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. 2021 May 26;13(6):992.
doi: 10.3390/v13060992.

Presence and Diversity of Different Enteric Viruses in Wild Norway Rats (Rattus norvegicus)

Sandra Niendorf  1 , Dominik Harms  1 , Katja F Hellendahl  1 , Elisa Heuser  2   3 , Sindy Böttcher  1 , C-Thomas Bock  1 , Rainer G Ulrich  2   3
Affiliations

Presence and Diversity of Different Enteric Viruses in Wild Norway Rats (Rattus norvegicus)

Sandra Niendorf et al. Viruses. .

Abstract

Rodents are common reservoirs for numerous zoonotic pathogens, but knowledge about diversity of pathogens in rodents is still limited. Here, we investigated the occurrence and genetic diversity of enteric viruses in 51 Norway rats collected in three different countries in Europe. RNA of at least one virus was detected in the intestine of 49 of 51 animals. Astrovirus RNA was detected in 46 animals, mostly of rat astroviruses. Human astrovirus (HAstV-8) RNA was detected in one, rotavirus group A (RVA) RNA was identified in eleven animals. One RVA RNA could be typed as rat G3 type. Rat hepatitis E virus (HEV) RNA was detected in five animals. Two entire genome sequences of ratHEV were determined. Human norovirus RNA was detected in four animals with the genotypes GI.P4-GI.4, GII.P33-GII.1, and GII.P21. In one animal, a replication competent coxsackievirus A20 strain was detected. Additionally, RNA of an enterovirus species A strain was detected in the same animal, albeit in a different tissue. The results show a high detection rate and diversity of enteric viruses in Norway rats in Europe and indicate their significance as vectors for zoonotic transmission of enteric viruses. The detailed role of Norway rats and transmission pathways of enteric viruses needs to be investigated in further studies.

Keywords: Norway rat; astrovirus; enterovirus; hepatitis E virus; norovirus; rodent; rotavirus; zoonosis.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Phylogenetic tree of a 970 nucleotide (nt) alignment of the ORF1/ORF2 junction region of the novel astrovirus (AstV) strains detected in animals of this study (denoted by dot) and AstV reference sequences (accession numbers are indicated). The tree was reconstructed using the Maximum Likelihood method based on the Kimura 2-parameter model with Bootstrap test (1000 replicates). Bootstrap values above 70 are shown. The bar indicates the number of substitutions per site. An avian astrovirus sequence (AAstV|AB033998) was used as outgroup. Abbreviations: cec = cecum; cont = content; col = colon; duo = duodenum; fec = feces; ile = ileum; jej = jejunum.
Figure 2
Figure 2
Phylogenetic tree of a 581 nt alignment of ORF1b region of the novel astrovirus (AstV) strains detected in this study (denoted by dot) and AstV reference sequences (accession numbers are indicated). The tree was reconstructed using the Maximum Likelihood method based on the Tamura-3-parameter model with Bootstrap test (1000 replicates). Bootstrap values above 70 are shown. An avian astrovirus sequence (AAstV|AB033998) was used as outgroup. The bar indicates the number of substitutions per site. Abbreviations: cec = cecum; cont = content; col = colon; duo = duodenum; fec = feces; ile = ileum; jej = jejunum.
Figure 3
Figure 3
Phylogenetic analysis of a 820 nt fragment of VP7 gene from the novel rotavirus strain identified in this study (marked with a dot) and reference sequences. The phylogenetic tree was reconstructed using the Maximum Likelihood method and Tamura–Nei parameter with Bootstrap test (1000 replicates) method available in MEGA7. The bar indicates the number of substitutions per site. Bootstraps values above 70 are shown. Abbreviations: cec cont = content of cecum.
Figure 4
Figure 4
Phylogenetic analysis of a 312 nt fragment of ORF1 from HEV strains detected in this study (marked with dot) and reference sequences of species Orthohepevirus C and Orthohepevirus A. The phylogenetic tree was reconstructed using the Neighbor-Joining method with Bootstrap test (1000 replicates) and the Tamura–Nei parameter method available in MEGA7. The bar indicates the number of substitutions per site. Bootstraps values above 70 are shown. Abbreviations: cec = cecum; cont = content; fec = feces; ile = ileum; jej = jejunum.
Figure 5
Figure 5
Phylogenetic analysis of the entire genome from ratHEV strains detected in this study (marked with dot) and reference sequences of representative strains of species Orthohepevirus C and Orthohepevirus A. The phylogenetic tree was reconstructed using the Neighbor-Joining method with Bootstrap test (1000 replicates) and the Tamura–Nei parameter method available in MEGA7. The bar indicates the number of substitutions per site. Bootstraps values above 70 are shown. Abbreviations: cont = content; fec = feces; ile = ileum.
Figure 6
Figure 6
Phylogenetic analysis of a 263 nt fragment of ORF1 from norovirus strains detected in this study (marked with dot), human norovirus reference sequences and a single sequence that was detected in a rat from Copenhagen, Denmark (GI.P11|KC294198). The phylogenetic tree was reconstructed using the Neighbor-Joining method with Bootstrap test (1000 replicates) and the Kimura 2-parameter method available in MEGA7. The bar indicates the number of substitutions per site. Bootstraps values above 70 are shown. The bovine norovirus sequence III.2|AY126474 was used as an outgroup. Abbreviations: cec = cecum; cont = content; fec = feces; ile = ileum.
Figure 7
Figure 7
Phylogenetic analysis of a 255 nt fragment of ORF2 from norovirus strains detected in this study (marked with a dot), human norovirus reference sequences and a single sequence that was detected in a rat from Copenhagen, Denmark (GI.6|KC294198). The phylogenetic tree was reconstructed using the Neighbor-Joining method with Bootstrap test (1000 replicates) and the Kimura 2-parameter method available in MEGA7. The bar indicates the number of substitutions per site. A bovine norovirus sequence (GIII.1|EU360814) was used as an outgroup. Bootstraps values above 70 are shown. Abbreviations: cec = cecum; cont = content; fec = feces.
Figure 8
Figure 8
Phylogenetic analysis of a 737 nt fragment of VP1 gene from the enterovirus strain (marked with a dot) and the enterovirus isolate from this study (marked with a rhombus) and human enterovirus reference sequences. The phylogenetic tree was reconstructed using Maximum Likelihood method with General-Time-Reversible model with Bootstrap test (1000 replicates) available in MEGA7. The bar indicates the number of substitutions per site. Bootstraps values above 70 are shown. Abbreviations: cec = cecum; cont = content.
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