From a61526f2a5d328b7a633f93951b95a0192f289de Mon Sep 17 00:00:00 2001 From: LianeHughes <68756672+LianeHughes@users.noreply.github.com> Date: Mon, 2 Sep 2024 12:00:47 +0200 Subject: [PATCH] adding news and other information about mpox Also minor corrections to lineage competition text (news to follow) --- .../english/dashboards/lineage_competition.md | 22 ++++++------ content/english/pathogens/mpox.md | 35 ++++++++++--------- content/english/topics/mpox.md | 19 +++++----- content/english/updates/mpox_aug24.md | 13 +++++++ data/mpox_page_announcements.json | 5 +++ 5 files changed, 56 insertions(+), 38 deletions(-) create mode 100644 content/english/updates/mpox_aug24.md diff --git a/content/english/dashboards/lineage_competition.md b/content/english/dashboards/lineage_competition.md index 9f955b7f..3d963dbb 100644 --- a/content/english/dashboards/lineage_competition.md +++ b/content/english/dashboards/lineage_competition.md @@ -10,13 +10,13 @@ menu: name: SARS-CoV-2 variant competition dashboards_topics: [COVID-19, Infectious diseases] data_status: "updating" # or "historic" - --- +
All data last updated: {{< last_modified_lineage >}}
SARS-CoV-2 is constantly evolving, with new variants competing against one another for domiance in different regions. This model integrates SARS-CoV-2 genotype sequencing data from around the world to estimate the growth advantage of different variants, which is then used to provide regional estimates of variant frequencies and how these are changing over time. This can be used by researchers who might wish to know which variants to focus on in their studies, or by public health officials who might wish to know which variants are likely to become dominant in their region. -The full set of model estimates can be found in the [GitHub repository](https://github.com/MurrellGroup/lineages). +The full set of model estimates, which includes estimates for countries other than Sweden, can be found in the [GitHub repository of the Murrell research group](https://github.com/MurrellGroup/lineages), who conduct this research. ## Global statistics on lineage competition @@ -26,11 +26,11 @@ Growth rate advantages are estimated from all variant frequency data, globally.
Growth advantage estimates for the top variants
-For convergent mutations (occuring independently at least three times), we estimate the contribution to growth rate advantage of each mutation. +For convergent mutations (occuring independently at least three times), the contribution to the growth rate advantage of each mutation is estimated.
Estimates of contribution to growth of convergently occuring mutations
-The relatedness of SARS-CoV-2 variants, with their estimated growth rate advantages, can be visualized in a phylogenetic tree. We show only recent variants, and key ancestral variants, and we exclude lineage with low growth rate estimates. +The relatedness of SARS-CoV-2 variants, with their estimated growth rate advantages, can be visualised in a phylogenetic tree. Only recent variants, and key ancestral variants, are shown. Lineage with low growth rate estimates are excluded.
Growth-annotated phylogeny
@@ -38,7 +38,7 @@ The relatedness of SARS-CoV-2 variants, with their estimated growth rate advanta The "model average" variant frequencies are forecasts from the model with all region-specific effects set to zero. This provides a single "snapshot" of the global variant situation. This is not meant to representative of the true global variant frequencies, since it is influenced by different sequencing coverage in different regions, but it is useful to understand the model's estimates of how quickly one variant might be expected to replace others. -Variants are colored such that related variants should be similar in color. +Variants are coloured such that related variants should be similar in colour.
Model average variant trajectories
@@ -46,7 +46,7 @@ Variants are colored such that related variants should be similar in color. ## Results from Sweden -We always include estimates of variant frequencies and growth rate advantages for Sweden. Swedish genotype data comes, as with all other data, from GISAID. Note that sequencing volumes are often low, especially when case counts themselves are low (and there are not many infections to sequence), and in such cases the estimates for variant frequencies in Sweden can be very uncertain. +Estimates of variant frequencies and growth rate advantages for Sweden are always included in the model. As with all data used in the model, Swedish genotype data comes from [GISAID](https://gisaid.org). Sequencing volumes are often low for Sweden, especially when the case counts themselves are low (and there are not many infections to sequence). In such cases, the estimates for variant frequencies in Sweden can be very uncertain. It is therefore important to treat the results of the model with caution when sequencing volumes are low.
SARS-CoV-2 genotype volumes
@@ -56,12 +56,12 @@ We always include estimates of variant frequencies and growth rate advantages fo ## Methods -Lineage dynamics are modelled using a Bayesian multinomial logistic regression over lineage counts. The latest global [GISAID](https://gisaid.org/) SARS-CoV-2 dataset (obtained via bulk download) is filtered to include only sequences with collection dates within the last 100 days. Lineage assignment is performed using [NextClade](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli/index.html), retaining sequences with a “good” overall QC status, and >90% coverage. Daily lineage counts are aggregated by region (including only countries with sufficient recent sequencing volumes), with low-frequency sub-lineages (too rare to model) merged into their most recent ancestors. +Lineage dynamics are modelled using a Bayesian multinomial logistic regression over lineage counts. The latest global [GISAID](https://gisaid.org/) SARS-CoV-2 dataset (obtained via bulk download) is filtered to include only sequences with collection dates within the last 100 days. Lineage assignment is performed using [NextClade](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli/index.html), retaining sequences with a “good” overall quality control (QC) status, and >90% coverage. Daily lineage counts are aggregated by region (including only countries with sufficient recent sequencing volumes), with low-frequency sub-lineages (too rare to model) merged into their most recent ancestors. -Growth rates are modelled with a hierarchical approach. Each lineage's growth rate in a given region is the sum of a global rate and a region-specific random effect. The global rate for each lineage comprises three components: i) branch-specific terms for each branch ancestral to the lineage, ii) terms for convergent spike mutations occurring 3 or more times independently that are present in the lineage, and iii) a lineage-specific term. This parameterization allows for shared evidence when mutations occur across multiple branches, and phylogenetic heritability of growth rates, such that growth rates for closely-related lineages are more likely, under the model’s prior, to be similar to one another. Recombinants inherit weighted mixtures of their multiple parents' growth terms. Lineage-specific intercept terms, which contorl the relative timing of the emergence of variants, comprise a global shared term and region-specific random effects. +Growth rates are modelled with a hierarchical approach. Each lineage's growth rate in a given region is the sum of a global rate and a region-specific random effect. The global rate for each lineage comprises three components: i) branch-specific terms for each branch ancestral to the lineage, ii) terms for convergent spike mutations occurring 3 or more times independently that are present in the lineage, and iii) a lineage-specific term. This parameterisation allows for shared evidence when mutations occur across multiple branches, and phylogenetic heritability of growth rates, such that growth rates for closely-related lineages are more likely, under the model’s prior, to be similar to one another. Recombinants inherit weighted mixtures of their multiple parents' growth terms. Lineage-specific intercept terms, which control the relative timing of the emergence of variants, comprise a global shared term and region-specific random effects. -Gaussian priors (centered on zero) are used for each parameter type, with Gaussian hyperpriors over the log of their standard deviations. Posterior distributions are jointly sampled (for global and local parameters for all global data) using Hamiltonian Monte Carlo with the No-U-Turn sampler, implemented in [Julia's](https://julialang.org/) [AdvancedHMC.jl](https://github.com/TuringLang/AdvancedHMC.jl) package. +Gaussian priors (centred on zero) are used for each parameter type, with Gaussian hyperpriors over the log of their standard deviations. Posterior distributions are jointly sampled (for global and local parameters for all global data) using Hamiltonian Monte Carlo with the No-U-Turn sampler, implemented in the [AdvancedHMC.jl](https://github.com/TuringLang/AdvancedHMC.jl) package of [Julia](https://julialang.org/). -For all plots, we use the [Pango designations](https://github.com/cov-lineages/pango-designation/) for lineage names. +The [Pango designations](https://github.com/cov-lineages/pango-designation/) are used for lineage names in all of the plots produced using the model. -We gratefully acknowledge all data contributors, i.e. the Authors and their Originating Laboratories responsible for obtaining the specimens, and their Submitting Laboratories that generated the genetic sequence and metadata and shared via the GISAID Initiative the data on which this research is based. +The Murrell group gratefully acknowledges all data contributors, i.e. the Authors and their Originating Laboratories responsible for obtaining the specimens, and their Submitting Laboratories that generated the genetic sequence and metadata and shared via the GISAID Initiative the data on which this research is based. diff --git a/content/english/pathogens/mpox.md b/content/english/pathogens/mpox.md index 17902d55..8d0ce690 100644 --- a/content/english/pathogens/mpox.md +++ b/content/english/pathogens/mpox.md @@ -3,18 +3,18 @@ title: "Mpox: ongoing research, data, publications and preprints" toc: true recaptcha: true aliases: - - /pathogens/monkeypox + - /pathogens/monkeypox --- ## General information -Mpox a.k.a. Monkeypox is a zoonotic disease (i.e. one that is transmitted from animals to humans) caused by the mpox virus. The virus is a member of the *Orthopoxvirus* genus in the family *Poxviridae*. There are currently two clades of mpox virus: the West African clade and the Congo Basin (Central African) clade [according to WHO](https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON385). It is closely related to the virus that causes smallpox (*variola virus*), which has had a major negative impact on human populations throughout history. +Mpox a.k.a. Monkeypox is a zoonotic disease (i.e. one that is transmitted from animals to humans) caused by the mpox virus. The virus is a member of the _Orthopoxvirus_ genus in the family _Poxviridae_. There are currently two clades of mpox virus: the West African clade and the Congo Basin (Central African) clade [according to WHO](https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON385). It is closely related to the virus that causes smallpox (_variola virus_), which has had a major negative impact on human populations throughout history. -The mpox virus is endemic to certain areas of west and central Africa, but not elsewhere. Outbreaks in other regions are rare. However, in May 2022, multiple cases were detected in different European countries, including Sweden. This led to fears that the virus could become more widespread across the world ([WHO, 2022](https://www.who.int/health-topics/monkeypox#tab=tab_1); [Adler et al., 2022](https://doi.org/10.1016/s1473-3099(22)00228-6)). Over 20,000 cases have been detected in Europe since the start of the outbreak. As of September 2022, 161 cases have been detected in Sweden and reported to the Swedish Public Health Agency. +The mpox virus is endemic to certain areas of west and central Africa, but not elsewhere. Outbreaks in other regions are rare. However, in May 2022, multiple cases were detected in different European countries, including Sweden. This led to fears that the virus could become more widespread across the world ([WHO, 2022](https://www.who.int/health-topics/monkeypox#tab=tab_1); [Adler et al., 2022]()). Over 20,000 cases have been detected in Europe since the start of the outbreak. As of September 2022, 161 cases have been detected in Sweden and reported to the Swedish Public Health Agency. Clinically, mpox is typically characterised by fever, unexplained acute rash, and lymphadenopathy. Additional symptoms and complications may also occur (see [the pages from the Centers for Disease Control (CDC)](https://www.cdc.gov/poxvirus/monkeypox/symptoms/index.html) for more detailed information). The incubation time of the virus is normally 5-13 days, but can be up to three weeks. Close personal contact with an infected individual is the most common means of human-human transmission. -Information regarding mortality rate is limited, but there is significant variation in the rates that have been reported (from 1 - 10%) ([Adler et al., 2022](https://doi.org/10.1016/s1473-3099(22)00228-6)). There are currently no licenced treatments for human mpox, although brincidofovir and tecovirimat (both drugs approved in the USA for use against smallpox) show promise in animal studies ([Adler et al., 2022](https://doi.org/10.1016/s1473-3099(22)00228-6)). Whilst no vaccine has been approved in Europe by European Medicines Agency (EMA) to date, EU healthcare has access to doses of [Jynneosvaccine](https://www.cdc.gov/poxvirus/monkeypox/vaccines/jynneos.html). This vaccine is approved by the U.S. Food and Drug Administration (FDA) for both mpox and smallpox. The doses available to EU healthcare were donated by the USA and Canada via the European Health Emergency Preparedness and Response Authority (HERA). +Information regarding mortality rate is limited, but there is significant variation in the rates that have been reported (from 1 - 10%) ([Adler et al., 2022]()). There are currently no licenced treatments for human mpox, although brincidofovir and tecovirimat (both drugs approved in the USA for use against smallpox) show promise in animal studies ([Adler et al., 2022]()). Whilst no vaccine has been approved in Europe by European Medicines Agency (EMA) to date, EU healthcare has access to doses of [Jynneosvaccine](https://www.cdc.gov/poxvirus/monkeypox/vaccines/jynneos.html). This vaccine is approved by the U.S. Food and Drug Administration (FDA) for both mpox and smallpox. The doses available to EU healthcare were donated by the USA and Canada via the European Health Emergency Preparedness and Response Authority (HERA). ## Ongoing research and data efforts @@ -49,23 +49,23 @@ These tools have been adapted/developed for use with the mpox virus. They could ## Relevant publications and preprints -- Miura, F., van Ewijk, C.E., Backer J. A., Xiridou, M., Franz, E., Op de Coul, E., Brandwagt, D., van Cleef, B., van Rijckevorsel. G., Swaan. C., van den Hof, S., Wallinga, J. (2022). Estimated incubation period for monkeypox cases confirmed in the Netherlands, May 2022. *Eurosurveillance*, *27*, 2200448. [https://doi.org/10.2807/1560-7917.ES.2022.27.24.2200448](https://doi.org/10.2807/1560-7917.ES.2022.27.24.2200448) +- Miura, F., van Ewijk, C.E., Backer J. A., Xiridou, M., Franz, E., Op de Coul, E., Brandwagt, D., van Cleef, B., van Rijckevorsel. G., Swaan. C., van den Hof, S., Wallinga, J. (2022). Estimated incubation period for monkeypox cases confirmed in the Netherlands, May 2022. _Eurosurveillance_, _27_, 2200448. [https://doi.org/10.2807/1560-7917.ES.2022.27.24.2200448](https://doi.org/10.2807/1560-7917.ES.2022.27.24.2200448) -- Pfaff, F., Hoffmann, D., Beer, M. (2022). Monkeypox genomic surveillance will challenge lessons learned from SARS-CoV-2. *Lancet*, *400*, 10345. [https://doi.org/10.1016/s0140-6736(22)01106-0](https://doi.org/10.1016/s0140-6736(22)01106-0) +- Pfaff, F., Hoffmann, D., Beer, M. (2022). Monkeypox genomic surveillance will challenge lessons learned from SARS-CoV-2. _Lancet_, _400_, 10345. [https://doi.org/10.1016/s0140-6736(22)01106-0]() -- Kraemer, M.U.G., Tegally, H., Pigott, D.M., Dasgupta, A., Sheldon, J., Wilkinson, E., Schultheiss, M., Han, A., Oglia, M., Marks, S., Kanner, J., O'Brien, K., Dandamudi, S., Rader, B., Sewalk, K., Bento, A.I., Scarpino, S.V., de Oliveira, T., Bogoch, I.I., Katz, R., Brownstein, J.S. (2022). Tracking the 2022 monkeypox outbreak with epidemiological data in real-time. *The Lancet Infectious Diseases*. [https://doi.org/10.1016/S1473-3099(22)00359-0](https://doi.org/10.1016/S1473-3099(22)00359-0) +- Kraemer, M.U.G., Tegally, H., Pigott, D.M., Dasgupta, A., Sheldon, J., Wilkinson, E., Schultheiss, M., Han, A., Oglia, M., Marks, S., Kanner, J., O'Brien, K., Dandamudi, S., Rader, B., Sewalk, K., Bento, A.I., Scarpino, S.V., de Oliveira, T., Bogoch, I.I., Katz, R., Brownstein, J.S. (2022). Tracking the 2022 monkeypox outbreak with epidemiological data in real-time. _The Lancet Infectious Diseases_. [https://doi.org/10.1016/S1473-3099(22)00359-0]() -- Rodríguez-Morales, A.J., Ortiz-Martínez, Y., Bonilla-Aldana, D.K. (2022). What has been researched about monkeypox? a bibliometric analysis of an old zoonotic virus causing global concern. *New Microbes and New Infections*, *47*, 100993. [https://doi.org/10.1016/j.nmni.2022.100993](https://doi.org/10.1016/j.nmni.2022.100993) +- Rodríguez-Morales, A.J., Ortiz-Martínez, Y., Bonilla-Aldana, D.K. (2022). What has been researched about monkeypox? a bibliometric analysis of an old zoonotic virus causing global concern. _New Microbes and New Infections_, _47_, 100993. [https://doi.org/10.1016/j.nmni.2022.100993](https://doi.org/10.1016/j.nmni.2022.100993) -- Perez Duque, M., Ribeiro, S., Martins, J. V., Casaca, P., Leite, P.P., Tavares, M., Mansinho, K., Duque, L.M., Fernandes, C., Cordeiro, R., Borrego, M.J., Pelerito, A., de Carvalho, I.L., Núncio, S., Manageiro, V., Minetti, C., Machado, J., Haussig, J.M., Croci, R., Spiteri, G., Casal, A.S., Mendes, D., Souto, T., Pocinho, S., Fernandes, T., Firme, A., Vasconcelos, P., Freitas, G. (2022). Ongoing monkeypox virus outbreak, Portugal, 29 April to 23 May 2022. *Eurosurveillance, 27* 2200424. [https://doi.org/10.2807/1560-7917.ES.2022.27.22.2200424](https://doi.org/10.2807/1560-7917.ES.2022.27.22.2200424) +- Perez Duque, M., Ribeiro, S., Martins, J. V., Casaca, P., Leite, P.P., Tavares, M., Mansinho, K., Duque, L.M., Fernandes, C., Cordeiro, R., Borrego, M.J., Pelerito, A., de Carvalho, I.L., Núncio, S., Manageiro, V., Minetti, C., Machado, J., Haussig, J.M., Croci, R., Spiteri, G., Casal, A.S., Mendes, D., Souto, T., Pocinho, S., Fernandes, T., Firme, A., Vasconcelos, P., Freitas, G. (2022). Ongoing monkeypox virus outbreak, Portugal, 29 April to 23 May 2022. _Eurosurveillance, 27_ 2200424. [https://doi.org/10.2807/1560-7917.ES.2022.27.22.2200424](https://doi.org/10.2807/1560-7917.ES.2022.27.22.2200424) -- Vivancos, R., Anderson, C., Blomquist, P., Balasegaram, S., Bell, A., Bishop, L., Brown, C.S., Chow, Y., Edeghere, O., Florence, I., Logan, S., Manley, P., Crowe, W., McAuley, A., Shankar, A.G., Mora-Peris, B., Paranthaman, K., Prochazka, M., Ryan, C., Simons, D., Vipond, R., Byers, C., Watkins, N.A., UKHSA Monkeypox Incident Management team, Welfare, W., Whittaker, E., Dewsnap, C., Wilson, A., Young, Y., Chand, M., Riley, S., Hopkins, S. (2022). Community transmission of monkeypox in the United Kingdom, April to May 2022. *Eurosurveillance, 27* 2200422. [https://doi.org/10.2807/1560-7917.ES.2022.27.22.2200422](https://doi.org/10.2807/1560-7917.ES.2022.27.22.2200422) +- Vivancos, R., Anderson, C., Blomquist, P., Balasegaram, S., Bell, A., Bishop, L., Brown, C.S., Chow, Y., Edeghere, O., Florence, I., Logan, S., Manley, P., Crowe, W., McAuley, A., Shankar, A.G., Mora-Peris, B., Paranthaman, K., Prochazka, M., Ryan, C., Simons, D., Vipond, R., Byers, C., Watkins, N.A., UKHSA Monkeypox Incident Management team, Welfare, W., Whittaker, E., Dewsnap, C., Wilson, A., Young, Y., Chand, M., Riley, S., Hopkins, S. (2022). Community transmission of monkeypox in the United Kingdom, April to May 2022. _Eurosurveillance, 27_ 2200422. [https://doi.org/10.2807/1560-7917.ES.2022.27.22.2200422](https://doi.org/10.2807/1560-7917.ES.2022.27.22.2200422) -- Yang, L., Tian, L., Li, L., Liu, Q., Guo, X., Zhou, Y., Pei, R., Chen, X., Wang, Y. (2022). Efficient assembly of a large fragment of monkeypox virus genome as a qPCR template using dual-selection based transformation-associated recombination. *Virologica Sinica*. [https://doi.org/10.1016/j.virs.2022.02.009](https://doi.org/10.1016/j.virs.2022.02.009) +- Yang, L., Tian, L., Li, L., Liu, Q., Guo, X., Zhou, Y., Pei, R., Chen, X., Wang, Y. (2022). Efficient assembly of a large fragment of monkeypox virus genome as a qPCR template using dual-selection based transformation-associated recombination. _Virologica Sinica_. [https://doi.org/10.1016/j.virs.2022.02.009](https://doi.org/10.1016/j.virs.2022.02.009) -- Adler, H., Gould, S., Hine, P., Snell, L. B., Wong, W., Houlihan, C.F., Osborne, J.C., Rampling, T., Beadsworth, M.B.J., Duncan, C.J.A., Dunning, J., Fletcher, T.E., Hunter, E.R., Jacobs, M., Khoo, S.H., Newsholme, W., Porter, D., Porter, R.J., Ratcliffe, L., Schmid, M.L., Semple, M.G., Tunbridge, A.J., Wingfield, T., Price, N.M., NHS England High Consequence Infectious Diseases (Airborne) (2022). Clinical features and management of human monkeypox: a retrospective observational study in the UK. *The Lancet Infectious Diseases*. [https://doi.org/10.1016/s1473-3099(22)00228-6](https://doi.org/10.1016/s1473-3099(22)00228-6) +- Adler, H., Gould, S., Hine, P., Snell, L. B., Wong, W., Houlihan, C.F., Osborne, J.C., Rampling, T., Beadsworth, M.B.J., Duncan, C.J.A., Dunning, J., Fletcher, T.E., Hunter, E.R., Jacobs, M., Khoo, S.H., Newsholme, W., Porter, D., Porter, R.J., Ratcliffe, L., Schmid, M.L., Semple, M.G., Tunbridge, A.J., Wingfield, T., Price, N.M., NHS England High Consequence Infectious Diseases (Airborne) (2022). Clinical features and management of human monkeypox: a retrospective observational study in the UK. _The Lancet Infectious Diseases_. [https://doi.org/10.1016/s1473-3099(22)00228-6]() -- Mauldin, M.R., McCollum, A.M., Nakazawa, Y.J., Mandra, A., Whitehouse, E.R., Davidson, W., Zhao, H., Gao, J., Li, Y., Doty, J., Yinka-Ogunleye, A., Akinpelu, A., Aruna, O., Naidoo, D., Lewandowski, K., Afrough, B., Graham, V., Aarons, E., Hewson, R., Vipond, R., Dunning, J., Chand, M., Brown, C., Cohen-Gihon, I., Erez, N., Shifman, O., Israeli, O., Sharon, M., Schwartz, E., Beth-Din, A., Zvi, A., Minn Mak, T., Kai Ng, Y., Cui, L. Lin, R.T.P., Olson, V.A., Brooks, T., Paran, N., Ihekweazu, C., Reynolds, M. G. (2022). Exportation of monkeypox virus from the African continent. *The Journal of infectious diseases, 225*, 1367-1376. [https://doi.org/10.1093/infdis/jiaa559](https://doi.org/10.1093/infdis/jiaa559) +- Mauldin, M.R., McCollum, A.M., Nakazawa, Y.J., Mandra, A., Whitehouse, E.R., Davidson, W., Zhao, H., Gao, J., Li, Y., Doty, J., Yinka-Ogunleye, A., Akinpelu, A., Aruna, O., Naidoo, D., Lewandowski, K., Afrough, B., Graham, V., Aarons, E., Hewson, R., Vipond, R., Dunning, J., Chand, M., Brown, C., Cohen-Gihon, I., Erez, N., Shifman, O., Israeli, O., Sharon, M., Schwartz, E., Beth-Din, A., Zvi, A., Minn Mak, T., Kai Ng, Y., Cui, L. Lin, R.T.P., Olson, V.A., Brooks, T., Paran, N., Ihekweazu, C., Reynolds, M. G. (2022). Exportation of monkeypox virus from the African continent. _The Journal of infectious diseases, 225_, 1367-1376. [https://doi.org/10.1093/infdis/jiaa559](https://doi.org/10.1093/infdis/jiaa559) - Khalil, A., Samara, A., O’Brien, P. et al. Call for a unified approach to Monkeypox infection in pregnancy: Lessons from the COVID-19 pandemic. Nat Commun 13, 5038 (2022). [https://doi.org/10.1038/s41467-022-32638-w](https://doi.org/10.1038/s41467-022-32638-w) @@ -75,13 +75,14 @@ These tools have been adapted/developed for use with the mpox virus. They could ## Other useful resources -- News from Swedish Public Health Agency FoHM on mpox ([in Engish](https://www.folkhalsomyndigheten.se/the-public-health-agency-of-sweden/communicable-disease-control/disease-information-about-monkeypox/)) ([in Swedish](https://www.folkhalsomyndigheten.se/smittskydd-beredskap/smittsamma-sjukdomar/apkoppor/)) -- [Swedish Public Health Agency information about mpox cases](https://www.folkhalsomyndigheten.se/smittskydd-beredskap/utbrott/aktuella-utbrott/apkoppor-internationellt-maj-2022-/) (only in Swedish) -- [Information about PCR detection of mpox from the Swedish Public Health Agency FoHM](https://www.folkhalsomyndigheten.se/mikrobiologi-laboratorieanalyser/laboratorieanalyser-och-tjanster/analyskatalog/pcr/orthopoxvirus/) (only in Swedish) +- News from Swedish Public Health Agency FoHM on mpox ([in Engish](https://www.folkhalsomyndigheten.se/the-public-health-agency-of-sweden/communicable-disease-control/disease-information-about-monkeypox/)) ([in Swedish](https://www.folkhalsomyndigheten.se/smittskydd-beredskap/smittsamma-sjukdomar/apkoppor/)) +- [Swedish Public Health Agency information about mpox cases April 2024 - July 2024](https://www.folkhalsomyndigheten.se/smittskydd-beredskap/utbrott/utbrottsarkiv/mpox-sverige-april-2024/) (only in Swedish). +- [Swedish Public Health Agency information about mpox cases May 2022 - May 2023](https://www.folkhalsomyndigheten.se/smittskydd-beredskap/utbrott/aktuella-utbrott/apkoppor-internationellt-maj-2022-/) (only in Swedish). +- [Information about PCR detection of mpox from the Swedish Public Health Agency FoHM](https://www.folkhalsomyndigheten.se/mikrobiologi-laboratorieanalyser/laboratorieanalyser-och-tjanster/analyskatalog/pcr/orthopoxvirus/) (only in Swedish) - [WHO - Factsheet on mpox](https://www.who.int/news-room/fact-sheets/detail/monkeypox) - [WHO - Multi-country outbreak of mpox bi-weekly situation reports](https://www.who.int/emergencies/situation-reports) - [WHO - Q&A related to mpox](https://www.who.int/news-room/questions-and-answers/item/monkeypox) -- [ECDC & WHO - Mpox report](https://monkeypoxreport.ecdc.europa.eu/) +- [ECDC & WHO - Mpox report](https://monkeypoxreport.ecdc.europa.eu/) - [ECDC - Mpox infection prevention and control guidance](https://www.ecdc.europa.eu/en/publications-data/monkeypox-infection-prevention-and-control-guidance-primary-and-acute-care) - [ECDC update on the outbreak](https://www.ecdc.europa.eu/en/publications-data/monkeypox-multi-country-outbreak-second-update) from October 2022 - [ECDC - Factsheet on mpox for health professionals](https://www.ecdc.europa.eu/en/all-topics-z/monkeypox/factsheet-health-professionals) diff --git a/content/english/topics/mpox.md b/content/english/topics/mpox.md index cb3762e8..3bf11728 100644 --- a/content/english/topics/mpox.md +++ b/content/english/topics/mpox.md @@ -6,22 +6,21 @@ credits: Image by UK Research and Innovation toc: false topic: Mpox menu: - topics_menu: - name: Mpox - identifier: mpox + topics_menu: + name: Mpox + identifier: mpox aliases: - - /topics/monkeypox/ + - /topics/monkeypox/ --- -
-  -  This page is under development, with more resources being added shortly. In the meantime, check out the mpox page in our 'emerging pathogens' section. That page contains more extensive information and useful links to other related resources. -
+## Mpox as an emerging disease + +Check out the mpox page in our 'emerging pathogens' section. That section provides recent information on pathogens that are considered to be 'emerging' (i.e. data is not necessarily available for Sweden, though early information about outbreaks is available). ## Background Mpox a.k.a. Monkeypox is caused by the mpox virus, and is a zoonotic disease (i.e. it is transmitted from animals to humans). The mpox virus is a member of the *Orthopoxvirus* genus in the family *Poxviridae*. It is closely related to the variola virus, which causes smallpox and has had a marked impact on human populations throughout history. [According to WHO](https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON385) there are currently two clades of mpox virus; the West African clade and the Congo Basin (Central African) clade. An outbreak began in Europe during May 2022. As of Septmber 2022, more than 20,000 cases have been detected in Europe, with 161 cases detected in Sweden and reported to the [Swedish Public Health Agency](https://www.folkhalsomyndigheten.se/smittskydd-beredskap/utbrott/aktuella-utbrott/apkoppor-internationellt-maj-2022-/). -Clinically, mpox is typically characterised by fever, an unexplained acute rash, and lymphadenopathy. Additional symptoms and complications may also occur, though. For more information about the clinical symptoms of mpox, see [information from the CDC](https://www.cdc.gov/poxvirus/monkeypox/symptoms/index.html). The incubation period of the virus is typically 5-13 days, but can be as long as three weeks. Close personal contact with an infected individual is currently (September, 2022) the most common way of transmission and limited information is available regarding mortality ([Adler et al., 2022](https://doi.org/10.1016/S1473-3099(22)00228-6)). The European Medicines Agency has not yet approved a vaccine in Europe. However, EU healthcare has access to doses of [Jynneos vaccine](https://www.cdc.gov/poxvirus/monkeypox/vaccines/jynneos.html), which is approved by the FDA for both mpox and smallpox. These vaccine doses were donated by the USA and Canada via the European Health Emergency Preparedness and Response Authority (HERA). +Clinically, mpox is typically characterised by fever, an unexplained acute rash, and lymphadenopathy. Additional symptoms and complications may also occur, though. For more information about the clinical symptoms of mpox, see [information from the CDC](https://www.cdc.gov/poxvirus/monkeypox/symptoms/index.html). The incubation period of the virus is typically 5-13 days, but can be as long as three weeks. Close personal contact with an infected individual is currently (September, 2022) the most common way of transmission and limited information is available regarding mortality ([Adler et al., 2022]()). The European Medicines Agency has not yet approved a vaccine in Europe. However, EU healthcare has access to doses of [Jynneos vaccine](https://www.cdc.gov/poxvirus/monkeypox/vaccines/jynneos.html), which is approved by the FDA for both mpox and smallpox. These vaccine doses were donated by the USA and Canada via the European Health Emergency Preparedness and Response Authority (HERA). -There are no approved treatments for human mpox as of September 2022. However, brincidofovir and tecovirimat, which are both drugs approved in the USA for use against smallpox, have been repurposed and show promise in animal studies ([Adler et al., 2022](https://doi.org/10.1016/S1473-3099(22)00228-6)). +There are no approved treatments for human mpox as of September 2022. However, brincidofovir and tecovirimat, which are both drugs approved in the USA for use against smallpox, have been repurposed and show promise in animal studies ([Adler et al., 2022]()). diff --git a/content/english/updates/mpox_aug24.md b/content/english/updates/mpox_aug24.md new file mode 100644 index 00000000..fb2e384e --- /dev/null +++ b/content/english/updates/mpox_aug24.md @@ -0,0 +1,13 @@ +--- +title: "Information about mpox in Sweden" +date: 2024-09-02 +summary: A case of clade 1 mpox has recently been detected in Sweden. See here to see the resources currently available on the Swedish Pathogens Portal. +banner: /topic_thumbs/topic_mpox.jpg +banner_caption: "Depiction of mpox virus from UK Research and Innovation." +--- + +Mpox is a zoonotic disease caused by the mpox virus. It has 2 clades (clades 1 and 2), each with two subclades. Clade 1 is the most contagious, and has a higher mortality rate. It is usually transmitted from animals to humans, although it can be transmitted between humans upon close contact. More general information about mpox is available on our [mpox topic](/topics/mpox/) and [mpox emerging pathogens](/pathogens/mpox/) pages, and from [Folkhälsomyndigheten](https://www.folkhalsomyndigheten.se/the-public-health-agency-of-sweden/communicable-disease-control/disease-information-about-mpox/). + +In August 2024, the first case of clade 1 variant mpox was diagnosed outside of African continent. The case was detected in Sweden, although the individual was infected in Africa during clade 1 mpox outbreak. Sweden is fully prepared to diagnose, isolate people diagnosed with mpox. The threat to the general population is currently designated as low, with only occasional, imported cases, like that detected in Sweden, expected. More information about this particular case is available from [Folkhälsomyndigheten](https://www.folkhalsomyndigheten.se/the-public-health-agency-of-sweden/communicable-disease-control/disease-information-about-mpox/one-case-of-mpox-clade-i-reported-in-sweden/). + +The Swedish Pathogens Portal continues to monitor and investigate research resources linked to emergent diseases, like mpox. Information on such diseases, including on related data and other research resources, is added to our [emerging pathogens section](/pathogens/). Where possible, the portal will also create data dashboards, and other resources, to display data and accelerate research in the area. diff --git a/data/mpox_page_announcements.json b/data/mpox_page_announcements.json index 4c0d7466..328f995f 100644 --- a/data/mpox_page_announcements.json +++ b/data/mpox_page_announcements.json @@ -1,4 +1,9 @@ [ + { + "date_time": "2024-08-15", + "title": "Case of mpox in Sweden", + "text": "A single case of mpox clade 1 was detected in Sweden in August 2024. No additional control measures are needed for this case, which originated in an area in which mpox is endemic. More information about this case is available from Folkhalsomyndigheten. Data on the number of mpox cases in Sweden between April and July 2024 is also available from Folkhalsomyndigheten (information only available in Swedish)." + }, { "date_time": "2022-06-03", "title": "Workflows for sequence variant analysis",