Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka.

Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021. Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages. Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country. Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage

Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020

Background The transmission dynamics of SARS-CoV-2 varies depending on social distancing measures, circulating SARS-CoV-2 variants, host factors and other environmental factors. We sought to investigate the clinical and epidemiological characteristics of a SARS-CoV-2 outbreak that occurred in a highly dense population area in Colombo, Sri Lanka from April to May 2020. Methodology/principal findings We carried out RT-qPCR for SARS-CoV2, assessed the SARS-CoV-2 specific total and neutralizing antibodies (Nabs) in a densely packed, underserved settlement (n = 2722) after identification of the index case on 15th April 2020. 89/2722 individuals were detected as infected by RT-qPCR with a secondary attack rate among close contacts being 0.077 (95% CI 0.063–0.095). Another 30 asymptomatic individuals were found to have had COVID-19 based on the presence of SARS-CoV-2 specific antibodies. However, only 61.5% of those who were initially seropositive for SARS-CoV-2 had detectable total antibodies at 120 to 160 days, while only 40.6% had detectable Nabs. 74/89 (83.1%) of RT-qPCR positive individuals were completely asymptomatic and all 15 (16.9%) who experienced symptoms were classified as having a mild illness. 18 (20.2%) were between the ages of 61 to 80. 11/89 (12.4%) had diabetes, 8/89 (9%) had cardiovascular disease and 4 (4.5%) had asthma. Of the two viruses that were sequenced and were of the B.1 and B.4 lineages with one carrying the D614G mutation. Discussion/conclusion Almost all infected individuals developed mild or asymptomatic illness despite the presence of comorbid illnesses. Since the majority of those who were in this underserved settlement were not infected despite circulation of the D614G variant, it would be important to further study environmental and host factors that lead to disease severity and transmission

Genomic and epidemiological analysis of SARS-CoV-2 viruses in Sri Lanka

Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021. Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages. Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country. Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage

Immune responses to a single dose of the AZD1222/Covishield vaccine in health care workers

Several COVID-19 vaccines have received emergency approval. Here we assess the immunogenicity of a single dose of the AZD1222 vaccine, at one month, in a cohort of health care workers (HCWs) (629 naïve and 26 previously infected). 93.4% of naïve HCWs seroconverted, irrespective of age and gender. Haemagglutination test for antibodies to the receptor binding domain (RBD), surrogate neutralization assay (sVNT) and ex vivo IFNγ ELISpot assays were carried out in a sub-cohort. ACE2 blocking antibodies (measured by sVNT) were detected in 67/69 (97.1%) of naïve HCWs. Antibody levels to the RBD of the wild-type virus were higher than to RBD of B.1.1.7, and titres to B.1.351 were very low. Ex vivo T cell responses were observed in 30.8% to 61.7% in naïve HCWs. Previously infected HCWs, developed significantly higher (p