Whole-genome sequencing of SARS-CoV-2 in the Republic of Ireland during waves 1 and 2 of the pandemic

Mallon, Patrick; Crispie, Fiona; González, Gabriel; Tinago, Willard; A, Garcia Leon; McCabe, Matthew S.; E, de Barra; Yousif, Obada; Lambert, John S; Walsh, Calum J.; Kenny, John; Feeney, Eoin R.; Carr, Michael J.; Doran, Peter; Cotter, Paul D.

doi:10.1101/2021.02.09.21251402

Cited by 21 publications

(21 citation statements)

References 17 publications

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“…Our estimation for the 1st July is 2.1% (95% CI: 1.2-3.6%) and is in complete accordance with a survey study that shows a sero-prevalence of 1.7% (95% CI: 1.1-2.4%) between 22nd June and 16th July 2020 [19]. Figure 4 displays our estimation of the time evolution of the sero-prevalence that shows a large increase from the beginning of January 2020 due to the high propagation of the UK variant [15,16] but, also, it would seem, due to the rolling out of the vaccination.…”

Section: T) (B) Infected Non Infectious E(t) = E 1 (T) + E 2 (T) C Symptomatic Infectious I(t) = I 1 (T) + I 2 (T) D Asymptomatic Infectisupporting

confidence: 86%

Dynamics of the COVID-19 epidemic in Ireland under mitigation

et al. 2021

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Background In Ireland and across the European Union the COVID-19 epidemic waves, driven mainly by the emergence of new variants of the SARS-CoV-2 have continued their course, despite various interventions from governments. Public health interventions continue in their attempts to control the spread as they wait for the planned significant effect of vaccination. Methods To tackle this challenge and the observed non-stationary aspect of the epidemic we used a modified SEIR stochastic model with time-varying parameters, following Brownian process. This enabled us to reconstruct the temporal evolution of the transmission rate of COVID-19 with the non-specific hypothesis that it follows a basic stochastic process constrained by the available data. This model is coupled with Bayesian inference (particle Markov Chain Monte Carlo method) for parameter estimation and utilized mainly well-documented Irish hospital data. Results In Ireland, mitigation measures provided a 78–86% reduction in transmission during the first wave between March and May 2020. For the second wave in October 2020, our reduction estimation was around 20% while it was 70% for the third wave in January 2021. This third wave was partly due to the UK variant appearing in Ireland. In June 2020 we estimated that sero-prevalence was 2.0% (95% CI: 1.2–3.5%) in complete accordance with a sero-prevalence survey. By the end of April 2021, the sero-prevalence was greater than 17% due in part to the vaccination campaign. Finally we demonstrate that the available observed confirmed cases are not reliable for analysis owing to the fact that their reporting rate has as expected greatly evolved. Conclusion We provide the first estimations of the dynamics of the COVID-19 epidemic in Ireland and its key parameters. We also quantify the effects of mitigation measures on the virus transmission during and after mitigation for the three waves. Our results demonstrate that Ireland has significantly reduced transmission by employing mitigation measures, physical distancing and lockdown. This has to date avoided the saturation of healthcare infrastructures, flattened the epidemic curve and likely reduced mortality. However, as we await for a full roll out of a vaccination programme and as new variants potentially more transmissible and/or more infectious could continue to emerge and mitigation measures change silent transmission, challenges remain.

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Section: T) (B) Infected Non Infectious E(t) = E 1 (T) + E 2 (T) C Symptomatic Infectious I(t) = I 1 (T) + I 2 (T) D Asymptomatic Infectisupporting

confidence: 86%

Dynamics of the COVID-19 epidemic in Ireland under mitigation

et al. 2021

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“…Similar studies have been reported from a plethora of countries around the world including the UK, Ireland, Russia, India, Qatar etc. [26,[33][34][35][36]. These studies provide valuable information on the routes of importation of new strains and the emergence of critical mutations that change key parameters such as transmissibility or virulence, as was recently highlighted by the discovery of the B.1.617 variant and its B.1.617.2 sub-lineage in India [37], which led to a surge of SARS-CoV-2 infections in Delhi.…”

Section: Resultsmentioning

confidence: 97%

“…The B.1.177 lineage, which is characterized by the A222V spike mutation, was previously been shown to have emerged in Spain in early summer and subsequently became widespread across Europe as well as Canada, accounting for the majority of sequences by autumn 2020 [25,26]. However, no evidence of increased transmissibility of this variant was reported [27].…”

Section: Resultsmentioning

confidence: 99%

Molecular epidemiology of SARS-CoV-2 in Cyprus

et al. 2021

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Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV-2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.

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“…The B.1.177 lineage, which is characterized by the A222V spike mutation, was previously been shown to have emerged in Spain in early summer and subsequently became widespread across Europe as well as Canada, accounting for the majority of sequences by autumn 2020 [16,17]. However, no evidence of increased transmissibility of this variant was reported [18].…”

Section: Resultsmentioning

confidence: 99%

Molecular Epidemiology of SARS-CoV-2 in Cyprus

Richter

Fanis

Tryfonos

et al. 2021

Preprint

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Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.

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Whole-genome sequencing of SARS-CoV-2 in the Republic of Ireland during waves 1 and 2 of the pandemic

Cited by 21 publications

References 17 publications

Dynamics of the COVID-19 epidemic in Ireland under mitigation

Dynamics of the COVID-19 epidemic in Ireland under mitigation

Molecular epidemiology of SARS-CoV-2 in Cyprus

Molecular Epidemiology of SARS-CoV-2 in Cyprus

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