updating papers that have been published

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).

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

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 {
 
 </style>
 
+The published article is available [here](https://doi.org/10.12688/wellcomeopenres.15786.1)
 
 ## Aim
 

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)
-<https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-as-they-happen>
-
-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: <https://ssrn.com/abstract=3550308> or <http://dx.doi.org/10.2139/ssrn.3550308>
-
-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: <https://ssrn.com/abstract=3551767> or <http://dx.doi.org/10.2139/ssrn.3551767>
-
-4 Araujo MB and Naimi B. Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate (March 16, 2020) Available at 		 <https://doi.org/10.1101/2020.03.12.20034728>
 
-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 <https://doi.org/10.1101/2020.02.04.20020479>
-
-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. <https://www.who.int/emergencies/diseases/novel-coronavirus-2019/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. <https://cds.climate.copernicus.eu/cdsapp#>
-
-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)
+<https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-as-they-happen>
+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: <https://ssrn.com/abstract=3550308> or <http://dx.doi.org/10.2139/ssrn.3550308>
+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: <https://ssrn.com/abstract=3551767> or <http://dx.doi.org/10.2139/ssrn.3551767>
+4.  Araujo MB and Naimi B. Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate (March 16, 2020) Available at 		 <https://doi.org/10.1101/2020.03.12.20034728>
+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 <https://doi.org/10.1101/2020.02.04.20020479>
+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. <https://www.who.int/emergencies/diseases/novel-coronavirus-2019/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. <https://cds.climate.copernicus.eu/cdsapp#>
+9. Alduchov OA and Eskridge RE. Improved Magnus' form approximation of saturation vapor pressure. J. Appl. Meteor., 1996; 35; 601–609.

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:
 <img src="figures/losreview_distributions.png" width="75%"> <br>
 **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: <https://www.medrxiv.org/content/10.1101/2020.04.30.20084780v1.article-info>
+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)
 

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:
 <img src="figures/pandemic_travel_china_fig3.png" width="80%"/>
 **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.

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).**
 
 <img src="figures/SocialBubbles.png" width="70%" style="display: block; margin: auto;" />
 ***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.*

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).**
 
 <img src="figures/surveillance.JPG" width="70%" style="display: block; margin: auto;" />
 **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.