| Title: |
Molecular epidemiology of AY.28 and AY.104 delta sub-lineages in Sri Lanka |
| Authors: |
Ranasinghe, D; Jayathilaka, DJ; Jeewandara, C; Gunasinghe, D; Ariyaratne, D; Jayadas, TTP; Kuruppu, H; Wijesinghe, A; Bary, FF; Madhusanka, D; Pushpakumara, PD; Guruge, D; Wijayamuni, R; Ogg, GS; Malavige, GN |
| Publisher Information: |
Frontiers Media |
| Publication Year: |
2023 |
| Collection: |
Oxford University Research Archive (ORA) |
| Description: |
Background: The 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. Methods: 705 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. Results: AY.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. Conclusions: Therefore, AY.28 and AY.104 appear to have a fitness advantage over the parental delta variant (B.1.617.2), while AY.28 also had a higher expression of sg-RNA compared to other sub-lineages. The clinical implications of these should be further investigated. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
https://doi.org/10.3389/fpubh.2022.873633 |
| DOI: |
10.3389/fpubh.2022.873633 |
| Availability: |
https://doi.org/10.3389/fpubh.2022.873633; https://ora.ox.ac.uk/objects/uuid:959c26bf-59ff-48c9-a19a-b10f8bb3fe0d |
| Rights: |
info:eu-repo/semantics/openAccess ; CC Attribution (CC BY) |
| Accession Number: |
edsbas.722CB528 |
| Database: |
BASE |