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Public-health topic

Genomic epidemiology

Published Research Radar records connected to the Genomic epidemiology topic through the auditable classification pipeline.

Published evidence
109
Diseases
48
Countries
62
Topics
12

Evidence stream

Published literature

109

30 of 109 publications shown

Whole-genome analysis of mumps virus genotype F in Shandong, China (2006–2018)

Suting Wang, Ping Xiong, Yao Liu +7 more

Frontiers in Microbiology

Type
Genomic study
Scope
China, Shandong, China

Why it matters nowMumps incidence in Shandong declined after vaccine introduction but remained above WHO elimination thresholds; the study provides whole-genome evidence that genotype F strains did not detectably diverge or drift away from the vaccine strain over ~12 years, while illustrating that SH-gene typing alone lacks resolution for closely related isolates.

Co-occurrence of pfkelch13 and pfmdr1 variants in a recurrent Plasmodium falciparum infection following standard artemether-lumefantrine treatment

Joana Laranjinha, Andréa Luciana S. da Silva, Sara B. Lopes +7 more

International Journal of Infectious Diseases

Type
Journal article
Scope
Not classified

Why it matters nowThe co-occurrence of resistance-associated markers and treatment failure in one patient is presented as justification for ongoing genomic surveillance of antimalarial resistance.

Clustering and Source Association of Clinical and Nonclinical Listeria monocytogenes Isolates, New York, USA, 2000-2021<sup>1</sup>.

Samut H, Mendez-Vallellanes DV, Hoyt H +10 more

Emerging infectious diseases

Type
Genomic study
Scope
United States

Why it matters nowThe authors suggest that whole-genome sequencing may strengthen outbreak investigation and source attribution for L. monocytogenes and that produce-associated transmission may reflect distinct pathways.

The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California

Jesse Elder, Rahil Ryder, Mayuri Panditrao +25 more

PLOS Digital Health

Type
Genomic study
Scope
Not classified

Why it matters nowCentralizing genomic and clinical data streams allows continuous assessment of viral behavior and transmission networks across a large jurisdiction. The established pipeline offers a replicable template for health departments aiming to strengthen routine variant tracking and resource allocation.

Autochthonous chikungunya virus outbreak in Verona province, Italy, 2025

Concetta Castilletti, Leonardo Ancillotti, Antonio Mori +30 more

Journal of Travel Medicine

Type
Genomic study
Scope
Italy, Réunion

Why it matters nowThe report illustrates how coordinated monitoring networks can quickly characterize emerging arboviral activity in non-endemic areas, offering insights into optimal diagnostic windows and the importance of continuous pathogen tracking.

First detection and molecular characterization of influenza D virus in livestock from Kazakhstan reveals circulation of the D/Yama2019 lineage

Yermukhammet Kassymbekov, Temirlan Sabyrzhan, Sardor Nuralibekov +6 more

Frontiers in Veterinary Science

Type
Genomic study
Scope
Kazakhstan

Why it matters nowIdentifying the virus in a new territory emphasizes the necessity for sustained genomic monitoring to evaluate ecological spread, animal health implications, and potential cross-species dynamics.

Phylogenetic and phylogeographic analysis of equine influenza in Colombia.

Gonzalez-Obando J, Carrillo M, Diaz FJ +9 more

Equine veterinary journal

Type
Genomic study
Scope
Colombia, United States

Why it matters nowThe genetic proximity to foreign viral strains highlights cross-border animal trade as a potential introduction pathway, emphasizing the need for continuous genomic monitoring to track strain evolution and guide control measures.

Molecular identification and phylogenetic analysis of Anopheles mosquitoes from malaria endemic-areas of Limpopo Province, South Africa

Mzwandile Thabani Hadebe, Samson Anjikwi Malgwi, Moses Okpeku

The Journal of Basic and Applied Zoology

Type
Genomic study
Scope
South Africa

Why it matters nowThe findings indicate that molecular testing may complement morphological identification in mosquito vector monitoring in the reported Limpopo setting. The abstract states that using additional, more variable markers alongside morphology could improve species discrimination and support malaria-control programmes.

Tularemia: a re-emerging zoonosis.

Hernández M, Oteo JA, Eiros JM

Medicina clinica

Type
Genomic study
Scope
Austria, Spain, France

Why it matters nowTularemia is classified as a CDC Category A bioterrorism agent due to extreme virulence (infection possible with as few as 10 cells) and 30% mortality in untreated cases. The documented re-emergence across multiple Northern Hemisphere regions underscores the need for updated clinical awareness and early diagnostic capacity.

Isolation and molecular characterization of West Nile Virus with evidence of vertical transmission in the Coastal region, Kenya.

Wanjiru T, Langat S, Koka H +9 more

Microbiology spectrum

Type
Genomic study
Scope
Kenya

Why it matters nowThe findings provide genomic and vector-associated information about West Nile virus detected in the sampled Kenyan settings, including two reported viral lineages and a reported vertical-transmission event. The authors identify continued genomic surveillance, vector competence research, and integrated arbovirus monitoring as relevant areas for prevention and control planning.

Genomic characterisation of vancomycin-resistant Enterococcus faecium with Tn1546-plasmid rep17 in obstetrics and gynaecology settings in Algeria.

Boutefnouchet C, Berredjem H, Aouras H +1 more

Molecular genetics and genomics : MGG

Type
Genomic study
Scope
Algeria

Why it matters nowThe findings document the presence of epidemic VREfm ST80 clone evolving in Algerian healthcare settings, with vancomycin resistance severely limiting treatment options for a major global health threat. The rep17 plasmid carrying both vancomycin and aminoglycoside resistance genes raises concern for potential horizontal gene transfer to other pathogens.

Genomic and epidemiological evidence linking a pre-season dengue case to local overwintering transmission in Guangdong, China

Liling Lin, Man Liu, Jianqian Chen +13 more

PLOS Neglected Tropical Diseases

Type
Genomic study
Scope
China

Why it matters nowThe observation indicates that viral persistence across off-season periods may occur in warming subtropical zones, highlighting the necessity for continuous mosquito monitoring programs.

Wastewater-Based Genomic Surveillance of SARS-CoV-2 Antiviral Resistance Determinants in Ontario: Towards a Scalable Framework for Population-Level Antiviral Resistance Monitoring

Opeyemi U. Lawal, Valeria R. Parreira, Alyssa K. Overton +8 more

Viruses

Type
Journal article
Scope
Not classified

Why it matters nowThe methodology supports large-scale tracking of pharmaceutical resistance and viral adaptation markers, indicating potential value for expanding community-level monitoring initiatives.

Emergence and phylogeography of the dengue vector Aedes aegypti in Southeastern Iran

Jalil Nejati, Mona Koosha, Nayyereh Choubdar +3 more

PLOS Neglected Tropical Diseases

Type
Genomic study
Scope
Iran, Brazil, Mexico

Why it matters nowThe confirmed establishment of genetically diverse Ae. aegypti populations in southeastern Iran represents an emerging invasion corridor that elevates arbovirus transmission risk, including dengue, chikungunya, Zika, and yellow fever. The genetic connectivity with endemic regions in Latin America, Africa, and South Asia underscores the need for integrated vector monitoring and genomic surveillance to inform prevention strategies.

Genomic epidemiology reveals geographically structured co-circulation of AFR10 and AFR13 Vibrio cholerae lineages driving cholera outbreaks in Tanzania (2022–2024)

Ibrahim I. Mauki, Reuben Abednego, Lawrence Mapunda +15 more

Microbial Genomics

Type
Genomic study
Scope
Tanzania, Democratic Republic of the Congo, Zambia

Why it matters nowResults inform public health interventions by clarifying transmission dynamics and antimicrobial resistance patterns relevant to treatment strategies. The authors emphasize the necessity for enhanced national and cross-border genomic surveillance to manage control efforts effectively.

A family cluster of brucellosis in an underserved urban community in Guayaquil city, Ecuador

Naomi Mora Jaramillo, Solon Alberto Orlando, Katherin Lucin +4 more

Frontiers in Public Health

Type
Genomic study
Scope
Ecuador

Why it matters nowUrban municipalities must incorporate food safety measures into their zoonotic monitoring strategies to address non-agricultural transmission routes.

Optimizing culture-free approaches to recover high-quality Mycobacterium tuberculosis genomic variation

Katharine S. Walter, Paulo César Pereira Dos Santos, Allison Carey +6 more

Microbial Genomics

Type
Genomic study
Scope
Not classified

Why it matters nowReducing reliance on lengthy culture procedures may accelerate pathogen genome recovery for epidemiological tracking.

Whole Genome Sequencing of Influenza Virus Transmission Pairs Confirms the Efficacy of Baloxavir in Reducing Household Transmission

Adam S Lauring, Leigh Papalambros, William J Fitzsimmons +5 more

Clinical Infectious Diseases

Type
Genomic study
Scope
Not classified

Why it matters nowThe findings provide evidence that genomic sequencing can be used to refine classification of suspected household influenza transmission events. Within the supplied article, the results are relevant to evaluating household transmission and treatment effects, but they do not establish a broader population-level surveillance signal.

Unravelling the genomic epidemiology and antigenic evolution of Chandipura virus: A genetically constrained neurotropic threat

Pooja Rani Kuri, Amit Sharma

PLOS Neglected Tropical Diseases

Type
Genomic study
Scope
India, Kenya, Nigeria

Why it matters nowAntigenic variations identified in key viral proteins indicate possible challenges for existing diagnostic assays and immunization platforms, reinforcing the value of continuous genomic tracking for health planning.

Molecularepidemiology and antimicrobial resistance determinants of Corynebacterium diphtheriae causing infections in Karachi, Pakistan, 2023-2024

Sobia Muhammad Asad Khan, Seema Irfan, Javaria Ashraf +9 more

International Journal of Infectious Diseases

Type
Genomic study
Scope
Pakistan

Why it matters nowThe widespread presence of resistant strains and genetic diversity suggests that local infection control strategies and laboratory testing protocols may require updates to address emerging transmission patterns.

Comparison of phylogenetic metrics of transmission between symptomatic and asymptomatic tuberculosis in individuals who were incarcerated in Brazil in 2008–24: a retrospective genomic epidemiology study

Kesia Esther da Silva, Paulo César Pereira dos Santos, Daniel Henrique Tsuha +11 more

The Lancet Microbe

Type
Cohort study
Scope
Brazil, United States

Why it matters nowExclusive reliance on clinical symptoms for identifying infected persons may overlook a major driver of ongoing dissemination, indicating that systematic screening protocols are essential in congregate environments.

Tuberculosis enhanced transmission due to interterritorial mobility and prolonged diagnostic delay: A call for an integrated genomic analysis

Sheri M. Saleeb, Silvia Vallejo-Godoy, Andrea Marcos Abellán +18 more

International Journal of Infectious Diseases

Type
Genomic study
Scope
Not classified

Why it matters nowThe findings illustrate the need for integrated cross-regional genomic surveillance and improved diagnostic timeliness to address tuberculosis transmission in increasingly mobile and diverse populations.

Closing Critical Gaps in the 2026 Bundibugyo Ebola Response: Five Actionable Priorities.

Mohapatra PR, Mishra B

Cureus

Type
Commentary
Scope
Uganda, Democratic Republic of the Congo

Why it matters nowOutlining rapid, scalable measures deployable through current infrastructure, the discussion highlights how targeted operational shifts may improve immediate outbreak management while strengthening long-term regional readiness.

The spread of sexually transmissible drug-resistant shigellosis in England: a genomic epidemiology study

Julia E Marshall, Noemie Lefrancq, Lewis C E Mason +5 more

The Lancet Infectious Diseases

Type
Genomic study
Scope
United Kingdom

Why it matters nowThe abstract frames sexually transmissible shigellosis as a public health concern requiring interventions beyond traditional enteric-disease measures. It also highlights antimicrobial stewardship as relevant across pathogens in a syndemic setting.

Diphtheria outbreak, Northern Territory of Australia, 2025 to 2026

Anthony DK Draper, Mark Sistrom, Kimberley McMahon +35 more

Eurosurveillance

Type
Genomic study
Scope
Australia

Why it matters nowThe event demonstrates that sustained immunization programs can be circumvented by specific socioeconomic and environmental risk factors, necessitating targeted monitoring of cutaneous manifestations.

Outbreak investigation of reemerging chikungunya virus in Malaysia in 2019–2020

Yik-Zheng Lim, Boon-Teong Teoh, Chee-Sieng Khor +13 more

BMC Infectious Diseases

Type
Genomic study
Scope
Malaysia, Bangladesh, China

Why it matters nowTracking these adapted viral lineages helps clarify regional transmission pathways and highlights potential shifts in pathogen behavior affecting community health planning.

Genomic epidemiology reveals the origins and transmission dynamics of chikungunya virus in China

Wei Chang, Mengyuan Zheng, Yanxian Jiang +7 more

Infectious Diseases of Poverty

Type
Genomic study
Scope
China, Myanmar, Taiwan, China

Why it matters nowIncorporating molecular tracking alongside travel history may strengthen early detection frameworks for emerging domestic clusters. Targeting monitoring resources at major transit corridors and high-incidence zones could support more proactive containment strategies.

Identification and drug resistance profiling of <i>Mycobacterium orygis</i> from an African elephant using whole-genome sequencing.

Ghayas H, Ashraf J, Saeed N +12 more

Microbiology spectrum

Type
Genomic study
Scope
Not classified

Why it matters nowDocumenting this rare tuberculosis complex variant in a captive species highlights the necessity for refined diagnostic protocols and precise antimicrobial testing. The authors propose that coordinated monitoring of affected wildlife facilities and associated personnel may help limit potential cross-species spread.

Dual-route H5N1 vaccination induces systemic and mucosal immunity in murine and bovine models

Joshua Wiggins, Adthakorn Madapong, Eric A. Weaver

npj Vaccines

Type
Genomic study
Scope
Not classified

Why it matters nowThe investigation addresses agricultural economic concerns and zoonotic transmission potential by evaluating livestock-targeted immunization strategies against expanding avian influenza lineages.

Genomic epidemiology and evolutionary dynamics of Bordetella pertussis: A comparative study between China and Global Strains (2018–2024)

Jianguang Cai, Yanwei Zhang, Shuang Wu +13 more

International Journal of Infectious Diseases

Type
Genomic study
Scope
China, Japan, United States

Why it matters nowThe convergence of resistance, hypervirulence, and potential vaccine escape within a dominant lineage is framed by the authors as grounds to revisit antibiotic stewardship and pertussis vaccination strategies.