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Author affiliation: ANSES, EnvA, INRAE, Maisons-Alfort, France (M. Pellerin, V. Doceul, N. Pavio); Institut Pasteur, Université Paris Cité, Environment and Infectious Risk Research Unit—Laboratory for Urgent Response to Biological Threats, Paris, France (A. Kwasiborski, V. Hourdel, S. Temmam, J.-C. Manuguerra); University of Lyon, Marcy l’Etoile, France (V. Lattard, S. Lefebvre, S.D. Soro); Institut Pasteur, Université Paris Cité, Environment and Infectious Risk Research Unit—National Reference Center for Hantaviruses, Paris (V. Sauvage); Office Français de la Biodiversité—Muséum National d’Histoire Naturelle, Paris (B. Pisanu); University of Strasbourg, Strasbourg, France (K. Toudji, C. Habold); LTSER France Zone Atelier Environnementale Urbaine, Strasbourg (K. Toudji, C. Habold); Centre de Biologie et de Gestion des Populations, Montferrier-sur-Lez, France (G. Castel, C. Tatard, N. Charbonnel); Muséum National d’Histoire Naturelle, Paris (A. Lalis); ANSES, Malzéville, France (E. Monchatre-Leroy); UniLaSalle, Mont-Saint-Aignan, France (E. Monchatre-Leroy)
Hepatitis E virus (HEV) is responsible for enterically acquired hepatitis in humans. The disease is frequently acute and self-limiting, but it can evolve to fulminant hepatitis or cause chronic hepatitis occurring primarily in immunocompromised persons (1). HEV belongs to the Hepeviridae family and Orthohepevirinae subfamily that comprise 4 genera, including Paslahepevirus and Rocahepevirus genera that infect humans. Most human cases are attributed to the species P. balayani (2). The genus Rocahepevirus includes Rocahepevirus ratti, formerly genotype C1 rat HEV (rHEV), which was identified in Rattus norvegicus rats in Germany in 2010 (3). It is phylogenetically distinct from other HEV viruses, sharing »60% sequence identity with Paslahepevirus. Since 2010, studies performed in Europe, Asia, Canada, and the United States in several rat species (R. norvegicus, R. rattus, and others) have shown rHEV genomic positivity rates of 2.6%–26% (4–10). In France, 2 studies conducted in Lyon during 2010–2012 reported a rHEV genomic positivity rate of 14% (11,12) in R. norvegicus rats.
In 2018, rHEV was identified in humans as the cause of persistent hepatitis in a liver transplant recipient in Hong Kong (13). Additional cases of rHEV hepatitis were reported in both immunocompetent and immunocompromised patients from Asia, North America (after infection in Central Africa), and Europe (14). In France, 2 human cases of rHEV infections have been described, but no direct contact with rats was documented (15,16).
Rats (including the species R. norvegicus and R. rattus) are the main reservoirs of rHEV; direct or indirect contact with them could be a potential risk for exposure. Spatiotemporal data and high genetic identity between rHEV sequences from rats and humans suggest zoonotic transmission (17,18). Although rats are the primary reservoir, rHEV has been detected sporadically in other animal species such as pigs (19,20).
Sequences of rHEV obtained from different geographic areas show a high degree of genetic variability. rHEV can be classified into multiple evolutionary groups (G1–G6); human strains are distributed across multiple phylogenetic groups (21). Within a country, genetic diversity of rat rHEV sequences can be high (9).
We conducted this large-scale study to assess rHEV virus circulation in rats in France and provide baseline data to better characterize the risk for human exposure. We investigated the presence of rHEV in livers from brown rats (R. norvegicus) captured in 8 large cities during 2021–2023. We determined positivity rate of rHEV RNA and RHEV antibodies and analyzed individual parameters such as weight and sex to determine the dynamics of rat infection in natural settings. We obtained full genome sequences and performed phylogenetic analyses.
Study Design, Population, and Trapping Method
We conducted rat captures during April 2021–July 2023 in 8 cities with >200,000 populations: Paris, Nantes, Lyon, Strasbourg, Bordeaux, Besancon, Nancy, and Marseille. We sampled rats in various habitat types: social housing developments (Lyon, Strasbourg, Bordeaux), sewers (Lyon, Besancon, Nancy, Nantes), and urban parks (Lyon, Paris, Strasbourg, Marseille) (Appendix). All rat procedures complied with international guidelines (European Directive 2010/63/EU) and were approved by local ethics committees and national authorities (authorization nos. 37713-2022042712262465, 34416-2021112911335464, and 30187-2021021512421700).
We captured rats by using 2 complementary methods: live trapping in Lyon, Besancon, Nancy, Nantes, Paris and Strasbourg, and ferret-assisted trapping in Lyon, Bordeaux, and Marseille (22,23). We trapped a total of 686 rats (Table 1). We registered sex and weight for each animal and considered bodyweight as a proxy for age progression in rats (24). That approach provided a standardized measure across collection sites and operators.
We conducted full necropsy and collected liver samples, which we immediately immersed in liquid nitrogen or in RNAShield (Zymo Research, https://www.zymoresearch.com) and stored at −80°C or −20°C. We analyzed a total of 686 liver samples. We also collected serum samples from some of the rats from which liver samples were taken. We analyzed a total of 317 serum specimens from 4 cities, in the different habitat types. We centrifuged blood samples at 2,500 rpm for 5 minutes at 4°C to obtain serum specimens.
Molecular Analyses
Viral RNA Extraction and Real-Time Reverse Transcription PCR
We homogenized »50 mg of liver tissue in Lysing Matrix E tubes (MP Biomedicals, https://www.mpbio.com) using a FastPrep-24 (MP Biomedicals) or Pre-Filled Bead Mill Tubes (Fisherbrand, https://www.fishersci.com) using Precellys 24 homogenizer (Bertin Technologies, https://www.bertin-technologies.com). We extracted RNA from liver tissue using either the KingFisher Duo (Thermo Fisher Scientific, https://www.thermofisher.com) with the MagMAX core nucleic acid purification kit (Thermo Fisher Scientific) or manually with the NucleoSpin Dx virus kit (Macherey-Nagel, http://www.mn-net.com), according to the manufacturer’s recommendations. We performed RHEV RNA detection using a specific real‐time quantitative reverse transcription PCR (qRT-PCR) as described previously (25).
rHEV Whole-Genome Sequencing and Phylogenetic Analyses
We performed whole-genome sequencing of 22 rHEV-positive liver samples by a random metagenomics sequencing approach using the SMARTer Stranded Total RNA-Seq kit version 3, Pico Input Mammalian (Takara Bio, https://www.takarabio.com), according to the manufacturer’s recommendations. We assembled complete genomes from reads using the Microseek pipeline (26) (Appendix).
We conducted phylogenetic analyses on whole genomes to investigate both the evolutionary origin of rHEV in France within the global diversity of Rocahepevirus strains and at the national level to investigate geographic clustering. We conducted an additional phylogenetic analysis on a 1122-nt fragment (positions 4105–5229 pb on reference sequence NC_038504 from the GenBank RefSeq database [https://www.ncbi.nlm.nih.gov/refseq]), to include partial genomes published. We aligned sequences with MAFFT version 7.526 in auto mode and manually cured them, as described previously (27). We inferred trees using IQ-TREE 2 version 2.2.0 and 1,000 ultrafast bootstrap replicates (28). We performed pairwise nucleotide and amino acid comparisons using CLC Genomics Workbench version 25.0.02 (QIAGEN, https://www.qiagen.com) to assess rHEV diversity.
Serologic Analysis
We detected HEV antibodies using the Wantai HEV-IgG ELISA WE-7296 kit (Wantai BioPharm, https://www.ystwt.cn) adapted for rat serum. Because that assay uses pE2 as a capture antigen, it enables the detection of cross-reactive antibody responses (29) (Appendix).
Statistical Analysis and Visualizations
We performed statistical analyses in R version 4.3.0 (The R Project for Statistical Computing, https://www.r-project.org). Univariable and multivariable logistic regression models assessed associations between rHEV liver positivity and explanatory variables. We reported odds ratios (ORs) and adjusted ORs (aORs) with 95% CIs and Wald test p values. The multivariable model included sex, sampling context (position2), and binary weight class. We assessed multicollinearity using variance inflation factors
rHEV RNA Positivity Rate in Rats
We evaluated rHEV infection in rats by detection of viral RNA by specific qRT-PCR in liver tissue samples. Among the 686 animals analyzed, 209 were positive; cycle threshold (Ct) values were 12–35, resulting in an overall positivity rate of 30.5% (95% CI 27.1%–34.0%) (Table 2). rHEV RNA–positive animals were captured in all types of habitats. We observed significant differences by simple linear regression analysis (SRL) and generalized linear model (GLM) analyses in positivity rate between urban parks and sewers or social housing areas: 9.7% (95% CI 6.7%–13.8%) in urban parks and »44% (95% CI 33.9%–55.3%) in both sewers and social housing areas. Positive animals were found in all cities sampled; however, we could not perform statistical comparison between cities because of inconsistent sampling. Positivity rate significantly differed by weight class, from 9.0% (95% CI 5.8%–13.8%) in rats >100 g, but not by sex.
To further investigate the distribution of rHEV in rat populations, we performed an in-depth statistical analysis with the samples obtained using a biologic trapping method with trained ferrets. This approach enabled the near-complete capture of all rats, young and adults, within each colony; we captured a total of 188 rats trapped in the targeted area in Lyon and 93 in the area in Bordeaux (Appendix Table 1). We classified rats into 5 categories according to their bodyweight, corresponding to different physiologic stages. The distribution of rats among weight categories did not differ significantly between the 2 cities (χ2 = 11.74, d.f. = 6; p = 0.068).
Figure 1
Figure 1. rHEV RNA and HEV antibody positivity by weight category in rats in Lyon and Bordeaux in study of rHEV circulation in brown rats from 8 cities, France, 2021–2023. A) rHEV…
Overall rHEV virus positivity rate differed significantly between the 2 cities (pFigure 1). In Lyon, 99/188 (52.7% [95% CI 45.5%–59.7%]) rats were rHEV RNA–positive; in Bordeaux, 29/93 (31.2% [95% CI 22.7%–41.2%]) rats were positive (Appendix Table 2). When we considered bodyweight pooled across cities, rHEV RNA positivity rate increased strongly with weight (Figure 1, panel A). Positivity rate was lower in rats weighing 400 g. The 400 g, for which p = 0.003), indicating that infection was less frequent in the smallest (youngest) rats. City-specific analysis revealed contrasting weight-related positivity rate patterns (Figure 1, panels B, C). In Lyon, positivity rate exceeded 50% across all weight categories >100 g. In contrast, Bordeaux showed peak positivity rate in the 200–300 g category; positivity rate decreased progressively in heavier (older) animals to 11.8% [95% CI 2.1%–37.7%] in rats >400 g.
rHEV Antibody in Rats
Among the 317 available rat serum samples, overall rHEV seropositivity rate was estimated at 45.4% (95% CI 40.0%–51.0%) (Table 3). Seropositivity increased significantly by weight class, from 21.6% (95% CI 13.8–32.3) in rats with bodyweight >100 g. Seropositivity rate ranged from 23.2% (95% CI 14.1%–35.8%) in urban parks to 48.9% (95% CI 42.4%–55.4%) in sewers and 57.9% (95% CI 42.2%–72.1%) in social housing areas; we observed statistically significant differences between urban parks and sewers or social housing. As for viral RNA positivity rate, no difference was observed between sexes. Among the 142 seropositive rats tested for rHEV antibodies, 63 (44.4%) were found to be positive; in the 170 seronegative rats, 63 (37.1%) were positive.
To further investigate rHEV antibody distribution in rat populations, we conducted an in-depth statistical analysis in Lyon and Bordeaux. The overall rHEV seropositivity rate among the 200 rats with available serum, 90 from Lyon and 72 from Bordeaux, was 51% (95% CI 43.9%–58.1%). Seropositivity rate increased progressively across weight categories; it was 28.6% (95% CI 12.2%–52.3%) in rats 50% (95% CI 36.3%–68.2%) in rats weighing 300–400 g, and 70% (95% CI 57.8%–84.9%) in rats >400 g (Figure 1, panel D). The differences between rats weighing 400 g were statistically significant (p
Viral Load
Figure 2
Figure 2. Distribution of rHEV-positive rats in Lyon and Bordeaux in study of RHEV circulation in brown rats from 8 cities, France, 2021–2023. Median Ct values were calculated after excluding animals with…
qRT-PCR Ct values correlate with viral load; low Ct values reflect high viral load in the sample. Rats were grouped by Ct range (35/negative) and by bodyweight (Figure 2, panel A). GLM analysis revealed a significant effect of both weight category and city on Ct values but no significant effect of sex (Appendix Figure 1). In Lyon, the median Ct was 17.38 (95% CI 14.70–20.90), (Figure 2, panel B) whereas in Bordeaux it was 25.10 (95% CI 21.60–29.0) (Figure 2, panel C); the difference was statistically significant (χ2 = 921 by Mann-Whitney test; d.f. = 3; p = 0.004). In Lyon, where the number of trapped animals was higher, we observed significant differences between animals of different weight categories (χ2 = 12.90 by Kruskal-Wallis test; d.f. = 6, p = 0.012).
rHEV Partial and Full Genome Sequences and Phylogenetic Analyses
Figure 3
Figure 3. Whole-genome phylogenetic analysis of rHEV sequences generated in study of rHEV circulating in brown rats from 8 cities, France, 2021–2023. We used 67 sequences covering the genera Rocahepevirus, …
Figure 4
Figure 4. Whole-genome phylogenetic analysis of 20 rat hepatitis E virus (rHEV) sequences generated in study of RHEV circulating in brown rats from 8 cities, France, 2021–2023. The tree, a subset of…
From the liver of R. norvegicus rats captured in 6 of the 8 cities analyzed (Lyon, Strasbourg, Nancy, Bordeaux, Besançon, and Nantes), we obtained 20 complete (GenBank accession nos. PX955492–511) and 2 partial (accession nos. PZ016892–3) rHEV genomes. Whole-genome phylogenetic analyses confirmed that the sequences belong to the rHEV species with a strongly supported bootstrap percentage (100%). They clustered into a monophyletic clade comprising sequences originating from R. rattus and R. norvegicus rats sampled in Asia, America, and Europe, along with human isolates (Figures 3, 4).
Overall, sequences from France were distributed across 5 distinct clusters (named a–e), likely clustering by city (Figure 4). Cluster a comprised sequences from Bordeaux and was closely related to strains detected in Germany in 2009. Cluster b included sequences from Lyon and Nantes, generally structured by city. Cluster c comprised sequences from Strasbourg and Nancy, with subclades observed by city. Sequences from Hungary (2010 and 2017) were positioned at the root of clades b and c, indicating a closer origin. Cluster d included only sewer-derived sequences from Lyon district 3 that were genetically closer to strains from South Korea and Spain rather than to other Lyon strains. Finally, cluster e comprised sequences from Besançon. The RHEV sequence detected in a human kidney-transplant patient who had cirrhosis (16) clustered in the same subclade e as the 2 rHEV sequences from Besançon (this study) (Figure 3). Pairwise comparison of complete genomes or at the open reading frame (ORF) 1 and ORF2 levels showed up to 14% nucleotide diversity among the 20 full genome sequences (Appendix Figure 2) and were consistent with phylogenetic analyses. Amino acid divergence reached 5.6% for ORF1 and 4.1% for ORF2.
Figure 5
![Phylogenetic analyses of RHEV sequences generated in study of rHEV circulating in brown rats from 8 cities, France, 2021–2023. Analysis is based on a 1,122-nt fragment spanning portions of open reading frame (ORF) 1, ORF3, and ORF2 of Orthohepevirinae genomes (positions 4105–5229 in in a reference strain from the GenBank RefSeq database [https://www.ncbi.nlm.nih.gov/refseq], NC_038504). We analyzed 100 partial sequences, 78 retrieved from GenBank covering the genera Rocahepevirus, Avihepevirus, Paslahepevirus, and Chirohepevirus and 22 generated in this study (GenBank accession nos. PZ016892–3). We aligned strains using MAFFT version 7.526 and inferred the tree with IQ-TREE 2 version 2.2.0 for 1,000 ultrafast bootstrap replicates (28). For clarity, only Rocahepevirus ratti sequences (RHEV, FrHEV, and VHEV) are shown (https://ictv.global/report/chapter/hepeviridae/hepeviridae/orthohepevirinae/rocahepevirus). Colors indicate source for sequences from this study: burgundy, Bordeaux; blue, Lyon; green, Nantes; purple, Strasbourg; light green, Nancy; gray, Besançon. Lowercase letters a–f indicate clusters. Numbers at nodes indicate bootstrap values >70. Scale bar indicates numbers of substitutions per nucleotide. FrHEV, ferret hepatitis E virus; rHEV, rat hepatitis E virus; VHEV, vole hepatitis E virus.](https://wwwnc.cdc.gov/eid/images/26-0926-F5-tn.jpg)
Figure 5. Phylogenetic analyses of RHEV sequences generated in study of rHEV circulating in brown rats from 8 cities, France, 2021–2023. Analysis is based on a 1,122-nt fragment spanning portions of open…
Figure 6
![Phylogenetic analyses of 22 rat hepatitis E virus (rHEV) sequences generated in study of rHEV circulating in brown rats from 8 cities, France, 2021–2023. Analysis is based on a 1,122-nt fragment spanning portions of open reading frame (ORF) 1, ORF3, and ORF2 of Orthohepevirinae genomes (positions 4105–5229 in a reference strain from GenBank RefSeq database [https://www.ncbi.nlm.nih.gov/refseq], NC_038504). The tree, a subset of the full analysis (Figure 5), highlights subclustering of sequences from Lyon, irrespective of whether rats were captured on the surface or in the sewer system. Colors indicate source for sequences from this study: burgundy, Bordeaux; blue, Lyon; green, Nantes; purple, Strasbourg; light green, Nancy; gray, Besançon. Lowercase letters a–f indicate clusters. Numbers at nodes indicate bootstrap values >70. Scale bar indicates numbers of substitutions per nucleotide.](https://wwwnc.cdc.gov/eid/images/26-0926-F6-tn.jpg)
Figure 6. Phylogenetic analyses of 22 rat hepatitis E virus (rHEV) sequences generated in study of rHEV circulating in brown rats from 8 cities, France, 2021–2023. Analysis is based on a 1,122-nt…
Additional phylogenetic analysis based on the 1,122-nt fragment overlapping ORF1/ORF3/ORF2 region (Figures 5, 6) resulted in similar topology as whole-genome analysis, except that fine resolution of internal nodes was less robust than in the whole genome, as previously described (30). However, we identified another highly supported cluster (cluster f) among sewer-captured rats in Lyon district 4. Those sequences were closely related to a strain in R. norvegicus detected in Lyon in 2012 and to a human strain in 2022 (15) and distant from other rHEV strains circulating in Lyon, suggesting concomitant circulation of several strains in Lyon.
In 2010, a novel hepevirus was first identified in rats in Germany (3), but it was considered at low zoonotic potential because it failed to infect nonhuman primates (31). However, that Rocahepevirus has drawn attention after being associated with several cases of human hepatitis (32). In our study, we provide evidence of a high positivity rate of 30% (209/686) of rHEV RNA in rats from 8 major cities, suggesting that rats are an important source of the virus. Previous molecular surveys conducted in rat populations across European countries reported an rHEV positivity rate of 2.6%–26% (4–10). The global positivity rate of 30% we observed is one of the highest in studies in Europe. Two previous studies conducted in Lyon, France, reported a positivity rate of 14% in 2010–2012 (11,12). The positivity rate observed in Lyon in 2021–2023 is high (52.7%), but the rat populations sampled, the relative weight categories of the animal, the type of habitats, or the molecular detection protocol were different, limiting the comparison with 2010–2012.
We observed different rHEV positivity rates according to habitat, with higher positivity rate in sewers and social housing (44%) than in urban parks (9,7%). This low positivity rate in urban parks confirms findings from the Netherlands, where rats from greener urban areas were less frequently infected by rHEV (33). Conversely, high rates of rHEV infections have been observed in Spain, in both urban areas and on farms (9), where high population density, combined with an abundance of food and waste, promotes rat proliferation. In agreement, a previous study conducted in Lyon (12) had observed a strong positive correlation between areas with high human population density, predominantly low-income, and the number of infected rats.
In our study, we observed a high rate of rHEV infection in sewer-dwelling rats; that novel finding might help to explain the high levels of rHEV measured in wastewater observed in France, Sweden, Italy, Spain, and Portugal (34). In those countries, a predominance of rHEV over HEV (Paslahepevirus) was detected in sewage samples. The exact role of wastewater in rHEV exposure, beyond exposure of persons working in sewage and wastewater treatment plants, remains to be investigated.
Examining rHEV infection dynamics in rats, we observed that positivity rates were higher in rats >100 g than those 400 g, depending on the city. A similar weight/age effect was identified in Canada; sexually mature rats were significantly more likely than immature rats to be infected with rHEV (7). A possible reason is cumulative exposure to rHEV with age, leading to increased risk for infections. Age-related changes in rat behavior, including increased exploratory range, social interactions, and aggressive behaviors, might further enhance viral transmission. Finally, the contrasting distribution patterns of RHEV positivity rate observed between Lyon and Bordeaux suggest that other ecologic factors, such as their abundance and environmental conditions, substantially influence viral infection dynamics. High rates of RHEV infections observed in all age categories >100 g, as observed in Lyon, suggest early infection with possible reinfection or viral persistence. Because HEV infection can be modulated in the context of exposure to immunomodulatory substances or pathogens (35), further investigations are needed to explore the persistence potential of rHEV in rats (33,36).
Consistent with the widespread circulation of rHEV within rat populations in France, we estimated seropositivity rate as >45%. In young rats (37) or 80% (31) were found but the test used to detect rHEV antibodies were different, making comparison difficult. We identified many rats carrying both rHEV RNA and HEV antibodies, suggesting that viral neutralization is not completely efficient.
rHEV sequences show geographic clustering within each city. Similarly, rat sequences from Berlin, Germany, obtained in 2009 and 2023 (10) clustered by location rather than by year. In contrast, a study of rodent population across Spain reported less pronounced geographic structuring; substantial rHEV genetic diversity was detected within sampling regions, and up to 7 distinct clades identified in 1 area (9). The rHEV virus identified in 2012 in Lyon does not cluster within the clade of viruses detected in Lyon in 2022–2023 but was very close to viruses from Nancy, suggesting that several introductions of the virus might occur in large cities. Of note, the rHEV strain associated with the human case described in France in 2025 is close to cluster e including rat-associated strains we identified in Besançon (Figure 3); that high genetic similarity suggests that human-associated and rat-associated rHEV strains are related, thus supporting that zoonotic transmission occurs. Sequences obtained from rats sampled either above ground or from sewers were interspersed within the same subclades. However, representative samplings across all cities were limited, which prevents drawing definitive conclusions about the patterns of circulation between the environments. It is not yet known whether rats living above ground are the same individuals that move between and spread the virus in the sewers.
This study provides comprehensive characterization of rHEV circulation in its reservoir, the urban brown rat, in France. Our results reveal widespread and abundant rHEV presence across most of the cities investigated, highlighting a previously underappreciated source of potential human exposure. That finding is particularly significant given the close proximity between rat populations and human habitats, which can enable zoonotic transmission. Considering that the mechanisms underlying rHEV transmission from rats to humans remain poorly understood, the absence of data on human exposure is a limitation of this study. The link between the circulation of rHEV in rat populations and the risk for zoonotic transmission remains to be elucidated. Overall, this study provides baseline data on rHEV circulation in its main reservoir that are of value for future investigations. Future research should prioritize environmental studies to assess the infectivity of viral RNA detected in urban sewers, as well as investigations into potential intermediate hosts, such as pigs.
A major public health concern arises from the current diagnostic gap: routine molecular and serologic assays for HEV (Paslahepevirus) do not target rHEV, leading to underestimation of human rHEV infections. The high number of hepatitis cases with unknown etiology further underscores the need for improved diagnostic tools. The development and validation of rHEV-specific molecular and serologic assays are therefore critical to elucidate the true burden and clinical spectrum of rHEV infection in humans (17).
Because rHEV is an RNA virus with a high mutation rate and a large animal reservoir, and given the potential high frequency of direct or indirect human-rat contacts, rHEV represents a substantial zoonotic threat. Addressing the risk for rHEV spillover in humans requires a multifaceted approach, including the development of sensitive detection methods, the characterization of transmission dynamics, and assessment of potential cross-protection conferred by HEV exposure. Such efforts are essential to guide public health strategies and mitigate the threat posed by rHEV.
Ms. Pellerin is an engineer in biotechnology studying hepatitis E virus at ANSES Animal Health Laboratory. Her primary research interest is animal reservoirs of zoonotic pathogens.
We thank all field assistants from the Assessment of Rats Management Associated to a Genomics-Urban Ecology-Disease Occurrence Network (ARMAGUEDON) Project, Museum National d’Histoire Naturelle, and Institut Pasteur Paris. We are also grateful to the staff and gardeners of the City of Paris for their logistical support. We thank the Comité d’Éthique pour la Recherche Fédérative de l’Institut pluridisciplinaire Hubert Curien (IPHC’s CERF) team and the interns, including Mathieu Béraud, for collecting the samples. We thank the local authorities and the staff of the cities of Lyon, Marseille, and Nancy; the wastewater department and the sewer maintenance teams of Lyon, Besançon, Nantes, and Nancy; and the pest control operators and the zoological park team of Lyon.
Funding was provided by Assessment of Rats Management Associated to a Genomics-Urban Ecology-Disease Occurrence Network in Paris (ARMAGUEDON, ANR-20-CE03-0007); Agence Nationale de Recherches sur le SIDA et les hépatites virales et les maladies infectieuses émergentes (ANRS MIE) Emergen programme, RATVAR (projet ANRS0163); ANRS-MIE Contrat d’Initiation 24115 ZORRO; ANR-10-LABX-0062: LABEX Integrative Biology of Emerging Infectious Diseases; LTSER France, Zone Atelier Environnementale Urbaine, France; and ANR- BioRodDis-BiodivERsA3 ERA-Net COFUND program.