Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola Virus Disease (EVD) outbreak on 04 September 2025 after PCR confirmation of Ebola virus (EBOV), formely Zaïre ebolavirus, in patient’s specimens from Bulape Heath Zone, in Kasai Province. The re-emergence of EBOV in remote areas with very limited access is not unprecedent since 15 Ebola outbr...| Virological - Latest posts
Mpox_A2.PDF (423.7 KB) On 13 June 2025, CERFIG (Centre de Recherche et de Formation en Infectiologie de Guinée confirmed Mpox infection in a 53‑year‑old patient attending the Dermatology Department of CHU Donka, Conakry. Whole‑genome sequencing performed on crust lesion samples with Oxford Nanopore (metagenomic approach) and Illumina iSeq100 (targeted capture) recovered 99.9 % and 97.8 % of the viral genome, respectively. Phylogenetic analysis placed the virus in lineage A.2.2 of Clade...| Virological - Latest posts
National Institutes of Health National Library of Medicine Division of Intramural Research Bethesda, MD Supervisor: Martha Nelson Apply: https://www.training.nih.gov/jobs/pdf-cb-091625/ The post-doctoral scholar will study how rapidly evolving RNA viruses (e.g., H5N1 avian influenza, coronavirus) transmit and evolve at the human-animal interface, using advanced Bayesian phylodynamic approaches and large-scale genomic data. This project is part of a longstanding government-academic partnership...| Virological - Latest posts
This post has been updated to include new sequences, new analysis, and revised estimates. Background Sierra Leone confirmed its first Mpox case on January 10, 2025, with the Minister of Health declaring a Public Health Emergency shortly thereafter. Cases have surged in recent weeks, with over 2,800 new infections reported as of May 22, 2025, strongly indicating ongoing human-to-human transmission similar to patterns observed in the early stages of the ongoing outbreaks in Nigeria and the DRC ...| Virological - Latest posts
SARS-CoV-2 Spike displays multiple adaptive changes in addition to the furin cleavage site. Robert F. Garry1-3 1Department of Microbiology and Immunology, Tulane University Medical Center, 1430 Tulane Avenue, New Orleans, Louisiana 70112 USA. 2Zalgen Labs, LLC, Germantown, MD, USA. 3Global Viral Network, Tampa, Florida Abstract SARS-CoV-2 is a pandemic pathogen with highly transmissibility by the respiratory route and ability to replicate in many animals, including humans. The evolution of SA...| Virological - Latest posts
Jonathan E. Pekar, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK Thomas P. Peacock, The Pirbright Institute, Woking, UK, GU24 0NF; Department of Infectious Disease, Imperial College London, UK, W2 1PG Louise Moncla, University of Pennsylvania, PA 19104, USA Praneeth Gangavarapu, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA Divya Venkatesh, Department of Biology, University of Oxford, Oxford OX1 3SY, UK Daniel H. Gold...| Virological - Latest posts
Introduction Case History: On January 30, 2025, the Ministry of Health declared an outbreak of Sudan Ebola Virus (SUDV) Disease in Kampala, Uganda, following the death of a healthcare worker at Mulago National Referral Hospital. The index case, a 32-year-old male nurse, presented with fever and other symptoms on 19th January 2025 and sought care at three healthcare facilities, one in Kampala one in Wakiso and another in Mbale district, before succumbing to the illness 10 days later (29th Janu...| Virological - Latest posts
> Fieldbioinformatics updated to 1.6.0 Fieldbioinformatics has been the first line recommendation by the artic network for generation of consensus sequences from Nanopore viral amplicon sequencing data since the west african ebola outbreak in 2016. The pipeline has changed a great deal since then, but had remained mostly unchanged from the early stages of the SARS-CoV-2 (SC2) outbreak when the sudden need for reliable analysis pipelines prompted rapid development of the pipeline. Its widespre...| Virological - Latest posts
Preliminary analysis of 98 genomic sequences of MPXV clade Ib cases from Burundi, July to September 2024 Introduction A large mpox clade Ib virus outbreak started in the province of South Kivu in the Democratic Republic of the Congo (DRC) and is rapidly geographically expanding to other areas within the DRC as well as to other countries surrounding the DRC. Especially Burundi is severely affected with close to 1531 confirmed cases of mpox Clade Ib virus infections since the first detection at...| Virological - Latest posts
On October 28, 2024, Lassa virus (LASV) was identified in an individual residing in Iowa, USA with travel history from Liberia. Initial diagnostic testing was performed at the University of Nebraska Medical Center and the specimen was confirmed LASV positive by the Viral Special Pathogens Branch (VSPB) at the US Centers for Disease Control and Prevention (CDC). No secondary transmission cases were identified over the following 3-week time span. The virus was sequenced using unbiased next gene...| Virological - Latest posts
Keywords: Monkeypox virus, Mpox, Outbreak, Human-to-Human, Genomic, APOBEC3, Kinshasa, DRC. The ongoing mpox outbreaks in the Democratic Republic of Congo (DRC) has raised significant public health concerns, particularly due to the emergence of the newly identified viral subclade Ib. Recently, we reported human-to-human transmission through sexual contact involving this subclade (1). This transmission route may be an important factor contributing to the virus’s spread from its initial hotsp...| Virological - Latest posts
Since 2005, there have been eight public health emergency of international concern (PHEIC) declarations. The tow last are related to mpox outbreaks, the first one from 2022-2023with clade IIb that spread globally in more than 100 countries and more recently since 14th august 2024 an outbreak with clade Ib (WHO, 2024). The current declaration followed the declaration of a Public Health Emergency of Continental Security (PHECS) by Africa CDC on August 13th and both were consecutive to the conce...| Virological - Latest posts
We are announcing Pathoplexus, a specialised genomic database for viruses of public health importance. By combining modern open-source software with transparent governance structures, Pathoplexus fills a niche within the existing genomic sequencing database landscape, aiming to meet requests from both data submitters and users and striving to improve equity. Today we launch with four virus species, Ebolavirus sudan, Ebolavirus zaire, West Nile virus and Crimean-Congo haemorrhagic fever virus....| Virological - Latest posts
On 29 July 2024, the Kenyan Ministry of Health confirmed a case of mpox in Taita Taveta County which borders Tanzania (Mpox – African Region). The reported case was from a 42-year-old male, a long-distance truck driver who had travelled from Kampala, Uganda to Mombasa, Kenya and was enroute to Rwanda at the time of detection. The date of onset of symptoms was 3 July 2024 and the case was detected and isolated by the Kenyan Ministry of Health officials on 22 July 2024 after presenting with c...| Virological - Latest posts
Preliminary analysis of full genome sequences of 58 MPXV clade Ib cases from Kamituga and Kamanyola, South-Kivu , DRC Recently, we showed that the MPXV outbreak in South Kivu is associated with a novel sub- lineage of clade I viruses (Murhula Masirika et al, 2024). The majority of these cases seem to be transmitted through heterosexual contact, with also person-to-person transmission within and outside the households. Here we provide an update of the ongoing sequencing effort. We sequenced MP...| Virological - Latest posts
Due to length constraints on virological.org posts, we are splitting this report into two parts that should be read as a single report. This is Part 2, containing Findings sections 6 through 9, Concluding remarks, Acknowledgements, and References. For Background, Data, Methods, and Findings sections 1 through 5. See Part 1 Michael Worobey, University of Arizona, Tucson, AZ 85705, USA Karthik Gangavarapu, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, ...| Virological - Latest posts
(Replace this first paragraph with a brief description of your new category. This guidance will appear in the category selection area, so try to keep it below 200 characters.) Use the following paragraphs for a longer description, or to establish category guidelines or rules: Why should people use this category? What is it for? How exactly is this different than the other categories we already have? What should topics in this category generally contain? Do we need this category? Can we merge ...| Virological - Latest posts
This category is for posts about viruses that don’t have their own category. They may get their own category in future and then these posts will be moved there.| Virological - Latest posts
On Sunday, April 21st, 2024, “in the interest of public transparency and ensuring the scientific community has access to this information as quickly as possible to encourage disease research and development to benefit the U.S. dairy industry”, the National Veterinary Services Laboratories (NVSL) of the Animal and Plant Health Inspection Service (APHIS) of the U.S. Department of Agriculture (USDA) shared H5N1 sequence reads from 239 Biosamples related to the ongoing H5N1 clade 2.3.4.4b inf...| Virological - Latest posts
This category is for analysis and discussion about the H5N1 avian lineage of Influenza A that emerged in around 2020 and has spread globally including the recent outbreak in cattle in the USA.| Virological - Latest posts
Solomon K. Langat1, Genay Pilarowski2, Samson Limbaso1, Paul Oluniyi2, Daniele Jones2, Albert Nyunja1, Edith Koskei1, Samuel Owaka1, Hellen Koka1, Francis Mulwa1, James Mutisya1, Victor Ofula1, Edith Chepkorir1, Joel Lutomiah1, Cristina M. Tato2, Samoel Khamadi1. Affiliations Centre for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya Chan Zuckerberg Biohub, San Francisco, CA, United States of America Introduction Hepatitis A is a vaccine-preventable liver disease caus...| Virological - Latest posts
First mpox virus clade Ib cases in Goma, Nord Kivu, DRC: Potential risk for a larger outbreak Since the identification of the first human case of mpox in 1970, the Democratic Republic of the Congo (DRC) has borne the greatest burden of disease among endemic countries, which experiencing sporadic outbreaks almost every year. From January 2023, the DRC has seen a drastic increase in the number of suspected mpox cases, with an estimated 20,000 cases and 1,000 deaths reported at the time of writi...| Virological - Latest posts
Dear Colleagues, Viruses invites the submission of original research and review articles to this Special Issue, covering challenges in HIV diversity. The articles can cover any level of diversity, from intrapatient immune evasion and development of drug resistance, to global challenges for vaccine design. Reports of research on HIV recombination at all levels, from intrapatient to inter-subtype, are encouraged. Although HIV-1 M-group viruses comprise the majority of global AIDS cases, submiss...| Virological - Latest posts
The ongoing mpox virus outbreak of Kamituga in South Kivu province, Democratic Republic of Congo, is associated with a novel Clade I sublineage Authors: Leandre Murhula Masirika1,2, Jean Claude Udahemuka3,4, Leonard Schuele5, Pacifique Ndishimye4,6,7, Saria Otani8, Justin Bengehya Mbiribindi9, Jean M. Marekani10, Léandre Mutimbwa Mambo11, Marjan Boter5, David F. Nieuwenhuijse5, Trudie Lang12 ,Bilembo Kitwanda Steeven9, Nadine Malyamungu Bubala9, Ernest Balyahamwabo Kalalizi2, Jean Pierre Mus...| Virological - Latest posts
There is now a paper on the outbreak described in this post and another one on virological.| Virological - Latest posts
Felipe Gomes Naveca1,2 Tatiana Amaral Pires de Almeida1,3, Victor Souza1, Valdinete Nascimento1, Dejanane Silva1, Fernanda Nascimento1, Matilde Mejía1, Yasmin Silva de Oliveira1, Luisa Rocha4, Natana Xavier4, Janis Lopes4, Rodrigo Maito4, Cátia Meneses4, Tatyana Amorim5, Daniel Barros5, Luciana Fé5, Ana Ruth Arcanjo5, Guilherme Araújo5, Rosiane Rodrigues6, Stella Albuquerque6, Cristiane Mattos6, Ciciléia Silva6, Aline Linhares6, Taynã Rodrigues7, Francy Mariscal7, Karolina Sabino7, Sels...| Virological - Latest posts
On August 15th, 2023, the Chad Ministry of Public Health and Prevention has declared an outbreak of dengue virus (DENV) in the health district of Abéché, Ouaddaï province in eastern Chad [1]. As reported on 19th December 2023, there have been 2037 suspected cases, including 100 DENV-confirmed cases across four provinces (N’Djamena (n=49), Ouaddaï (n=33), Wadi Fira (n=12), and Sila (n=6)). As part of the Africa CDC - Africa Pathogen Genomics Initiative (Africa PGI) regional sequencing pr...| Virological - Latest posts
UPDATE - 2023-12-04 NEW FEATURE ANNOUNCEMENT We have an exciting update to these RSV primer schemes! The ARTIC-RSV tiled amplicon scheme has now been validated for multiplexing the RSV A and RSV B primer scheme into a single reaction, facilitating sequencing without the need for prior typing of samples and thus removing an extra step in some workflows. We also provide a solution for the additional bioinformatic complexity and have developed a pipeline that makes RSV genome analysis quick and ...| Virological - Latest posts
Preprint_CHIK_NGS_KDG_2023.pdf (276.4 KB) Idrissa Dieng1*, Bacary Djilocalisse Sadio1*, Alioune Gaye2, Samba Niang Sagne3, Marie Henriette Dior Ndione1, Mouhamed Kane1, Mamadou Korka Diallo3, Bocar Sow3, Safietou Sankhe1, Amadou Diallo3, Madeleine Dieng1, Serge Freddy Moukaha Doukanda1, Maimouna Mbanne1, Seynabou Mbaye Ba Souna Diop1, Diamilatou Balde1, Mignane Ndiaye1, Khalidou Djibril Sow4, Maryam Diarra3, Abdoulaye Sam5, Ababacar Mbaye6, Boubacar Diallo7, Yoro Sall5, Ousmane Faye7, Boly Di...| Virological - Latest posts
For those who might be interested I had a go at remaking Figure 1 but including BA.2.86 (as the most extreme example of a second generation BA.2 lineage). As you can see it really stretches what its possible to show in these types of schematics. Also notable among all these lineages is the massive overrepresentation of non-synonymous relative to synonymous mutations (mostly absent except in BA.2.86 which has just 1).| Virological - Latest posts
NIAID Data Ecosystem Discovery Portal Emily Haag, Candice Czech, Ginger Tsueng, Nichollette Acosta, Jason Lin, Dylan Welzel, Everaldo Rodolpho, Chunlei Wu, Andrew I. Su, Laura D. Hughes, Wilbert Van Panhuis, Asiyah Lin, Meghan Hartwick, Jack DiGiovanna, Sai Subrahmanian, Deepti Jain, Poro Burman, Eric Tobin, Sudha Venkatachari, Maria Giovanni, Zorana Mitrovic Vucicevic Introduction The world is sitting on a wealth of knowledge that has yet to be fully realized. Researchers around the globe ge...| Virological - Latest posts
Genomic analysis of selected Vibrio cholerae isolates from the 2023 Cholera outbreak in Zambia: A use-case for integration of whole-genome sequencing in cholera outbreak response Background Vibrio cholerae is a Gram-negative bacterium responsible for causing the infectious disease cholera. It is estimated that V. cholerae causes millions of cases of cholera each year, resulting in thousands of deaths globally. To combat this disease, the isolation and serotyping of V. cholerae are crucial for...| Virological - Latest posts
Towards Pandemic-Scale Ancestral Recombination Graphs of SARS-CoV-2 Shing H. Zhan1, Anastasia Ignatieva2,3,*, Yan Wong1,*, Katherine Eaton4, Benjamin Jeffery1, Duncan S. Palmer1, Carmen L. Murall4, Sarah P. Otto5, Jerome Kelleher1,† 1Big Data Institute , Li Ka Shing Centre for Health Information and Discovery, University of Oxford, United Kingdom 2Department of Statistics, University of Oxford, United Kingdom 3School of Mathematics and Statistics, University of Glasgow, United Kingdom 4Nati...| Virological - Latest posts
Sarah Nadeau Visiting Postdoc, Fred Hutchinson Cancer Research Center sarahnadeau266@gmail.com This is a write-up I put together during a two-month visit to Erick Matsen’s group. Many thanks to Erick and his group for supporting the project. Thanks also to Jakob McBroome, Christopher Gulvik, and Jay Gee for helpful comments. Any errors are entirely my own. Problem statement Identifying transmission clusters in a pathogen outbreak - epidemiologically linked cases - is key to identifying at-r...| Virological
A discussion forum for analysis and interpretation of virus molecular evolution and epidemiology.| Virological
New York City (NYC) experienced a large mpox outbreak in 2022, with 3821 cases. Case counts remained low through most of 2023 at only 184 cases, a mean of 3.5 cases per week. However, incidence increased in 2024, with 191 cases as of 4 May 2024, a mean of 10.6 cases per week. To investigate the evolutionary dynamics underlying this increase in case count, we performed phylogenetic and phylodynamic analysis of the 81 mpox virus (MPXV) genomes sampled in 2023 and 2024 in NYC, sequenced by the N...| Virological
Due to length constraints on virological.org posts, we are splitting this report into two parts that should be read as a single report. This is Part 1, containing Background, Data, Methods, and Findings sections 1 through 5. See Part 2 for Findings sections 6 through 9, Concluding remarks, Acknowledgements, and References. Michael Worobey, University of Arizona, Tucson, AZ 85705, USA Karthik Gangavarapu, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, ...| Virological