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Article ; Online: Preliminary case report on the SARS-CoV-2 cluster in the UK, France, and Spain

Hodcroft, Emma B

2020 Volume 150, Page(s) w20212

Abstract: Almost half of the confirmed COVID-19 cases detected so far in the United Kingdom are part of a large cluster of 13 British nationals who tested positive for SARS-CoV-2 in the UK, Spain, and France. Transmissions among this cluster occurred at a ski ... ...

Abstract	Almost half of the confirmed COVID-19 cases detected so far in the United Kingdom are part of a large cluster of 13 British nationals who tested positive for SARS-CoV-2 in the UK, Spain, and France. Transmissions among this cluster occurred at a ski resort in France, and originated from a single infected traveller returning from a conference in Singapore where he acquired the virus. At least 21 individuals were exposed to the virus, tested, and quarantined, with 13 of those testing positive between the period of 6th February and 15th February. Here, all publicly available information about the primarily UK/France cluster is consolidated, providing a complete and accessible summary of the cases and their connections. Notable in this cluster are the number of individuals infected, the apparent absence of any severe illness among those infected, and a case of a “delayed positive” test during isolation after initially testing negative, at least 7 days after last possible contact.
MeSH term(s)	Betacoronavirus ; COVID-19 ; Contact Tracing ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Coronavirus Infections/transmission ; Disease Outbreaks ; France/epidemiology ; Humans ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/transmission ; Quarantine ; SARS-CoV-2 ; Singapore ; Spain/epidemiology ; Travel ; United Kingdom/epidemiology
Keywords	covid19
Language	English
Publishing date	2020-02-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2036179-8
ISSN	1424-3997 ; 1424-7860
ISSN (online)	1424-3997
ISSN	1424-7860
DOI	10.4414/smw.2020.20212
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Article ; Online: Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: Phylogenetic analysis and intervention scenarios.

Reichmuth, Martina L / Hodcroft, Emma B / Althaus, Christian L

PLoS pathogens

2023 Volume 19, Issue 8, Page(s) e1011553

Abstract: The SARS-CoV-2 pandemic has led to the emergence of various variants of concern (VoCs) that are associated with increased transmissibility, immune evasion, or differences in disease severity. The emergence of VoCs fueled interest in understanding the ... ...

Abstract	The SARS-CoV-2 pandemic has led to the emergence of various variants of concern (VoCs) that are associated with increased transmissibility, immune evasion, or differences in disease severity. The emergence of VoCs fueled interest in understanding the potential impact of travel restrictions and surveillance strategies to prevent or delay the early spread of VoCs. We performed phylogenetic analyses and mathematical modeling to study the importation and spread of the VoCs Alpha and Delta in Switzerland in 2020 and 2021. Using a phylogenetic approach, we estimated between 383-1,038 imports of Alpha and 455-1,347 imports of Delta into Switzerland. We then used the results from the phylogenetic analysis to parameterize a dynamic transmission model that accurately described the subsequent spread of Alpha and Delta. We modeled different counterfactual intervention scenarios to quantify the potential impact of border closures and surveillance of travelers on the spread of Alpha and Delta. We found that implementing border closures after the announcement of VoCs would have been of limited impact to mitigate the spread of VoCs. In contrast, increased surveillance of travelers could prove to be an effective measure for delaying the spread of VoCs in situations where their severity remains unclear. Our study shows how phylogenetic analysis in combination with dynamic transmission models can be used to estimate the number of imported SARS-CoV-2 variants and the potential impact of different intervention scenarios to inform the public health response during the pandemic.
MeSH term(s)	Humans ; Phylogeny ; SARS-CoV-2/genetics ; Switzerland/epidemiology ; COVID-19/epidemiology ; Pandemics
Language	English
Publishing date	2023-08-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1011553
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genetic Variants of SARS-CoV-2-What Do They Mean?

Lauring, Adam S / Hodcroft, Emma B

JAMA

2021 Volume 325, Issue 6, Page(s) 529–531

MeSH term(s)	Animals ; COVID-19/veterinary ; COVID-19/virology ; COVID-19 Vaccines/immunology ; Genetic Variation ; Humans ; Mink ; Mutation ; Phylogeny ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	COVID-19 Vaccines ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-01-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2958-0
ISSN	1538-3598 ; 0254-9077 ; 0002-9955 ; 0098-7484
ISSN (online)	1538-3598
ISSN	0254-9077 ; 0002-9955 ; 0098-7484
DOI	10.1001/jama.2020.27124
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Article ; Online: Preliminary case report on the SARS-CoV-2 cluster in the UK, France, and Spain

Hodcroft, Emma B.

Swiss Medical Weekly ; ISSN 1424-3997

2020

Keywords	General Medicine ; covid19
Language	English
Publisher	EMH Swiss Medical Publishers, Ltd.
Publishing country	ch
Document type	Article ; Online
DOI	10.4414/smw.2020.20212
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Evolution and Biology of SARS-CoV-2 Variants.

Telenti, Amalio / Hodcroft, Emma B / Robertson, David L

Cold Spring Harbor perspectives in medicine

2022 Volume 12, Issue 5

Abstract: Our understanding of the still unfolding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic would have been extremely limited without the study of the genetics and evolution of this new human coronavirus. Large-scale genome-sequencing ... ...

Abstract	Our understanding of the still unfolding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic would have been extremely limited without the study of the genetics and evolution of this new human coronavirus. Large-scale genome-sequencing efforts have provided close to real-time tracking of the global spread and diversification of SARS-CoV-2 since its entry into the human population in late 2019. These data have underpinned analysis of its origins, epidemiology, and adaptations to the human population: principally immune evasion and increasing transmissibility. SARS-CoV-2, despite being a new human pathogen, was highly capable of human-to-human transmission. During its rapid spread in humans, SARS-CoV-2 has evolved independent new forms, the so-called "variants of concern," that are better optimized for human-to-human transmission. The most important adaptation of the bat coronavirus progenitor of both SARS-CoV-1 and SARS-CoV-2 for human infection (and other mammals) is the use of the angiotensin-converting enzyme 2 (ACE2) receptor. Relaxed structural constraints provide plasticity to SARS-related coronavirus spike protein permitting it to accommodate significant amino acid replacements of antigenic consequence without compromising the ability to bind to ACE2. Although the bulk of research has justifiably concentrated on the viral spike protein as the main determinant of antigenic evolution and changes in transmissibility, there is accumulating evidence for the contribution of other regions of the viral proteome to virus-host interaction. Whereas levels of community transmission of recombinants compromising genetically distinct variants are at present low, when divergent variants cocirculate, recombination between SARS-CoV-2 clades is being detected, increasing the risk that viruses with new properties emerge. Applying computational and machine learning methods to genome sequence data sets to generate experimentally verifiable predictions will serve as an early warning system for novel variant surveillance and will be important in future vaccine planning. Omicron, the latest SARS-CoV-2 variant of concern, has focused attention on step change antigenic events, "shift," as opposed to incremental "drift" changes in antigenicity. Both an increase in transmissibility and antigenic shift in Omicron led to it readily causing infections in the fully vaccinated and/or previously infected. Omicron's virulence, while reduced relative to the variant of concern it replaced, Delta, is very much premised on the past immune exposure of individuals with a clear signal that boosted vaccination protects from severe disease. Currently, SARS-CoV-2 has proven itself to be a dangerous new human respiratory pathogen with an unpredictable evolutionary capacity, leading to a risk of future variants too great not to ensure all regions of the world are screened by viral genome sequencing, protected through available and affordable vaccines, and have non-punitive strategies in place for detecting and responding to novel variants of concern.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Animals ; COVID-19 ; Evolution, Molecular ; Humans ; Mammals/metabolism ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-05-27
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ISSN	2157-1422
ISSN (online)	2157-1422
DOI	10.1101/cshperspect.a041390
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sharing, synthesis and sustainability of data analysis for epidemic preparedness in Europe.

Kucharski, Adam J / Hodcroft, Emma B / Kraemer, Moritz U G

The Lancet regional health. Europe

2021 Volume 9, Page(s) 100215

Language	English
Publishing date	2021-10-07
Publishing country	England
Document type	Journal Article ; Review
ISSN	2666-7762
ISSN (online)	2666-7762
DOI	10.1016/j.lanepe.2021.100215
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Preliminary case report on the SARS-CoV-2 cluster in the UK, France, and Spain

Emma, Hodcroft B.

Swiss Medical Weekly

Abstract: Almost half of the confirmed COVID-19 cases detected so far in the United Kingdom are part of a large cluster of 13 British nationals who tested positive for SARS-CoV-2 in the UK, Spain, and France Transmissions among this cluster occurred at a ski ... ...

Abstract	Almost half of the confirmed COVID-19 cases detected so far in the United Kingdom are part of a large cluster of 13 British nationals who tested positive for SARS-CoV-2 in the UK, Spain, and France Transmissions among this cluster occurred at a ski resort in France, and originated from a single infected traveller returning from a conference in Singapore where he acquired the virus At least 21 individuals were exposed to the virus, tested, and quarantined, with 13 of those testing positive between the period of 6th February and 15th February Here, all publicly available information about the primarily UK/France cluster is consolidated, providing a complete and accessible summary of the cases and their connections Notable in this cluster are the number of individuals infected, the apparent absence of any severe illness among those infected, and a case of a "delayed positive" test during isolation after initially testing negative, at least 7 days after last possible contact
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #10337
Database	COVID19

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Article ; Online: Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: phylogenetic analysis and intervention scenarios

Reichmuth, Martina / Hodcroft, Emma B / Althaus, Christian L

medRxiv

Abstract	The SARS-CoV-2 pandemic has led to the emergence of various variants of concern (VoCs) that are associated with increased transmissibility, immune evasion, or differences in disease severity. The emergence of VoCs fueled interest in understanding the potential impact of travel restrictions and surveillance strategies to prevent or delay the early spread of VoCs. We performed phylogenetic analyses and mathematical modeling to study the importation and spread of the VoCs Alpha and Delta in Switzerland in 2020 and 2021. Using a phylogenetic approach, we estimated 383-1,038 imports of Alpha and 455-1,347 imports of Delta into Switzerland. We then used the results from the phylogenetic analysis to parameterize a dynamic transmission that accurately described the subsequent spread of Alpha and Delta. We modeled different counterfactual intervention scenarios to quantify the potential impact of border closures and surveillance of travelers on the spread of Alpha and Delta. We found that implementing border closures after the announcement of VoCs would have been of limited impact to mitigate the spread of VoCs. In contrast, increased surveillance of travelers could prove to be an effective measure for delaying the spread of VoCs in situations where their severity remains unclear. Our study shows how phylogenetic analysis in combination with dynamic transmission models can be used to estimate the number of imported SARS-CoV-2 variants and the potential impact of different intervention scenarios to inform the public health response during the pandemic.
Keywords	covid19
Language	English
Publishing date	2023-03-17
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.03.13.23287198
Database	COVID19

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Article ; Online: Impact of cross-border-associated cases on the SARS-CoV-2 epidemic in Switzerland during summer 2020 and 2021.

Reichmuth, Martina L / Hodcroft, Emma B / Riou, Julien / Neher, Richard A / Hens, Niel / Althaus, Christian L

Epidemics

2022 Volume 41, Page(s) 100654

Abstract: During the summers of 2020 and 2021, the number of confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Switzerland remained at relatively low levels, but grew steadily over time. It remains unclear to what extent ...

Abstract	During the summers of 2020 and 2021, the number of confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Switzerland remained at relatively low levels, but grew steadily over time. It remains unclear to what extent epidemic growth during these periods was a result of the relaxation of local control measures or increased traveling and subsequent importation of cases. A better understanding of the role of cross-border-associated cases (imports) on the local epidemic dynamics will help to inform future surveillance strategies. We analyzed routine surveillance data of confirmed cases of SARS-CoV-2 in Switzerland from 1 June to 30 September 2020 and 2021. We used a stochastic branching process model that accounts for superspreading of SARS-CoV-2 to simulate epidemic trajectories in absence and in presence of imports during summer 2020 and 2021. The Swiss Federal Office of Public Health reported 22,919 and 145,840 confirmed cases of SARS-CoV-2 from 1 June to 30 September 2020 and 2021, respectively. Among cases with known place of exposure, 27% (3,276 of 12,088) and 25% (1,110 of 4,368) reported an exposure abroad in 2020 and 2021, respectively. Without considering the impact of imported cases, the steady growth of confirmed cases during summer periods would be consistent with a value of R
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/epidemiology ; Epidemics ; Travel ; Public Health ; Switzerland/epidemiology
Language	English
Publishing date	2022-11-17
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2467993-8
ISSN	1878-0067 ; 1755-4365
ISSN (online)	1878-0067
ISSN	1755-4365
DOI	10.1016/j.epidem.2022.100654
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Article ; Online: Understanding disclosed and cryptic HIV transmission risk via genetic analysis: what are we missing and when does it matter?

Ragonnet-Cronin, Manon / Hodcroft, Emma B / Wertheim, Joel O

Current opinion in HIV and AIDS

2019 Volume 14, Issue 3, Page(s) 205–212

Abstract: Purpose of review: To discuss the recent HIV phylogenetic analyses examining HIV transmission patterns among and within risk groups.: Recent findings: Phylodynamic analysis has recently been applied to multiple HIV outbreaks among people who inject ... ...

Abstract	Purpose of review: To discuss the recent HIV phylogenetic analyses examining HIV transmission patterns among and within risk groups. Recent findings: Phylodynamic analysis has recently been applied to multiple HIV outbreaks among people who inject drugs to determine whether HIV transmission is ongoing. Large-scale analyses of datasets of HIV sequences collected for drug-resistance testing provide population-level insights into transmission patterns. One focus across world regions has been to investigate whether age-disparity is a driver of HIV transmission. In sub-Saharan Africa, researchers have examined transmission between heterosexuals and MSM and between high prevalence fishing communities and inland communities. In the US and the UK, cryptic risk groups such as nondisclosed MSM and the partners of transgender women are increasingly being uncovered based on their position in densely sampled molecular transmission networks. Summary: Analysis of HIV genetic sequence can resolve viral transmission patterns between risk groups at unprecedented scales and levels of detail. Future research should focus on understanding the effect of missing data on inferences and the biases of different methods. Uncovering groups and patterns obscured from traditional epidemiolocal analyses is exciting but should not compromise the privacy of the groups in question.
MeSH term(s)	Female ; Genotype ; HIV/classification ; HIV/genetics ; HIV/isolation & purification ; HIV/physiology ; HIV Infections/psychology ; HIV Infections/transmission ; HIV Infections/virology ; Homosexuality, Male/statistics & numerical data ; Humans ; Male ; Phylogeny ; Risk Factors
Language	English
Publishing date	2019-04-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Review
ZDB-ID	2502511-9
ISSN	1746-6318 ; 1746-630X
ISSN (online)	1746-6318
ISSN	1746-630X
DOI	10.1097/COH.0000000000000537
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