A before-after study to evaluate the effect of pharmacy workflow redesign to improve pharmacy waiting time and reduce medication near misses in Malaysia.

OBJECTIVES: This study aimed to evaluate the effectiveness of workflow redesign (eaST system) on pharmacy waiting time and near-missed events. We also investigated other factors that may potentially affect these study outcomes. METHODS: A quasi-experimental (before-after) study design was adopted. Pre-intervention data were collected over 7 months (January-July 2017). Subsequently, the workflow redesign (eaST system) was implemented and the effect of the intervention (August 2017-February 2018) was evaluated. Univariate analysis was used to compare the differences between pre-intervention and post-intervention of pharmacy waiting time and near-missed events. Significant factors affecting study outcomes were analysed using linear regression analysis. KEY FINDINGS: A total of 210,530 prescriptions were analysed. The eaST system significantly increases the percentage of prescriptions dispensed within 30 min per day (median = 68 (interquartile range (IQR) = 41) vs. median = 93 (IQR = 33), P < 0.001) and reduced the mean percentage of near-missed events (mean = 50.71 (standard deviation (SD) = 23.95) vs. mean = 27.87 (SD = 12.23), P < 0.001). However, the eaST system's effects on related outcomes were conditional on a three-way interaction effect. The eaST system's effects on pharmacy waiting time were influenced by the number of prescriptions received and the number of PhIS server disruptions. Conversely, the eaST system's effects on near-missed events were influenced by the number of pharmacy personnel and number of controlled medications. CONCLUSIONS: Overall, the eaST system improved the pharmacy waiting time and reduced near-missed events.

Clinical testing on SARS-CoV-2 swab samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP).

BACKGROUND: High cost of commercial RNA extraction kits limits the testing efficiency of SARS-CoV-2. Here, we developed a simple nucleic acid extraction method for the detection of SARS-CoV-2 directly from nasopharyngeal swab samples. METHODS: A pH sensitive dye was used as the end point detection method. The obvious colour changes between positive and negative reactions eliminates the need of other equipment. RESULTS: Clinical testing using 260 samples showed 92.7% sensitivity (95% CI 87.3-96.3%) and 93.6% specificity (95% CI 87.3-97.4%) of RT-LAMP. CONCLUSIONS: The simple RNA extraction method minimizes the need for any extensive laboratory set-up. We suggest combining this simple nucleic acid extraction method and RT-LAMP technology as the point-of care diagnostic tool.

Colorimetric detection of SARS-CoV-2 by uracil-DNA glycosylase (UDG) reverse transcription loop-mediated isothermal amplification (RT-LAMP).

OBJECTIVES: Preventing reverse transcription loop-mediated isothermal amplification (RT-LAMP) carryover contamination could be solved by adding deoxyuridine triphosphate (dUTP) and uracil-DNA glycosylase (UDG) into the reaction master mix. METHODS: RNA was extracted from nasopharyngeal swab samples by a simple RNA extraction method. RESULTS: Testing of 77 samples demonstrated 91.2% sensitivity (95% confidence interval [CI]: 78-98.2%) and 100% specificity (95% confidence interval: 92-100%) using UDG RT-LAMP. CONCLUSION: This colorimetric UDG RT-LAMP is a simple-to-use, fast, and easy-to-interpret method, which could serve as an alternative for diagnosis of SARS-CoV-2 infection, especially in remote hospitals and laboratories with under-equipped medical facilities.

RNA purification-free detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP).

BACKGROUND: Current diagnosis of SARS-CoV-2 infection relies on RNA purification prior to amplification. Typical extraction methods limit the processing speed and turnaround time for SARS-CoV-2 diagnostic testing. METHODS: Here, we applied reverse transcription loop-mediated isothermal amplification directly onto human clinical swabs samples to amplify the RNA from SARS-CoV-2 swab samples after processing with chelating resin. RESULTS: By testing our method on 64 samples, we managed to develop an RT-LAMP assay with 95.9% sensitivity (95% CI 86 to 99.5%) and 100% specificity (95% CI 78.2-100%). CONCLUSION: The entire process including sample processing can be completed in approximately 50 min. This method has promising potential to be applied as a fast, simple and inexpensive diagnostic tool for the detection of SARS-CoV-2.

Two extraction-free reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2.

BACKGROUND: Current assays for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on time consuming, costly and laboratory based methods for virus isolation, purification and removing inhibitors. To address this limitation, we propose a simple method for testing RNA from nasopharyngeal swab samples that bypasses the RNA purification step. METHODS: In the current project, we have described two extraction-free reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of SARS-CoV-2 by using E gene and RdRp gene as the targets. RESULTS: Here, results showed that reverse transcription loop-mediated isothermal amplification assays with 88.4% sensitive (95% CI: 74.9-96.1%) and 67.4% sensitive (95% CI: 51.5-80.9%) for E gene and RdRp gene, respectively. CONCLUSION: Without the need of RNA purification, our developed RT-LAMP assays for direct detection of SARS-CoV-2 from nasopharyngeal swab samples could be turned into alternatives to qRT-PCR for rapid screening.

Serology surveillance of SARS-CoV-2 antibodies among healthcare workers in COVID-19 designated facilities in Malaysia.

BACKGROUND: Asymptomatic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections are well documented. Healthcare workers (HCW) are at increased risk of infection due to occupational exposure to infected patients. We aim to determine the prevalence of SARS-CoV-2 antibodies among HCW who did not come to medical attention. METHODS: We prospectively recruited 400 HCW from the National Public Health Laboratory and two COVID-19 designated public hospitals in Klang Valley, Malaysia between 13/4/2020 and 12/5/2020. Quota sampling was used to ensure representativeness of HCW involved in direct and indirect patient care. All participants answered a self-administered questionnaire and blood samples were taken to test for SARS-CoV-2 antibodies by surrogate virus neutralization test. FINDINGS: The study population comprised 154 (38.5%) nurses, 103 (25.8%) medical doctors, 47 (11.8%) laboratory technologists and others (23.9%). A majority (68.9%) reported exposure to SARS-CoV-2 in the past month within their respective workplaces. Adherence to personal protection equipment (PPE) guidelines and hand hygiene were good, ranging from 91-100% compliance. None (95% CI: 0, 0.0095) of the participants had SARS-CoV-2 antibodies detected, despite 182 (45.5%) reporting some symptoms one month prior to study recruitment. One hundred and fifteen (29%) of participants claimed to have had contact with known COVID-19 persons outside of their workplace. INTERPRETATION: Zero seroprevalence among HCW suggests a low incidence of undiagnosed COVID-19 infection in our healthcare setting during the first local wave of SARS-CoV-2 infection. The occupational risk of SARS-CoV-2 transmission within healthcare facilities can be prevented by adherence to infection control measures and appropriate use of PPE.

Correction: Development of a reverse transcription recombinase polymerase amplification assay for rapid and direct visual detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

[This corrects the article DOI: 10.1371/journal.pone.0245164.].

Development of a reverse transcription recombinase polymerase amplification assay for rapid and direct visual detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

Rapid diagnosis is an important intervention in managing the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak. Real time reverse transcription polymerase chain reaction (RT-qPCR) remains the primary means for diagnosing the new virus strain but it is time consuming and costly. Recombinase polymerase amplification (RPA) is an isothermal amplification assay that does not require a PCR machine. It is an affordable, rapid, and simple assay. In this study, we developed and optimized a sensitive reverse transcription (RT)-RPA assay for the rapid detection of SARS-CoV-2 using SYBR Green I and/or lateral flow (LF) strip. The analytical sensitivity and specificity of the RT-RPA assay were tested by using 10-fold serial diluted synthetic RNA and genomic RNA of similar viruses, respectively. Clinical sensitivity and specificity of the RT-RPA assay were carried out using 78 positive and 35 negative nasopharyngeal samples. The detection limit of both RPA and RT-qPCR assays was 7.659 and 5 copies/µL RNA, respectively with no cross reactivity with other viruses. The clinical sensitivity and specificity of RT-RPA were 98% and 100%, respectively. Our study showed that RT-RPA represents a viable alternative to RT-qPCR for the detection of SARS-CoV-2, especially in areas with limited infrastructure.

A Sensitive Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Direct Visual Detection of SARS-CoV-2.

A simple and rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of SARS-CoV-2. The RT-LAMP assay was highly specific for SARS-CoV-2 and was able to detect one copy of transcribed SARS-CoV-2 RNA within 24 minutes. Assay validation performed using 50 positive and 32 negative clinical samples showed 100% sensitivity and specificity. The RT-LAMP would be valuable for clinical diagnosis and epidemiological surveillance of SARS-CoV-2 infection in resource-limited areas as it does not require the use of sophisticated and costly equipment.

Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2.

BACKGROUND: Highly sensitive real-time reverse transcription polymerase chain reaction (RT-qPCR) methods have been developed for the detection of SARS-CoV-2. However, they are costly. Loop-mediated isothermal amplification (LAMP) assay has emerged as a novel alternative isothermal amplification method for the detection of nucleic acid. METHODS: A rapid, sensitive and specific real-time reverse transcription LAMP (RT-LAMP) assay was developed for SARS-CoV-2 detection. RESULTS: This assay detected one copy/reaction of SARS-CoV-2 RNA in 30 min. Both the clinical sensitivity and specificity of this assay were 100%. The RT-LAMP showed comparable performance with RT-qPCR. Combining simplicity and cost-effectiveness, this assay is therefore recommended for use in resource resource-limited settings.

Performance of the HIV Blot 2.2, INNO-LIA HIV I/II Score, and Geenius HIV 1/2 Confirmatory Assay for use in HIV confirmation.

In view of recent revised recommendations for human immunodeficiency virus (HIV) confirmatory testing, the performance of 3 HIV confirmatory assays was compared. Using the HIV Blot 2.2 (MP-WB), the INNO-LIA HIV I/II Score (INNO), and the Geenius HIV 1/2 Confirmatory Assay (Geenius), we tested 199 HIV-1 positive, 161 HIV negative, 65 HIV western blot indeterminate, 26 HIV seroconversion, 34 early HIV infection and 4 HIV-2 positive archived specimens. We show that all 3 assays had comparable test sensitivity in the detection of HIV-1 positive cases. However, less non-specific reactivity was observed with the INNO and Geenius assays, where both of them were able to resolve MP-WB indeterminate cases. When early HIV cases were considered, INNO and Geenius were more likely to confirm an early-stage infection as positive. Nevertheless, overall poor sensitivity (25.5% - 44.7%) of these assays for the detection of early cases was observed, likely because these cases had very low or non-detectable levels of HIV antibodies. Hence, further testing by a nucleic acid test or a p24 antigen test of specimens reactive on screening with a fourth generation Ag/Ab assay that are negative on confirmatory testing for HIV-specific antibody, may be useful. In conclusion, INNO and Geenius had comparable test performance, although the ease of use and shorter assay time for Geenius may make it the preferred choice for laboratories. In that regard, of note is our observation of non-specific reactivity of lipaemic specimens to the HIV-2 gp140 band in the Geenius assay, which should prompt caution when interpreting results of such specimens.