Genomic Surveillance Unit (Wellcome Sanger Institute)

Could another mosquito species be confounding malaria vector control efforts in West Africa? 🦟 Members of the Anopheles gambiae complex, including An. gambiae and An. coluzzii, are the most important vectors of malaria in Africa. These species cannot be distinguished without genomics as they look similar to other species within the group. For our final Journal Club of 2024, join Professor Alessandra della Torre from the Sapienza Università di Roma, who will explore recent genomic evidence identifying a distinct cryptic taxon within the Anopheles gambiae complex, provisionally named the ‘Bissau molecular form’, in the coastal regions of far-west Africa. The study analysed the whole genome sequences of Anopheles mosquitoes available through the MalariaGEN Vector Observatory and the results have been published in Nature Communications Biology: https://lnkd.in/eAUsBxed While the Bissau molecular form hasn’t been officially named or classified yet, the study found that this cryptic species lacks common insecticide resistance mechanisms found in An. gambiae and An. coluzzii. Register to learn more about how this species was identified using genomic evidence and what this means for malaria control in far-west Africa. https://lnkd.in/eM_zyQPn Beniamino Caputo, PhD, Carlo Maria De Marco, Giordano Bottà PhD, Alfred Amambua-Ngwa, Dr. Sessinou Benoît ASSOGBA, PhD, Chris Clarkson, Jacob Tennessen, David Weetman, Alistair Miles

Growing capacity for genomic data analysis in Africa = improved #malaria vector control 🖥️ Today, participants from the 3rd cohort of the PAMCA Pan-African Mosquito Control Association-MalariaGEN training course in data analysis for the genomic surveillance of African malaria vectors met for a virtual hackathon. 👏 The hackathon was an opportunity for this year's training cohort to apply concepts learned during the course to work on genomic data analysis projects. Participants and teaching assistants engaged in a series of productive sessions collaborating with each other to explore, discuss findings, and share feedback on their genomic data analysis projects. These projects aim to fill gaps in current knowledge on malaria mosquitoes by identifying any new patterns and trends in the genomic data that may have a public health significance. The focus of the projects ranges from: 🌍 Extensive exploratory analysis on samples from specific countries 🧪 Investigating resistance patterns to specific insecticides 🧬 Identifying potential new genes linked with insecticide resistance across multiple countries 🦟 Analysing the geographic population structures and genetic diversity of lesser-studied Anopheles species "It is yet another great opportunity to dive into malaria vector genomics data from projects across Africa. Initiatives like these are important for strengthening data analysis capacity building efforts on the continent to maximise the public health impact of vector genomics work." Elijah Juma, PhD, Manager, Vector Genomics Program, PAMCA "Through our close, continuing collaboration with PAMCA, we're delighted to have held this hackathon for the third time. Beyond the learning and exchange of ideas, it is also a platform for initiating and extending collaboration with other individuals and groups in African institutions - this is a key part of what this PAMCA-MalariaGEN training course is all about." Alistair Miles, Malaria Vector Surveillance Lead, Genomic Surveillance Unit (Wellcome Sanger Institute) An exciting announcement on the next iteration of the training course is coming soon - keep an eye on our channels 👀 Meanwhile, workshop modules and data materials remain openly accessible on GitHub for anyone interested in self-directed learning: https://lnkd.in/etfDbaDK

The Global Preparedness Monitoring Board, which works to track and monitor global pandemic preparedness, has launched its 2024 annual report. The report lays out 15 complex and interconnected drivers of pandemic risk, including biosecurity threats, rapid technological innovation, misinformation, and entrenched social and economic inequity. It also provides a roadmap for the global response to ensure that efforts to prevent pandemics today are strong and flexible enough to respond to the next pandemic. Here are some takeaways from the report: - The emergence and spread of pathogens are not random events. An increasingly interconnected world contributes to the spread of pathogens. "The interconnectedness of our world is a double-edged sword. It spreads diseases faster, but it also gives us the tools to respond swiftly if we invest in the right technologies." Dr Palitha Abeykoon, GPMB Board Member. - Adapt, protect, connect. The next pandemic will be different from the last, so responses must be adaptable to changing local, national, and global contexts. - Maximum equity equals maximum security. Social and economic inequities are intertwined with pandemic vulnerability. Prioritising equity, including in access to technological innovation, will improve global health security. - Advances in biotechnological innovation during the COVID-19 pandemic, including in genomic surveillance, are crucial for effective epidemic and pandemic preparedness and response. However, the report emphasises that their momentum must be maintained, and more attention needs to be directed towards areas with relatively less innovation such as information management and trust-building approaches. Read the full report: https://lnkd.in/eaVeEQYe What are your takeaways from the report? Comment below ⤵️ #pandemicpreparedness #genomicsurveillance 

The October edition of our monthly Journal Club series is all about drug resistance in #malaria parasites 💊 A recent review by the GSU's Malaria Parasite Surveillance Team provided the most comprehensive overview of kelch13 genetic markers, which are closely linked to artemisinin partial resistance (ART-R) in Plasmodium falciparum. Full pre-print: https://lnkd.in/eyfrF4Pv Explainer article: https://lnkd.in/eD3kK72x In this session, Dr Andrew Balmer will delve into the findings from this review, which maps data from over 112,000 P. falciparum genome sequences worldwide to track kelch13 mutations. By evaluating the spread of kelch13 mutations across different regions and over time, the review follows the emergence of ART-R in Southeast Asia and the concerning parallels now being seen in East and Northeast Africa. Our Journal Clubs are an interactive forum to learn and discuss the latest research on malaria genomic epidemiology - register to join the webinar on the 22nd: 📝 https://lnkd.in/e_-xFhzU Nina White | Eyyüb Selim Ünlü | Chiyun Lee | Richard Pearson | Jacob Almagro-Garcia | Cristina Ariani

From cutting-edge training and new analytical tools to impactful research results, we’re making genomic surveillance more accessible. This month members of our team attended the 9th Genomic Epidemiology of Malaria #GEM2024 conference and presented on a variety of topics. The first set of posters highlighted the outstanding efforts being made to develop and publish tools and learning materials that increase the accessibility of genomic analyses. Chiyun Lee, Senior Data Scientist, showed off the Pf-Haploatlas: a free, interactive web app for analysing P.falciparum genes: https://lnkd.in/eejVbK5D Eyyüb Selim Ünlü, Data Scientist, highlighted a collection of free-to-use Jupyter notebooks focused on guiding new users through common analyses of genomic data without having to download anything: https://lnkd.in/eQbGwcqB Looking forward, our Parasite Data Lead Dr Richard Pearson presented on the upcoming plan to release Pf8, the next MalariaGEN data resource. It will include more than 33,000 samples from 99 partner studies. This will be 60% more samples than Pf7, the current version of the data resource. Paballo Chauke is our Training coordinator and he shone a spotlight on the excellent efforts of the joint collaboration between MalariaGEN and PAMCA Pan-African Mosquito Control Association. This includes a free online training course about African malaria vectors: https://lnkd.in/etfDbaDK Whilst the GSU builds a variety of tools and resources to expand the capacity and capabilities for genomic surveillance worldwide, we also perform groundbreaking research that advances the field of malaria genomics. Dr Nina White, Senior Data Scientist, presented her work analysing differing drug resistance markers and identifying the most common haplotypes. Our Translational Research Lead Dr Jacob Almagro-Garcia introduced a new beta-mixture model that accurately separates two-strain malaria infections by using whole-genome sequencing data. This helps researchers identify relatedness patterns within and between infections in malaria. Dr Brenas Jon presented his work comparing mosquitoes caught in a high-altitude balloon to those found at ground level from across the West African Sahel. His findings suggest that mosquitos in these areas were genetically similar, building on our knowledge about how migration patterns can contribute to endemic malaria. Dr Andrew Balmer shared efforts to understand the extent of artemisinin resistance. He shared how the recent increases in resistance in Africa mirror those in Southeast Asia 10-15 years ago: https://lnkd.in/eeVUBnW5 #GEM24 was a whirlwind of a conference, but proved to us yet again that genomic surveillance is an exciting and important field. Make sure you’re following our page for the latest genomic surveillance news.

The first day of the Genomic Epidemiology of Malaria #GEM2024 conference has kicked off with a deep dive into the Malaria Vector Genome Observatory by Anastasia Hernandez Koutoucheva 🦟 The Observatory is a collaborative effort to sequence the genomes of thousands of Anopheles mosquitoes and use those data to improve malaria control. 💬 “Community-driven development is key to sustained progress.” Explore the Anopheles genomic data, tools, research, and more built and shared by a global network of Malaria Vector Genome Observatory partners: https://lnkd.in/e2SfDAEN Over the next three days, follow along for live updates and cutting-edge malaria genomics insights from the presentations, posters, and discussion at #GEM2024

Could there be a genetic link between how #malaria parasites and mosquitoes spread across regions? Learn more about this at our September Journal Club with Clara Rehmann 👥 Clara, a PhD researcher at the University of Oregon, will explore a recent study on how the shared evolutionary history between parasites and vectors provides clues about their similar geographic patterns. Clara and colleagues investigated a possible genetic link between their distribution in sub-Saharan Africa by analysing the location and whole genome data of Anopheles gambiae mosquitoes and Plasmodium falciparum parasites. Read the full study published in G3 Genes|Genomes|Genetics: https://lnkd.in/eA92b7Sd Register to join the Journal Club 👉 https://lnkd.in/eAJvyZQa

New pre-print by the GSU's Malaria Parasite Surveillance Team 📃 A review of over 112,000 published genomes reveals the rapid spread of artemisinin resistance 🔗 https://lnkd.in/eyfrF4Pv The review offers the most comprehensive overview yet of kelch13 genetic markers, which are closely linked to artemisinin partial resistance in Plasmodium falciparum parasites. Read more about the paper and what this means for malaria control ⬇️ Andrew Balmer | Nina White | Eyyüb Selim Ünlü | Chiyun Lee | Richard Pearson | Jacob Almagro-Garcia | Cristina Ariani

Join us for the West African Centre for Cell Biology of Infectious Pathogens (WACCBIP) - University of Ghana Ghana Workshop on Amplicon Sequencing and Genomic Surveillance of malaria - scaling up malaria drug and insecticide resistance surveillance using cutting-edge techniques that are shaping the future of malaria surveillance. Learn how genomic tools are being used to track and combat the spread of antimalarial and insecticide resistance and gain hands-on experience with illumina amplicon sequencing. #MalariaResearch #AmpliconSequencing #GenomicSurveillance

Today is #WorldMosquitoDay. 🦟 On this day in 1897, Sir Ronald Ross discovered that female Anopheles mosquitoes transmit malaria between humans 🩸 There are several thousand species of mosquitoes in the world, but far fewer can transmit diseases like malaria, dengue, and chikungunya. Being able to identify mosquito types is important for public health, as it gives an idea of the risk of diseases that may be circulating in the area. Have you ever wondered how to tell the difference? To learn your three P’s of mosquito identification, check out our in-depth mosquito identification guide created by experts at the Genomic Surveillance Unit (Wellcome Sanger Institute). ⬇️ https://lnkd.in/e54YKVyC