Surveillance of emerging SARS-CoV-2 variants by nanopore technology-based genome sequencing

Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Methods:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves.The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria.Viral RNA was extracted,and elutes were subjected to nanopore sequencing.All the sequencing data were uploaded in the publicly accessible database,GISAID.Results:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the period.Less than 1%were Kappa variant and 16%of the study samples remained unassigned.Omicron variant was circulated among all age groups and in all the provinces.Ct value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over 25.Conclusions:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.

Evaluation of the diagnostic performance of a commercial molecular assay for the screening of suspected monkeypox cases in Sri Lanka

Background:The main objective of the present study was to compare the diagnostic performance of the commercial LightMix Modular Monkeypox Virus(MPXV)qPCR(TIB Molbiol,Germany)assay with the in-house non-variola orthopox/monkeypox generic real-time PCR assay(ICMR-NIV,Pune)for the screening of(MPXV)cases at Medical Research Institute(MRI)in Sri Lanka.Furthermore,clinical and sociodemographic data of suspected/confirmed cases received at MRI for the MPXV screening were also analyzed.Methods:The diagnostic performance of the commercial LightMix Modular MPXV qPCR assay with the in-house nonvariola orthopox/monkeypox generic real-time PCR assay for the screening of suspected MXPV cases was evaluated using standard methods with minor modifications.Socio-demographic and clinical profiles of suspected and confirmed MPXV cases were also analyzed.Results:The commercial LightMix Modular MPXV assay was able to detect MPXV with 100%sensitivity and specificity with non-variola orthopox/monkeypox generic rtPCR assay.During the period of study,from the total of 25 samples tested,only 2 were MPXV-positive(males).The most common symptoms of suspected MPXV cases were lesions or rashes(92%).Conclusions:With the continually increasing number of cases,access to MPXV testing should be made more widely available.The commercial LightMix Modular MPXV(TIB Molbiol)qPCR assay offers comparable performance to the non-variola orthopox/monkeypox generic real time PCR assay for MPXV detection during the present outbreak.