Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020

Background In the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data. Aim We applied genomic epidemiology to trace SARS-CoV-2 spread on an international, national and local level, to illustrate how transmission chains can be resolved to the level of a single event and single person using integrated sequence data and spatio-temporal metadata. Methods We investigated 289 COVID-19 cases at a university hospital in Munich, Germany, between 29 February and 27 May 2020. Using the ARTIC protocol, we obtained near full-length viral genomes from 174 SARS-CoV-2-positive respiratory samples. Phylogenetic analyses using the Auspice software were employed in combination with anamnestic reporting of travel history, interpersonal interactions and perceived high-risk exposures among patients and healthcare workers to characterise cluster outbreaks and establish likely scenarios and timelines of transmission. Results We identified multiple independent introductions in the Munich Metropolitan Region during the first weeks of the first pandemic wave, mainly by travellers returning from popular skiing areas in the Alps. In these early weeks, the rate of presumable hospital-acquired infections among patients and in particular healthcare workers was high (9.6% and 54%, respectively) and we illustrated how transmission chains can be dissected at high resolution combining virus sequences and spatio-temporal networks of human interactions. Conclusions Early spread of SARS-CoV-2 in Europe was catalysed by superspreading events and regional hotspots during the winter holiday season. Genomic epidemiology can be employed to trace viral spread and inform effective containment strategies.

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Risk factors for norovirus infection in healthcare workers during nosocomial outbreaks: a cross-sectional study

Antimicrobial Resistance and Infection Control ◽

10.1186/s13756-021-00979-8 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Kjell Torén ◽

Linus Schiöler ◽

Nancy P. Nenonen ◽

Charles Hannoun ◽

Anette Roth ◽

...

Keyword(s):

Risk Factors ◽

Healthcare Workers ◽

Close Contact ◽

Phylogenetic Analyses ◽

Gastrointestinal Symptoms ◽

Cross Sectional Study ◽

University Hospital ◽

Sectional Study ◽

Cross Sectional ◽

Norovirus Gii

Abstract Background Norovirus outbreaks cause severe medico-socio-economic problems affecting healthcare workers and patients. The aim of the study was to investigate prevalence of norovirus infection and risk factors for infection in healthcare workers during nosocomial outbreaks. Methods A cross-sectional study of norovirus infections in healthcare workers was performed in seven outbreak wards in a large university hospital. Packs (swab for rectal sampling, and questionnaire) were posted to healthcare workers on notification of a ward outbreak. Rectal samples were examined with norovirus-specific real-time PCR. Replies from questionnaires were analysed using logistic regression models with norovirus genogroup (G)II positive findings as dependent variable. The results are expressed as odds ratios (OR) with 95% confidence intervals (CI). Sequencing and phylogenetic analyses (1040 nucleotides) were used to characterize norovirus strains from healthcare workers. Cluster analyses included norovirus GII.4 strains detected in ward patients during the ongoing outbreaks. Results Of 308 packs issued to healthcare workers, 129 (42%) were returned. norovirus GII was detected in 26 healthcare workers (20.2%). Work in cohort care (OR 4.8, 95% CI 1.4–16.3), work in wards for patients with dementia (OR 13.2, 95% CI 1.01–170.7), and having diarrhoea, loose stools or other gastrointestinal symptoms the last week (OR 7.7, 95% CI 2.5–27.2) were associated with increased norovirus prevalence in healthcare workers. Sequencing revealed norovirus GII.4 in healthcare workers samples, and strains detected in healthcare workers and ward patients during a given ward outbreak showed ≥ 99% similarity. Conclusion Norovirus positive findings in healthcare workers were strongly associated with symptomatic infection, close contact with sick patients, and dementia nursing.

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VIRULIGN: fast codon-correct alignment and annotation of viral genomes

10.1101/409052 ◽

2018 ◽

Cited By ~ 2

Author(s):

Pieter Libin ◽

Koen Deforche ◽

Ana B. Abecasis ◽

Kristof Theys

Keyword(s):

Open Source Software ◽

Sequence Data ◽

Heterogeneous Data ◽

Software Project ◽

Viral Genomes ◽

Viral Spread ◽

Treatment And Prevention ◽

Correct Alignment ◽

Virus Sequence ◽

Essential Resource

AbstractVirus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit for these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codoncorrect alignments of large datasets, with standardized genome annotation and various alignment export formats.VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project.

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The ability of single genes vs full genomes to resolve time and space in outbreak analysis

BMC Evolutionary Biology ◽

10.1186/s12862-019-1567-0 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 6

Author(s):

Gytis Dudas ◽

Trevor Bedford

Keyword(s):

Genome Sequencing ◽

Statistical Power ◽

Ebola Virus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Viral Genomes ◽

Whole Genomes ◽

Temporal And Spatial ◽

Pathogen Genome ◽

Insight Into

Abstract Background Inexpensive pathogen genome sequencing has had a transformative effect on the field of phylodynamics, where ever increasing volumes of data have promised real-time insight into outbreaks of infectious disease. As well as the sheer volume of pathogen isolates being sequenced, the sequencing of whole pathogen genomes, rather than select loci, has allowed phylogenetic analyses to be carried out at finer time scales, often approaching serial intervals for infections caused by rapidly evolving RNA viruses. Despite its utility, whole genome sequencing of pathogens has not been adopted universally and targeted sequencing of loci is common in some pathogen-specific fields. Results In this study we highlighted the utility of sequencing whole genomes of pathogens by re-analysing a well-characterised collection of Ebola virus sequences in the form of complete viral genomes (≈19 kb long) or the rapidly evolving glycoprotein (GP, ≈2 kb long) gene. We have quantified changes in phylogenetic, temporal, and spatial inference resolution as a result of this reduction in data and compared these to theoretical expectations. Conclusions We propose a simple intuitive metric for quantifying temporal resolution, i.e. the time scale over which sequence data might be informative of various processes as a quick back-of-the-envelope calculation of statistical power available to molecular clock analyses.

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The ability of single genes vs full genomes to resolve time and space in outbreak analysis

10.1101/582957 ◽

2019 ◽

Cited By ~ 5

Author(s):

Gytis Dudas ◽

Trevor Bedford

Keyword(s):

Genome Sequencing ◽

Statistical Power ◽

Ebola Virus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Viral Genomes ◽

Whole Genomes ◽

Temporal And Spatial ◽

Pathogen Genome ◽

Insight Into

AbstractInexpensive pathogen genome sequencing has had a transformative effect on the field of phylodynamics, where ever increasing volumes of data have promised real-time insight into outbreaks of infectious disease. As well as the sheer volume of pathogen isolates being sequenced, the sequencing of whole pathogen genomes, rather than select loci, has allowed phylogenetic analyses to be carried out at finer time scales, often approaching serial intervals for infections caused by rapidly evolving RNA viruses. Despite its utility, whole genome sequencing of pathogens has not been adopted universally and targeted sequencing of loci is common in some pathogen-specific fields. In this study we aim to highlight the utility of sequencing whole genomes of pathogens by re-analysing a well-characterised collection of Ebola virus sequences in the form of complete viral genomes (~19kb long) or the rapidly evolving glycoprotein (GP, ~2kb long) gene. We quantify changes in phylogenetic, temporal, and spatial inference resolution as a result of this reduction in data and compare these to theoretical expectations. We propose a simple intuitive metric for quantifying temporal resolution,i.e.the time scale over which sequence data might be informative of various processes as a quick back-of-the-envelope calculation of statistical power available to molecular clock analyses.

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Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

Systematic Botany ◽

10.1600/036364419x15710776741477 ◽

2019 ◽

Vol 44 (4) ◽

pp. 930-942

Author(s):

Geraldine A. Allen ◽

Luc Brouillet ◽

John C. Semple ◽

Heidi J. Guest ◽

Robert Underhill

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Evidence ◽

South American ◽

New Combinations ◽

The North ◽

Hybridization Event ◽

Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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Prevalence of Thyroid Diseases in an Occupationally Radiation Exposed Group: A Cross-Sectional Study in a University Hospital of Southern Italy

Endocrine Metabolic & Immune Disorders - Drug Targets ◽

10.2174/1871530318666181102114627 ◽

2019 ◽

Vol 19 (6) ◽

pp. 803-808 ◽

Cited By ~ 1

Author(s):

Luigi Vimercati ◽

Luigi De Maria ◽

Francesca Mansi ◽

Antonio Caputi ◽

Giovanni M. Ferri ◽

...

Keyword(s):

Ionizing Radiation ◽

Healthcare Workers ◽

Southern Italy ◽

Cross Sectional Study ◽

Thyroid Diseases ◽

University Hospital ◽

Control Group ◽

Sectional Study ◽

Cross Sectional ◽

Exposed Workers

Background: Thyroid diseases occur more frequently in people exposed to ionizing radiation, but the relationship between occupational exposure to ionizing radiation and thyroid pathologies still remains unclear. Objective: To evaluate the prevalence of thyroid diseases in healthcare workers exposed to low-level ionizing radiation compared with a control group working at the University Hospital of Bari, Southern Italy, and living in the same geographical area, characterized by mild iodine deficiency. Methods: We ran a cross-sectional study to investigate whether healthcare workers exposed to ionizing radiation had a higher prevalence of thyroid diseases. Four hundred and forty-four exposed healthcare workers (241 more exposed, or “A Category”, and 203 less exposed, or “B Category”) and 614 nonexposed healthcare workers were enrolled during a routine examination at the Occupational Health Unit. They were asked to fill in an anamnestic questionnaire and undergo a physical examination, serum determination of fT3, fT4 and TSH, anti-TPO ab and anti-TG ab and ultrasound neck scan. Thyroid nodules were submitted to fine needle aspiration biopsy when indicated. Results: The prevalence of thyroid diseases was statistically higher in the exposed workers compared to controls (40% vs 29%, adPR 1.65; IC95% 1.34-2.07). In particular, the thyroid nodularity prevalence in the exposed group was approximately twice as high as that in the controls (29% vs 13%; adPR 2.83; IC95% 2.12-3.8). No statistically significant association was found between exposure to ionizing radiation and other thyroid diseases. Conclusion: In our study, mild ionizing radiation-exposed healthcare workers had a statistically higher prevalence of thyroid diseases than the control group. The results are likely due to a closer and more meticulous health surveillance programme carried out in the ionising radiation-exposed workers, allowing them to identify thyroid alterations earlier than non-exposed health staff.

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Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Science ◽

10.1126/science.abf2946 ◽

2021 ◽

pp. eabf2946

Author(s):

Louis du Plessis ◽

John T. McCrone ◽

Alexander E. Zarebski ◽

Verity Hill ◽

Christopher Ruis ◽

...

Keyword(s):

Large Scale ◽

Phylogenetic Analyses ◽

Transmission Dynamics ◽

Genetic Lineage ◽

Size Dependent ◽

Spatio Temporal ◽

The Uk ◽

Lineage Structure ◽

And Control ◽

Lineage Diversity

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

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Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

Microorganisms ◽

10.3390/microorganisms9030666 ◽

2021 ◽

Vol 9 (3) ◽

pp. 666

Author(s):

Niccolò Forin ◽

Alfredo Vizzini ◽

Federico Fainelli ◽

Enrico Ercole ◽

Barbara Baldan

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Illumina Miseq ◽

Botanical Garden ◽

Molecular Study ◽

Its2 Sequence ◽

Type Specimens ◽

Its1 Sequence ◽

Dna Sequence Data ◽

Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

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Preventing SARS-CoV-2 transmission in the emergency department by implementing a separate pathway for patients with respiratory conditions

Journal of Complementary and Integrative Medicine ◽

10.1515/jcim-2020-0422 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Fulwah Alqahtani ◽

Marzouqah Alanazi ◽

Wajdan Alassaf ◽

Fadilah Sfouq Aleanizy ◽

Muna Aljahany ◽

...

Keyword(s):

Emergency Department ◽

Longitudinal Study ◽

Healthcare Workers ◽

Respiratory Symptoms ◽

Control Measures ◽

University Hospital ◽

Respiratory Pathway ◽

Infection Control Measures ◽

Separate Pathway ◽

Respiratory Conditions

Abstract Objectives This study aimed to describe the development and implementation of a separated pathway to check and treat patients with a suspected/confirmed coronavirus disease 2019 (COVID-19) in the emergency department (ED) at King Abdullah bin Abdulaziz University Hospital in Riyadh. Methods We conducted a retrospective, descriptive longitudinal study from March to July 2020 by analyzing data of all confirmed cases of COVID-19 among ED visitors and healthcare workers in King Abdullah bin Abdulaziz University Hospital. Results During the study period, a total of 1,182 swab samples were collected for testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), of which 285 (24.1%) tested positive. Of the 285 cases of confirmed SARS-CoV-2 infection, 18 were healthcare workers and 267 were patients. As a result of using the respiratory pathway for COVID-19 patients, the hospital managed to limit transmission of SARS-CoV-2 not only between patients but also between patients and healthcare workers, while also containing the pandemic. There were no cases of nosocomial SARS-CoV-2 infection recorded among the patients who visited the ED or the flu clinic. All confirmed cases were community acquired and patients were cared for under constrained measures. Conclusions Implementing infection control measures and restricting those with respiratory symptoms to the ED pathway prevented nosocomial spread of SARS-CoV-2 infection in the ED.

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Burnout of Healthcare Workers amid the COVID-19 Pandemic: A Japanese Cross-Sectional Survey

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18052434 ◽

2021 ◽

Vol 18 (5) ◽

pp. 2434

Author(s):

Yoshito Nishimura ◽

Tomoko Miyoshi ◽

Hideharu Hagiya ◽

Yoshinori Kosaki ◽

Fumio Otsuka

Keyword(s):

Healthcare Workers ◽

Healthcare Professionals ◽

Healthcare Delivery ◽

General Medicine ◽

Maslach Burnout Inventory ◽

University Hospital ◽

Survey Study ◽

Cross Sectional Survey ◽

Cross Sectional ◽

The Past

The coronavirus disease 2019 (COVID-19) global pandemic has drastically changed how we live and work. Amid the prolonged pandemic, burnout of the frontline healthcare professionals has become a significant concern. We conducted a cross-sectional survey study to provide data about the relationship between the COVID-19 pandemic and the prevalence of burnout in healthcare professionals in Japan. Healthcare workers in a single Japanese national university hospital participated in the survey, including basic demographics, whether a participant engaged in care of COVID-19 patients in the past 2 weeks and the Maslach Burnout Inventory. Of those, 25.4% fully answered the survey; 33.3% were doctors and 63.6% were nurses, and 36.3% engaged in care of COVID-19 patients in the past 2 weeks. Compared to those belonging to General Medicine, those in Emergency Intensive Care Unit were at higher risk of burnout (odds ratio (OR), 6.7; 95% CI, 1.1–42.1; p = 0.031). Of those who engaged in care of COVID-19 patients, 50% reported burnout while 6.1% did not (OR 8.5, 95% CI; 1.3–54.1; p = 0.014). The burnout of healthcare workers is a significant concern amid the pandemic, which needs to be addressed for sustainable healthcare delivery.

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