Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR.

BACKGROUND: Although active surveillance SARS-CoV-2 variants of concern (VOCs) is required for proper outbreak control measures, many lower income countries find it challenging to detect VOCs by carrying genomic sequencing alone, due to limited resources. METHODS: VOCs can also be identified by the unique mutations in the spike protein by real-time PCR that detect these single nucleotide polymorphisms (SNPs). We used a multiplex, real-time PCR assay for detection of these SNPs for identification of the prevalence of different SARS-CoV-2 VOCs in 16/26 districts in Sri Lanka. RESULTS: Of the 664/934 that were subjected to the multiplex qRT-PCR, 638 (96.1 %) detected L452R and K417 in the channels and were identified as the delta variant. 25 samples (3.9 %) detected N501Y, with K417 were considered as the alpha variant. Of 10/16 districts in Sri Lanka, the delta variant was the only VOC detected. CONCLUSIONS: This multiplex real-time qRT-PCR which identifies certain SNPs specific to the VOCs appears to be a fast, cheaper and less technically demanding method to generate data regarding the spread of different SARS-CoV-2 variants, and is a suitable method for lower income countries, to supplement the data generated by genomic sequencing.

Defining Obesity Using a Biological End Point in Sri Lankan Children.

OBJECTIVE: To identify the percentage of body fat mass (FM) that would define obesity among Sri Lankan children. METHODS: A cross-sectional study was conducted among 5-15 y old children in the district of Colombo. FM was assessed using Bio Impedance Assay (BIA). After a 12 h overnight fast, blood was drawn for fasting blood glucose (FBS) and lipid profile. Oral-glucose-tolerance test (OGTT) was done along with 2 h random blood sugar (RBS). Metabolic syndrome (MetS) was diagnosed by a high waist circumference (WC) with ≥2 metabolic derangements [FBS/RBS, high density lipoprotein-cholesterol (HDL-C), triglyceride, and systolic and diastolic blood pressure (SBP/DBP)]. Receiver-Operator Characteristics (ROCs) were drawn to determine the best %FM that predicted MetS. RESULTS: Nine hundred twenty children were studied (547 boys). Fifteen (1.6 %) had MetS. Ninety five (10.3 %) had two and 16(1.7 %) had ≥3 metabolic derangements. MetS in boys was associated with %FM of 28.6 (sensitivity 1.000; specificity 0.870) and in girls 33.7 (sensitivity 0.875; specificity 0.808). CONCLUSIONS: FM associated with adverse health outcomes in this population is comparable to other available data. A %FM of 28.6 % for boys and 33.7 % for girls would be acceptable cutoff limits.