1 research outputs found
Molecular epidemiology of SARSâCoVâ2 in Mongolia, first experience with nanopore sequencing in lowerâ and middleâincome countries setting
Abstract Background Coronavirus disease (COVIDâ19) has had a significant impact globally, and extensive genomic research has been conducted on severe acute respiratory syndrome coronavirus 2 (SARSâCoVâ2) lineage patterns and its variants. Mongolia's effective response resulted in low prevalence until vaccinations became available. However, due to the lack of systematically collected data and absence of whole genome sequencing capabilities, we conducted a twoâstepped, nationally representative molecular epidemiologic study of SARSâCoVâ2 in Mongolia for 2020 and 2021. Methods We used retrospective analysis of stored biological samples from November 2020 to October 2021 and a variantâspecific realâtime reverse transcription polymerase chain reaction (RTâPCR) test to detect SARSâCoVâ2 variants, followed by whole genome sequencing by Nanopore technology. Samples were retrieved from different sites and stored at â70°C deep freezer, and tests were performed on samples with cycle threshold <30. Results Out of 4879 nucleic acid tests, 799 whole genome sequencing had been carried out. Among the stored samples of earlier local transmission, we found the 20B (B.1.1.46) variant predominated in the earlier local transmission period. A slower introduction and circulation of alpha and delta variants were observed compared to global dynamics in 2020 and 2021. Beta or Gamma variants were not detected between November 2020 and September 2021 in Mongolia. Conclusions SARSâCoVâ2 variants of concerns including alpha and delta were delayed in circulation potentially due to public health stringencies in Mongolia. We are sharing our initial experience with whole genome sequencing of SARSâCoVâ2 from Mongolia, where sequencing data is sparse