Revisiting the genetic diversity of emerging hantaviruses circulating in Europe using a pan-viral resequencing microarray

Spread of Puumala Hantavirus to New Areas in a Large Croatian Outbreak of Hemorrhagic Fever with Renal Syndrome, 2021

Background: The largest documented outbreak of hemorrhagic fever with renal syndrome occurred in Primorje-Gorski Kotar County, Croatia, in 2021, marking the first-time cases of hantavirus infection recorded outside of the known endemic region in the north of the county. Aim: To identify the factors contributing to the spread of the outbreak and to compare risk factors for acquiring hantavirus infection in the endemic and newly affected regions. Methods and Results: A total of 189 cases were confirmed by positive Puumala IgM/IgG antibodies (93.6%), and 13 probable cases were identified by clinical and epidemiological data (6.4%) using a structured questionnaire. Of the 179 cases with available clinical data, 59 (33.0%) were hospitalized. Three cases received hemodialysis, and no deaths were reported. Among 170 cases with information on exposures, 66 (38.8%) reported occupational risk. Cases in the northern part of county were more likely to have been infected in early spring (OR 27.1, 95% CI 2.93-250.7), to report seeing a rodent (OR 6.5; 95%CI 2.3-18.4), and to know someone with hemorrhagic fever with renal syndrome (HFRS) (OR 3.0; 95%CI 1.2-8.0) than cases from the southern part of the county. Data from Croatian Forests Ltd. suggested that an unusually good production of beech seeds in 2020 may have contributed to an increased rodent population in 2021. However, average temperature, rainfall, and humidity data from 2021 did not illustrate a significant difference from previous years (Kruskal-Wallis p = 0.837, p = 0.999, p = 0.108). Conclusion: The 2021 HFRS outbreak was likely fueled by an abundant rodent population and virus transmission in rodent hosts. Human activity, environmental factors, and the ensuing animal-human interactions have spread hantavirus infection from Croatia's mountainous region to a previously nonendemic coastal area with a Mediterranean climate.

Mathematical Model of the Spread of Hantavirus Infection

A mathematical epidemiological model incorporating the mobility of rodents and human groups among zones of less or major contact between them is presented. The hantavirus infection dynamics is expressed using a model type SEIR (Susceptible-Exposed-Infectious-Removed), which incorporates the displacement of the rodent and the human, between the urban and rural sector, the latter being subdivided in populated and non-populated. The results show the impact that rodent or human displacement may have on the propagation of hantavirus infection. Human mobility is more significant than rodents in increasing the number of hantavirus infection cases. The results found may be used as a reference by the health authorities to develop more specific campaigns on the territorial dynamics of the rodent, attend to the mobility of humans in these territories, mainly agricultural and forestry workers, and strengthen control-prevention actions in the community, to prevent future outbreaks that are fatal.

Modeling of hantavirus cardiopulmonary syndrome

Introduction Hantavirus cardiopulmonary syndrome is an infection caused by rodents of the Bunyanvirales family towards humans. This disease in Chile is considered endemic, which has a high fatality rate. At present, some studies show the contagion between people of the Andes virus, whose locality is concentrated in Argentina and Chile. Objectives Analyze the possibility of hantavirus transmission between humans using an SEIR-type mathematical model. Methods An SEIR (Susceptible, Exposed, Infectious and Recovered) mathematical model to express the dynamics of hantavirus disease is proposed, including the possibility of human-to-human transmission and the perception of risk. Results The peak of human-to-human contagion decreases by about 25% after increasing people’s perception of risk by reducing the rate of resistance to changeand increasing the speed of people’s reaction. Conclusions It is urgent to review risk communication strategies and prevention measures in the face of this possibility of massive human-tohuman infections, in addition to strengthening research and planning the development of a vaccine to protect populations exposed to this disease with a high fatality rate.

Genetic Diversity of Puumala orthohantavirus in Rodents and Human Patients in Austria, 2012-2019

Puumala orthohantavirus (PUUV) has a wide distribution throughout Europe. Distinctive temporal patterns of spillover into the human population are related to population dynamics of the reservoir host, the bank vole (Clethrionomys glareolus). As the rodent host is tied to specific habitats with small individual ranges, PUUV genetic diversity is also highly correlated with geographic distance. Using sequenced portions of viral S and M segments, we determined whether geographic clusters were supported. Human cases of PUUV infections are concentrated in southeastern Austria. We detected four distinct genotypes: two genotypes of the Alpe-Adria (ALAD) lineage typically associated with southeast Europe, and two sublineages of the Central Europe (CE) lineage. One cluster of CE genotypes represents a phylogenetically distinct sublineage compared to previously reported CE clades, and extends the boundary of the CE lineage further south than previously reported.

Assessing Genome-Wide Diversity in European Hantaviruses through Sequence Capture from Natural Host Samples

Research on the ecology and evolution of viruses is often hampered by the limitation of sequence information to short parts of the genomes or single genomes derived from cultures. In this study, we use hybrid sequence capture enrichment in combination with high-throughput sequencing to provide efficient access to full genomes of European hantaviruses from rodent samples obtained in the field. We applied this methodology to Tula (TULV) and Puumala (PUUV) orthohantaviruses for which analyses from natural host samples are typically restricted to partial sequences of their tri-segmented RNA genome. We assembled a total of ten novel hantavirus genomes de novo with very high coverage (on average >99%) and sequencing depth (average >247×). A comparison with partial Sanger sequences indicated an accuracy of >99.9% for the assemblies. An analysis of two common vole (Microtus arvalis) samples infected with two TULV strains each allowed for the de novo assembly of all four TULV genomes. Combining the novel sequences with all available TULV and PUUV genomes revealed very similar patterns of sequence diversity along the genomes, except for remarkably higher diversity in the non-coding region of the S-segment in PUUV. The genomic distribution of polymorphisms in the coding sequence was similar between the species, but differed between the segments with the highest sequence divergence of 0.274 for the M-segment, 0.265 for the S-segment, and 0.248 for the L-segment (overall 0.258). Phylogenetic analyses showed the clustering of genome sequences consistent with their geographic distribution within each species. Genome-wide data yielded extremely high node support values, despite the impact of strong mutational saturation that is expected for hantavirus sequences obtained over large spatial distances. We conclude that genome sequencing based on capture enrichment protocols provides an efficient means for ecological and evolutionary investigations of hantaviruses at an unprecedented completeness and depth.