RESUMEN
BACKGROUND: More than a year after its first appearance in December 2019, the COVID-19 pandemic is still on a rampage in many parts of the world. Although several vaccines have been approved for emergency use, the emergence and rapid spread of new SARS-CoV-2 variants have sparked fears of vaccine failure due to immune evasion. Massive viral genome sequencing has been recommended to track the genetic changes that could lead to adverse consequences. METHODS: We sequenced SARS-CoV-2 respiratory isolates from the National Public Health Laboratory, Malaysia and examined them together with viral genomes deposited in GISAID by other Malaysian researchers, to understand the evolutionary trend of the virus circulating in the country. We studied the distribution of virus lineages and site-wise mutations, analysed genetic clustering with the goeBURST full Minimum Spanning Tree algorithm, examined the trend of viral nucleotide diversity over time and performed nucleotide substitution association analyses. RESULTS: We identified 22 sub-lineages, 13 clonal complexes, 178 sequence types and seven sites of linkage disequilibrium in 277 SARS-CoV-2 genomes sequenced between January and December 2020. B.1.524 was the largest lineage group. The number of mutations per genome ranged from 0 to 19. The mean genomic diversity value over 12 months was 3.26 × 10-4. Of 359 mutations detected, 60.5% of which were non-synonymous, the most frequent were in the ORF1ab (P4715L), S (D614G and A701V) and N (S194L) genes. CONCLUSION: The SARS-CoV-2 virus accumulated an abundance of mutations in the first year of the COVID-19 pandemic in Malaysia. Its overall genetic diversity, however, is relatively low compared to other Asian countries with larger populations. Continuous genomic and epidemiological surveillance will help to clarify the evolutionary processes determining viral diversity and impacting on human health.
RESUMEN
BACKGROUND: The standard for SARS-CoV-2 diagnosis is RT-PCR from nasopharyngeal or oropharyngeal swabs. Major airports require COVID-19 screening, and saliva has the potential as a substitute specimen for SARS-CoV-2 diagnosis. We investigated the utility of fresh drooled saliva against NPS for COVID-19 screening of travelers. METHODS: We recruited 81 travelers and 15 non-travelers (including ten controls) prospectively within a mean of 3·22 days of RT-PCR confirmed COVID-19. Each study participant provided 2 mls of early morning fresh drooled whole saliva separately into a sterile plastic container and GeneFiX™ saliva collection kit. The saliva specimens were processed within 4 h and tested for SARS-CoV-2 genes (E, RdRP, and N2) and the results compared to paired NPS RT-PCR for diagnostic accuracy. RESULTS: Majority of travellers were asymptomatic (75·0%) with a mean age of 34·26 years. 77 travelers were RT-PCR positive at the time of hospitalization whilst three travelers had positive contacts. In this group, the detection rate for SARS-CoV-2 with NPS, whole saliva, and GeneFiX™ were comparable (89·3%, 50/56; 87·8%, 43/49; 89·6%, 43/48). Both saliva collection methods were in good agreement (Kappa = 0·69). There was no statistical difference between the detection rates of saliva and NPS (p > 0·05). Detection was highest for the N2 gene whilst the E gene provided the highest viral load (mean = 27·96 to 30·10, SD = 3·14 to 3·85). Saliva specimens have high sensitivity (80·4%) and specificity (90·0%) with a high positive predictive value of 91·8% for SARS-CoV-2 diagnosis. CONCLUSION: Saliva for SARS-CoV-2 screening is a simple accurate technique comparable with NPS RT-PCR.
