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Mpox: ongoing research, data, publications and preprints

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. 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; 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) 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). 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. 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

In this section, we present announcements about ongoing research efforts primarily by (but not limited to) researchers and institutions based in Sweden. The intention is to ‘highlight’ these efforts as soon as possible, so that we can maximise their usefulness to researchers.

Please feel free to submit an announcement using the form below or by sending an e-mail to

Lists of data, tools, publications, and other potentially useful information are provided further down on the page and likely to be more complete.

Workflows for sequence variant analysis


Two Galaxy workflows for mpox sequence variant analysis have been made available. One workflow (Illumina metatranscriptomic PE) deals with variant analysis from metatranscriptomic data. The other workflow (Report generation) can be used to generate the final variant analysis reports/plots. The workflows, and instructions on how to use them, are found here. More workflows will be added here over time

Mpox viral data submission


Since 13 May 2022, 92 laboratory confirmed cases of mpox have been reported to the WHO from Member States that are not endemic for mpox virus. With epidemiological investigations ongoing we are repurposing the pipelines built during the COVID-19 pandemic to demonstrate preparedness for other infectious disease outbreaks. Therefore we are seeking your help in connecting us to laboratories or individuals who are active in sequencing mpox virus. We have created a document outlining the data submission into our open databases with a particular focus on attribution for data producers and can provide technical support to streamline the data submission process. If you are aware of ongoing sequencing efforts of mpox virus or would like to suggest any other data resources that should be connected please contact

Contact: European COVID-19 Data Portal/BY-COVID,

Nextstrain build


Nextstrain have updated their mpox build with additional available genomes from Portugal and a genome from Germany associated with the current multi-country outbreak. The latest Nextstrain build can found here.

Datasets available

Tools available

These tools have been adapted/developed for use with the mpox virus. They could potentially be adapted for use with other viruses, and with other types of infectious disease. They are thus key in aiding future pandemic preparedness.

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.

  • Pfaff, F., Hoffmann, D., Beer, M. (2022). Monkeypox genomic surveillance will challenge lessons learned from SARS-CoV-2. Lancet, 400, 10345.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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).

  • Karan A, Styczynski AR, Huang CH, Sahoo MK, Srinivasan K, Pinsky BA, et al. Human monkeypox without viral prodrome or sexual exposure, California, USA, 2022. Emerg Infect Dis. 2022 Oct.

  • Kaler J, Hussain A, Flores G, et al. (July 03, 2022) Monkeypox: A Comprehensive Review of Transmission, Pathogenesis, and Manifestation. Cureus 14(7): e26531.

Other useful resources