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Molecular epidemiology of AY.28 and AY.104 delta sub-lineages in Sri Lanka
Preprint
em Inglês
| medRxiv
| ID: ppmedrxiv-22270436
ABSTRACT
BackgroundThe worst SARS-CoV-2 outbreak in Sri Lanka was due to the two Sri Lankan delta sub-lineages AY.28 and AY.104. We proceeded to further characterize the mutations and clinical disease severity of these two sub-lineages. Methods705 delta SARS-CoV-2 genomes sequenced by our laboratory from mid-May to November 2021 using Illumina and Oxford Nanopore were included in the analysis. The clinical disease severity of 440/705 individuals were further analyzed to determine if infection with either AY.28 or AY.104 was associated with more severe disease. Sub-genomic RNA (sg-RNA) expression was analyzed using periscope. ResultsAY.28 was the dominant variant throughout the outbreak, accounting for 67.7% of infections during the peak of the outbreak. AY.28 had three lineage defining mutations in the spike protein A222V (92.80%), A701S (88.06%), and A1078S (92.04%) and seven in the ORF1a R24C, K634N, P1640L, A2994V, A3209V, V3718A, and T3750I. AY.104 was characterized by the high prevalence of T95I (90.81%) and T572L (65.01%) mutations in the spike protein and by the absence of P1640L (94.28%) in ORF1a with the presence of A1918V (98.58%) mutation. The mean sgRNA expression levels of ORF6 in AY.28 were significantly higher compared to AY.104 (p < 0.0001) and B.1.617.2 (p < 0.01). Also, ORF3a showed significantly higher sgRNA expression in AY.28 compared to AY.104 (p < 0.0001). There was no difference in the clinical disease severity or duration of hospitalization in individuals infected with these sub lineages. ConclusionsTherefore, AY.28 appears to have a fitness advantage over the parental delta variant (B.1.617.2) and AY.104 possibly due to the A222V mutation. AY.28 also had a higher expression of sg-RNA compared to other sub-lineages. The clinical implications of these should be further investigated.
cc_by_nc_nd
Texto completo:
Disponível
Coleções:
Preprints
Base de dados:
medRxiv
Tipo de estudo:
Estudo observacional
/
Estudo prognóstico
Idioma:
Inglês
Ano de publicação:
2022
Tipo de documento:
Preprint