Now 261 confirmed cases of
#Dengue
in Italy of which 49 are locally acquired. New data on where introductions were from included now on the official dashboard:
Using real-time mobility data and detailed case data we elucidate "The effect of human mobility and control measures on the COVID-19 epidemic in China". Out today in
@ScienceMagazine
w/
@svscarpino
@EvolveDotZoo
and many others
Thanks to our LATAM open COVID-19 data working group we have updated our line list for Latin America. This outbreak has been a success in collaboration!
We made a big push updating detailed line-list entries now including ~2.3 million COVID cases. Great to see increasing momentum for open-data sharing across many countries. Thanks to the team and all the volunteers involved. Data for download here:
We continue to curate a global open-access database for
#monkeypox
. A short description of why and how we do that is now published in
@TheLancetInfDis
.
Open-access data here:
Thanks to all the volunteers from around the world we keep a line list of the current COVID-19 pandemic. A full description of methods used are now published in
@ScientificData
(thanks also to
@alhufton
for rapid turnaround). Data:
We are recruiting a 2-3 year Postdoctoral Fellow in Computational Epidemiology
@UniofOxford
@OxZooDept
to work on exciting questions regarding the importation dynamics of infectious diseases. Please share widely and DM or email for more details:
We have added more information to the global B.1.1.7 lineage tracker including travel data from the UK to countries around the world in October 2020 (latest data). See more details here . Will update as new data comes in.
Countries the B.1.1.7 variant has been found in:
UK, Denmark, Singapore, Australia, Netherlands, Sweden, Spain, Switzerland, Lebanon, France, Israel, Italy.
Hard to imagine it has not reached US by this time
Global maps of the past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus driven by accelerated climate change, urbanization and human movements out today in
@NatureMicrobiol
Free to read here:
and
Very insightful piece by
@sciencecohen
in
@ScienceMagazine
News on the ongoing spread of bird flu in the US with specific mention of South-North movements of cattle at this time of year, coinciding with bird movements (see below)?
We have collected and tabulated epidemiological data from the ongoing nCoV-2019 outbreak. Data in link to download. We will regularly update. Please DM and get in touch if you have any additional information.
Some countries now reporting cases of B.1.1.529 (Israel, Botswana, SA, HK, maybe Malawi; ). Likely many more countries will be reporting cases soon looking at passenger flight data out of JNB.
As of 2022-05-19 5pm, we counted 75 suspected and confirmed cases reported across 7 countries. Curious that there are a few with symptom onset date in late April.
Outbreaks of
#monkeypox
continue to grow rapidly across many countries. US catching up fast with reports now in 34 states. Total number of cases confirmed at ~13,000 from only 11, 100 days ago.
Excited to be one of the 2018 recipients of the
#Google
Faculty Grants to work on the use of
#ai
to improve the control of infectious diseases.
@GoogleAI
Herculean effort by all keeping the dots appearing. Please get in touch if you have a couple of hours time to help out geocoding, entering and updating new cases.
Our team has started curating an open line list for the Ebola 2022 outbreak in Uganda. Data are updated regularly. Downloadable here: and source list here:
"With this virus, you have to react early. You can see this by comparing Germany and Britain, two countries that are structured similarly. Germany simply implemented measures earlier in the spring."
Easily one of the most important tools to track Variants of Concern around the world. Congratulations for keeping this system up and running (
@EvolveDotZoo
@arambaut
@AineToole
++) with >1M published genomes. Open source, peer-reviewed and transparent.
"Which interventions work best in a pandemic?". Very much an open question. Interdisciplinary work on potential ways to combine methods from economics, medicine and infectious disease modelling:
1,679 reported cases of
#dengue
have been imported into France between Jan 1 and late April 2024, compared to 131 in 2023.
The mosquito (Ae. albopictus) transmitting it has been established in 80% of metropolitan departments (out of 96)
81 local cases of
#dengue
in Italy in 2023, including some reported in the Autumn indicating transmission potential outside the summer months. France reported 41 local dengue cases over the same timeframe.
And another. Super-spreading, mobility and geographic spread of COVID in the USA. More evidence for the importance of multiple seedings to drive large outbreaks
We started curating a range of openly available Omicron datasets (SGTF, genomes) including data from Austria, Denmark, UK, ECDC_EU, USA and TravelHistory for genomes uploaded to GISAID. Find downloadable data here: Suggestions and contributions welcome.
Fascinating preprint on the introduction and establishment dynamics of B.1.1.7 in Denmark using large scale genomic data. Many introductions contributed to fast growth and dispersal across the country:
Two years of COVID-19 in Africa: "Certainly, Africa’s successes in the COVID-19 pandemic have not been reported in the mainstream media in a way that could enable the world to learn from them."
Important reports on B.1.617.2 in the UK. Critically, as conclusive evidence for transmission advantage is hard to derive in the early phase of a new VOC spreading urgent and pre-emptive action has shown greatest success to prevent large outbreaks
Github repository now live with updated linelist with geographic location.
Massive thanks to all contributors across many institutions.
We will keep uploading basic epidemiological summaries spatially resolved:
"Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study" together with
@vcolizza
@mariusgilbert
and many others in
@TheLancet
:
V important study on patient outcomes across high and intensive care units in ten African countries (Egypt, Ethiopia, Ghana, Kenya, Libya, Malawi, Mozambique, Niger, Nigeria, and South Africa)
Some very good practical considerations to estimate Rt. I found the section on adjusting for reporting delays especially useful: work by
@sarahcobey
@KatieMG
+ many more
Results from Dalziel et al. 2018 in Science showing that intensities of FLU transmission depend on level of urbanization/crowding may become increasingly relevant for COVID-19 in US now:
We are hiring one Postdoc (up to 36 months, 3years!) and one Research Assistant (24 months) to work on the spatial dynamics of infectious diseases (incl. COVID-19).
@UniofOxford
In 2024 alone Italy has documented 197 imported cases of
#dengue
. Many of them from countries with large outbreaks such as Brazil.
With temperatures rising local outbreaks in Italy and elsewhere are likely.
Excited to announce our new genomic epidemiology project to design public health interventions in Mexico. We will be investigating the determinants of spread of arboviruses w/ help of genetic, serological and spatial data. Follow us on
@GEAPH2020
1/2
New preprint: Optimal disease surveillance with graph-based Active Learning
DPhil student
@JoeTLH
led a study on how to sample on networks for tracking infectious diseases with limited testing budgets.
Summary and timeline of publicly available information on nCoV cases 'outside' of Wuhan (travel history, visit to market, date of onset of symptoms where available). Please re-use, amend, and add information as you see fit. DM for PDF. Latest update: Jan 21, 12:30pm GMT.
Top 20 passenger destination cities and direct + total flight volume from Wuhan, China, where novel coronavirus was confirmed. Many thanks to Journal of Travel Medicine for rapid turnaround. Corr. author:
@BogochIsaac
Fantastic work by
@NadineRujeni
and colleagues: "Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity"
Shorter estimated latent period and incubation period for the Delta variant. New data from Guangdong, China. These analyses we need in real-time and from different contexts as they have many downstream implications for modelling.
Our team have just collaborated with Guangdong CDC on a new preprint (not yet peer-reviewed) on the COVID outbreak in Guangzhou in May-June, and in this thread I’m going describe one of the findings relevant to quarantine durations (1/16)
We analysed how conflict impacted the
#Ebola
epidemic in eastern
#DRC
in 2018-2019. We find evidence for both, conflict events driving larger epidemics and presence of disease increasing frequency of conflict events.
#openaccess
w/
@SCauchemez
@BMCMedicine
Our team at is
#hiring
two DataScientists/PostDocs based in Oxford (or remote). Exciting opportunity to advance decentralised computing infrastructure for pandemic preparedness. Find out more here:
@viralverity
wrote a nice piece on "Progress and challenges in virus genomic epidemiology"; highlights how integrated data streams can be used to make inference on transmission dynamics, and what is needed to move towards predictive phylodynamics:
Important work on seroprevalence of anti–SARS-CoV-2 IgG antibodies in Kenyan blood donors: National "..4.3% (95% CI 2.9–5.8%) and was highest in urban counties, Mombasa (8.0%), Nairobi (7.3%) and Kisumu (5.5%)."
We are hiring two RA's (UK based). One 50% FTE and one 100% FTE to help curate data on the open line list of COVID-19. Please get in touch with CV and short statement of motivation directed to
@B_Gutierrez_G
and me. See details👇
Fantastic work by
@BNODesk
tracking Omicron. Thank you for all your work. Many new countries reporting Omicron which is not unexpected. Local contact tracing and isolation may help get early clusters under control. Ideally accompanied by financial support.
Elegant and insightful: "Awareness-driven behavior changes can shift the shape of epidemics away from peaks and toward plateaus, shoulders, and oscillations"
Using
#openly
available human movement data to better predict the spread of infectious disease in resource poor settings, including source and sink dynamics. Out today
@SciReports
We are looking to compile countries case definitions for
#monkeypox
here: and monitor them as they are changing.
Please add any links here or comment directly on GitHub.
Ahead of the summer holidays and many returning travelers from large
#dengue
outbreak settings in South America, Caribbean, Asia, Ae. albopictus newly to UK, near ports and channel travel, major cities (incl. Berlin).
Global dynamics of
#monkeypox
are now becoming increasingly heterogeneous.
Encouraging signs from Germany over the last week (PH interventions may be working?)
Global cases still rising.
Data from:
The importance of open line list data to understand the origins and early dynamics of an outbreak. Our team has made an effort to curate them during this pandemic, making it accessible to everyone:
Very excited to host Jessica Metcalf on May 1st, 4-5pm at the
@oxmartinschool
for a talk on 'Infection dynamics and control in a changing world'.
@OxfordTalks
See details below:
Incredibly detailed report on "Reproduction number (R) and growth rate (r) of the COVID-19 epidemic in the UK: methods of estimation, data sources, causes of heterogeneity, and use as a guide in policy formulation" by the
@royalsociety
SET-C