update bibliography

_data/biblio.yml

@@ -318,7 +318,10 @@
   year: "2022"
   title: "COVID-19 in the 47 countries of the WHO African region: a modelling analysis of past trends and future patterns"
   journal: "Lancet Global Health"
-  doi: "https://doi.org/10.1016/S2214-109X(22)00233-9"
+  volume: "10"
+  number: "8"
+  pages: "e1099–e1114"
+  doi: "https://doi.org/10.1016/s2214-109x(22)00233-9"
 
 - key: Cai2007
   author: "X. Cai and Z. Xu"
@@ -918,6 +921,15 @@
   pages: "20190151"
   doi: "https://doi.org/10.1098/rsif.2019.0151"
 
+- key: Magpantay2023
+  author: "F. M. G. Magpantay, J. Mao, S. Ren, S. Zhao, and T. Meadows"
+  year: "2023"
+  title: "The reinfection threshold, revisited"
+  journal: "Mathematical Biosciences"
+  volume: "363"
+  pages: "109045"
+  doi: "https://doi.org/10.1016/j.mbs.2023.109045"
+
 - key: Marin2012
   author: "J.-M. Marin, P. Pudlo, C. P. Robert, and R. J. Ryder"
   year: "2012"
@@ -967,11 +979,13 @@
   pages: "e1002172"
   doi: "https://doi.org/10.1371/journal.pbio.1002172"
 
-- key: Molodecky2021
+- key: Molodecky2023
   author: "N. A. Molodecky, H. Jafari, R. M. Safdar, J. A. Ahmed, A. Mahamud, A. S. Bandyopadhyay, H. Shukla, A. Quddus, M. Zaffran, R. W. Sutter, N. C. Grassly, and I. M. Blake"
-  year: "2021"
+  year: "2023"
   title: "Modelling the spread of serotype-2 vaccine derived-poliovirus outbreak in Pakistan and Afghanistan to inform outbreak control strategies in the context of the COVID-19 pandemic"
   journal: "Vaccine"
+  volume: "41"
+  pages: "A93–A104"
   doi: "https://doi.org/10.1016/j.vaccine.2021.09.037"
 
 - key: Musa2020
@@ -1348,6 +1362,16 @@
   pages: "1102–1104"
   doi: "https://doi.org/10.1038/nature09319"
 
+- key: Wu2023
+  author: "D. Wu, H. Petousis-Harris, J. Paynter, V. Suresh, and O. J. Maclaren"
+  year: "2023"
+  title: "Likelihood-based estimation and prediction for a measles outbreak in Samoa"
+  journal: "Infectious Disease Modelling"
+  volume: "8"
+  number: "1"
+  pages: "212–227"
+  doi: "https://doi.org/10.1016/j.idm.2023.01.007"
+
 - key: Xia2011
   author: "Y. Xia and H. Tong"
   year: "2011"

vignettes/pomp.bib

@@ -295,16 +295,19 @@ @Article{He2020
   pmid             = {32348302},
 }
 
-@Article{Molodecky2021,
+@Article{Molodecky2023,
   author           = {Molodecky, Natalia A. and Jafari, Hamid and Safdar, Rana M. and Ahmed, Jamal A. and Mahamud, Abdirahman and Bandyopadhyay, Ananda S. and Shukla, Hemant and Quddus, Arshad and Zaffran, Michel and Sutter, Roland W. and Grassly, Nicholas C. and Blake, Isobel M.},
   journal          = {Vaccine},
-  title            = {Modelling the spread of serotype-2 vaccine derived-poliovirus outbreak in {Pakistan} and {Afghanistan} to inform outbreak control strategies in the context of the {COVID-19} pandemic},
-  year             = {2021},
+  title            = {Modelling the spread of serotype-2 vaccine derived-poliovirus outbreak in {Pakistan} and {Afghanistan} to inform outbreak control strategies in the context of the {COVID}-19 pandemic},
+  year             = {2023},
+  month            = apr,
+  pages            = {A93--A104},
+  volume           = {41},
   abstract         = {Background Since July 2019, Pakistan and Afghanistan have been facing an outbreak of serotype-2 circulating vaccine derived poliovirus (cVDPV2) in addition to continued transmission of serotype-1 wild poliovirus (WPV1) and SARS-CoV-2 in 2020. Understanding the risks of cVDPV2 transmission due to pause of global vaccination efforts and the impact of potential vaccination response strategies in the current context of COVID-19~{m}itigation measures is critical. Methods We developed a stochastic, geographically structured mathematical model of cVDPV2 transmission which captures both mucosal and humoral immunity separately and allows for reversion of serotype-2 oral polio vaccine (OPV2) virus to cVDPV2 following vaccine administration. The model includes geographic heterogeneities in vaccination coverage, population immunity and population movement. The model was fitted to historic cVDPV2 cases in Pakistan and Afghanistan between January 2010\mbox{-}{A}pril 2016 and July 2019-March 2020~{us}ing iterated particle filtering. The model was used to simulate spread of cVDPV2 infection from July 2019 to explore impact of various proposed vaccination responses on stopping transmission and risk of spread of reverted Sabin-2 under varying assumptions of impacts from COVID-19 lockdown measures on movement patterns as well as declines in vaccination coverage. Results Simulated monthly incidence of cVDPV2 from the best-fit model demonstrated general spatio-temporal alignment with observed cVDPV2 cases. The model predicted substantial spread of cVDPV2 infection, with widespread transmission through 2020 in the absence of any vaccination activities. Vaccination responses were predicted to substantially reduce transmission and case burden, with a greater impact from earlier responses and those with larger geographic scope. While the greatest risk of seeding reverted Sabin-2 was predicted in areas targeted with OPV2, subsequent spread was greatest in areas with no or delayed response. The proposed vaccination strategy demonstrated ability to stop the cVDPV2 outbreak (with low risk of reverted Sabin-2~{s}pread) by February 2021. Conclusion Outbreak response vaccination campaigns against cVDPV2 will be challenging throughout the COVID-19 pandemic but must be implemented urgently when feasible to stop transmission of cVDPV2.},
-  creationdate     = {2021-11-29T08:22:18},
+  creationdate     = {2023-08-03T08:22:27},
   doi              = {10.1016/j.vaccine.2021.09.037},
   groups           = {pomp},
-  modificationdate = {2021-11-29T08:24:23},
+  modificationdate = {2023-08-03T08:22:41},
   owner            = {kingaa},
   pmcid            = {PMC8463303},
   pmid             = {34629206},
@@ -1585,11 +1588,15 @@ @Article{Cabore2022
   journal          = {Lancet Global Health},
   title            = {{COVID-19} in the 47 countries of the {WHO} {African} region: a modelling analysis of past trends and future patterns},
   year             = {2022},
+  month            = aug,
+  number           = {8},
+  pages            = {e1099--e1114},
+  volume           = {10},
   abstract         = {Summary Background COVID-19 has affected the African region in many ways. We aimed to generate robust information on the transmission dynamics of COVID-19 in this region since the beginning of the pandemic and throughout 2022. Methods For each of the 47 countries of the WHO African region, we consolidated COVID-19 data from reported infections and deaths (from WHO statistics); published literature on socioecological, biophysical, and public health interventions; and immunity status and variants of concern, to build a dynamic and comprehensive picture of COVID-19~{b}urden. The model is consolidated through a partially observed Markov decision process, with a Fourier series to produce observed patterns over time based on the SEIRD (denoting susceptible, exposed, infected, recovered, and dead) modelling framework. The model was set up to run weekly, by country, from the date the first infection was reported in each country until Dec 31, 2021. New variants were introduced into the model based on sequenced data reported by countries. The models were then extrapolated until the end of 2022 and included three scenarios based on possible new variants with varying transmissibility, severity, or immunogenicity. Findings Between Jan 1, 2020, and Dec 31, 2021, our model estimates the number of SARS-CoV-2 infections in the African region to be 505$\cdot$6~{m}illion (95% CI 476$\cdot$0-536$\cdot$2), inferring that only 1$\cdot$4% (one in 71) of SARS-CoV-2 infections in the region were reported. Deaths are estimated at 439 500 (95% CI 344 374-574 785), with 35$\cdot$3% (one in three) of these reported as COVID-19-related deaths. Although the number of infections were similar between 2020 and 2021, 81% of the deaths were in 2021. 52$\cdot$3% (95% CI 43$\cdot$5-95$\cdot$2) of the region's population is estimated to have some SARS-CoV-2 immunity, given vaccination coverage of 14$\cdot$7% as of Dec 31, 2021. By the end of 2022, we estimate that infections will remain high, at around 166$\cdot$2~{m}illion (95% CI 157$\cdot$5-174$\cdot$9) infections, but deaths will substantially reduce to 22\hspace{0.167em}563 (14\hspace{0.167em}970-38\hspace{0.167em}831). Interpretation The African region is estimated to have had a similar number of COVID-19 infections to that of the rest of the world, but with fewer deaths. Our model suggests that the current approach to SARS-CoV-2 testing is missing most infections. These results are consistent with findings from representative seroprevalence studies. There is, therefore, a need for surveillance of hospitalisations, comorbidities, and the emergence of new variants of concern, and scale-up of representative seroprevalence studies, as core response strategies. Funding},
   creationdate     = {2022-06-27T09:43:25},
-  doi              = {10.1016/S2214-109X(22)00233-9},
+  doi              = {10.1016/s2214-109x(22)00233-9},
   groups           = {pomp},
-  modificationdate = {2022-07-22T08:18:11},
+  modificationdate = {2023-08-03T08:39:42},
   owner            = {kingaa},
 }
 
@@ -2830,6 +2837,21 @@ @InCollection{Liu2001b
   modificationdate = {2023-08-02T09:59:38},
 }
 
+@Article{Magpantay2023,
+  author           = {Magpantay, F. M. G. and Mao, J. and Ren, S. and Zhao, S. and Meadows, T.},
+  journal          = {Mathematical Biosciences},
+  title            = {The reinfection threshold, revisited},
+  year             = {2023},
+  month            = sep,
+  pages            = {109045},
+  volume           = {363},
+  creationdate     = {2023-08-03T08:21:12},
+  doi              = {10.1016/j.mbs.2023.109045},
+  groups           = {pomp},
+  modificationdate = {2023-08-03T08:21:12},
+  owner            = {kingaa},
+}
+
 @Article{Marin2012,
   author           = {Marin, Jean-Michel and Pudlo, Pierre and Robert, Christian P. and Ryder, Robin J.},
   journal          = {Stat Comput},
@@ -3068,6 +3090,22 @@ @Article{Wood2010
   groups       = {pomp},
 }
 
+@Article{Wu2023,
+  author           = {Wu, David and Petousis-Harris, Helen and Paynter, Janine and Suresh, Vinod and Maclaren, Oliver J.},
+  journal          = {Infectious Disease Modelling},
+  title            = {Likelihood-based estimation and prediction for a measles outbreak in {Samoa}},
+  year             = {2023},
+  month            = mar,
+  number           = {1},
+  pages            = {212--227},
+  volume           = {8},
+  creationdate     = {2023-08-03T08:21:12},
+  doi              = {10.1016/j.idm.2023.01.007},
+  groups           = {pomp},
+  modificationdate = {2023-08-03T08:21:12},
+  owner            = {kingaa},
+}
+
 @Article{Xia2011,
   author           = {Xia, Yingcun and Tong, Howell},
   journal          = {Stat Sci},