ABSTRACT
Objectives. The main goal of the study was to develop laboratory-developed tests (LDT) for monitoring SARS-CoV-2 variants of concern (VOC) currently present in Latvia. METHODS. We have studied the latest scientific articles to prognose specific mutations that could be indicators of VOC. Mutations responsible for immune escape were chosen as targets for our LDTs. Multiple TaqMan RT-PCR LDTs detecting alfa, beta, gamma, delta and omicron strains in nasopharyngeal swab and saliva samples were developed and validated in our laboratory. RESULTS. More than 15,000 SARS-CoV-2 positive samples were tested. In total, 10,874 different VOCs of SARS-CoV-2 were found by our LDTs. Beta, delta and omicron strains were first detected in Latvia by E. Gulbis Laboratory. Sanger sequencing methods for RT-PCR result confirmation were also developed. The first cases of VOCs detected by the RT-PCR method were also confirmed in our laboratory by Sanger sequencing. Our results were later confirmed by the National Reference Laboratory. CONCLUSIONS. Using our laboratory capacity and intellectual potential, we have developed skills for an urgent response to future VOCs of SARS-CoV-2 or other potentially harmful infectious diseases.
ABSTRACT
Objectives. The goal was to introduce an automated and effective solution for the management of self-collected samples. E. Gulbja Laboratory collected the data of using automated self-sampling kit collection from 1st January 2021 until 31st December 2021. We have formulated conclusions about the data and the use of automation in self-sample kit collection. MATERIALS AND METHODS. E. Gulbja Laboratory collected data about SARS-CoV-2 saliva sample kit collection in automated devices, average processing time between sample collection and result reception by the patient, proportion of positive tests, the age distribution of patients who used automated collection devices, and the ratio of sample kits that were collected outside of regular working hours (20:00-08:00). RESULT. Results were collected from 18 automated (contactless) sample collection devices used by E. Gulbja Laboratory. 64,257 saliva kits for SARS-CoV-2 PCR testing were conducted, and 3.92% of them were positive (SARS-CoV-2 virus RNA found in saliva sample). The average processing time in automated devices located in the capital city was 11.13 hours, in the suburbs - 15.52 hours, and the rest of the country -17.60 hours. The average age of patients that chose an automatic device to hand in their saliva sample kits was 33.94 years. CONCLUSIONS. By using automated devices, patient contacts were decreased, and direct communication with medical staff was excluded, which reduced the risk of infection during processing. Automated devices make sample kit distribution available 24 hours. It saves workforce resources in the laboratory that are already very limited, especially during a pandemic.