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Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020.

ABSTRACT: By October 2021, 230 million SARS-CoV-2 diagnoses have been reported. Yet, a considerable proportion of cases remains undetected. Here, we propose GInPipe, a method that rapidly reconstructs SARS-CoV-2 incidence profiles solely from publicly available, time-stamped viral genomes. We validate GInPipe against simulated outbreaks and elaborate phylodynamic analyses. Using available sequence data, we reconstruct incidence histories for Denmark, Scotland, Switzerland, and Victoria (Australia) and demonstrate, how to use the method to investigate the effects of changing testing policies on case ascertainment. Specifically, we find that under-reporting was highest during summer 2020 in Europe, coinciding with more liberal testing policies at times of low testing capacities. Due to the increased use of real-time sequencing, it is envisaged that GInPipe can complement established surveillance tools to monitor the SARS-CoV-2 pandemic. In post-pandemic times, when diagnostic efforts are decreasing, GInPipe may facilitate the detection of hidden infection dynamics.

SUBMITTER: Smith MR

PROVIDER: S-EPMC8517019 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020.

Smith Maureen Rebecca MR Trofimova Maria M Weber Ariane A Duport Yannick Y Kühnert Denise D von Kleist Max M

Nature communications 20211014 1

By October 2021, 230 million SARS-CoV-2 diagnoses have been reported. Yet, a considerable proportion of cases remains undetected. Here, we propose GInPipe, a method that rapidly reconstructs SARS-CoV-2 incidence profiles solely from publicly available, time-stamped viral genomes. We validate GInPipe against simulated outbreaks and elaborate phylodynamic analyses. Using available sequence data, we reconstruct incidence histories for Denmark, Scotland, Switzerland, and Victoria (Australia) and dem ...[more]

PMID: 34650062

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Project description:Although France was one of the most affected European countries by the COVID-19 pandemic in 2020, the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) movement within France, but also involving France in Europe and in the world, remain only partially characterized in this timeframe. Here, we analyzed GISAID deposited sequences from January 1 to December 31, 2020 (n = 638,706 sequences at the time of writing). To tackle the challenging number of sequences without the bias of analyzing a single subsample of sequences, we produced 100 subsamples of sequences and related phylogenetic trees from the whole dataset for different geographic scales (worldwide, European countries, and French administrative regions) and time periods (from January 1 to July 25, 2020, and from July 26 to December 31, 2020). We applied a maximum likelihood discrete trait phylogeographic method to date exchange events (i.e., a transition from one location to another one), to estimate the geographic spread of SARS-CoV-2 transmissions and lineages into, from and within France, Europe, and the world. The results unraveled two different patterns of exchange events between the first and second half of 2020. Throughout the year, Europe was systematically associated with most of the intercontinental exchanges. SARS-CoV-2 was mainly introduced into France from North America and Europe (mostly by Italy, Spain, the United Kingdom, Belgium, and Germany) during the first European epidemic wave. During the second wave, exchange events were limited to neighboring countries without strong intercontinental movement, but Russia widely exported the virus into Europe during the summer of 2020. France mostly exported B.1 and B.1.160 lineages, respectively, during the first and second European epidemic waves. At the level of French administrative regions, the Paris area was the main exporter during the first wave. But, for the second epidemic wave, it equally contributed to virus spread with Lyon area, the second most populated urban area after Paris in France. The main circulating lineages were similarly distributed among the French regions. To conclude, by enabling the inclusion of tens of thousands of viral sequences, this original phylodynamic method enabled us to robustly describe SARS-CoV-2 geographic spread through France, Europe, and worldwide in 2020.

Project description:BackgroundDuring the COVID-19 pandemic, face-to-face delivery of education in schools across Wales was disrupted with repeated school closures to limit risk of infection. Evidence describing the incidence of infection amongst school staff during times when schools were open is limited. A previous research study found infection rates were higher in English primary school settings when compared with secondary. An Italian study suggested teachers weren't at greater risk of infection in comparison to the general population. The aim of this study was to identify whether educational staff had higher incidence rates than their counterparts in the general population in Wales, and secondly whether incidence rates amongst staff differed between primary and secondary school settings and by teacher age.MethodsWe performed a retrospective observational cohort study using the national case detection and contact tracing system implemented during the COVID pandemic. Age stratified person-day COVID-19 incidence rates amongst teaching staff linked to primary or secondary schools in Wales were calculated for the autumn and summer terms during 2020-2021.ResultsThe observed pooled COVID-19 incidence rates for staff across both terms was 23.30 per 100,000 person days (95% CI: 22.31-24.33). By comparison, the rate in the general population aged 19-65, was 21.68 per 100,000 person days (95%: CI 21.53-21.84). Incidence among teaching staff was highest in the two youngest age groups (< 25 years and 25-29 years). When compared to the age matched general population, incidence was higher in the autumn term amongst primary school teachers aged ≤ 39 years, and in the summer term higher only in the primary school teachers aged < 25 years.ConclusionThe data were consistent with an elevated risk of COVID-19 amongst younger teaching staff in primary schools when compared to the general population, however differences in case ascertainment couldn't be excluded as a possible reason for this. Rate differences by age group in teaching staff mirrored those in the general population. The risk in older teachers (≥ 50 years) in both settings was the same or lower than in the general population. Amongst all age groups of teachers maintaining the key risk mitigations within periods of COVID transmission remain important.

Project description:Background: Lyme borreliosis (LB) is the most common tick-borne disease in Europe, but the burden of disease is incompletely described. Methods: We conducted a systematic review across PubMed, EMBASE, and CABI Direct (Global Health) databases, from January 1, 2005, to November 20, 2020, of epidemiological studies reporting incidence of LB in Europe (PROSPERO, CRD42021236906). Results: The systematic review yielded 61 unique articles describing LB incidence (national or subnational) in 25 European countries. Substantial heterogeneity in study designs, populations sampled, and case definitions restricted data comparability. The European Union Concerted Action on Lyme Borreliosis (EUCALB)-published standardized LB case definitions were used by only 13 (21%) of the 61 articles. There were 33 studies that provided national-level LB incidence estimates for 20 countries. Subnational LB incidence was available from an additional four countries (Italy, Lithuania, Norway, and Spain). The highest LB incidences (>100 cases per 100,000 population per year [PPY]) were reported in Belgium, Finland, the Netherlands, and Switzerland. Incidences were 20-40/100,000 PPY in the Czech Republic, Germany, Poland, and Scotland and <20/100,000 PPY in Belarus, Croatia, Denmark, France, Ireland, Portugal, Russia, Slovakia, Sweden, and the United Kingdom (England, Northern Ireland, and Wales); markedly higher incidences were observed at the subnational level (up to 464/100,000 PPY in specific local areas). Conclusions: Although countries in Northern (Finland) and Western (Belgium, the Netherlands, and Switzerland) Europe reported the highest LB incidences, high incidences also were reported in some Eastern European countries. There was substantial subnational variation in incidence, including high incidences in some areas of countries with low overall incidence. This review, complemented by the incidence surveillance article, provides a comprehensive view into LB disease burden across Europe that may guide future preventive and therapeutic strategies-including new strategies on the horizon.

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Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020.

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Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020.

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