Mammalian orthoreoviruses (MRVs) belong to the genus Orthoreovirus in the family Reoviridae. MRVs are nonenveloped, double-stranded (ds) RNA viruses that cause symptomatic or asymptomatic infection in mammals [1]. They are classified into four serotypes: MRV serotype 1 (MRV1) (Lang, T1L), MRV serotype 2 (MRV2) (Jones, T2J), MRV serotype 3 (MRV3) (Dearing, T3D), and MRV serotype 4 (MRV4) (Ndelle, T4N) [2]. The genome of MRVs is approximately 23,500 bp in total and contains 10 segments: three large (L) segments (L1-L3), three medium (M) segments (M1-M3), and four small (S) segments (S1-S4) [3]. Segments L1-L3 encode the λ3, λ2, and λ1 protein, respectively; segments M1-M3 encode the μ2, μ1, and μNS protein, respectively; and segments S1-S4 encode the σ1, σ2, σNS, and σ3 protein, respectively. Neutralization and hemagglutinin activities are restricted to the σ1 protein, which is located on the outer capsid of the virion [4]. The σ1 protein is responsible for attachment of the virus to the cell receptor and is used for serotype determination of MRVs [5].

MRVs are considered to be nonpathogenic, causing mild respiratory and enteric symptoms only occasionally [6]. However, some reports have shown that they can cause severe illness in animals and children. MRV was detected in a child with acute gastroenteritis, and this virus showed the highest similarity to an MRV recently reported in European bats [7]. Furthermore, an increasing number of reports have indicated that MRV is the cause of diarrhea in newborn piglets. In 2015, a novel pathogenic MRV was found in diarrheic pigs in the United States [8], and in 2017, a novel reassortant MRV3 was identified in diarrheic pigs in eastern China [2]. To study the biological characteristics of MRV in China, further investigation of MRV diversity is necessary.

In 2017, 19 fecal samples from suckling piglets with diarrhea were collected from pig farms in Heilongjiang Province in China. The positivity rate of MRV in Heilongjiang Province was found to be 15.79% (3/19) by RT-PCR using previously described primers [9]. MRV-positive fecal samples were inoculated onto MDBK cells. After five passages, a cytopathic effect (CPE) was found with one MRV-positive fecal sample, as evidenced by enlargement of the cells, cell rupture, and granular changes. Electron microscopic observation revealed the presence of virus particles with a diameter of approximately 70 nm (Supplementary Fig. S1A). The virus strain was named HLJYC2017.

The whole genome of MRV HLJYC2017 was amplified and sequenced (Supplementary Table S1, Fig. S1B). The sequence of each segment of HLJYC2017 was deposited in the GenBank database (Supplementary Table S2). The nucleotide sequences of MRV HLJYC2017 S1, S2, S3 and S4 are 1413 nt, 1257 nt, 1101 nt, and 1098 nt in length, respectively, encoding predicted σ1, σ2, σNS, and σ3 proteins consisting of 470 aa, 418 aa, 366 aa, and 365 aa, respectively. The nucleotide sequences of the MRV HLJYC2017 M1, M2, and M3 genes are 2211 nt, 2127, and 2166 nt in length, respectively, encoding predicted μ2, μ1, and μNS proteins of 736 aa, 708 aa, and 721 aa, respectively. The nucleotide sequences of the MRV HLJYC2017 L1, L2, and L3 genes are 3804 nt, 3870 nt, and 3828 nt in length, respectively, encoding predicted λ3, λ2, and λ1 proteins of 1267 aa, 1289 aa, and 1275 aa, respectively.

Phylogenetic analysis based on complete nucleotide sequences of the MRV HLJYC2017 S1 gene and the S1 genes of other MRVs with sequences available in the GenBank database (Supplementary Table S3) indicated a close relationship with the MRV isolate T1/T28/KM/2013 (Supplementary Table S2, Fig. 1) (86.9% nt and 92.8% aa sequence identity) (host: Tupaia sp.). The serotype was classified as MRV1. Phylogenetic analysis based on complete nucleotide sequences of the MRV HLJYC2017 S2, S3, S4, M1, M3, L1 and L2 genes showed that this strain is closely related to the MRV isolate WIV3 (Supplementary Table S2, Supplementary Fig. S2) isolated in Wuhan, China (host: Hipposideros sp.). Phylogenetic analysis based on the complete MRV HLJYC2017 M2 gene showed that it is closely related to the isolate GD-1 (Supplementary Table S2) isolated in China (host: pig), and phylogenetic analysis based on the complete MRV HLJYC2017 L3 gene indicated that it is closely related to the MRV2 isolate OV204 (Supplementary Table S2) isolated at the University of Florida in the USA (host: Odocoileus virginianus). These results indicate that MRV HLJYC2017 is a reassortant strain.

Fig. 1
figure 1

Phylogenetic analysis of MRV HLJYC2017 based on the S1 sequence. Phylogenetic trees were constructed using MEGA 5.2 software, using the Construct/Test neighbor-joining method (bootstrap method with 1000 replications). Bootstrap values > 70% are shown

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Reassortment of genome segments might play an important role in the emergence of new reovirus variants [1, 10,11,12,13,14], and reassortment events between MRV strains have been reported previously [2, 8, 15,16,17,18,19,20]. In this study, of the 10 segments of the MRV HLJYC2017 strain, seven (S2, S3, S4, M1, M3, L1, and L2) possess sequences that are nearly identical to those of WIV3 (host: Hipposideros), indicating that MRV HLJYC2017 might be of bat origin. The S1 gene of the MRV HLJYC2017 strain appears to have murine origins, because it exhibits the closest relationship to the S1 gene of MRV isolate T1/T28/KM/2013 (host: Tupaia), and its M2 gene appears to have a porcine origin, because M2 has the closest relationships to the MRV isolate GD-1 (host: pig). Furthermore, the L3 gene of the MRV HLJYC2017 strain appears to be of deer origin, because it is most closely related to that of the MRV isolate OV204 (host: Odocoileus virginianus). These results indicate that MRV HLJYC2017 might be a reassortant strain with segments derived from bat, murine, porcine, and deer viruses (Fig. 2). These results suggest that MRV infection on farms in China is becoming increasingly complex.

Fig. 2
figure 2

The 10 segments of HLJYC2017 that are closely related to those of bat, murine, porcine and deer MRVs. HLJYC2017 is likely to have been formed by a reassortment process, with L1, L2, M1, M3, S2, S3, and S4 from a bat MRV; L3 from a deer MRV; M2 from a porcine MRV; and S1 from a murine MRV

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The trimeric σ1 protein is divided into two domains: an N-terminal tail and a C-terminal head [21]. Through aa sequence comparisons, we found two large differences in the N-terminal tails of MRV1, MRV2 and MRV3 (Supplementary Fig. S3A). The first difference is that, compared with MRV1 and MRV2 strains, all MRV3 strains have an insertion of 4 aa (GLES) located between 26K and 27E (aa numbering based on MRV1). The second difference is that there is a large gap in the S1 protein between 155D and 171R of MRV1 compared to MRV2 and MRV3 (Supplementary Fig. S3A). There is also a 7-aa deletion (156SLINSGQ162, between 155D and 171R) in the S1 protein of MRV2 compared with that of MRV1 strains, and there is a 14-aa deletion (157LINSGQSSIGELSA170, between 156S and 171R) in the S1 protein of MRV3 compared with that of MRV1 strains (Supplementary Fig. S3A).

Serotype-dependent differences in MRV are related to the S1 gene fragment encoding the σ1 protein, which is responsible for viral attachment to cellular receptors [22]. Further analysis of the influence of these aa changes on the spatial structure of the N-terminal tail of the S1 protein was performed. The S1 protein sequences of MRV1 strain HLJYC20172017 and MRV3 strain MPC/04 [23] were used to search the SWISS-MODEL template library using PyMOL software [18]. The solution structure of the outer capsid protein sigma-1 (VP4) (SMTL ID: 6gao.1 and 6gap.1) [24] was selected for model construction, which showed that the spatial structure of the S1 protein N-terminal tail of HLJYC20172017 is different from that of the MRV3 MPC/04 strain. Specifically, a longer α-helix forms in the N-terminal tail of the MRV1 HLJYC20172017 strain than in that of the MRV3 MPC/04 strain (Supplementary Fig. S3B).

Structures of two neutralizing epitopes (5C6 and 9BG5) have been identified on the σ1 protein [21]. The two neutralizing epitope regions of the σ1 protein of HLJYC2017 were compared with those of MRV strains (encoding the full-length σ1 protein) from China obtained from the GenBank database. In the 5C6 neutralizing epitope, 13 aa positions (415A, 417Q, 424R, 426D, 429R, 430I, 446Y, 447G, 448G, 449T, 450Y, 458W and 459A) are conserved between MRV1 and MRV2 strains (Supplementary Fig. S4A), and 5 aa positions (415A, 422G, 447G, 448G and 458W) are conserved between MRV1 and MRV3 strains (Supplementary Fig. S4A). In the 9BG5 neutralizing epitope, 14 aa positions (344Q, 346P, 354V, 355T, 368S, 381G, 382K, 408P, 410S, 432G, 434S, 435E, 442E, and 446Y) are conserved between MRV1 and MRV2 strains (Supplementary Fig. S4B) and four (351R, 354V, 381G, and 407) are conserved between MRV1 and MRV3 strains (Supplementary Fig. S4B). There is a partial overlap of neutralizing antibody epitopes among MRV1, MRV2 and MRV3, suggesting some cross-protection among them.

Recombination is a common process that produces diversity in most RNA viruses and creates new opportunities for them to overcome selective pressures and adapt to new environments and hosts [25]. Recombination analysis was performed using RDP4 software [26], revealing recombination in the L3 gene sequence, as shown in Fig. 3. A breakpoint for a potential recombination zone was detected in the L3 gene (nt 1619–1663). The recombinant strain is the MRV BatMRV1-IT2011 strain (KT900697). The major parental strain for the recombination site located in the L3 gene is HLJYC2017, and the minor parental strain is the MRV strain FS-03 (KM820756).

Fig. 3
figure 3

Recombination analysis of MRV HLJYC2017 and other MRV strains

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Analysis of viral recombination has attracted the interest of epidemiologists, molecular biologists, and evolutionary biologists. Under field conditions, mixed infections are required to give rise to recombination events [27, 28]. Some MRV strains have been found in China, such as MRV-ZJ2013 [2], MRV variant B/03 [29], MRV3 SD-14 [30, 31], BtMRV WIV2-5, WIV7 and WIV8 [31], MRV3 MPC/04 [23], RpMRV-YN2012 [32], MRV2tou05 [33], MRV-HLJ/2007 [34], and BYD1 [35], providing increased opportunities for genome reorganization. In addition, the transmission of MRV from one host to another is not limited to close contact but may occur due to indirect contamination [15]. As infectious particles of MRV are found in environmental samples, it is likely that infection can be transmitted in the environment through contaminated food, water, or other factors [36]. This provides sufficient opportunity for the occurrence of recombination. In avian orthoreoviruses, several reports have identified recombinant sequences in L1 from Muscovy duck reovirus [11]; L1, L2, M1, M2, M3, and S2 from chicken orthoreovirus [12]; and M1 and S2 from avian orthoreovirus [1] (Supplementary Table S4). In MRVs, recombination in the L1, L2, M1, M2, M3 and S1 genes has also been found [2, 15]. In this study, recombination in the L3 gene of MRV was identified for the first time. Further studies of the genetic evolution of new MRVs in China are necessary.

In summary, a novel reassortant of MRV from China was isolated in this study. The insertion and deletion of specific amino acids in the σ1 protein have occurred between different serotypes of MRV. Neutralizing antibody epitope analysis showed partial cross-protection between MRV1, MRV2, and MRV3 in China. These results provide valuable information on MRV evolution and will facilitate future investigation of the molecular pathogenesis of MRVs.