better than the molecular diagnosis test, it could not identify the causative agent and did not show a difference between pathogens for better antibiotic treatment, and also the possibility of diagnosis is low at the beginning of the disease. Therefore, according to the results of the current study, the best way to diagnose lobar pneumonia is to use both methods, simultaneously.

Assessing a chip based rapid RTPCR test for SARS CoV-2 detection (TrueNat assay): A diagnostic accuracy study

COVID-19 testing is required before admission of a patient in the hospitals, invasive procedures, major and minor surgeries etc. Real Time Polymerase chain reaction is the gold standard test for the diagnosis, but requires well equipped biosafety laboratory along with trained manpower. In this study we have evaluated the diagnostic accuracy of novel TrueNat molecular assay for detecting SARS CoV-2. TrueNat is a chip-based real time PCR test and works on portable, light weight, battery powered equipment and can be used in remote areas with poor infrastructure. In this study 1807 patients samples were collected for both TrueNat and RTPCR COVID-19 testing during study period. Of these 174 (9.7%) and 174 (15%) were positive by RTPCR and TrueNat respectively and taking results of RTPCR as gold standard TrueNat test showed a sensitivity, specificity and diagnostic accuracy of 69.5, 90.9% and 89.2% respectively. It can be concluded that TrueNat is a simple, easy to use, good rapid molecular diagnostic test for diagnosis of COVID-19 especially in resource limited settings and will prove to be a game changer of molecular diagnostics in future.

Prevention of COVID-19 by mRNA-based vaccines within the general population of California

Background Estimates of COVID-19 vaccine effectiveness under real-world conditions, and understanding of barriers to uptake, are necessary to inform vaccine rollout. Methods We enrolled cases (testing positive) and controls (testing negative) from among the population whose SARS-CoV-2 molecular diagnostic test results from 24 February-29 April 2021 were reported to the California Department of Public Health. Participants were matched on age, sex, and geographic region. We assessed participants’ self-reported history of mRNA-based COVID-19 vaccine receipt (BNT162b2 and mRNA-1273). Participants were considered fully vaccinated two weeks after second dose receipt. Among unvaccinated participants, we assessed willingness to receive vaccination. We measured vaccine effectiveness (VE) via the matched odds ratio of prior vaccination, comparing cases with controls. Results We enrolled 1023 eligible participants aged ≥18 years. Among 525 cases, 71 (13.5%) received BNT162b2 or mRNA-1273; 20 (3.8%) were fully vaccinated with either product. Among 498 controls, 185 (37.1%) received BNT162b2 or mRNA-1273; 86 (16.3%) were fully vaccinated with either product. Two weeks after second dose receipt, VE was 87.0% (95% confidence interval: 68.6-94.6%) and 86.2% (68.4-93.9%) for BNT162b2 and mRNA-1273, respectively. Fully vaccinated participants receiving either product experienced 91.3% (79.3-96.3%) and 68.3% (27.9-85.7%) VE against symptomatic and asymptomatic infection, respectively. Among unvaccinated participants, 42.4% (159/375) residing in rural regions and 23.8% (67/281) residing in urban regions reported hesitancy to receive COVID-19 vaccination. Conclusions Authorized mRNA-based vaccines are effective at reducing documented SARS-CoV-2 infections within the general population of California. Vaccine hesitancy presents a barrier to reaching coverage levels needed for herd immunity.

Comparison of Quidel Sofia SARS FIA Test to Hologic Aptima SARS-CoV-2 TMA Test for Diagnosis of COVID-19 in Symptomatic Outpatients

The Quidel Sofia SARS FIA test (SOFIA) is a rapid antigen immunoassay for detection of SARS-CoV-2 viral proteins from nasal or nasopharyngeal swab specimens. The purpose of this study was to compare the results of the SOFIA test to the Hologic Aptima SARS-CoV-2 TMA test (APTIMA TMA), a high-throughput molecular diagnostic test that uses transcription mediated amplification for detection of SARS-CoV-2 nucleic acid from upper respiratory specimens. Three hundred and 40-seven symptomatic patients, from an urgent care center in an area with a high prevalence of SARS-CoV-2 infections, were tested in parallel using nasal swabs on the SOFIA test and nasopharyngeal swabs on the APTIMA TMA test. The SOFIA test demonstrated an 82.0% positive percent agreement (PPA) compared to the APTIMA TMA test for symptomatic patients tested ≤ 5 days from symptom onset and a 54.5% PPA for symptomatic patients > 5 days from symptom onset. The Cepheid Xpert Xpress SARS-CoV-2 RT-PCR test was used to determine the cycle threshold (Ct) value from any specimens that were discrepant between the SOFIA and APTIMA TMA tests. Using a Ct value of ≤ 35 as a surrogate for SARS-CoV-2 culture positivity, we estimate that the SOFIA test detected 87.2% of symptomatic patients tested ≤ 5 days from symptom onset that were likely to be culture positive.

An enhanced isothermal amplification assay for viral detection

Rapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. Here we report the development of a molecular diagnostic test for SARS-CoV-2 based on an enhanced recombinase polymerase amplification (eRPA) reaction. eRPA has a detection limit on patient samples down to 5 viral copies, requires minimal instrumentation, and is highly scalable and inexpensive. eRPA does not cross-react with other common coronaviruses, does not require RNA purification, and takes ~45 min from sample collection to results. eRPA represents a first step toward at-home SARS-CoV-2 detection and can be adapted to future viruses within days of genomic sequence availability.

Suitcase Lab: new, portable, and deployable equipment for rapid detection of specific harmful algae in Chilean coastal waters

Phytoplankton blooms, including harmful algal blooms (HABs), have serious impacts on ecosystems, public health, and productivity activities. Rapid detection and monitoring of marine microalgae are important in predicting and managing HABs. We developed a toolkit, the Suitcase Lab, to detect harmful algae species in the field. We demonstrated the Suitcase Lab’s capabilities for sampling, filtration, DNA extraction, and loop-mediated isothermal amplification (LAMP) detection in cultured Alexandrium catenella cells as well as Chilean coastal waters from four sites: Repollal, Isla García, Puerto Montt, and Metri. A LAMP assay using the Suitcase Lab in the field confirmed microscopic observations of A. catenella in samples from Repollal and Isla García. The Suitcase Lab allowed the rapid detection of A. catenella, within 2 h from the time of sampling, even at a single cell per milliliter concentrations, demonstrating its usefulness for quick and qualitative on-site diagnosis of target toxic algae species. This method is applicable not only to detecting harmful algae but also to other field studies that seek a rapid molecular diagnostic test.

Use of predictive tools in the management of COVID-19 patients: a key role of clinical laboratories

ObjectivesCoronavirus disease 2019 (COVID-19) is widely spreading and represents a critical threat to global health. In the fight against this pandemic, provincial hospitals urgently need rapid diagnostic of COVID-19 infected patients to avoid collapsing of emergency units. However, the high demand of patients with severe acute respiratory symptoms limits the fast delivery of results by the gold standard method reverse transcription-polymerase chain reaction real time (rRT-PCR) for the identification of COVID-19 positive pneumonia. The principal aim is to find other useful laboratory indicators to assist rRT-PCR tests and to help controlling of this outbreak.MethodsBlood, coagulation and inflammatory parameters were collected from a total of 309 patients classified as negative (128) and positive (181) rRT-PCR test groups. Patients were classified as positive by molecular diagnostic test.ResultsLeukocyte count (WBC), neutrophils count, lymphocytes count and lactate dehydrogenase (LDH) were statistically different between both groups of patients. The use of LDH/WBC ratio increases the diagnostic performance with the best area under the curve (0.783), sensibility (82%) and the best percentage (80.5%) of correctly identified COVID-19 positive patients.ConclusionsThe combination of predictive LDH/WBC ratio with clinical illness features could help in medical management of patients and improve the technical resources of hospitals, especially in a critical scenario with a large shortage of medical equipment and lack of reagents for performing rRT-PCR.

427. Variation in SARS-CoV-2 molecular diagnostic test performance in symptomatic versus asymptomatic populations

Background Growing recognition of the importance of asymptomatic and pre-symptomatic transmission for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led to a substantial expansion of testing from symptomatic to asymptomatic patients, and particularly those with risk factors for infection. Viral burden in asymptomatic individuals can differ from symptomatic patients, which can impact test performance. We therefore evaluated the impact of expanded testing indications upon the sensitivity and specificity of molecular diagnostic assays for SARS-CoV-2. Methods We performed a retrospective review of laboratory results from 5,122 emergency room patients and inpatients tested for SARS-CoV-2 between 05/03/2020 and 06/13/2020 using the Hologic Panther Fusion and the Cepheid Xpert assays at the Brigham & Women’s Hospital in Boston, MA. Descriptive analyses were performed for trends in testing volume, rates of positivity and cycle thresholds (Cts) over time based on symptom status. We calculated the proportion of new diagnoses made on a patient’s first test as an indirect measure of sensitivity. We calculated the proportion of first tests that are positive with a Ct value < 35 as an indirect measure of specificity. Results The overall rate of positivity over the study period was 8.7% (599/7,510 tests; 440/4,795 people) and declined by 1.8% (95% CI -2.2% - -1.4%, P< 0.0001) each week. Relative to tests in symptomatic people, the asymptomatic population had a higher mean Ct value (35.1 vs 32.3; P < 0.0001). Ct values increased by 0.7 (95% CI -0.1 - +1.4, P=0.07) and 0.8 (95% CI +0.3 - +1.4; p=0.01), sensitivity declined by 4% (95% CI -9% - +1%, P=0.08) and 12% (95% CI -20% - -5%, P-0.01) and specificity declined by 8% (95% CI -3% to 20%; P=0.13) and 9% (95% CI 7% - 11%; P=0.0002), over the time period of the study for asymptomatic and symptomatic patients, respectively. Figure 1: Trends in Ct values by symptoms Figure 2: Trends in diagnosis by first versus second test by symptoms Figure 3: Trends in proportion of people with their first test having Ct < 35 by symptoms Conclusion We show that the proportion of patients with low SARS-CoV-2 viral loads has increased as testing has expanded to the asymptomatic population and as transmission wanes in the community. This negatively impacts the performance of molecular assays by increasing the risk of false negatives and the detection of non-viable virus. Decision algorithms based on molecular assay results may need re-evaluation in light of these dynamics. Disclosures All Authors: No reported disclosures