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Dairy cows from 19 farms from different locations in North West Syria were tested for BVD. BRSV, PI3, IBR, BHV4, BPS andadeno viruses (IIFandAGID methods). BRSV and BHV4 were the prevalent infections with 88 % and 83.2 % of sero- positiveness, respectively. PI3 and BVD infections were also frequent, showing 62 % and 58 %, respectively. IBR, adeno and BPS showed a lowerprevalence (31 %, 26 % and 11 %).

In the one health approach, which summarizes the concept that human, animal, and plant health are interdependent and linked to the ecosystems in which they exist, animal welfare assumes an important role. In addition, the Farm to Fork Strategy of the European Union recognizes animal welfare as an essential component. Transport of animals involves a number of issues related to welfare. Animals are subjected to continuous stress, not only during transit on vehicles, vessels, trains, or airplanes, but also during loading and unloading operations. The handling and transport conditions have improved from basic and relatively rudimentary systems, with elements to attenuate the discomfort of animals having been gradually introduced, especially for long-distance transport. Despite several improvements in animal welfare standards during transportation there are still pressing issues in current EU legislation which deserve reviewing. Recently, several scientific opinions on animal welfare, including during transport, have been published by the European Food Safety Agency, following requests by the European Commission. In addition, the European Court of Auditors published its last report focused on animal welfare during transport. These reports underline the need to review current legislation governing the topic and highlight a number of outstanding issues in the European Union and in Third Countries. This article summarizes the history and current status of this complex issue., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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., Competing Interests: Authors declare that there is no conflict of interest.

Background: In 2015, an unprecedented epidemic of microcephaly occurred in Brazil. Preliminary observations suggested the involvement of cofactors in the etiopathology of Zika virus-associated microcephaly. Bovine viral diarrhea virus (BVDV) was identified in fetal samples with microcephaly, originating in the state of Paraíba, and two virus sequences, obtained from the amniotic fluid collected from mothers with babies affected by Zika and microcephaly, have been characterized as two different species of BVDV, types 1 and 2., Aim: The involvement of BVDV as a co-factor in the etiopathogenesis of Zika virus-associated microcephaly was explored., Methods: A serological screening using an ELISA test was undertaken to detect antibodies against BVDV among patients referred to the Central Laboratory of Natal, Rio Grande do Norte, encompassing microcephalic babies and their mothers, mothers and pregnants not associated with microcephaly and general patients as a control group., Results: Two samples were positive out of 382 tested (0.52%). No specific relation with birth defects could be established., Conclusions: The study might suggest serological evidence of BVDV in humans. Further studies and the application of improved diagnostic tests adapted to humans are necessary to clarify the epidemiological extent and impact of BVDV., Competing Interests: The authors declare that there is no conflict of interest.

Bovine viral diarrhea virus (BVDV) and classical swine fever virus (CSFV) are members of the genus Pestivirus that cause disease in wild and domestic animals and are responsible for extensive economic losses of livestock and biological industry. BVDV is also a significant laboratory contaminant. Currently, no effective antiviral therapeutics are available to control their infection. Ginsenosides, as major pharmacological ingredients in the plants of ginseng, have various biological activities. In the present work, the antiviral activity of 9 ginsenosides and 3 other saponins from Araliaceae plants was investigated against Pestivirus . Ginsenoside Rb2 and Rb3 showed low cytotoxicity and obvious antiviral effect. They were able to inhibit the replication and proliferation of BVDV and CSFV. In addition, our results suggest that the possible antiviral mechanism of Rb2 might be related to its ability to affect the translation of these viruses. Obtained results suggest that ginsenoside Rb2 and Rb3 have a potential for effective treatment against Pestivirus infection., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Tan, Giangaspero, Sun, Jin, Liu, Wang, Cheng, Wang and Zhang.)

Background: Classical swine fever virus (CSFV), species member of the family Flaviviridae , is generally considered restricted to domestic and wild suids. The circulation of CFSV has been detected in cattle herds in China and India. Natural infection appeared associated with clinical signs in some cases., Aim: The secondary structures of the internal ribosome entry site in the 5' untranslated region (UTR) were used for the genomic characterization of bovine strains., Methods: Sequences have been compared to the representative CSFV strains isolated from pigs, vaccines, and contaminants from porcine cell lines and an ovine strain isolated in Spain., Results: The observed sequences from cattle showed a genetic relatedness with live-attenuated vaccine strains used in pigs. Sequence characteristics of the Chinese strain S171 are genetically distant from the previously reported CSFV genotypes, suggesting a new outgroup in the species, described for the first time, and named CSFV-d. Other Chinese strains were genetically closely related to CSFV genotype a2 (Alfort type) pig strains. Indian strains, reported from the states of Tamil Nadu and Meghalaya, were genetically closely related to CSFV genotype a1 (Brescia type) and a5 pig strains, respectively., Conclusion: These preliminary observations are new and relevant in countries, where CSFV control and eradication strategies are applied., Competing Interests: Authors declare that there is no conflict of interest.

Applying palindromic nucleotide substitutions (PNS) method, variable loci of the internal ribosome entry site (IRES) secondary structure in the 5' untranslated region (UTR) of Border disease virus sequences were analysed allowing their allocation into ten IRES classes within the species. Sequence characteristics of Turkish and Chinese strains were highly divergent from other genogroups, indicating geographic segregation and micro-evolutive steps within the species. Observed heterogeneity in the BDV species has to be considered for potential implications on diagnostic tests, control and preventive measures., (Crown Copyright © 2019. Published by Elsevier B.V. All rights reserved.)

Pestiviruses are responsible for widespread diseases affecting cattle, pigs and other ruminants, presenting a wide range of clinical manifestations, with significant impact on animal production. Given the recent various reports of a relatively high number of new strains and atypical genomic variants, in the present study, ninety-seven genomic sequences from southern Italy have been evaluated applying the palindromic nucleotide substitutions method, based on 5'-UTR secondary structure alignment and computing genetic distance among strains in the internal ribosome entry site. Sequence analysis revealed a highly heterogeneous virus population, indicating the introduction of virus variants of Bovine viral diarrhea virus and Border disease virus species from foreign countries. The application of different analytical procedures was useful to avoid interpretation difficulties. Circulation of heterogeneous virus populations showed the need for more accurate epidemiological investigations and stringent veterinary controls to protect animal health and welfare., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

In 2015, a young female Alpine chamois ( Rupicapra rupicapra rupicapra ), originated from the Aosta Valley Region, Northernwestern Italy, was conferred to the National Reference Centre for Wild Animal Diseases for pathologic examinations. Histological analysis revealed a severe meningoencephalitis characterized by lymphocytic and plasmacellular infiltration, gliosis, perivascular cuffs, and leptomeningitis at the level of brain and brain stem. Laboratory investigations included polymerase chain reaction, sequencing and characterization by phylogenetic analysis, and evaluation of the internal ribosome entry site secondary structure in the 5' untranslated region. These tests identified the pathological agent as border disease virus, a known health risk in domestic small ruminants. Genetic characteristics of the isolated strains, closely related to ovine and caprine strain sequences from neighboring regions of Piedmont, France, and Switzerland, suggested geographic segregation and micro-evolutive steps within the species.

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., (Copyright © 2018 Elsevier B.V. All rights reserved.)

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., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Two-hundred and eighty-one strains of bovine viral diarrhea virus type 1 (BVDV-1) were evaluated according to the palindromic nucleotide substitutions (PNS) method, a simple and practical genotyping procedure, at the three variable loci, V1, V2 and V3, in the 5'-untranslated region of genomic RNA. Ten PNSs were characteristic to the Pestivirus genus, located in the V1 and V2 loci. The BVDV-1 species shared a U-A pairing, a species-characteristic PNS, in position fifteen common to the V1 locus, and a G-C pairing in position five common to the V2 and V3 loci. Within the BVDV-1 species, 15 genotypes, BVDV-1a, BVDV-1b, BVDV-1c, BVDV-1d, and the newly described from BVDV-1e to BVDV-1o were identified based on characteristic nucleotide base pairings. The nomenclature reflected the genotypes' level of divergence within the species. Genotypes BVDV-1l, BVDV-1m and BVDV-1o were borderline in the species., (Copyright © 2013 Elsevier B.V. All rights reserved.)

The genus Pestivirus from the family Flaviviridae is represented by four established species; Bovine viral diarrhea virus 1 (BVDV-1); Bovine viral diarrhea virus 2 (BVDV-2); Border disease virus (BDV); and Classical swine fever virus (CSFV); as well a tentative species from a Giraffe. The palindromic nucleotide substitutions (PNS) in the 5' untranslated region (UTR) of Pestivirus RNA has been described as a new, simple and practical method for genotyping. New software is described, also named PNS, that was prepared specifically for this PNS genotyping procedure. Pestivirus identification using PNS was evaluated on five hundred and forty-three sequences at genus, species and genotype level using this software. The software is freely available at www.pns-software.com., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Ovine sera collected in the Prefectures of Hokkaido, Aomori and Iwate in the Northern Japan were examined for the presence of antibodies against Respiratory syncytial virus (RSV), bovine Herpesvirus type 1 (infectious bovine rhinotracheitis: IBR) and Parainfluenza virus type 3 (PIV3) using serum neutralisation (SN) and enzyme-linked immunosorbent assay (ELISA) tests. Twenty-three animals (11.73%) out of the 196 tested were sero-positive to PIV3. Sixteen animals (8.69%) out of the 184 tested reacted to RSV. No animals were positive to IBR antigen. Sero-conversions to PIV3 were detected in Hokkaido and Iwate (14.92% and 8.82%, respectively). Antibodies against RSV were detected in Hokkaido (9.23%) and Aomori (14.28%). Although no diagnostic measures were in place, the infections did not appear to be related to any reduction in sheep productivity.

Ovine herpesvirus 2 (OvHV-2) causes sheep-associated malignant catarrhal fever (SA-MCF), and is responsible for economic losses in cattle and other susceptible species around the world. A survey of 154 serum samples from 14 flocks in 3 Japanese prefectures (Hokkaido, Aomori and Iwate) was undertaken between 2007 and 2008 to test for antibodies to OvHV-2. OvHV-2 was present in 56 sheep and 2 goats, with 37.66% of samples having a positive reaction using a serum neutralization test. The immune reaction reported in goats could result from Caprine herpesvirus-2. These results indicate that sheep are reservoirs for OvHV-2 in the field in Japan, and they might transmit the virus to susceptible cattle and wild fauna.

A serological survey was carried out in the northern prefectures of Hokkaido, Iwate and Aomori in Japan, for the presence of antibodies against Toxoplasma gondii, Chlamydiapsittaci var. ovis, Mycobacterium paratuberculosis, Coxiella burnetii, Brucella spp., Leptospirosis and Orf virus (ORFV). Out of 267 samples tested, highest overall prevalence (28.78%) was found for T. gondii. The 12.59% of tested sheep were positive for C. psittaci var. ovis. A total of 8.67% were found to be seropositive for C. burnetii. Levels of these infections were found in all three prefectures. Seroconversion to ORFV was detected in Hokkaido and Iwate Prefectures (2.57%). Animals were positive only for L. ballum (1.50%), in Hokkaido and Aomori Prefectures. No animals tested positive for Brucella spp. and M. paratuberculosis.

Ovine sera collected from the northern Prefectures of Hokkaido, Iwate and Aomori in Japan, were examined for the presence of antibodies against Coxiella burnetii (Q fever) using the complement fixation test and, against Brucella spp., using both the rapid serum agglutination test and the complement fixation test. None of the sera tested were serologically positive to Brucella spp. A total of 21 animals (8.64%) out of 243 samples tested were seropositive to the C. burnetii antigen. Levels of infection were observed in all of the three Prefectures and in ten flocks of the fourteen sampled. Although no diagnostic measures were in place, the infection could not be linked to losses in sheep production or to the decreased fertility in ewes, a lower lambing rate and mortality in lambs. These data confirmed that Q fever is widespread in the sheep population in the area studied. Considering the zoonotic potential of the disease, further studies to investigate the epidemiology of Q fever in this region are required.

Sheep flocks from Hokkaido, Iwate and Aomori, three northern prefectures of Japan, were screened for antibodies to Mycoplasma ovipneumoniae and Mycoplasma agalactiae by ELISA. Sixty four animals out of 246 (26%) were seropositive to M. ovipneumoniae, with positive results obtained from all three prefectures. None of the sera tested were serologically positive to M. agalactiae.

The first epidemiological survey of Border disease virus (BDV) was undertaken in small ruminants in Japan. Ovine sera, collected from the northern prefectures of Hokkaido, Aomori and Iwate, were examined for the presence of antibodies against BDV using the neutralization peroxidase-linked antibody test. Twenty-nine (17.6%) of one hundred and sixty-five samples were seropositive for BDV. Results were specific, excluding cross-reactions with bovine viral diarrhea virus (BVDV). Only one sample (0.6%) was positive for BVDV, and was negative for BDV. Despite serological evidence of virus circulation, there have been no clinical cases of border disease in sheep in Japan. Although no diagnostic measures were performed, the infection did not appear to be associated with a reduction in ewe fertility nor with lamb mortality.

The 5'-untranslated region of Pestivirus strains isolated from domestic and wild animals were analysed to determine their taxonomic status according to nucleotide changes in the secondary genomic structure using the palindromic nucleotide substitutions (PNS) method. A total of 131 isolates out of 536 Pestivirus strains evaluated, were clustered as Border disease virus (BDV) species. The BDV strains were further divided into at least 8 genotypes or subspecies. Thirty-two isolates from small ruminants suffering from clinical symptoms of Border disease were clustered into bovine viral diarrhoea virus 1 (BVDV-1), BVDV-2 and classical swine fever (hog cholera) virus species and also into the tentative BDV-2 species. Since the definition of an infectious disease is based primarily on a specific causative pathogen and taking into account the heterogeneity of the genus Pestivirus, clinical cases should be named according to the laboratory results. The PNS procedure could be useful for laboratory diagnosis of Border disease in domestic and wild ruminants.

Ovine sera collected from the northern Prefectures of Hokkaido, Iwate and Aomori in Japan, were examined for the presence of antibodies against visna-maedi virus using the agar gel immunodiffusion test and enzyme-linked immunosorbent assays. Three animals (1.12%), out of 267 samples tested, were found to be seropositive to the visna-maedi antigens in both tests. Levels of infection were found in flocks from Hokkaido and Iwate Prefectures, but not in the Aomori Prefecture. Nucleic acid detection by polymerase chain reaction on serum samples did not give positive results. Although no diagnostic measures were in place, the infection could not be related to losses in sheep production or to reduced survival rates. The very limited visna-maedi distribution indicates a highly favourable condition for the application of eradication strategies in this area.

The palindromic nucleotide substitutions (PNS) at the three variable loci (V1, V2 and V3) in the 5'-untranslated region (UTR) of the Pestivirus genome have been considered for taxonomical segregation of the species, through the evaluation of 534 strains. On the basis of qualitative and quantitative secondary structure characteristics, species have been identified within the genus, determining genetic distances between species isolates, clarifying borderline and multirelated sequences, and characterizing and clustering the Pestivirus strains showing unexpected genomic sequences. Nine genomic groups have been identified: the species Bovine viral diarrhea virus 1 (BVDV-1), Bovine viral diarrhea virus 2 (BVDV-2), Border disease virus (BDV) and Classical swine fever virus (CSFV) and the tentative species Pronghorn, Giraffe, Bovine viral diarrhea virus 3 (BVDV-3) (HoBi group), Border disease virus 2 (BDV-2) (Italian small ruminant isolates) and Bungowannah. Palindromic positions have been characterized according to changes in nucleotide base-pairs identifying low variable positions (LVP) including base-pairs present in less than 80% of the genus. The determination of divergence between single strain sequences or genetic groups was obtained easily by comparing base-pairing combinations from aligned secondary structures. This provided clear information such as the level of heterogeneity within a species, the relatedness between species, or facilitating the characterization and clustering of specific strains. The BVDV-1 and BDV species resulted heterogeneous, showing isolates located on a borderline in the species. Within the BVDV-2 species, two main genogroups were identified, with strains showing common sequence characteristics to both groups (multirelated strains). They could be allocated correctly by quantitative analysis. Similarly, the relation between CSFV and BDV species appeared very clearly. Also in this case, ambiguous strain sequences could be clustered in the species showing the lowest divergence values. In conclusion, the proposed taxonomical procedure is based on the evaluation of only the strategic and highly conserved genome regions in the 5'-UTR. Furthermore, the application of quantitative analytical procedure allowed for a better determination of relation among species., (Copyright © 2011 Elsevier B.V. All rights reserved.)

In 2005 a Mycoplasma species was isolated from ocular-conjunctival swabs from an adult male Alpine ibex (Capra ibex) from the Valle d'Aosta Region, Northern Italy. The animal suffered from bilateral ocular discharge with diffuse inflammation, severe corneal involvement of the left eye and mild corneal opacity of the right eye. Histologic examination revealed a keratoconjunctivitis characterized by lymphocytic and plasmacellular infiltration. Laboratory investigations of the isolate included culture, transmission electron microscopy, PCR, and denaturing gradient gel electrophoresis, as well as DNA sequencing of the 16S rDNA gene. These tests identified the isolate as Mycoplasma mycoides subsp. capri large-colony serovar, an organism that has occasionally been associated with keratoconjunctivitis in goats. For a correct diagnosis, it is necessary to carry out laboratory investigations, as clinical cases of keratoconjunctivitis in wild ruminants are not always ascribable to Mycoplasma conjunctivae.

Bovine viral diarrhea virus 2 (BVDV-2) strains demonstrated in cattle, sheep, and adventitious contaminants of biological products have been evaluated by the palindromic nucleotide substitutions (PNS) method at the three variable loci (V1, V2 and V3) in the 5' untranslated region (UTR), to determine their taxonomical status. Variation in conserved genomic sequences was used as parameter for epidemiological evaluation of the species in relation with geographical distribution, animal host and virulence. Four genotypes, BVDV-2a, BVDV-2b, BVDV-2c, and BVDV-2d have been identified within the species. Taxonomical segregation corresponded to geographical distribution of genotype variants. Genotype 2a was present worldwide, and was the only circulating also in sheep, in addition to cattle. Genotypes 2b, 2c and 2d were restricted to South America. Contamination of biological products was related to genotypes 2a and 2d. Genetic variation could be related with chronological diffusion of the BVDV-2 species variants in different geographic areas. Chronologically, the species emerged in North America in 1978, spreading in UK and Japan, continental Europe, South America and New Zealand. Correlation between clinical features related with isolation of BVDV-2 strains and genetic variation indicated that subgenotype 1, variant 4 of genotype 2a was related with hemorrhagic syndrome. These observations suggest that evaluation of genomic secondary structure, by identifying markers for expression of virus biological activities and species evolutionary history, may be applied as useful tool for epidemiological evaluation of the BVDV-2 species, and possibly for other species of the genus Pestivirus.

Forty-three strains of classical swine fever (hog cholera) virus (CSFV) from outbreaks in pigs in Europe, Asia and America, two strains from commercial CSFV modified live vaccines and a strain isolated from a diseased lamb from Spain were subjected to analyses of nucleotide sequence variations in the 5' terminal region of the genome. These isolates were divided into three clusters, namely: CSFV-1, CSFV-2, and CSFV-3, based on palindromic nucleotide substitutions in the 5' untranslated region (UTR). The homology degree, according to nucleotide base pairing variation in the secondary palindromic structure of the three variable loci V1, V2 and V3, was 60% in the CSFV species, with a mean divergence value of 6.19 base pairs (bp). relatedness within genotypes ranged from 71.11% to 100%, with mean divergence values from 5.5 to 0.73 base pairs. Subgenotypes showed a divergence ranging from 1 to 9 base pairs within the genotype. Genotype CSFV-1 revealed 15 base pair combinations with 13 divergent base pairs, resulting in 4 subgenotypes with 6 variants in subgenotype CSFV-1.1, including the reference strain Brescia and 6 variants in subgenotype CSFV-1.2, including the Alfort reference strain. Subgenotypes CSFV-1.3 and CSFV-1.4 comprised one and two variants, respectively. Genotype CSFV-2 was represented by the Spanish ovine isolate 5440/99 and the genotype CSFV-3 included the Japanese strains Okinawa/86 and Kanagawa/74. CSFV genotypes revealed a strong relationship with Border disease virus strains, showing relatively low divergence values when compared to other pestivirus species. Evaluation of nucleotide base pair divergence among genotypes and expression of evolutionary changes in the CSFV species led to the construction of a phylogenetic tree based on secondary structure.

Bovine viral diarrhoea virus 2 (BVDV-2) strains demonstrated in cattle, sheep and adventitious contaminants of biological products were evaluated by the palindromic nucleotide substitutions (PNS) method at the three variable loci (V1, V2 and V3) in the 5' untranslated region (UTR), to determine their taxonomic status. Variation in conserved genomic sequences was used as a parameter for the epidemiological evaluation of the species in relation to geographic distribution, animal host and virulence. Four genotypes were identified within the species. Taxonomic segregation corresponded to geographic distribution of genotype variants. Genotype 2a was distributed worldwide and was also the only genotype that was circulating in sheep and cattle. Genotypes 2b, 2c and 2d were restricted to South America. Genotypes 2a and 2d were related to the contamination of biological products. Genetic variation could be related to the spread of BVDV-2 species variants in different geographic areas. Chronologically, the species emerged in North America in 1978 and spread to the United Kingdom and Japan, continental Europe, South America and New Zealand. Correlation between clinical features related with isolation of BVDV-2 strains and genetic variation indicated that subgenotype 1, variant 4 of genotype 2a, was related to a haemorrhagic syndrome. These observations suggest that the evaluation of genomic secondary structures, by identifying markers for expression of virus biological activities and species evolutionary history, may be a useful tool for the epidemiological evaluation of BVDV-2 species and possibly of other species of the genus Pestivirus.

The palindromic nucleotide substitutions (PNS) at the three variable loci (V1, V2 and V3) in the 5' untranslated region (UTR) of Pestivirus RNA have been considered for taxonomical segregation of species, through the evaluation of 430 genomic sequences. On the basis of qualitative and quantitative secondary structure characteristics, six species have been identified: Bovine viral diarrhea virus 1 (BVDV-1), Bovine viral diarrhea virus 2 (BVDV-2), Classical swine fever virus (CSFV), Border disease virus (BDV), the tentative species Giraffe and a new proposed taxon named Pronghorn. The first step was qualitative and consisted in the characterization of the different positions of the three stems and loops in the 5' UTR sequences of all the strains under consideration belonging to the genus. Secondary structure sequences showing divergent base-pair combinations have been aligned for comparison. Palindromic positions have been characterized according to changes in nucleotide base-pairs identifying low-variable positions (LVP) including base-pairs present in less than 80% of the genus. The second step was quantitative, allowing the identification of genomic groups by clustering the base-pair combinations according to LVP. Relatedness among types was evaluated to identify homogeneous groups. Cross comparisons between types within the genus have been evaluated by computing the divergence percentage thus clarifying borderline and multirelated sequences.

The Parsonage-Turner syndrome, a rare form of neuralgic amyotrophy of unknown aetiology, was diagnosed in a patient involved in an outbreak of bovine viral diarrhoea virus (BVDV). The patient, suffering from inflammation of the right shoulder with a permanent atrophy, developed anti-BVDV antibody titres which remained very high during the four following years of monitoring.

The 5'-untranslated region (5'-UTR) of the pestivirus strains isolated from wisent and reindeer suffering from severe diarrhoea in the Duisburg zoo in Germany were amplified by reverse transcription-polymerase chain reaction and sequenced for comparison with those of other pestiviruses from cattle, sheep, goats and swine. Phylogenetic trees constructed from the primary nucleotide sequences of these strains demonstrated that the 5'-UTR of both the wisent and reindeer isolates were identical and suggested that the isolates were allocated to a new cluster of Border disease virus (BDV). The BDV strains were further divided into at least three genotypes or subspecies by phylogenetic analysis and a newly proposed method based on palindromic nucleotide substitutions was used at the variable regions in the 5'-UTR.