MOOD project is at the forefront of European research of infectious disease surveillance and modelling from a data science perspective, investigating the impact of global warming on disease outbreaks, and proposing innovations for building of One Health systems across Europe and the world.
In the table below all publications to which the MOOD project contributed are listed. Use the filter to select the most relevant articles.
101.
Domenico, Laura Di
Adherence and sustainability of interventions informing optimal control against the COVID-19 pandemic Journal Article
In: Nature Communications, vol. 1, no. 57, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Adherence and sustainability of interventions informing optimal control against the COVID-19 pandemic},
author = {Laura Di Domenico et al.},
url = {https://www.nature.com/articles/s43856-021-00057-5},
doi = {10.1038/s43856-021-00057-5},
year = {2021},
date = {2021-12-06},
urldate = {2021-12-06},
journal = {Nature Communications},
volume = {1},
number = {57},
abstract = {After one year of stop-and-go COVID-19 mitigation, in the spring of 2021 European countries still experienced sustained viral circulation due to the Alpha variant. As the prospect of entering a new pandemic phase through vaccination was drawing closer, a key challenge remained on how to balance the efficacy of long-lasting interventions and their impact on the quality of life.
We show that moderate interventions would require a much longer time to achieve the same result as high intensity lockdowns, with the additional risk of deteriorating control as adherence wanes. Shorter strict lockdowns are largely more effective than longer moderate lockdowns, for similar intermediate distress and infringement on individual freedom.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
After one year of stop-and-go COVID-19 mitigation, in the spring of 2021 European countries still experienced sustained viral circulation due to the Alpha variant. As the prospect of entering a new pandemic phase through vaccination was drawing closer, a key challenge remained on how to balance the efficacy of long-lasting interventions and their impact on the quality of life.
We show that moderate interventions would require a much longer time to achieve the same result as high intensity lockdowns, with the additional risk of deteriorating control as adherence wanes. Shorter strict lockdowns are largely more effective than longer moderate lockdowns, for similar intermediate distress and infringement on individual freedom.
We show that moderate interventions would require a much longer time to achieve the same result as high intensity lockdowns, with the additional risk of deteriorating control as adherence wanes. Shorter strict lockdowns are largely more effective than longer moderate lockdowns, for similar intermediate distress and infringement on individual freedom.
102.
Cereda, Danilo; Manica, Mattia; Tirani, Marcello; Rovida, Francesca; Demicheli, Vittorio; Ajelli, Marco; Poletti, Piero; Trentini, Filippo; Guzzetta, Giorgio; Marziano, Valentina; Piccarreta, Raffaella; Barone, Antonio; Magoni, Michele; Deandrea, Silvia; Diurno, Giulio; Lombardo, Massimo; Faccini, Marino; Pan, Angelo; Bruno, Raffaele; Pariani, Elena; Grasselli, Giacomo; Piatti, Alessandra; Gramegna, Maria; Baldanti, Fausto; Melegaro, Alessia; Merler, Stefano
The early phase of the COVID-19 epidemic in Lombardy, Italy Journal Article
In: Epidemics, vol. 37, pp. 100528, 2021, ISSN: 1755-4365.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{@article{CEREDA2021100528,,
title = {The early phase of the COVID-19 epidemic in Lombardy, Italy},
author = {Danilo Cereda and Mattia Manica and Marcello Tirani and Francesca Rovida and Vittorio Demicheli and Marco Ajelli and Piero Poletti and Filippo Trentini and Giorgio Guzzetta and Valentina Marziano and Raffaella Piccarreta and Antonio Barone and Michele Magoni and Silvia Deandrea and Giulio Diurno and Massimo Lombardo and Marino Faccini and Angelo Pan and Raffaele Bruno and Elena Pariani and Giacomo Grasselli and Alessandra Piatti and Maria Gramegna and Fausto Baldanti and Alessia Melegaro and Stefano Merler},
url = {https://www.sciencedirect.com/science/article/pii/S1755436521000724},
doi = {https://doi.org/10.1016/j.epidem.2021.100528},
issn = {1755-4365},
year = {2021},
date = {2021-12-01},
urldate = {2021-12-01},
journal = {Epidemics},
volume = {37},
pages = {100528},
abstract = {Background
In the night of February 20, 2020, the first epidemic of the novel coronavirus disease (COVID-19) outside Asia was uncovered by the identification of its first patient in Lombardy region, Italy. In the following weeks, Lombardy experienced a sudden increase in the number of ascertained infections and strict measures were imposed to contain the epidemic spread.
Methods
We analyzed official records of cases occurred in Lombardy to characterize the epidemiology of SARS-CoV-2 during the early phase of the outbreak. A line list of laboratory-confirmed cases was set up and later retrospectively consolidated, using standardized interviews to ascertained cases and their close contacts. We provide estimates of the serial interval, of the basic reproduction number, and of the temporal variation of the net reproduction number of SARS-CoV-2.
Results
Epidemiological investigations detected over 500 cases (median age: 69, IQR: 57–78) before the first COVID-19 diagnosed patient (February 20, 2020), and suggested that SARS-CoV-2 was already circulating in at least 222 out of 1506 (14.7%) municipalities with sustained transmission across all the Lombardy provinces. We estimated the mean serial interval to be 6.6 days (95% CrI, 0.7–19). Our estimates of the basic reproduction number range from 2.6 in Pavia (95% CI, 2.1–3.2) to 3.3 in Milan (95% CI, 2.9–3.8). A decreasing trend in the net reproduction number was observed following the detection of the first case.
Conclusions
At the time of first case notification, COVID-19 was already widespread in the entire Lombardy region. This may explain the large number of critical cases experienced by this region in a very short timeframe. The slight decrease of the reproduction number observed in the early days after February 20, 2020 might be due to increased population awareness and early interventions implemented before the regional lockdown imposed on March 8, 2020.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Background
In the night of February 20, 2020, the first epidemic of the novel coronavirus disease (COVID-19) outside Asia was uncovered by the identification of its first patient in Lombardy region, Italy. In the following weeks, Lombardy experienced a sudden increase in the number of ascertained infections and strict measures were imposed to contain the epidemic spread.
Methods
We analyzed official records of cases occurred in Lombardy to characterize the epidemiology of SARS-CoV-2 during the early phase of the outbreak. A line list of laboratory-confirmed cases was set up and later retrospectively consolidated, using standardized interviews to ascertained cases and their close contacts. We provide estimates of the serial interval, of the basic reproduction number, and of the temporal variation of the net reproduction number of SARS-CoV-2.
Results
Epidemiological investigations detected over 500 cases (median age: 69, IQR: 57–78) before the first COVID-19 diagnosed patient (February 20, 2020), and suggested that SARS-CoV-2 was already circulating in at least 222 out of 1506 (14.7%) municipalities with sustained transmission across all the Lombardy provinces. We estimated the mean serial interval to be 6.6 days (95% CrI, 0.7–19). Our estimates of the basic reproduction number range from 2.6 in Pavia (95% CI, 2.1–3.2) to 3.3 in Milan (95% CI, 2.9–3.8). A decreasing trend in the net reproduction number was observed following the detection of the first case.
Conclusions
At the time of first case notification, COVID-19 was already widespread in the entire Lombardy region. This may explain the large number of critical cases experienced by this region in a very short timeframe. The slight decrease of the reproduction number observed in the early days after February 20, 2020 might be due to increased population awareness and early interventions implemented before the regional lockdown imposed on March 8, 2020.
In the night of February 20, 2020, the first epidemic of the novel coronavirus disease (COVID-19) outside Asia was uncovered by the identification of its first patient in Lombardy region, Italy. In the following weeks, Lombardy experienced a sudden increase in the number of ascertained infections and strict measures were imposed to contain the epidemic spread.
Methods
We analyzed official records of cases occurred in Lombardy to characterize the epidemiology of SARS-CoV-2 during the early phase of the outbreak. A line list of laboratory-confirmed cases was set up and later retrospectively consolidated, using standardized interviews to ascertained cases and their close contacts. We provide estimates of the serial interval, of the basic reproduction number, and of the temporal variation of the net reproduction number of SARS-CoV-2.
Results
Epidemiological investigations detected over 500 cases (median age: 69, IQR: 57–78) before the first COVID-19 diagnosed patient (February 20, 2020), and suggested that SARS-CoV-2 was already circulating in at least 222 out of 1506 (14.7%) municipalities with sustained transmission across all the Lombardy provinces. We estimated the mean serial interval to be 6.6 days (95% CrI, 0.7–19). Our estimates of the basic reproduction number range from 2.6 in Pavia (95% CI, 2.1–3.2) to 3.3 in Milan (95% CI, 2.9–3.8). A decreasing trend in the net reproduction number was observed following the detection of the first case.
Conclusions
At the time of first case notification, COVID-19 was already widespread in the entire Lombardy region. This may explain the large number of critical cases experienced by this region in a very short timeframe. The slight decrease of the reproduction number observed in the early days after February 20, 2020 might be due to increased population awareness and early interventions implemented before the regional lockdown imposed on March 8, 2020.
103.
Pullano, Giulia; Domenico, Laura Di; Colizza, Vittoria
Telework and other measures reducing the presence at work to slow down COVID-19pdm in France (Sept 2020) Technical Report
2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@techreport{nokey,
title = {Telework and other measures reducing the presence at work to slow down COVID-19pdm in France (Sept 2020)},
author = {Giulia Pullano and Laura Di Domenico and Vittoria Colizza},
url = {http://www.epicx-lab.com/uploads/9/6/9/4/9694133/inserm_covid-19-telework.pdf},
year = {2021},
date = {2021-11-28},
urldate = {2021-11-28},
abstract = {COVID-19 pandemic shows a clear and substantial increase of activity in France since summer 2020.
Certain regions are in highly vulnerable situations, with large number of hospitalizations per day,
important fraction of ICU beds occupied, and short doubling times (<2 weeks). At the same time,
activities are increasing since the beginning of September, with the reopening of schools and the return
to work after summer holidays (not yet reaching pre-pandemic levels), leaving further opportunities for
the virus to spread. Using mathematical models calibrated to the observed epidemic trajectory in each
region, this report analyzes possible scenarios of telework and other means to reduce the presence at
work, and assesses their impact on the epidemic trajectory in the following weeks. Numerical results
confirm that telework and other measures reducing the presence at work under realistic assumptions
may decelerate the epidemic curve gaining few weeks of time, but would not be enough to revert the
increasing tendency of the curve, unless coupled with other contact reduction measures. The situation is
particularly critical in IDF. In these conditions, if nothing changes, the level of hospitalizations of the peak
of the first wave is expected to be reached in IDF in about a month from now (earlier, if return to work
increases in the following weeks as suggested by the trend in the data and if not contrasted by telework).
Explicit guidance on telework and interventions to facilitate its application to all professional categories
who can adopt it should be urgently provided. This standard should be kept as a routine measure of
epidemic control for several months. More restrictive measures involving the closure of certain activities
to reduce avoidable contacts are urgently needed to slow down the epidemic increase to levels that are
manageable by the healthcare system. This analysis cannot account for the effect of the measures
implemented today},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {techreport}
}
COVID-19 pandemic shows a clear and substantial increase of activity in France since summer 2020.
Certain regions are in highly vulnerable situations, with large number of hospitalizations per day,
important fraction of ICU beds occupied, and short doubling times (<2 weeks). At the same time,
activities are increasing since the beginning of September, with the reopening of schools and the return
to work after summer holidays (not yet reaching pre-pandemic levels), leaving further opportunities for
the virus to spread. Using mathematical models calibrated to the observed epidemic trajectory in each
region, this report analyzes possible scenarios of telework and other means to reduce the presence at
work, and assesses their impact on the epidemic trajectory in the following weeks. Numerical results
confirm that telework and other measures reducing the presence at work under realistic assumptions
may decelerate the epidemic curve gaining few weeks of time, but would not be enough to revert the
increasing tendency of the curve, unless coupled with other contact reduction measures. The situation is
particularly critical in IDF. In these conditions, if nothing changes, the level of hospitalizations of the peak
of the first wave is expected to be reached in IDF in about a month from now (earlier, if return to work
increases in the following weeks as suggested by the trend in the data and if not contrasted by telework).
Explicit guidance on telework and interventions to facilitate its application to all professional categories
who can adopt it should be urgently provided. This standard should be kept as a routine measure of
epidemic control for several months. More restrictive measures involving the closure of certain activities
to reduce avoidable contacts are urgently needed to slow down the epidemic increase to levels that are
manageable by the healthcare system. This analysis cannot account for the effect of the measures
implemented today
Certain regions are in highly vulnerable situations, with large number of hospitalizations per day,
important fraction of ICU beds occupied, and short doubling times (<2 weeks). At the same time,
activities are increasing since the beginning of September, with the reopening of schools and the return
to work after summer holidays (not yet reaching pre-pandemic levels), leaving further opportunities for
the virus to spread. Using mathematical models calibrated to the observed epidemic trajectory in each
region, this report analyzes possible scenarios of telework and other means to reduce the presence at
work, and assesses their impact on the epidemic trajectory in the following weeks. Numerical results
confirm that telework and other measures reducing the presence at work under realistic assumptions
may decelerate the epidemic curve gaining few weeks of time, but would not be enough to revert the
increasing tendency of the curve, unless coupled with other contact reduction measures. The situation is
particularly critical in IDF. In these conditions, if nothing changes, the level of hospitalizations of the peak
of the first wave is expected to be reached in IDF in about a month from now (earlier, if return to work
increases in the following weeks as suggested by the trend in the data and if not contrasted by telework).
Explicit guidance on telework and interventions to facilitate its application to all professional categories
who can adopt it should be urgently provided. This standard should be kept as a routine measure of
epidemic control for several months. More restrictive measures involving the closure of certain activities
to reduce avoidable contacts are urgently needed to slow down the epidemic increase to levels that are
manageable by the healthcare system. This analysis cannot account for the effect of the measures
implemented today
104.
Pullano, Giulia; Domenico, Laura Di; Sabbatini, Chiara E.; Colizza, Vittoria
Expected impact of exit strategies after the second lockdown - France, Nov 2020 Technical Report
2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@techreport{nokey,
title = {Expected impact of exit strategies after the second lockdown - France, Nov 2020},
author = {Giulia Pullano and Laura Di Domenico and Chiara E. Sabbatini and Vittoria Colizza},
url = {https://www.epicx-lab.com/uploads/9/6/9/4/9694133/inserm_covid-19-lockdown_schools_open-20201117.pdf},
year = {2021},
date = {2021-11-17},
urldate = {2021-11-17},
abstract = {This report is an update of previous reports (Report #19, Report #21) on the expected impact of the
second lockdown implemented in France on Friday, October 30 to suppress the second wave of COVID-19
epidemic. We provide updated projections simulating a mild lockdown with schools open informed on the
estimates on mobility reduction recorded during the first week of lockdown from mobile phone data
(Report #22), and explore different exit strategies. The current report focuses on Île-de-France; analyses
for other regions will follow. },
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {techreport}
}
This report is an update of previous reports (Report #19, Report #21) on the expected impact of the
second lockdown implemented in France on Friday, October 30 to suppress the second wave of COVID-19
epidemic. We provide updated projections simulating a mild lockdown with schools open informed on the
estimates on mobility reduction recorded during the first week of lockdown from mobile phone data
(Report #22), and explore different exit strategies. The current report focuses on Île-de-France; analyses
for other regions will follow.
second lockdown implemented in France on Friday, October 30 to suppress the second wave of COVID-19
epidemic. We provide updated projections simulating a mild lockdown with schools open informed on the
estimates on mobility reduction recorded during the first week of lockdown from mobile phone data
(Report #22), and explore different exit strategies. The current report focuses on Île-de-France; analyses
for other regions will follow.
105.
Kraemer, Moritz U. G.; Fraser, Oliver G. Pybusand; Cauchemez, Christophe; Rambaut, Simon; Cowling, Andrew; Benjamin, J.
Monitoring key epidemiological parameters of SARS-CoV-2 transmission Journal Article
In: Nature Medicine, vol. 27, no. 1854–1855 , pp. 1–2, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{kraemer2021monitoring,
title = {Monitoring key epidemiological parameters of SARS-CoV-2 transmission},
author = {Moritz U.G. Kraemer and Oliver G. Pybusand Fraser and Christophe Cauchemez and Simon Rambaut and Andrew Cowling and J. Benjamin},
doi = {https://doi.org/10.1038/s41591-021-01545-w},
year = {2021},
date = {2021-11-08},
urldate = {2021-11-08},
journal = {Nature Medicine},
volume = {27},
number = {1854–1855 },
pages = {1--2},
abstract = {Control of the SARS-CoV-2 pandemic requires targeted interventions, which in turn require precise estimates of quantities that describe transmission. Per-capita transmission rates are influenced by four quantities: (1) the latent period (time from infection to becoming infectious); (2) individual variability in infectiousness (defined by variation in intrinsic transmissibility and contact rate); (3) the incubation period (time from infection to symptom onset); and (4) the serial interval (time between symptom onset of an infector and an infected) (Fig. 1).},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
Control of the SARS-CoV-2 pandemic requires targeted interventions, which in turn require precise estimates of quantities that describe transmission. Per-capita transmission rates are influenced by four quantities: (1) the latent period (time from infection to becoming infectious); (2) individual variability in infectiousness (defined by variation in intrinsic transmissibility and contact rate); (3) the incubation period (time from infection to symptom onset); and (4) the serial interval (time between symptom onset of an infector and an infected) (Fig. 1).
106.
Camille, Schaeffer; Roberto, Interdonato; Lancelot, Renaud; Roche, Mathieu; Teisseire, Maguelonne.
Social network data and epidemiological intelligence: A case study of avian influenza Conference
vol. 116, 2021.
Abstract | BibTeX | Tags: HPAI (Avian Influenza)
@conference{nokey,
title = {Social network data and epidemiological intelligence: A case study of avian influenza},
author = {Schaeffer Camille and Interdonato Roberto and Lancelot, Renaud and Roche, Mathieu and Teisseire, Maguelonne.},
year = {2021},
date = {2021-11-06},
urldate = {2021-11-06},
journal = {International Journal of Infectious Diseases},
volume = {116},
pages = {99},
abstract = {Event Based Surveillance (EBS) systems detect and monitor diseases by analysing articles from online newspapers and reports from health organizations (e.g. FAO, OIE, etc.). However, they partially integrate data from social networks, even though these data are present in large quantities on the web. The purpose of this study is to exploit social network data, such as Twitter and YouTube, to provide epidemiological and additional information for Avian Influenza surveillance.},
keywords = {HPAI (Avian Influenza)},
pubstate = {published},
tppubtype = {conference}
}
Event Based Surveillance (EBS) systems detect and monitor diseases by analysing articles from online newspapers and reports from health organizations (e.g. FAO, OIE, etc.). However, they partially integrate data from social networks, even though these data are present in large quantities on the web. The purpose of this study is to exploit social network data, such as Twitter and YouTube, to provide epidemiological and additional information for Avian Influenza surveillance.
107.
Syed, Mehtab Alam; Decoupes, Remy; Arsevska, Elena; Roche, Mathieu; Teisseire, Maguelonne
Spatial opinion mining from COVID-19 twitter data Journal Article
In: International Journal of Infectious Diseases, vol. 116, iss. 549, pp. 527, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), Text mining
@article{nokey,
title = {Spatial opinion mining from COVID-19 twitter data},
author = {Mehtab Alam Syed and Remy Decoupes and Elena Arsevska and Mathieu Roche and Maguelonne Teisseire},
url = {https://www.ijidonline.com/article/S1201-9712(21)00957-7/pdf},
doi = {https://doi.org/10.1016/j.ijid.2021.12.065},
year = {2021},
date = {2021-11-06},
urldate = {2021-11-06},
journal = {International Journal of Infectious Diseases},
volume = {116},
issue = {549},
pages = {527},
abstract = {: In the first quarter of 2020, World Health Organization (WHO) declared COVID-19 as a public health emergency around the globe. Therefore, different users from all over the world shared their thoughts about COVID-19 on social media platforms i.e., Twitter, Facebook etc. So, it is important to analyze public opinions about COVID-19 from different regions over different period of time. To fulfill the spatial analysis issue, a previous work called H-TF-IDF (Hierarchy-based measure for tweet analysis) for term extraction from tweet data has been proposed. In this work, we focus on the sentiment analysis performed on terms selected by H-TFIDF for spatial tweets groups to know local situations during the ongoing epidemic COVID-19 over different time frames.},
keywords = {Covid-19 (Coronavirus), Text mining},
pubstate = {published},
tppubtype = {article}
}
: In the first quarter of 2020, World Health Organization (WHO) declared COVID-19 as a public health emergency around the globe. Therefore, different users from all over the world shared their thoughts about COVID-19 on social media platforms i.e., Twitter, Facebook etc. So, it is important to analyze public opinions about COVID-19 from different regions over different period of time. To fulfill the spatial analysis issue, a previous work called H-TF-IDF (Hierarchy-based measure for tweet analysis) for term extraction from tweet data has been proposed. In this work, we focus on the sentiment analysis performed on terms selected by H-TFIDF for spatial tweets groups to know local situations during the ongoing epidemic COVID-19 over different time frames.
108.
Faria, Nuno R.; Mellan, Thomas A.; Whittaker, Charles; Claro, Ingra M.; da S. Candido, Darlan; Mishra, Swapnil; Crispim, Myuki A. E.
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil Journal Article
In: Science, vol. 372, no. 6544, pp. 815-821, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil},
author = {Nuno R. Faria and Thomas A. Mellan and Charles Whittaker and Ingra M. Claro and Darlan da S. Candido and Swapnil Mishra and Myuki A. E. Crispim},
url = {https://www.science.org/doi/abs/10.1126/science.abh2644},
doi = {10.1126/science.abh2644},
year = {2021},
date = {2021-11-01},
urldate = {2021-11-01},
journal = {Science},
volume = {372},
number = {6544},
pages = {815-821},
abstract = {Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
109.
Hu, Maogui
Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Among Air Passengers in China Journal Article
In: Clinical Infectious Diseases, vol. 75, iss. 1, pp. e234–e240, 2021, ISSN: 1058-4838.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{@article{10.1093/cid/ciab836,,
title = {Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Among Air Passengers in China },
author = {Maogui Hu et al.},
url = {https://academic.oup.com/cid/article/75/1/e234/6373518},
doi = {https://doi.org/10.1093/cid/ciab836},
issn = {1058-4838},
year = {2021},
date = {2021-09-21},
urldate = {2021-09-21},
journal = {Clinical Infectious Diseases},
volume = {75},
issue = {1},
pages = {e234–e240},
abstract = {Modern transportation plays a key role in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and new variants. However, little is known about the exact transmission risk of the virus on airplanes.Using the itinerary and epidemiological data of coronavirus disease 2019 (COVID-19) cases and close contacts on domestic airplanes departing from Wuhan city in China before the lockdown on 23 January 2020, we estimated the upper and lower bounds of overall transmission risk of COVID-19 among travelers.In total, 175 index cases were identified among 5797 passengers on 177 airplanes. The upper and lower attack rates (ARs) of a seat were 0.60% (34/5622, 95% confidence interval [CI] .43–.84%) and 0.33% (18/5400, 95% CI .21–.53%), respectively. In the upper- and lower-bound risk estimates, each index case infected 0.19 (SD 0.45) and 0.10 (SD 0.32) cases, respectively. The seats immediately adjacent to the index cases had an AR of 9.2% (95% CI 5.7–14.4%), with a relative risk 27.8 (95% CI 14.4–53.7) compared to other seats in the upper limit estimation. The middle seat had the highest AR (0.7%, 95% CI .4%–1.2%). The upper-bound AR increased from 0.7% (95% CI 0.5%–1.0%) to 1.2% (95% CI .4–3.3%) when the co-travel time increased from 2.0 hours to 3.3 hours.The ARs among travelers varied by seat distance from the index case and joint travel time, but the variation was not significant between the types of aircraft. The overall risk of SARS-CoV-2 transmission during domestic travel on planes was relatively low. These findings can improve our understanding of COVID-19 spread during travel and inform response efforts in the pandemic.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Modern transportation plays a key role in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and new variants. However, little is known about the exact transmission risk of the virus on airplanes.Using the itinerary and epidemiological data of coronavirus disease 2019 (COVID-19) cases and close contacts on domestic airplanes departing from Wuhan city in China before the lockdown on 23 January 2020, we estimated the upper and lower bounds of overall transmission risk of COVID-19 among travelers.In total, 175 index cases were identified among 5797 passengers on 177 airplanes. The upper and lower attack rates (ARs) of a seat were 0.60% (34/5622, 95% confidence interval [CI] .43–.84%) and 0.33% (18/5400, 95% CI .21–.53%), respectively. In the upper- and lower-bound risk estimates, each index case infected 0.19 (SD 0.45) and 0.10 (SD 0.32) cases, respectively. The seats immediately adjacent to the index cases had an AR of 9.2% (95% CI 5.7–14.4%), with a relative risk 27.8 (95% CI 14.4–53.7) compared to other seats in the upper limit estimation. The middle seat had the highest AR (0.7%, 95% CI .4%–1.2%). The upper-bound AR increased from 0.7% (95% CI 0.5%–1.0%) to 1.2% (95% CI .4–3.3%) when the co-travel time increased from 2.0 hours to 3.3 hours.The ARs among travelers varied by seat distance from the index case and joint travel time, but the variation was not significant between the types of aircraft. The overall risk of SARS-CoV-2 transmission during domestic travel on planes was relatively low. These findings can improve our understanding of COVID-19 spread during travel and inform response efforts in the pandemic.
110.
Martin, Darren P; Weaver, Steven; Tegally, Houryiah; San, Emmanuel James; Shank, Stephen D; Wilkinson, Eduan; Giandhari, Jennifer; Naidoo, Sureshnee; Pillay, Yeshnee; Singh, Lavanya; Lessells, Richard J; NGS-SA,; (COG-UK), COVID-19 Genomics UK; Gupta, Ravindra K; Wertheim, Joel O; Nekturenko, Anton; Murrell, Ben; Harkins, Gordon W; Lemey, Philippe; MacLean, Oscar A; Robertson, David L; de Oliveira, Tulio; Pond, Sergei L Kosakovsky
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages Bachelor Thesis
2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@bachelorthesis{nokey,
title = {The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages},
author = {Darren P Martin and Steven Weaver and Houryiah Tegally and Emmanuel James San and Stephen D Shank and Eduan Wilkinson and Jennifer Giandhari and Sureshnee Naidoo and Yeshnee Pillay and Lavanya Singh and Richard J Lessells and NGS-SA and COVID-19 Genomics UK (COG-UK) and Ravindra K Gupta and Joel O Wertheim and Anton Nekturenko and Ben Murrell and Gordon W Harkins and Philippe Lemey and Oscar A MacLean and David L Robertson and Tulio de Oliveira and Sergei L Kosakovsky Pond},
url = {https://doi.org/10.1016/j.cell.2021.09.003},
doi = {10.1016/j.cell.2021.09.003},
year = {2021},
date = {2021-09-06},
urldate = {2021-09-06},
journal = {Cell},
volume = {184},
issue = {20},
abstract = {The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three “501Y lineages” coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {bachelorthesis}
}
The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three “501Y lineages” coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.
111.
Mazzoli, Mattia; Valdano, Eugenio; Colizza, Vittoria
Projecting the COVID-19 epidemic risk in France for the summer 2021 Journal Article
In: Journal of Travel Medicine, vol. 28, no. 7, 2021, ISSN: 1708-8305.
Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{@article{10.1093/jtm/taab129,
title = {Projecting the COVID-19 epidemic risk in France for the summer 2021},
author = {Mattia Mazzoli and Eugenio Valdano and Vittoria Colizza},
url = {https://academic.oup.com/jtm/article-pdf/28/7/taab129/41784325/taab129.pdf},
doi = {https://doi.org/10.1093/jtm/taab129},
issn = {1708-8305},
year = {2021},
date = {2021-08-19},
urldate = {2021-08-19},
journal = {Journal of Travel Medicine},
volume = {28},
number = {7},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
112.
Domenico, Laura Di; Colizza, Vittoria
Epidemic scenarios of Delta variant in France in the summer 2021 Technical Report
2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@techreport{nokey,
title = {Epidemic scenarios of Delta variant in France in the summer 2021},
author = {Laura Di Domenico and Vittoria Colizza},
url = {https://www.epicx-lab.com/uploads/9/6/9/4/9694133/inserm-covid-19-delta_projections_summer-20210710.pdf},
year = {2021},
date = {2021-07-10},
urldate = {2021-07-10},
abstract = {As the Delta variant rapidly progresses in France, with an estimated 43.2% of detected cases attributed to the L452R mutation in the week 26, concerns arise on the upcoming summer epidemic situation, also given the reported slowdown of vaccinations. This short report aims at presenting a range of possible epidemic scenarios, according to different hypotheses on vaccine administration rollout in the summer, conditions of mixing, seasonality and preventive measures, and considering different estimates for the transmissibility advantages of the circulating variants of concern. },
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {techreport}
}
As the Delta variant rapidly progresses in France, with an estimated 43.2% of detected cases attributed to the L452R mutation in the week 26, concerns arise on the upcoming summer epidemic situation, also given the reported slowdown of vaccinations. This short report aims at presenting a range of possible epidemic scenarios, according to different hypotheses on vaccine administration rollout in the summer, conditions of mixing, seasonality and preventive measures, and considering different estimates for the transmissibility advantages of the circulating variants of concern.
113.
Manica, Mattia; Pancheri, Serena; Poletti, Piero; Giovanazzi, Giulia; Guzzetta, Giorgio; Trentini, Filippo; Marziano, Valentina; Ajelli, Marco; Zuccali, Maria Grazia; Benetollo, Pier Paolo; Merler, Stefano; Ferro, Antonio
In: Clinical Infectious Diseases, vol. 74, no. 5, pp. 893-896, 2021, ISSN: 1058-4838.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{nokey,
title = {Risk of Symptomatic Infection During a Second Coronavirus Disease 2019 Wave in Severe Acute Respiratory Syndrome Coronavirus 2–Seropositive Individuals },
author = {Mattia Manica and Serena Pancheri and Piero Poletti and Giulia Giovanazzi and Giorgio Guzzetta and Filippo Trentini and Valentina Marziano and Marco Ajelli and Maria Grazia Zuccali and Pier Paolo Benetollo and Stefano Merler and Antonio Ferro},
url = {https://academic.oup.com/cid/article/74/5/893/6301134},
doi = {10.1093/cid/ciab556},
issn = {1058-4838},
year = {2021},
date = {2021-06-16},
urldate = {2021-06-16},
journal = {Clinical Infectious Diseases},
volume = {74},
number = {5},
pages = {893-896},
abstract = {We analyzed 221 coronavirus disease 2019 cases identified between June 2020 and January 2021 in 6074 individuals screened for immunoglobulin G antibodies in May 2020, representing 77% of residents of 5 Italian municipalities. The relative risk of developing symptomatic infection in seropositive participants was 0.055 (95% confidence interval, .014–.220)},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
We analyzed 221 coronavirus disease 2019 cases identified between June 2020 and January 2021 in 6074 individuals screened for immunoglobulin G antibodies in May 2020, representing 77% of residents of 5 Italian municipalities. The relative risk of developing symptomatic infection in seropositive participants was 0.055 (95% confidence interval, .014–.220)
114.
Dellicour, Simon; Linard, Catherine; Goethem, Nina Van; Re, Daniele Da; Artois, Jean; Bihin, Jérémie; Schaus, Pierre; Massonnet, François; Oyen, Herman Van; Vanwambeke, Sophie O.; Speybroeck, Niko; Gilbert, Marius
Investigating the drivers of the spatio-temporal heterogeneity in COVID-19 hospital incidence—Belgium as a study case Journal Article
In: International Journal of Health Geographics, iss. 20, no. 29, 2021, ISSN: 1476-072X.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Investigating the drivers of the spatio-temporal heterogeneity in COVID-19 hospital incidence—Belgium as a study case},
author = {Simon Dellicour and Catherine Linard and Nina Van Goethem and Daniele Da Re and Jean Artois and Jérémie Bihin and Pierre Schaus and François Massonnet and Herman Van Oyen and Sophie O. Vanwambeke and Niko Speybroeck and Marius Gilbert },
url = {https://ij-healthgeographics.biomedcentral.com/articles/10.1186/s12942-021-00281-1},
doi = {https://doi.org/10.1186/s12942-021-00281-1},
issn = {1476-072X},
year = {2021},
date = {2021-06-14},
urldate = {2021-06-14},
journal = {International Journal of Health Geographics},
number = {29},
issue = {20},
abstract = {Background
The COVID-19 pandemic is affecting nations globally, but with an impact exhibiting significant spatial and temporal variation at the sub-national level. Identifying and disentangling the drivers of resulting hospitalisation incidence at the local scale is key to predict, mitigate and manage epidemic surges, but also to develop targeted measures. However, this type of analysis is often not possible because of the lack of spatially-explicit health data and spatial uncertainties associated with infection.
Methods
To overcome these limitations, we propose an analytical framework to investigate potential drivers of the spatio–temporal heterogeneity in COVID-19 hospitalisation incidence when data are only available at the hospital level. Specifically, the approach is based on the delimitation of hospital catchment areas, which allows analysing associations between hospitalisation incidence and spatial or temporal covariates. We illustrate and apply our analytical framework to Belgium, a country heavily impacted by two COVID-19 epidemic waves in 2020, both in terms of mortality and hospitalisation incidence.
Results
Our spatial analyses reveal an association between the hospitalisation incidence and the local density of nursing home residents, which confirms the important impact of COVID-19 in elderly communities of Belgium. Our temporal analyses further indicate a pronounced seasonality in hospitalisation incidence associated with the seasonality of weather variables. Taking advantage of these associations, we discuss the feasibility of predictive models based on machine learning to predict future hospitalisation incidence.
Conclusion
Our reproducible analytical workflow allows performing spatially-explicit analyses of data aggregated at the hospital level and can be used to explore potential drivers and dynamic of COVID-19 hospitalisation incidence at regional or national scales.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Background
The COVID-19 pandemic is affecting nations globally, but with an impact exhibiting significant spatial and temporal variation at the sub-national level. Identifying and disentangling the drivers of resulting hospitalisation incidence at the local scale is key to predict, mitigate and manage epidemic surges, but also to develop targeted measures. However, this type of analysis is often not possible because of the lack of spatially-explicit health data and spatial uncertainties associated with infection.
Methods
To overcome these limitations, we propose an analytical framework to investigate potential drivers of the spatio–temporal heterogeneity in COVID-19 hospitalisation incidence when data are only available at the hospital level. Specifically, the approach is based on the delimitation of hospital catchment areas, which allows analysing associations between hospitalisation incidence and spatial or temporal covariates. We illustrate and apply our analytical framework to Belgium, a country heavily impacted by two COVID-19 epidemic waves in 2020, both in terms of mortality and hospitalisation incidence.
Results
Our spatial analyses reveal an association between the hospitalisation incidence and the local density of nursing home residents, which confirms the important impact of COVID-19 in elderly communities of Belgium. Our temporal analyses further indicate a pronounced seasonality in hospitalisation incidence associated with the seasonality of weather variables. Taking advantage of these associations, we discuss the feasibility of predictive models based on machine learning to predict future hospitalisation incidence.
Conclusion
Our reproducible analytical workflow allows performing spatially-explicit analyses of data aggregated at the hospital level and can be used to explore potential drivers and dynamic of COVID-19 hospitalisation incidence at regional or national scales.
The COVID-19 pandemic is affecting nations globally, but with an impact exhibiting significant spatial and temporal variation at the sub-national level. Identifying and disentangling the drivers of resulting hospitalisation incidence at the local scale is key to predict, mitigate and manage epidemic surges, but also to develop targeted measures. However, this type of analysis is often not possible because of the lack of spatially-explicit health data and spatial uncertainties associated with infection.
Methods
To overcome these limitations, we propose an analytical framework to investigate potential drivers of the spatio–temporal heterogeneity in COVID-19 hospitalisation incidence when data are only available at the hospital level. Specifically, the approach is based on the delimitation of hospital catchment areas, which allows analysing associations between hospitalisation incidence and spatial or temporal covariates. We illustrate and apply our analytical framework to Belgium, a country heavily impacted by two COVID-19 epidemic waves in 2020, both in terms of mortality and hospitalisation incidence.
Results
Our spatial analyses reveal an association between the hospitalisation incidence and the local density of nursing home residents, which confirms the important impact of COVID-19 in elderly communities of Belgium. Our temporal analyses further indicate a pronounced seasonality in hospitalisation incidence associated with the seasonality of weather variables. Taking advantage of these associations, we discuss the feasibility of predictive models based on machine learning to predict future hospitalisation incidence.
Conclusion
Our reproducible analytical workflow allows performing spatially-explicit analyses of data aggregated at the hospital level and can be used to explore potential drivers and dynamic of COVID-19 hospitalisation incidence at regional or national scales.
115.
Decoupes, Rémy; Rodrique, Kafando; Roche, Mathieu; Teisseire, Maguelonne
H-TFIDF: What makes areas specific over time in the massive flow of tweets related to the covid pandemic? Journal Article
In: AGILE: GIScience Series, vol. 2, no. 4, pp. 1-8, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{,
title = {H-TFIDF: What makes areas specific over time in the massive flow of tweets related to the covid pandemic?},
author = {Rémy Decoupes and Kafando Rodrique and Mathieu Roche and Maguelonne Teisseire },
doi = {10.5194/agile-giss-2-2-2021},
year = {2021},
date = {2021-06-01},
urldate = {2021-06-01},
journal = {AGILE: GIScience Series},
volume = {2},
number = {4},
pages = {1-8},
publisher = {European Centre for Disease Prevention and Control},
abstract = {Data produced by social networks may contain weak signals of possible epidemic outbreaks. In this paper, we focus on Twitter data during the waiting period before the appearance of COVID-19 first cases outside China. Among the huge flow of tweets that reflects a global growing concern in all countries, we propose to analyze such data with an adaptation of the TF-IDF measure. It allows the users to extract the discriminant vocabularies used across time and space. The results are then discussed to show how the specific spatio-temporal anchoring of the extracted terms make it possible to follow the crisis dynamics on different scales of time and space.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Data produced by social networks may contain weak signals of possible epidemic outbreaks. In this paper, we focus on Twitter data during the waiting period before the appearance of COVID-19 first cases outside China. Among the huge flow of tweets that reflects a global growing concern in all countries, we propose to analyze such data with an adaptation of the TF-IDF measure. It allows the users to extract the discriminant vocabularies used across time and space. The results are then discussed to show how the specific spatio-temporal anchoring of the extracted terms make it possible to follow the crisis dynamics on different scales of time and space.
116.
Domenico, Laura Di; Sabbatini, Chiara E.; Pullano, Giulia; Lévy-Bruhl, Daniel; Colizza, Vittoria
Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France Journal Article
In: Eurosurveillance, vol. 26, iss. 15, no. 2, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{,
title = {Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France},
author = {Laura Di Domenico and Chiara E. Sabbatini and Giulia Pullano and Daniel Lévy-Bruhl and Vittoria Colizza},
url = {https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.15.2100272},
doi = { 10.2807/1560-7917.ES.2021.26.15.2100272},
year = {2021},
date = {2021-04-15},
urldate = {2021-04-15},
journal = {Eurosurveillance},
volume = {26},
number = {2},
issue = {15},
publisher = {Cold Spring Harbor Laboratory Press},
abstract = {Facing B.1.1.7 variant, social distancing was strengthened in France in January 2021. Using a 2-strain mathematical model calibrated on genomic surveillance, we estimated that curfew measures allowed hospitalizations to plateau, by decreasing transmission of the historical strain while B.1.1.7 continued to grow. School holidays appear to have further slowed down progression in February. Without progressively strengthened social distancing, a rapid surge of hospitalizations is expected, despite the foreseen increase in vaccination rhythm.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Facing B.1.1.7 variant, social distancing was strengthened in France in January 2021. Using a 2-strain mathematical model calibrated on genomic surveillance, we estimated that curfew measures allowed hospitalizations to plateau, by decreasing transmission of the historical strain while B.1.1.7 continued to grow. School holidays appear to have further slowed down progression in February. Without progressively strengthened social distancing, a rapid surge of hospitalizations is expected, despite the foreseen increase in vaccination rhythm.
117.
Huang, Bo; Wang, Jionghua; Cai, Jixuan; Yao, Shiqi; Chan, Paul Kay Sheung; Tam, Tony Hong-wing; Hong, Ying-Yi; Ruktanonchai, Corrine W.; Carioli, Alessandra; Floyd, Jessica R.; Ruktanonchai, Nick W.; Yang, Weizhong; Li, Zhongjie; Tatem, Andrew J.; Lai, Shengjie
Integrated vaccination and physical distancing interventions to prevent future COVID-19 waves in Chinese cities Journal Article
In: Nature Human Behaviour, vol. 5, pp. 695–705, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Integrated vaccination and physical distancing interventions to prevent future COVID-19 waves in Chinese cities},
author = {Bo Huang and Jionghua Wang and Jixuan Cai and Shiqi Yao and Paul Kay Sheung Chan and Tony Hong-wing Tam and Ying-Yi Hong and Corrine W. Ruktanonchai and Alessandra Carioli and Jessica R. Floyd and Nick W. Ruktanonchai and Weizhong Yang and Zhongjie Li and Andrew J. Tatem and Shengjie Lai },
doi = {https://doi.org/10.1038/s41562-021-01063-2},
year = {2021},
date = {2021-02-18},
urldate = {2021-02-18},
journal = {Nature Human Behaviour},
volume = {5},
pages = {695–705},
abstract = {The coronavirus disease 2019 (COVID-19) pandemic has posed substantial challenges to the formulation of preventive interventions, particularly since the effects of physical distancing measures and upcoming vaccines on reducing susceptible social contacts and eventually halting transmission remain unclear. Here, using anonymized mobile geolocation data in China, we devise a mobility-associated social contact index to quantify the impact of both physical distancing and vaccination measures in a unified way. Building on this index, our epidemiological model reveals that vaccination combined with physical distancing can contain resurgences without relying on stay-at-home restrictions, whereas a gradual vaccination process alone cannot achieve this. Further, for cities with medium population density, vaccination can reduce the duration of physical distancing by 36% to 78%, whereas for cities with high population density, infection numbers can be well-controlled through moderate physical distancing. These findings improve our understanding of the joint effects of vaccination and physical distancing with respect to a city’s population density and social contact patterns.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
The coronavirus disease 2019 (COVID-19) pandemic has posed substantial challenges to the formulation of preventive interventions, particularly since the effects of physical distancing measures and upcoming vaccines on reducing susceptible social contacts and eventually halting transmission remain unclear. Here, using anonymized mobile geolocation data in China, we devise a mobility-associated social contact index to quantify the impact of both physical distancing and vaccination measures in a unified way. Building on this index, our epidemiological model reveals that vaccination combined with physical distancing can contain resurgences without relying on stay-at-home restrictions, whereas a gradual vaccination process alone cannot achieve this. Further, for cities with medium population density, vaccination can reduce the duration of physical distancing by 36% to 78%, whereas for cities with high population density, infection numbers can be well-controlled through moderate physical distancing. These findings improve our understanding of the joint effects of vaccination and physical distancing with respect to a city’s population density and social contact patterns.
118.
Dellicour, Simon; Gill, Mandev S; Faria, Nuno R; Rambaut, Andrew; Pybus, Oliver G; Suchard, Marc A; Lemey, Philippe
Relax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST Journal Article
In: Molecular Biology and Evolution, vol. 38, iss. 8, 2021, ISSN: 1537-1719.
Abstract | Links | BibTeX | Tags: OpenDataSet
@article{10.1093/molbev/msab031,
title = {Relax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST},
author = {Simon Dellicour and Mandev S Gill and Nuno R Faria and Andrew Rambaut and Oliver G Pybus and Marc A Suchard and Philippe Lemey},
editor = {Rasmus Nielsen},
url = {https://doi.org/10.1093/molbev/msab031},
doi = {10.1093/molbev/msab031},
issn = {1537-1719},
year = {2021},
date = {2021-02-02},
urldate = {2021-02-02},
journal = {Molecular Biology and Evolution},
volume = {38},
issue = {8},
abstract = {Spatially explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented 10 years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyze the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.},
keywords = {OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Spatially explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented 10 years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyze the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.
119.
Marini, Giovanni; Manica, Mattia; Delucchi, Luca; Pugliese, Andrea; Ros`a, Roberto
Spring temperature shapes West Nile virus transmission in Europe Journal Article
In: Acta Tropica, vol. 215, pp. 105796, 2021.
Abstract | Links | BibTeX | Tags: WNV (West Nile Virus)
@article{marini2021spring,
title = {Spring temperature shapes West Nile virus transmission in Europe},
author = {Giovanni Marini and Mattia Manica and Luca Delucchi and Andrea Pugliese and Roberto Ros`a},
doi = {https://doi.org/10.1016/j.actatropica.2020.105796},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Acta Tropica},
volume = {215},
pages = {105796},
publisher = {Elsevier},
abstract = {West Nile Virus (WNV) is now endemic in many European countries, causing hundreds of human cases every year, with a high spatial and temporal heterogeneity. Previous studies have suggested that spring temperature might play a key role at shaping WNV transmission. Specifically, warmer temperatures in April-May might amplify WNV circulation, thus increasing the risk for human transmission later in the year. To test this hypothesis, we collated publicly available data on the number of human infections recorded in Europe between 2011 and 2019. We then applied generalized linear models to quantify the relationship between human cases and spring temperature, considering both average conditions (over years 2003-2010) and deviations from the average for subsequent years (2011-2019). We found a significant positive association both spatial (average conditions) and temporal (deviations). The former indicates that WNV circulation is higher in usually warmer regions while the latter implies a predictive value of spring conditions over the coming season. We also found a positive association with WNV detection during the previous year, which can be interpreted as an indication of the reliability of the surveillance system but also of WNV overwintering capacity. Weather anomalies at the beginning of the mosquito breeding season might act as an early warning signal for public health authorities, enabling them to strengthen in advance ongoing surveillance and prevention strategies.},
keywords = {WNV (West Nile Virus)},
pubstate = {published},
tppubtype = {article}
}
West Nile Virus (WNV) is now endemic in many European countries, causing hundreds of human cases every year, with a high spatial and temporal heterogeneity. Previous studies have suggested that spring temperature might play a key role at shaping WNV transmission. Specifically, warmer temperatures in April-May might amplify WNV circulation, thus increasing the risk for human transmission later in the year. To test this hypothesis, we collated publicly available data on the number of human infections recorded in Europe between 2011 and 2019. We then applied generalized linear models to quantify the relationship between human cases and spring temperature, considering both average conditions (over years 2003-2010) and deviations from the average for subsequent years (2011-2019). We found a significant positive association both spatial (average conditions) and temporal (deviations). The former indicates that WNV circulation is higher in usually warmer regions while the latter implies a predictive value of spring conditions over the coming season. We also found a positive association with WNV detection during the previous year, which can be interpreted as an indication of the reliability of the surveillance system but also of WNV overwintering capacity. Weather anomalies at the beginning of the mosquito breeding season might act as an early warning signal for public health authorities, enabling them to strengthen in advance ongoing surveillance and prevention strategies.
120.
Ingelbeen, Brecht; Peckeu, Laur`ene; Laga, Marie; Hendrix, Ilona; Neven, Inge; Sande, Marianne AB; Kleef, Esther
Reducing contacts to stop SARS-CoV-2 transmission during the second pandemic wave in Brussels, Belgium, August to November 2020 Journal Article
In: Eurosurveillance, vol. 26, no. 7, pp. 2100065, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{ingelbeen2021reducing,
title = {Reducing contacts to stop SARS-CoV-2 transmission during the second pandemic wave in Brussels, Belgium, August to November 2020},
author = {Brecht Ingelbeen and Laur`ene Peckeu and Marie Laga and Ilona Hendrix and Inge Neven and Marianne AB Sande and Esther Kleef},
doi = {https://doi.org/10.1371/journal.pbio.3001115},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Eurosurveillance},
volume = {26},
number = {7},
pages = {2100065},
publisher = {European Centre for Disease Prevention and Control},
abstract = {To evaluate the effect of physical distancing and school reopening in Brussels between August and November 2020, we monitored changes in the number of reported contacts per SARS-CoV-2 case and associated SARS-CoV-2 transmission. The second COVID-19 pandemic wave in Brussels was the result of increased social contact across all ages following school reopening. Physical distancing measures including closure of bars and restaurants, and limiting close contacts, while primary and secondary schools remained open, reduced social mixing and controlled SARS-CoV-2 transmission.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
To evaluate the effect of physical distancing and school reopening in Brussels between August and November 2020, we monitored changes in the number of reported contacts per SARS-CoV-2 case and associated SARS-CoV-2 transmission. The second COVID-19 pandemic wave in Brussels was the result of increased social contact across all ages following school reopening. Physical distancing measures including closure of bars and restaurants, and limiting close contacts, while primary and secondary schools remained open, reduced social mixing and controlled SARS-CoV-2 transmission.