Genetic characterization of bovine viral diarrhea virus strains in Beijing, China and innate immune responses of peripheral blood mononuclear cells in persistently infected dairy cattle

Pestivirus A Bovine viral diarrhea virus type 1 species genotypes circulating in China and Turkey

Background

Pestivirus A Bovine viral diarrhea virus type 1 (BVDV-1) is a heterogeneous species within the genus, affecting cattle and other ruminants, with economic impact on livestock production.

Aim

The study aimed to update the taxonomy of the Pestivirus A, BVDV-1 species and to verify the clustering of the strains reported as genotype 1v, originating from different countries.

Methods

Recently deposited strains from China, Turkey, and Iran have been evaluated by the palindromic nucleotide substitutions (PNS) genotyping method.

Results

Based on secondary structure analysis of the 5'-UTR sequences, strains reported as 1v from China were clustered as sub genotype 1.7.3 (1o). Genotype 1.19 (1w) was restricted to China and genotype 1.21 (1v) was present only in Turkey and Iran.

Conclusion

The application of the PNS method clarified the taxonomical status of strains, revealing the homonymy of genetically different clusters. Furthermore, these observations indicated geographic segregation in the Pestivirus A species, and confirmed the occurrence of new atypical genetic variants, with potential implications on control and prophylaxis.

Host Cell Receptors Implicated in the Cellular Tropism of BVDV

Bovine viral diarrhea virus (BVDV) is one of the most hazardous viruses, which causes huge economic losses in the cattle industry around the world. In recent years, there has been a continuous increase in the diversity of pestivirus worldwide. As a member of the genus Pestivirus in the Flaviviridae family, BVDV has a wide range of host animals including cattle, goat, sheep, pig, camel and other cloven-hoofed animals, and it has multi-tissue tropism as well. The recognition of their permissive cells by viruses via interaction with the cellular receptors is a prerequisite for successful infection. So far, little is known about the cellular receptors essential for BVDV entry and their detailed functions during BVDV infection. Thus, discovery of the cellular receptors involved in the entry of BVDV and other pestiviruses is significant for development of the novel intervention. The viral envelope glycoprotein E^rns and E2 are crucial determinants of the cellular tropism of BVDV. The cellular proteins bound with E^rns and E2 potentially participate in BVDV entry, and their abundance might determine the cellular tropism of BVDV. Here, we summarize current knowledge regarding the cellular molecules have been described for BVDV entry, such as, complement regulatory protein 46 (CD46), heparan sulfate (HS), the low-density lipoprotein (LDL) receptor, and a disintegrin and metalloproteinase 17 (ADAM17). Furthermore, we focus on their implications of the recently identified cellular receptors for pestiviruses in BVDV life cycle. This knowledge provides a theoretical basis for BVDV prevention and treatment by targeting the cellular receptors essential for BVDV infection.

Th17 cell differentiation induced by cytopathogenic biotype BVDV-2 in bovine PBLCs

Background

Bovine viral diarrhea virus (BVDV) is a major pathogen that causes bovine viral diarrhea/mucosal disease (BVD-MD), which has become a global infectious disease due to its wide spread and the lack of effective treatment. The process of BVDV infection is complex. Once infected, host immune cells are activated and modulated. As a major immune cell, peripheral blood lymphocyte cells (PBLCs) are the primary target of BVDV. In order to further understand the mechanism of BVDV- host interaction, the expression profiles of host lymphocytes mRNAs associated with BVDV infection were investigated by transcriptomic sequencing analysis.

Results

The transcriptomic sequencing analysis was performed on bovine PBLCs infected with CP BVDV-2 GS2018 after 12 h of infection. Gene expression profiling demonstrated that 1052 genes were differentially expressed in GS2018 infected PBLCs compared with the control group. Of these genes, 485 genes were up-regulated and 567 were down-regulated. The 19 differential expressed genes (DEGs) were selected for validation using quantitative real-time PCR and the results were consistent with the results of RNA-Seq. Gene ontology enrichment and KEGG pathway analysis showed that 1052 DEGs were significantly enriched in 16 pathways, including cytokine-cytokine receptor interaction, IL17, PI3K-Akt, MAPK and TNF signaling pathway. PPI network analysis showed that IL17A, IFN-γ and TNF-α interacted with various proteins and may play crucial roles in BVDV-2 infection. Of note, we confirmed that GS2018 induced Th17 cell differentiation in PBLCs and persistently increased the expression levels of IL17A. In turn, the replication of GS2018 was inhibited by IL17A.

Conclusion

In this study, the transcription changes of DEGs related to host immune responses in bovine PBLCs were caused by CP BVDV-2 infection. In particular, the effector molecules IL17A of Th17 cells were significantly up-regulated, which inhibited viral replication. These results will contribute to exploration and further understanding of the host immune response mechanism and interaction between host and BVDV-2.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08194-w.

Transcriptomic profiling of bovine blood dendritic cells and monocytes following TLR stimulation

Dendritic cells (DC) and monocytes are vital for the initiation of innate and adaptive immune responses. Recently, we identified bona fide DC subsets in blood of cattle, revealing subset- and species-specific transcription of toll-like receptors (TLR). In the present study, we analyzed phenotypic and transcriptional responses of bovine DC subsets and monocytes to in vitro stimulation with four to six different TLR ligands. Bovine DC subsets, especially plasmacytoid DC (pDC), showed a clear increase of CCR7, CD25, CD40, CD80, CD86, and MHC-II expression both on mRNA and protein level. Flow cytometric detection of p38 MAPK phosphorylation 15 min after stimulation confirmed activation of DC subsets and monocytes in accordance with TLR gene expression. Whole-transcriptome sequencing of sorted and TLR-stimulated subsets revealed potential ligand- and subset-specific regulation of genes associated with inflammation, T-cell co-stimulation, migration, metabolic reprogramming, and antiviral activity. Gardiquimod was found to evoke strong responses both in DC subsets and monocytes, while Poly(I:C) and CpG preferentially triggered responses in cDC1 and pDC, respectively. This in-depth analysis of ligand responsiveness is essential for the rational design of vaccine adjuvants in cattle, and provides a solid basis for comparative studies on DC and monocyte biology across species.

Genetic Diversity of Bovine Pestiviruses Detected in Backyard Cattle Farms Between 2014 and 2019 in Henan Province, China

Bovine pestiviruses include Pestivirus A (BVDV-1), Pestivirus B (BVDV-2), and Pestivirus H, which was originally called HoBi-like pestivirus. We conducted an epidemiological investigation for pestiviruses circulating in backyard cattle farms in central China. RT-PCR assays and sequences analysis were conducted on 54 nasal swabs, 26 serum samples, and three lung samples from cattle with respiratory infections and identified 29 pestivirus strains, including 24 Pestivirus A and five Pestivirus H strains. Phylogenetic analysis based on partial 5'-UTR and Npro sequences showed that the genotypes of 24 Pestivirus A strains included Pestivirus A 1b (six isolates), Pestivirus A 1m (six isolates), Pestivirus A 1q (two isolates), Pestivirus A 1u (one isolates), and Pestivirus A 1o (nine isolates, a putative new sub-genotype). In addition, a single Pestivirus H agenotype included all five Pestivirus H strains. This study revealed extensive genetic variations within bovine pestivirus isolates derived from cattle in backyard farms in Central China, and this epidemiological information improves our understanding of the epidemics of bovine Pestiviruses, as well as will be useful in designing and evaluating diagnostic methods and developing more effective vaccines.

Prevalence and genetic diversity of bovine viral diarrhea virus in dairy herds of China

To determine the nationwide prevalence and genetic diversity of bovine viral diarrhea virus (BVDV) in China, 92 dairy farms with more than 500 animals in 19 provinces of China were surveyed in 2017. At each farm, ear notch samples from calves less than six months old and bulk tank milk (BTM) samples were collected. A total of 901 ear notch samples and 329 BTM samples from 183 tanks were sampled. A total of 20 (20/901, 2.22 %) ear notch samples from 10 (10/92, 10.86 %) farms tested positive for BVDV by IDEXX Antigen Point-of-Care (POC) Test kit and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). In addition, 80 of 183 (80/183, 43.7 %) BTM samples from 43 (43/92, 46.7 %) farms were identified as positive by qRT-PCR. The RNA of positive and suspect samples identified by qRT-PCR was subjected to 5'- untranslated region (UTR) amplification by nested RT-PCR and then sequenced. A total of 119 sequences were obtained and phylogenetic analysis of these 5'-UTR sequences revealed the presence of eight different subgenotypes of BVDV-1 including 1a (n = 37, 31.09 %), 1b (n = 5, 4.20 %), 1c (n = 34, 28.57 %), 1d (n = 2, 1.68 %), 1m (n = 25, 21.01 %), 1q (n = 6, 5.04 %), and two unknown subgenotypes which were tentatively typed as "BVDV-1v" (n = 8, 6.72 %) and "BVDV-1w" (n = 2, 1.68 %), respectively. BVDV-1a, 1c, and 1m were the dominant strains, collectively accounting for 80.67 % (96/119) of all sequences. Phylogenetic analysis based on selected N-terminal autoprotease (N^pro) sequences confirmed the classification of the 5'-UTR sequences. In conclusion, the prevalence of BVDV persistent infection in dairy cattle was high and genetic diversity was high and increasing, revealing a serious threat to the health of cattle in China and highlighting the need for BVDV control.

Who's who in the Bovine viral diarrhea virus type 1 species: Genotypes L and R

The bovine viral diarrhea virus type 1 species is responsible for cosmopolitan diseases affecting cattle and other ruminants, with relevant impact on animal production. The species presents high genomic heterogeneity, with implications on control and prophylactic programs. Genomic traits of different genetic groups are often related to geographic origin. Atypical sequences have been reported from Pestivirus isolates originated from cattle in Turkey. Based on phylogenetic analysis of 5' untranslated region and Npro and secondary structure analysis of the 5'-UTR RNA, Turkish isolates have been segregated in two distinct genotypes. Out of the twenty-three identified BVDV-1 genotypes, the Turkish clusters, named L and R or 1.16 and 1.14, according to palindromic nucleotide substitution genotyping method, represent genomic clusters so far, not described elsewhere, suggesting geographic segregation. In order to avoid confusion in the current taxonomy of the species, nomenclature of described homonymous genotypes, referred to different genomic clusters, should be corrected.

Bovine viral diarrhea virus type 1 current taxonomy according to palindromic nucleotide substitutions method

Pestivirus bovine viral diarrhea virus type 1 species is responsible for cosmopolitan diseases affecting cattle and other ruminants, presenting a wide range of clinical manifestations, with relevant impact on zootechnic production. Understanding genomic characteristic and virus taxonomy is fundamental in order to sustain control and prophylactic programs. Given the recent various studies reporting a relatively high number of new strains, in particular from Asian countries, in the present study, four hundred-eighty-two genomic sequences have been evaluated applying the palindromic nucleotide substitutions method for genotyping. Based on the secondary structure alignment and computing genetic distance among strains in the 5' untranslated region of Pestivirus RNA, the current taxonomy of the species was reviewed. Twenty-two genotypes have been identified, applying a nomenclature based on divergence in the genus.

Variability and Global Distribution of Subgenotypes of Bovine Viral Diarrhea Virus

Bovine viral diarrhea virus (BVDV) is a globally-distributed agent responsible for numerous clinical syndromes that lead to major economic losses. Two species, BVDV-1 and BVDV-2, discriminated on the basis of genetic and antigenic differences, are classified in the genus Pestivirus within the Flaviviridae family and distributed on all of the continents. BVDV-1 can be segregated into at least twenty-one subgenotypes (1a–1u), while four subgenotypes have been described for BVDV-2 (2a–2d). With respect to published sequences, the number of virus isolates described for BVDV-1 (88.2%) is considerably higher than for BVDV-2 (11.8%). The most frequently-reported BVDV-1 subgenotype are 1b, followed by 1a and 1c. The highest number of various BVDV subgenotypes has been documented in European countries, indicating greater genetic diversity of the virus on this continent. Current segregation of BVDV field isolates and the designation of subgenotypes are not harmonized. While the species BVDV-1 and BVDV-2 can be clearly differentiated independently from the portion of the genome being compared, analysis of different genomic regions can result in inconsistent assignment of some BVDV isolates to defined subgenotypes. To avoid non-conformities the authors recommend the development of a harmonized system for subdivision of BVDV isolates into defined subgenotypes.

Molecular Characterization of a Novel Bovine Viral Diarrhea Virus Isolate SD-15

As one of the major pathogens, bovine viral diarrhea virus caused a significant economic loss to the livestock industry worldwide. Although BVDV infections have increasingly been reported in China in recent years, the molecular aspects of those BVDV strains were barely characterized. In this study, we reported the identification and characterization of a novel BVDV isolate designated as SD-15 from cattle, which is associated with an outbreak characterized by severe hemorrhagic and mucous diarrhea with high morbidity and mortality in Shandong, China. SD-15 was revealed to be a noncytopathic BVDV, and has a complete genomic sequence of 12,285 nucleotides that contains a large open reading frame encoding 3900 amino acids. Alignment analysis showed that SD-15 has 93.8% nucleotide sequence identity with BVDV ZM-95 isolate, a previous BVDV strain isolated from pigs manifesting clinical signs and lesions resembling to classical swine fever. Phylogenetic analysis clustered SD-15 to a BVDV-1m subgenotype. Analysis of the deduced amino acid sequence of glycoproteins revealed that E2 has several highly conserved and variable regions within BVDV-1 genotypes. An additional N-glycosylation site (240NTT) was revealed exclusively in SD-15-encoded E2 in addition to four potential glycosylation sites (Asn-X-Ser/Thr) shared by all BVDV-1 genotypes. Furthermore, unique amino acid and linear epitope mutations were revealed in SD-15-encoded E^rns glycoprotein compared with known BVDV-1 genotype. In conclusion, we have isolated a noncytopathic BVDV-1m strain that is associated with a disease characterized by high morbidity and mortality, revealed the complete genome sequence of the first BVDV-1m virus originated from cattle, and found a unique glycosylation site in E2 and a linear epitope mutation in E^rns encoded by SD-15 strain. Those results will broaden the current understanding of BVDV infection and lay a basis for future investigation on SD-15-related pathogenesis.

Genomic characterization of three bovine viral diarrhea virus isolates from cattle

Three strains of the bovine viral diarrhea virus (BVDV) were isolated from cattle in Beijing, China. To investigate their genomic features, we sequenced and characterized the complete genome of each of the isolates. Each of the three virus genomes is about 12,220 bp in length, containing a 5' untranslated region (UTR), one open reading frame (ORF) encoding a 3897-amino-acid polypeptide, and a 3' UTR. The nucleotide sequence of the three isolates were 99.0 % identical to each and other shared nucleotide sequence identities of 73.4 % to 98.3 % with other BVDV-1 strains, about 70.0 % with BVDV-2 strains, about 67.0 % with BVDV-3, and less than 67.0 % with other pestiviruses. Phylogenetic analysis of the full-length genome, 3' UTR, and the N^pro gene demonstrated that the three viruses were BVDV-1 isolates. This is the first report of complete genome sequences of BVDV 1d isolates from China and might have implications for vaccine development.