ABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19. Identification of virus lineages is key to tracking the chains of transmission and for monitoring variants of interest as well as variants of concern. This study aimed to develop and validate a cost-effective method to determine SARS-CoV-2 lineages of virus samples from the first wave of the pandemic in Thailand (January -May 2020). A lineage-specific single nucleotide polymorphism (SNP) genotyping panel of SARS-CoV-2 was designed based on genomic surveillance data generated in the first wave. Viral RNA specimens obtained from the Department of Pathology, Faculty of Medicine Ramathibodi Hospital were analyzed by a MassARRAY (R) platform in comparison to a next generation sequencing of the virus genome. The MassARRAY (R) system was able to identify the SARS-CoV-2 lineages with high accuracy supporting its application as a rapid and cost-effective method for identification of circulating COVID-1 9 variants in the country, and has the ability to accommodate new SARS-CoV-2 variants by simple modifications of the assay protocol.
ABSTRACT
Coronavirus Disease 2019 (COVID-19) is a global public health threat. Genomic surveillance of SARS-CoV-2 was implemented in March of 2020 at a major diagnostic hub in Bangkok, Thailand. Several virus lineages supposedly originated in many countries were found, and a Thai-specific lineage, designated A/Thai-1, has expanded to be predominant in Thailand. A virus sample in the SARS-CoV-2 A/Thai-1 lineage contains a frame-shift deletion at ORF7a, encoding a putative host antagonizing factor of the virus.
ABSTRACT
Objectives: Amid the increasing number of pandemic coronavirus disease 2019 (COVID-19) cases, there is a need for a quick and easy method to obtain a non-invasive sample for the detection of this novel coronavirus (severe acute respiratory syndrome coronavirus 2;SARS-CoV-2). We aimed to investigate the potential use of saliva samples as a non-invasive tool for the diagnosis of COVID-19. Methods: From 27 March to 4 April 2020, we prospectively collected saliva samples and a standard nasopharyngeal and throat swab in persons seeking care at an acute respiratory infection clinic in a university hospital during the outbreak of COVID-19. Real-time polymerase chain reaction (RT-PCR) was performed, and the results of the two specimens were compared. Results: Two-hundred pairs of samples were collected. Sixty-nine (34.5%) individuals were male, and the median (interquartile) age was 36 (28–48) years. Using nasopharyngeal and throat swab RT-PCR as the reference standard, the prevalence of COVID-19 diagnosed by nasopharyngeal and throat swab RT-PCR was 9.5%. The sensitivity and specificity of the saliva sample RT-PCR were 84.2% (95% CI 60.4%–96.6%), and 98.9% (95% CI 96.1%–99.9%), respectively. An analysis of the agreement between the two specimens demonstrated 97.5% observed agreement (κ coefficient 0.851, 95% CI 0.723–0.979;p < 0.001). Conclusions: Saliva might be an alternative specimen for the diagnosis of COVID-19. The collection is non-invasive, and non-aerosol generating. This method could facilitate the diagnosis of the disease, given the simplicity of specimen collection and good diagnostic performance.