ABSTRACT
Introduction: Although whole genome sequencing (WGS) is the gold standard for genomic surveillance to detect SARS-CoV-2 variants, it is expensive and time-consuming to perform. Reverse transcription polymerase chain reaction (RT-PCR) based assays which detect mutations associated with SARS-CoV-2 variants of concern (VOC) are cost-effective alternatives to whole genome sequencing. In this study, we evaluated the Omicron detection using RT-PCR-based assays at the Kuala Lumpur International Airport among the international travelers during the November to December 2021 period. Material(s) and Method(s): All SARS-CoV-2 samples originated from KLIA with cycle threshold (CT) <30 were subjected to RT PCR-based assays to detect SARS-CoV-2 spike gene mutations. Subsequently, the detection of the mutations by RT-PCR was compared to VOC detection by WGS. Result(s): A total of 1764 COVID-19 positive samples were subjected to RT-PCR to detect SARS-CoV-2 variants based on spike protein mutations. Of these, 1264 samples were detected as presumptive Omicron cases with the first presumptive Omicron case detected on the 1st of December 2021. The detection of the first Omicron case and subsequent increase in the Omicron detection by RT-PCR corresponded well with data from WGS. The detection of Omicron cases using RTPCR was significantly faster than the detection by WGS. Conclusion(s): The rapid detection of SARS-CoV-2 variants of concern using RT-PCR may have an important impact on local public health policies. In addition, the variant diversity of Omicron and non-Omicron detected among international travelers at Kuala Lumpur International Airport correlated with global diversity indicating the importance of travel hubs for SARS-CoV-2 genomic surveillance.
ABSTRACT
Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a robust and cost-effective assay for rapid diagnosis of SARS-CoV-2 compared to reverse transcription quantitative (RT-q) PCR. The study evaluated the performance of RT-LAMP technique that incorporated a simple Chelex 100 resin-based RNA extraction step for SARS-CoV-2 detection targeting virus E (encoding envelope protein) and RdRP (encoding RNA-dependent RNA polymerase). Using primer sets for E and RdRP, the developed RT-LAMP assay had a limit of detection (LOD) of 1 copy/µl transcribed RNA. For nasopharyngeal and oropharyngeal swab samples (n = 58), in comparison to the gold standard RT-qPCR (amplifying E and RdRP) sensitivity, specificity, positive predictive value, and negative predictive value of SARS-CoV-2 RT-LAMP assay targeting E gene was 88% (95% confidence interval (CI): 75-96%), 87% (95% CI: 59-98%), 99% (95% CI: 97-100%), and 28% (95% CI: 14-48%), respectively and for RdRP gene was 67% (95% CI: 51-98%), 87% (95% CI: 59-98%), 100% (95% CI: 96-100%), and 12% (95% CI: 8-18%), respectively. The whole process of RT-LAMP assay was completed within ~60 minutes. This developed RT-LAMP method for on-site COVID-19 detection should be useful in resource limited settings. © 2022, SEAMEO TROPMED Network. All rights reserved.
ABSTRACT
In healthcare facilities, food waste and its packaging are mostly managed as non-infectious general waste. However, waste from SARS-CoV-2 positive patients, are treated as medical waste as they may be contaminated by the virus. We investigated the possibility of SARS-CoV-2 contamination from positive COVID-19 patients to their leftover food packages at a quarantine centre. Food packages surface was swabbed using prewetted cellular foam, placed into viral transport media and analysed using real time reverse transcription polymerase chain reaction. SARS-CoV-2 RNA was detected in two samples (4.5%) from asymptomatic patients who were at day-2 positive SARS-CoV-2 with cycle threshold (Ct) value (RdRp/E), 34.96/35.72 and 37.1/36.48 respectively. Detection of SARS-CoV-2 supports that there is contamination to the waste. These poses risk of exposure as SAR-COV-2 survive on the surfaces, thus, safe handling and disposal of food waste should be maintained. However, further study involving viral culture should be explored to determine the viability of the SARS-CoV-2 from leftover food packages. © 2021, Malaysian Journal of Public Health Medicine. All rights reserved.
ABSTRACT
COVID-19 has spread rapidly worldwide. The role of fomites in facilitating onward transmission is plausible. This study aimed to determine the presence of viable virus and its persistence on the surfaces of fomites in wards treating COVID-19 patients in Malaysia. This study was conducted in two stages. First, environmental sampling was performed on random days in the intensive care unit (ICU) and general wards. Then, in the second stage, samples were collected serially on alternate days for 7 days in two selected general wards. In Stage 1, a total of 104 samples were collected from the surfaces of highly touched and used areas by patients and healthcare workers. Only three samples were tested positive for SARS-COV-2. In Stage 2, three surface samples were detected positive, but no persistence of the virus was observed. However, none of the SARS-CoV-2 RNA was viable through tissue culture. Overall, the environmental contamination of SARS-CoV-2 was low in this hospital setting. Hospitals' strict infection control and the compliance of patients with wearing masks may have played a role in these findings, suggesting adherence to those measures to reduce occupational exposure of COVID-19 in hospital settings.
Subject(s)
COVID-19/transmission , Environmental Exposure/statistics & numerical data , Fomites/virology , Infection Control/methods , Equipment Contamination , Hospitals/statistics & numerical data , Humans , Intensive Care Units/statistics & numerical data , Malaysia , Patients' Rooms/statistics & numerical data , SARS-CoV-2/isolation & purificationABSTRACT
The emergence of a third wave of COVID-19 infection in Malaysia since September 2020 has led to imminent changes in public health prevention and control measures. As high as 96.2% of registered COVID-19 cases and 88.5% of confirmed deaths in Malaysia occurred during this third wave of infection. A phylogenomic study on 258 SARS-CoV-2 full genomes from February 2020-February 2021 has led to the discovery of a novel Malaysian lineage B.1.524. This lineage contains another spike mutation A701V that co-exists with the D614G spike mutation that was predominant in most of the third-wave clusters. The study provides vital genomic insights on the rapid spread of the SARS-CoV-2 variants in Malaysia in conjunction with the presence of a dominant SARS-CoV-2 lineage during the third wave of COVID-19 infection.