diff --git a/topics/covid19/_posts/2020-01-30-event-size-vs-duration.md b/topics/covid19/_posts/2020-01-30-event-size-vs-duration.md index cab2359..c74913b 100755 --- a/topics/covid19/_posts/2020-01-30-event-size-vs-duration.md +++ b/topics/covid19/_posts/2020-01-30-event-size-vs-duration.md @@ -3,11 +3,12 @@ title: "Understanding the duration and size of the spillover event at the start description: "The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan: Exploring initial point-source exposure sizes and durations using scenario analysis" -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal -update: 2020-01-30 +# update: 2020-01-30 +update: 2026-06-08 authors: - id: sam_abbott @@ -28,7 +29,7 @@ tags: [transmission-dynamics] *S. Abbott, J. Hellewell, J. Munday, CMMID nCoV working group, S. Funk* -*Last updated: 30 January 2020* +The study can be read [here](https://wellcomeopenresearch.org/articles/5-17) and the package code can be found [here](https://github.com/epiforecasts/WuhanSeedingVsTransmission). **Background:** The current novel coronavirus outbreak appears to have originated from a point-source exposure event at Huanan seafood wholesale market in Wuhan, China. There is still uncertainty around the scale and duration of this exposure event. This has implications for the estimated transmissibility of the coronavirus and as such, these potential scenarios should be explored. @@ -37,6 +38,3 @@ tags: [transmission-dynamics] **Results:** Using a pre-intervention SARS-like serial interval suggested a larger initial transmission event and a higher R0 estimate. Using a SARs-like serial interval we found that the most likely scenario produced an R0 estimate between 2-2.7 (90% credible interval (CrI)). A pre-intervention SARS-like serial interval resulted in an R0 estimate between 2-3 (90% CrI). There were other plausible scenarios with smaller events sizes and longer duration that had comparable R0 estimates. There were very few simulations that were able to reproduce the observed data when R0 was less than 1. **Conclusions:** Our results indicate that an R0 of less than 1 was highly unlikely unless the size of the initial exposure event was much greater than currently reported. We found that R0 estimates were comparable across scenarios with decreasing event size and increasing duration. Scenarios with a pre-intervention SARS-like serial interval resulted in a higher R0 and were equally plausible to scenarios with SARs-like serial intervals. - - -The study can be read [here](https://wellcomeopenresearch.org/articles/5-17) and the package code can be found [here](https://github.com/epiforecasts/WuhanSeedingVsTransmission). diff --git a/topics/covid19/_posts/2020-01-30-reporting-delays-and-temporal-variation.md b/topics/covid19/_posts/2020-01-30-reporting-delays-and-temporal-variation.md index 78129ec..d8fbe57 100755 --- a/topics/covid19/_posts/2020-01-30-reporting-delays-and-temporal-variation.md +++ b/topics/covid19/_posts/2020-01-30-reporting-delays-and-temporal-variation.md @@ -15,7 +15,7 @@ status: in-progress status: in-progress -update: 2019-01-30 +update: 2020-01-30 authors: - id: seb_funk diff --git a/topics/covid19/_posts/2020-03-03-cases-from-deaths.md b/topics/covid19/_posts/2020-03-03-cases-from-deaths.md index 8f70ec0..8f74c82 100755 --- a/topics/covid19/_posts/2020-03-03-cases-from-deaths.md +++ b/topics/covid19/_posts/2020-03-03-cases-from-deaths.md @@ -6,17 +6,17 @@ title: "Inferring cases from recent deaths" description: We infer the number of COVID-19 cases based on recently reported deaths. Results suggest that by the time a single COVID-19 death is reported, hundreds to thousands of cases may already be present in the population. # this is a legacy status and should be changed to one of the newer ones -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal #add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2020-03-04 +update: 2026-06-08 #add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -26,23 +26,25 @@ update: 2020-03-04 authors: - id: thibaut_jombart corresponding: true - - id: sam_abbott + - id: kevin_vanzandvoort equal: 1 - - id: amy_gimma + - id: tim_russell equal: 1 - id: chris_jarvis equal: 1 - - id: tim_russell + - id: amy_gimma equal: 1 - - id: kevin_vanzandvoort + - id: sam_abbott equal: 1 - id: sam_clifford - id: seb_funk - id: hamish_gibbs - id: yang_liu + - id: carl_ab_pearson + - id: nikos_bosse + - id: ncov-group - id: roz_eggo - id: adam_kucharski - - id: ncov-group - id: john_edmunds redirect_from: @@ -90,6 +92,7 @@ table.blueTable tfoot td { +The published article is available [here](https://doi.org/10.12688/wellcomeopenres.15786.1) ## Aim diff --git a/topics/covid19/_posts/2020-03-25-role-of-climate.md b/topics/covid19/_posts/2020-03-25-role-of-climate.md index c4923f4..531b3ea 100644 --- a/topics/covid19/_posts/2020-03-25-role-of-climate.md +++ b/topics/covid19/_posts/2020-03-25-role-of-climate.md @@ -5,12 +5,13 @@ title: Effective transmission across the globe: the role of climate in COVID description: We discussed the current evidence on the role of climate on COVID-19 transmission. -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal #add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2020-03-26 +# update: 2020-03-26 +update: 2026-06-08 #add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -28,9 +29,11 @@ authors: redirect_from: - /topics/covid19/current-patterns-transmission/role-of-climate.html -tags: [transmission-dynamics] +tags: [transmission-dynamics, comments-opinions] --- +The published version of this article is available [here](https://doi.org/10.1016/S2542-5196(20)30106-6) + COVID-19 has been declared a pandemic by the World Health Organization (WHO), owing to its rapid global spread and alarming ability to quickly overwhelm healthcare services with patients requiring critical care \[1\]. A pertinent question for COVID-19 mitigation strategies is whether the SARS-CoV-2 virus is less transmissible in hot and humid climates. Some studies support that notion. Sajadi et al.found that regions with established community outbreaks had a lower average temperature and specific humidity compared to areas that did not report significant community transmission \[2\] and similar findings have been observed using ecological niche modelling \[3\]. Similarly, Wang et al. reported a decrease in transmission intensity associated with an increase in temperature and relative humidity \[4\]. An environmental study of SARS-CoV-1 reported reduced survival of the virus at higher temperatures and humidity \[5\] . Such studies have been interpreted by some as sufficient evidence to assume that rising temperatures in boreal summer will likely facilitate COVID-19 control. However, these findings are prone to confounding, including the delay in spread to warmer regions of the world due to travel patterns \[6\] . Hence, it is essential to contextualize these with the current global spread of COVID-19. As of 24 March 2020, 117 countries and territories across the globe have reported local SARS-CoV-2 transmission, 71 have reported imported cases only, six are under investigation and the remainder has not yet reported any cases (Figure 1A) \[7\]. All WHO regions have at least six countries with confirmed local transmission, effectively spanning all climatic zones, from cold and dry to hot and humid regions. Notably, countries reporting local transmission include Malaysia, the Philippines, Indonesia and Thailand, with much movement between them and China. However other countries outside of Asia including Burkina Faso, Democratic Republic of Congo, Panama and Paraguay, with mean ambient temperatures between 1 January 2020 - 14 March 2020 greater than 25°C (Figure 1B) also report local transmission. @@ -43,21 +46,14 @@ The ability of SARS-CoV-2 to effectively spread globally, including in warm and References ---------- -1 WHO. WHO characterizes COVID-19 as a pandemic (11 March 2020) - - -2 Sajadi MM, Habibzadeh P, Vintzileos A, Shokouhi S, Miralles-Wilhelm F and Amoroso A. Temperature, Humidity and Latitude Analysis to Predict Potential Spread and Seasonality for COVID-19 (March 5, 2020). Available at SSRN: or - -3 Wang J, Tang K, Feng K and Lv W. High Temperature and High Humidity Reduce the Transmission of COVID-19 (March 9, 2020). Available at SSRN: or - -4 Araujo MB and Naimi B. Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate (March 16, 2020) Available at -5 Lai S, Bogoch I, Ruktanonchai N, Watts A, Lu X, Yang W, Yu H, Khan K and Tatem AJ. Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study (March 9, 2020). Available at medRxiv 2020.02.04.20020479 or - -6 Chan KH, Peiris JS, Lam SY, Poon LL, Yuen KY, Seto WH. The Effects of Temperature and Relative Humidity on the Viability of the SARS Coronavirus. Adv Virol. 2011; 2011: 734690. doi:10.1155/2011/734690 - -7 WHO. Coronavirus Disease (COVID-19) Situation Reports. accessed 26 March 2020. - -8 Copernicus Climate Change Service4 on the 22 Mar 2020 (C3S): ERA5: Fifth generation of ECMWF atmospheric reanalyses of the global climate. Copernicus Climate Change Service Climate Data Store (CDS), 2017; accessed 22 Mar 2020. - -9 Alduchov OA and Eskridge RE. Improved Magnus' form approximation of saturation vapor pressure. J. Appl. Meteor., 1996; 35; 601–609. +1. WHO. WHO characterizes COVID-19 as a pandemic (11 March 2020) + +2. Sajadi MM, Habibzadeh P, Vintzileos A, Shokouhi S, Miralles-Wilhelm F and Amoroso A. Temperature, Humidity and Latitude Analysis to Predict Potential Spread and Seasonality for COVID-19 (March 5, 2020). Available at SSRN: or +3. Wang J, Tang K, Feng K and Lv W. High Temperature and High Humidity Reduce the Transmission of COVID-19 (March 9, 2020). Available at SSRN: or +4. Araujo MB and Naimi B. Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate (March 16, 2020) Available at +5. Lai S, Bogoch I, Ruktanonchai N, Watts A, Lu X, Yang W, Yu H, Khan K and Tatem AJ. Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study (March 9, 2020). Available at medRxiv 2020.02.04.20020479 or +6. Chan KH, Peiris JS, Lam SY, Poon LL, Yuen KY, Seto WH. The Effects of Temperature and Relative Humidity on the Viability of the SARS Coronavirus. Adv Virol. 2011; 2011: 734690. doi:10.1155/2011/734690 +7. WHO. Coronavirus Disease (COVID-19) Situation Reports. accessed 26 March 2020. +8. Copernicus Climate Change Service4 on the 22 Mar 2020 (C3S): ERA5: Fifth generation of ECMWF atmospheric reanalyses of the global climate. Copernicus Climate Change Service Climate Data Store (CDS), 2017; accessed 22 Mar 2020. +9. Alduchov OA and Eskridge RE. Improved Magnus' form approximation of saturation vapor pressure. J. Appl. Meteor., 1996; 35; 601–609. diff --git a/topics/covid19/_posts/2020-05-06-los-systematic-review.md b/topics/covid19/_posts/2020-05-06-los-systematic-review.md index 08ff29d..40ec6b4 100644 --- a/topics/covid19/_posts/2020-05-06-los-systematic-review.md +++ b/topics/covid19/_posts/2020-05-06-los-systematic-review.md @@ -11,16 +11,17 @@ tags: [healthcare-settings] # these are the statuses you can choose from; delete/uncomment as necessary # defaults to paper-under-peer-review if not set -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal # add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2020-05-06 +# update: 2020-05-06 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -39,7 +40,7 @@ authors: - id: carl_ab_pearson - id: ncov-group - id: thibaut_jombart - - id: simon_procter + - id: simon_procter equal: 2 - id: gwen_knight equal: 2 @@ -65,5 +66,7 @@ authors:
**Figure 3: Combined LOS distributions.** Samples from the overall LoS distributions, split by location (China or rest of world) and type (ICU vs General). For each subset, 100000 draws were taken. The x-axis was cut at days = 60. -Preprint available at medRxiv: +Published article available at [BMC Medicine](https://doi.org/10.1186/s12916-020-01726-3) + +An earlier preprint is available at [medRxiv](https://www.medrxiv.org/content/10.1101/2020.04.30.20084780v1) diff --git a/topics/covid19/_posts/2020-05-11-pandemic-travel-china.md b/topics/covid19/_posts/2020-05-11-pandemic-travel-china.md index b4fdced..ab67568 100644 --- a/topics/covid19/_posts/2020-05-11-pandemic-travel-china.md +++ b/topics/covid19/_posts/2020-05-11-pandemic-travel-china.md @@ -1,7 +1,7 @@ --- # add the title of your project -title: Changing Travel Patterns in Mainland China During the Early Stages of the COVID-2019 Pandemic +title: Changing travel patterns in China during the early stages of the COVID-19 pandemic description: We examined human movement on multiple geographic scales to provide a complete picture of the overall dynamics while drawing links to their public health implications. @@ -11,16 +11,17 @@ tags: [transmission-dynamics, lmic-considerations, control-measures] # these are the statuses you can choose from; delete/uncomment as necessary # defaults to paper-under-peer-review if not set -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal # add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2020-05-11 +# update: 2020-05-11 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -33,6 +34,7 @@ authors: corresponding: true - id: yang_liu equal: 1 + corresponding: true - id: carl_ab_pearson - id: chris_jarvis - id: chris_grundy @@ -50,4 +52,4 @@ authors: **Figure 3. Human mobility, healthcare services availability, and COVID-19 related healthcare pressure.** A), The changes in traveller volume before (blue) and after (red) LNY. Net change is defined as inbound migration index minus outbound migration index. Thus, a negative change indicates more travellers leave than arrive while a positive value indicates more travellers arrive than leave. Solid line indicates the median level of healthcare access. B), The changes in the healthcare pressure (log10 scale) related to COVID-19 each week in low and high healthcare access prefectures. Healthcare access is measured by the number of hospitals per 100,000 residents. Healthcare pressure is measured by confirmed COVID-19 cases divided by healthcare access. Darker shade represents weeks when low healthcare access settings experienced significantly higher pressure than high healthcare access settings; lighter shade represents when differences are not significant based on Mann-Whitney U test. -This [pre-print](reports/pandemic_travel_china_Manuscript.pdf) and [supplemental materials](reports/pandemic_travel_china_Supplement.pdf) are being submitted to medrxiv and the links will be updated after screening. +Read the published article [here](https://doi.org/10.1038/s41467-020-18783-0). An earlier [pre-print](reports/pandemic_travel_china_Manuscript.pdf) and [supplemental materials](reports/pandemic_travel_china_Supplement.pdf) also available. diff --git a/topics/covid19/_posts/2020-06-05-SocialBubbles.md b/topics/covid19/_posts/2020-06-05-SocialBubbles.md index 7d73ad4..941b667 100644 --- a/topics/covid19/_posts/2020-06-05-SocialBubbles.md +++ b/topics/covid19/_posts/2020-06-05-SocialBubbles.md @@ -5,16 +5,17 @@ description: "We consider expanding the social bubble of either all households o # this is a legacy status and should be changed to one of the newer ones # status: in-progress -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal #add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2020-06-05 +# update: 2020-06-05 +update: 2026-06-08 #add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -45,7 +46,10 @@ tags: [transmission-dynamics, control-measures] **Conclusions:** Social bubbles can be an effective way of extending contacts beyond the household limiting the increase in epidemic risk, if managed appropriately. -**[Read the full preprint here](reports/SocialBubbles.pdf).** +**[Read the published here](https://doi.org/10.12688/wellcomeopenres.16164.2).** + + +**[Read an earlier preprint here](reports/SocialBubbles.pdf).** ***Figure 1. top panel: schematic of model structure and its stratification into different household sizes with three components of transmission dynamics, community transmission, bubble transmission and household transmission; left panel: household size distribution for all households in England and Wales, for those households with at least one child younger than 20 years old and for those with at least one child younger than 10 years old (about primary school age and younger). Right panel: illustrative transmission probability matrix A, composed of household and bubble contacts and including community transmission.* diff --git a/topics/covid19/_posts/2020-06-29-routine-surveillance.md b/topics/covid19/_posts/2020-06-29-routine-surveillance.md index 590fa63..16225fd 100644 --- a/topics/covid19/_posts/2020-06-29-routine-surveillance.md +++ b/topics/covid19/_posts/2020-06-29-routine-surveillance.md @@ -1,7 +1,7 @@ --- # add the title of your project -title: A Modelling Study for Designing a Multi-layered Surveillance Approach to Detect the Potential Resurgence of SARS-CoV-2 +title: Designing a multi-layered surveillance approach to detecting SARS-CoV-2: A modelling study description: We evaluated routine surveillance/ testing strategies that can act as early warning systems in China. @@ -11,16 +11,17 @@ tags: [control-measures, healthcare-settings] # these are the statuses you can choose from; delete/uncomment as necessary # defaults to paper-under-peer-review if not set -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal # add the date at which post is updated (or the date of the initial post, if its the initial post) in YYYY-MM-DD -update: 2020-08-19 +# update: 2020-08-19 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -58,7 +59,7 @@ authors: **Funding:** Bill & Melinda Gates Foundation, National Institute of Health Research (UK), National Institute of Health (US), the Royal Society, and Wellcome Trust. -**Read the full pre-print [here](https://www.medrxiv.org/content/10.1101/2020.06.27.20141440v1) and find the code used [here](https://github.com/yangclaraliu/covid_surveillance_strategy).** +**Read the published paper [here](https://doi.org/10.12688/wellcomeopenres.16256.1), an earlier pre-print [here](https://www.medrxiv.org/content/10.1101/2020.06.27.20141440v1), and find the code used [here](https://github.com/yangclaraliu/covid_surveillance_strategy).** **Figure 1.** Likely scope of outbreak by the time of first COVID-19 detection. In a city like Beijing, testing at the rate of 0.04 and 0.07 per 1000 roughly translates to testing 800 and 1600 patients per day. The current routine testing level is approximately 2000 per day. We showed that targeted testing such as the on-going efforts in fever clinics could lead to earlier detection of community transmission. However, with the current level of efforts, it is unlikely detection can occur before cumulative incidence has exceed 100 cases. diff --git a/topics/covid19/_posts/2020-08-05-backwardtracing.md b/topics/covid19/_posts/2020-08-05-backwardtracing.md index 5e5db8e..1540f56 100644 --- a/topics/covid19/_posts/2020-08-05-backwardtracing.md +++ b/topics/covid19/_posts/2020-08-05-backwardtracing.md @@ -5,9 +5,9 @@ title: "Implication of backward contact tracing in the presence of overdispersed description: "We explored the potential of combining backward contact tracing with more conventional forward contact tracing for control of COVID-19." -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal #add the date at which post is updated (if applicable), in YYYY-MM-DD update: 2020-08-05 @@ -20,6 +20,7 @@ update: 2020-08-05 authors: - id: akira_endo corresponding: true + - id: ncov-group - id: quentin_leclerc - id: gwen_knight - id: graham_medley @@ -33,9 +34,12 @@ tags: [control-measures] --- -**[Read the full preprint here](https://www.medrxiv.org/content/10.1101/2020.08.01.20166595v1.full.pdf).** +**[Read the published article here](https://doi.org/10.12688/wellcomeopenres.16344.3).** + +**[Read an earlier preprint here](https://www.medrxiv.org/content/10.1101/2020.08.01.20166595v1).** ### Abstract + Unlike forward contact tracing, backward contact tracing identifies the source of newly detected cases. This approach is particularly valuable when there is high individual-level variation in the number of secondary transmissions. By using a simple branching process model, we explored the potential of combining backward contact tracing with more conventional forward contact tracing for control of COVID-19. diff --git a/topics/covid19/_posts/2020-08-12-post-template.md b/topics/covid19/_posts/2020-08-12-post-template.md index 55344c7..ccdff44 100644 --- a/topics/covid19/_posts/2020-08-12-post-template.md +++ b/topics/covid19/_posts/2020-08-12-post-template.md @@ -11,16 +11,17 @@ tags: [control-measures] # these are the statuses you can choose from; delete/uncomment as necessary # defaults to paper-under-peer-review if not set -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal # add the date at which post is updated (or the date of the initial post, if its the initial post) in YYYY-MM-DD -update: 2020-08-19 +# update: 2020-08-19 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -53,4 +54,4 @@ authors: **Conclusion:** Understanding the impact that specific NPIs have had on SARS-CoV-2 transmission is complicated by temporal clustering, time-dependent variation in effects and differences in NPI intensity. However, the effectiveness of school closure and internal movement restrictions appears robust across different model specifications taking into account these effects, with some evidence that other NPIs may also be effective under particular conditions. This provides empirical evidence for the potential effectiveness of many although not all the actions policy-makers are taking to respond to the COVID-19 pandemic. -**Read the full pre-print [here](https://www.medrxiv.org/content/10.1101/2020.08.11.20172643v1) and find the code used [here](https://github.com/yangclaraliu/COVID19_NPIs_vs_Rt).** \ No newline at end of file +**Read the published paper [here](https://doi.org/10.1186/s12916-020-01872-8), an earlier pre-print [here](https://www.medrxiv.org/content/10.1101/2020.08.11.20172643v1), and find the code used [here](https://github.com/yangclaraliu/COVID19_NPIs_vs_Rt).** \ No newline at end of file diff --git a/topics/covid19/_posts/2020-08-13-synthetic-contact-matrices.md b/topics/covid19/_posts/2020-08-13-synthetic-contact-matrices.md index 4f92cbb..b96470f 100644 --- a/topics/covid19/_posts/2020-08-13-synthetic-contact-matrices.md +++ b/topics/covid19/_posts/2020-08-13-synthetic-contact-matrices.md @@ -11,16 +11,17 @@ tags: [mixing-patterns, control-measures, transmission-dynamics] # these are the statuses you can choose from; delete/uncomment as necessary # defaults to paper-under-peer-review if not set -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal # add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2020-08-13 +# update: 2020-08-13 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -39,7 +40,8 @@ authors: corresponding: true --- - **[You can read the full preprint here](https://www.medrxiv.org/content/10.1101/2020.07.22.20159772v2)** + **[You can read the published paper here](https://doi.org/10.1371/journal.pcbi.1009098)** + **[You can read an earlier preprint here](https://www.medrxiv.org/content/10.1101/2020.07.22.20159772v2)** **[and the supplementary information here](reports/synthetic_contact_matrices/synthetic_matrices_supplement_2020-07-22.pdf).** The risk of contracting a directly-transmitted infectious disease such as the Coronavirus Disease 2019 (COVID-19) depends on who interacts with whom. diff --git a/topics/covid19/_posts/2020-09-26-uk-vaccine-cost-effectiveness.md b/topics/covid19/_posts/2020-09-26-uk-vaccine-cost-effectiveness.md index f1725bd..c8144c3 100644 --- a/topics/covid19/_posts/2020-09-26-uk-vaccine-cost-effectiveness.md +++ b/topics/covid19/_posts/2020-09-26-uk-vaccine-cost-effectiveness.md @@ -11,16 +11,17 @@ tags: [control-measures, transmission-dynamics] # these are the statuses you can choose from; delete/uncomment as necessary # defaults to paper-under-peer-review if not set -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal # add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2020-10-23 +# update: 2020-10-23 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -31,10 +32,10 @@ authors: - id: frank_sandmann corresponding: true - id: nick_davies - - id: ncov-group - id: anna_vassall - id: john_edmunds - id: mark_jit + - id: ncov-group --- @@ -46,4 +47,4 @@ Findings. Without vaccination and physical distancing, we estimated 147.9 millio Interpretation. Our model findings highlight the substantial health and economic value of introducing SARS-CoV-2 vaccination. Given uncertainty around both characteristics of the eventually licensed vaccines and long-term COVID-19 epidemiology, our study provides early insights about possible future scenarios in a post-vaccination era from an economic and epidemiological perspective. -Read the full pre-print [here.](https://www.medrxiv.org/content/10.1101/2020.09.24.20200857v1) +Read the full paper [here](https://doi.org/10.1016/S1473-3099(21)00079-7), or an earlier pre-print [here.](https://www.medrxiv.org/content/10.1101/2020.09.24.20200857v1) diff --git a/topics/covid19/_posts/2020-10-26-Facebook-Geographic-Scales.md b/topics/covid19/_posts/2020-10-26-Facebook-Geographic-Scales.md index f78c94d..bd3ce60 100755 --- a/topics/covid19/_posts/2020-10-26-Facebook-Geographic-Scales.md +++ b/topics/covid19/_posts/2020-10-26-Facebook-Geographic-Scales.md @@ -1,7 +1,7 @@ --- # add the title of your project -title: Human movements can inform the spatial scale of interventions against COVID-19 transmission +title: Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19 description: We evaluated if Facebook for Good mobility data can provide information about movements within the UK during intervention periods and afterward. @@ -11,16 +11,17 @@ tags: [transmission-dynamics, control-measures] # these are the statuses you can choose from; delete/uncomment as necessary # defaults to paper-under-peer-review if not set -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal # add the date at which post is updated (or the date of the initial post, if its the initial post) in YYYY-MM-DD -update: 2020-10-26 +#update: 2020-10-26 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -51,4 +52,4 @@ authors: The UK enacted an intensive, nationwide lockdown on March 23 2020 to mitigate transmission of COVID-19. As restrictions began to ease, resurgence in transmission has been targeted by geographically-limited interventions of various stringencies. Determining the optimal spatial scale for local interventions is critical to ensure interventions reach the most at risk areas without unnecessarily restricting areas at low risk of resurgence. Here we use detailed human mobility data from Facebook to determine the spatially-explicit network community structure of the UK before and during the lockdown period, and how that has changed in response to the easing of restrictions and to locally-targeted interventions. We found that the mobility network became more sparse and the number of mobility communities decreased under the national lockdown. During this period, there was no evidence of re-routing in the network. Communities in which locally-targeted interventions have happened following resurgence did not show reorganization but did show small decreases in measurable mobility effects in the Facebook dataset. We propose that geographic communities detected in Facebook or other mobility data be part of decision making for determining the spatial extent or boundaries of interventions in the UK. These data are available in near real-time, and allow quantification of changes in the distribution of the population across the UK, as well as people's travel patterns to give data-driven metrics for geographically-targeted interventions. -Please download the [main text](reports/Facebook_movement_analysis_UK-20201026.pdf) and [supplement](reports/Facebook_movement_analysis_UK-Supplemental-20201026.pdf) for more information. +Please download the [published paper](https://doi.org/10.1371/journal.pcbi.1009162), [an earlier report](reports/Facebook_movement_analysis_UK-20201026.pdf) and [supplement](reports/Facebook_movement_analysis_UK-Supplemental-20201026.pdf) for more information. diff --git a/topics/covid19/_posts/2020-11-10-pcr-positivity-over-time.md b/topics/covid19/_posts/2020-11-10-pcr-positivity-over-time.md index e00a20e..f58fec6 100644 --- a/topics/covid19/_posts/2020-11-10-pcr-positivity-over-time.md +++ b/topics/covid19/_posts/2020-11-10-pcr-positivity-over-time.md @@ -6,13 +6,14 @@ description: "Using data on twice weekly PCR testing of front-line healthcare workers, we estimated individual infection times and probability of testing PCR positive through time since infection." -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2020-11-24 +#update: 2020-11-24 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -71,7 +72,7 @@ high proportion of infected individuals early in their infection, provided that the testing is frequent and the time from testing to notification of results is sufficiently fast. -**[Read the full preprint here](reports/pcr_profile/manuscript_main_text.pdf) +**[Read the published article here](https://doi.org/10.1186/s12916-021-01982-x), [an earlier preprint here](reports/pcr_profile/manuscript_main_text.pdf) and [the supplementary material here](reports/pcr_profile/manuscript_supplementary_material.pdf).** **[Download the median and 95% credible interval for our PCR-positivity curve (Figure 3) here](https://github.com/cmmid/pcr-profile/blob/main/PCR_curve_summary.csv) and [download the median and 95% credible interval for our lateral flow test positivity curve (Figure S3) here](https://github.com/cmmid/pcr-profile/blob/main/LFT_curve_summary.csv)** diff --git a/topics/covid19/_posts/2020-11-28-Slovakia.md b/topics/covid19/_posts/2020-11-28-Slovakia.md index 95b8d8c..933bddc 100644 --- a/topics/covid19/_posts/2020-11-28-Slovakia.md +++ b/topics/covid19/_posts/2020-11-28-Slovakia.md @@ -10,16 +10,17 @@ tags: [control-measures] # these are the statuses you can choose from; delete/uncomment as necessary # defaults to paper-under-peer-review if not set -status: paper-under-peer-review +# status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal # status: real-time-report # status: report # status: comment-opinion-online # status: comment-opinion-journal # add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2020-11-28 +#update: 2020-11-28 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -44,6 +45,8 @@ authors: equal: 1 --- +**[Published article](https://doi.org/10.1126/science.abf9648)** + **[medRxiv preprint](https://www.medrxiv.org/content/10.1101/2020.12.02.20240648v1)** Background: With the development of rapid antigen tests, population screening for SARS-CoV-2 infection has become logistically feasible and could reduce transmission with limited burden on the uninfected. We report the effects of mass testing on the prevalence of SARS-CoV-2 in Slovakia, the first country to implement such an approach. diff --git a/topics/covid19/_posts/2021-01-15-hospital-bed-pathways.md b/topics/covid19/_posts/2021-01-15-hospital-bed-pathways.md index 9f16ac8..d4eb619 100644 --- a/topics/covid19/_posts/2021-01-15-hospital-bed-pathways.md +++ b/topics/covid19/_posts/2021-01-15-hospital-bed-pathways.md @@ -8,10 +8,13 @@ tags: [healthcare-settings] # these are the statuses you can choose from; delete/uncomment as necessary # defaults to paper-under-peer-review if not set -status: paper-under-peer-review +# status: paper-under-peer-review +status: paper-published-at-journal # add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2021-01-15 +#update: 2021-01-15 +update: 2026-06-08 + # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -31,6 +34,8 @@ authors: --- + + **Objectives** Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length of stay (LoS) in particular bed types. LoS can vary depending on the patient's "bed pathway" - the sequence of transfers between bed types during a hospital stay. In this study, we characterise these pathways, and their impact on predicted hospital bed occupancy. @@ -50,5 +55,5 @@ For UCH, we found that using bed pathways improved the accuracy of bed occupancy We identified five bed pathways, with substantial variation in LoS by bed type, pathway, and geography. This might be caused by local differences in patient characteristics, clinical care strategies, or resource availability, and suggests that national LoS averages may not be appropriate for local forecasts of bed occupancy for COVID-19. -**Read the full pre-print [here](https://www.medrxiv.org/content/10.1101/2021.01.14.21249791v1) and access the code and data [here](https://github.com/qleclerc/COVID_bed_occupancy).** +**Read the full journal article [here](https://doi.org/10.1186/s12913-021-06509-x) and access the code and data [here](https://github.com/qleclerc/COVID_bed_occupancy).** diff --git a/topics/covid19/_posts/2021-02-15-comix-schools.md b/topics/covid19/_posts/2021-02-15-comix-schools.md index aa18469..e9e02b1 100644 --- a/topics/covid19/_posts/2021-02-15-comix-schools.md +++ b/topics/covid19/_posts/2021-02-15-comix-schools.md @@ -4,14 +4,15 @@ title: "Estimating the impact of reopening schools on the reproduction number of description: "Combining CoMix contact survey data with profiles in infectiousness and susceptibility to estimate the effect on the reproduction number." -status: paper-under-peer-review +#status: paper-under-peer-review # status: paper-accepted-at-journal -# status: paper-published-at-journal +status: paper-published-at-journal tags: [control-measures, mixing-patterns] # add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2021-02-15 +#update: 2021-02-15 +update: 2026-06-08 # add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -34,9 +35,9 @@ authors: --- -**[Read preprint here.](https://medrxiv.org/cgi/content/short/2021.03.06.21252964v1)** - +**[Read published article here.](https://doi.org/10.1186/s12916-021-02107-0)** +**[Read preprint here.](https://medrxiv.org/cgi/content/short/2021.03.06.21252964v1)** # Summary diff --git a/topics/covid19/_posts/2021-06-02-comix-england-march-2020-march-2021.md b/topics/covid19/_posts/2021-06-02-comix-england-march-2020-march-2021.md index 50788d7..bca4334 100644 --- a/topics/covid19/_posts/2021-06-02-comix-england-march-2020-march-2021.md +++ b/topics/covid19/_posts/2021-06-02-comix-england-march-2020-march-2021.md @@ -5,10 +5,12 @@ title: CoMix - Changes in social contacts as measured by the contact survey duri description: We present one full year of CoMix contact survey data from participants in England between March 2020 and March 2021 to track social contact behaviour during the Covid-19 pandemic. -status: paper-under-peer-review +#status: paper-under-peer-review +status: paper-published-at-journal #add the date at which post is updated (if applicable), in YYYY-MM-DD -update: 2021-06-02 +#update: 2021-06-02 +update: 2026-06-08 #add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -34,6 +36,9 @@ authors: tags: [transmission-dynamics, mixing-patterns, control-measures] --- +Click here to read the published article. + + Click here to read our full preprint. ### Background diff --git a/topics/covid19/_posts/2021-06-17-somalia-excess-mortality.md b/topics/covid19/_posts/2021-06-17-somalia-excess-mortality.md index f821c17..e74180b 100644 --- a/topics/covid19/_posts/2021-06-17-somalia-excess-mortality.md +++ b/topics/covid19/_posts/2021-06-17-somalia-excess-mortality.md @@ -1,6 +1,6 @@ --- -#add the title of your project +# add the title of your project title: Model fitting of early 2020 increase in burials in Mogadishu (Somalia) suggests possible early introduction of SARS-CoV-2 #add a description @@ -8,10 +8,12 @@ description: We fitted a dynamic transmission model to satellite imagery of the tags: [transmission-dynamics, severity, lmic-considerations, control-measures] -status: paper-under-peer-review +#status: paper-under-peer-review +status: paper-published-at-journal #add the date at which post is updated (or the date of the initial post, if its the initial post) in YYYY-MM-DD -update: 2021-06-17 +#update: 2021-06-17 +update: 2026-06-08 #add optional hash-array with authors # see /_data/authors.yml for list of ids, or to add/edit an author @@ -22,10 +24,11 @@ authors: - id: mihaly_koltai corresponding: true - id: collaborators_somalia_excess_mort_early_introd - - id: stefan_flasche - id: mark_jit - - id: francesco_checchi + - id: stefan_flasche + - id: nick_davies - id: ncov-group + - id: francesco_checchi # permalinks have changed # make sure old urls still work by redirecting to this post @@ -34,6 +37,8 @@ redirect_from: --- +**[The published version is available here.](https://doi.org/10.12688/wellcomeopenres.17247.2)** + ### **Background** In countries with weak surveillance systems confirmed COVID-19 deaths are likely to underestimate the death toll of the pandemic. Many countries also have incomplete vital registration systems, hampering excess mortality estimation, necessitating the use of alternative data sources of mortality. We obtained satellite imagery data of the main cemeteries of Mogadishu (Somalia), which showed a sustained rise in burials above the pre-pandemic baseline in the period February-July 2020. We fitted a dynamic transmission model to this indirect measure of excess mortality to estimate the date of introduction and transmissibility of SARS-CoV-2, as well as the effect of non-pharmaceutical interventions in this low-income, crisis-affected setting.