Bovine respiratory syncytial virus (BRSV) is an important respiratory pathogen in cattle, detrimentally affecting the economy and animal welfare. The virus is distributed worldwide and is a major pathogen of the bovine respiratory disease complex [1, 2]. Viral respiratory infections are also of concern with regards to antibiotic resistance, as they predispose cattle to secondary bacterial infections that are commonly treated with antibiotics. Bovine respiratory disease is traditionally handled with management measures, vaccination and metaphylactic antibiotic treatment. Another possible strategy is to prevent inter-herd transmission of the main pathogens by increasing biosecurity measures at herd level. Because live animal transport is considered one of the main modes of BRSV transmission between herds [5, 6], proper mitigation must ensure that live animal transport be performed without compromising biosecurity. This requires knowledge on transmission risk associated with animal contact at different stages of infection. Knowledge of BRSV shedding related to clinical features would also be useful in order to assess the transmission risk of an infected herd without the use of viral diagnostic assays. For both of these areas, several knowledge gaps exists. Although way of infection may affect both viral shedding and clinical signs compared to naturally exposed animals, challenge studies are superior in the sense that aetiology and time of exposure is known and clinical features and virus excretion can be followed closely. Challenge studies, many of them aiming to evaluate the efficacy of vaccines [7–11] seldom last longer than one to two weeks. Grissett et al. and Gershwin concluded that shedding of BRSV begins on day three or four post-infection (p.i.) and usually lasts until day nine or ten. Grissett et al. summarized that the median time to appearance, peak and resolution of clinical signs was 3, 6 and 12 days, respectively, based on information from 22 inoculation studies [7–11, 14–22]. As studies outlasting the acute phase of infection are lacking, it is not known how long an animal can transmit infectious viruses to other animals. Appearance of clinical signs is usually the only information available in the field, and finding a clinical parameter that indicates shedding of infectious BRSV would be valuable. The existence of chronic or persistent infections in individuals is likewise still unclear [23–26].

During the acute phase of a BRSV infection, immunological protection develops, but it is assumed to be short-lived. This might enable early reinfection and new shedding of the infective virus, which complicates the risk assessment. A few BRSV studies have been performed to shed light on this. In a study by Kimman et al. they reported a strong local IgA response in the respiratory tract, but no virus shedding, when calves were re-exposed 3–4 months after primary BRSV infection. Stott et al. indicated, referring to their own unpublished results, that reinfection in calves and heifers may occur as early as three weeks post-infection. However, early reinfection with BRSV is not well-documented, and more precise knowledge of the occurrence is needed.

The existing literature on BRSV shedding and transmission is based on various laboratory methods, such as detection of viral RNA and culturing of the virus. Although resource-demanding, virus transmission studies are preferably performed using live animals in sentinel trials.

The aim of the present study was, therefore, to study basic features of BRSV infection in calves infected by exposure to BRSV-shedding calves. This was performed by:Investigating the shedding of viral RNA and infective virions:related to clinical outcome during the experimental period, lasting for two monthsin calves rechallenged by inoculation seven weeks p.i.Investigating whether the calves and their environment are not infectious to naïve in-contact calves four to nine weeks post-infection despite rechallenge with BRSV and mild stress induction.

Bovine respiratory disease complex (BRDC) is a major cause of economic losses in the cattle industry worldwide. The most important viral agent include bovine herpesvirus type 1 (BHV-1), bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), and bovine parainfluenza-3 virus (BPI-3V). BRSV, belonging to the genus Pneumovirus within the family Paramyxoviridae, and is one of the most important causes of lower respiratory tract infections in calves; however, adult animals with subclinical infection are the main source of infection, since reinfections are common in the herds. It is highly prevalent in cattle, with a significant economic impact as the most important viral cause of BRDC worldwide. BVDV is a Pestivirus from the family Flaviviridae, which affects the digestive, respiratory, and reproductive systems in different production animals. Clinical signs include pyrexia, diarrhea, reduced production, and highly morbid disease but cause low mortality of infected animals. Infectious bovine rhinotracheitis (IBR) is an important infectious disease of domestic and wild cattle caused by BHV-1. This virus is a member of genus Varicellovirus, which belongs to the Herpesviridae family. Clinical signs infection includes symptoms of inflammatory reactions in respiratory, genital tracts, abortion, and neurological disorders. Betancur et al. found a statistical association between seropositive animals for BHV-1 with respect sex and age in Colombia, while Ochoa et al. reported higher infection in cows older than 5 years of age. BPI-3V is in the genus Respirovirus of the family Paramyxoviridae, which cause serious economic losses in small and large ruminants. Clinical disease is usually mild, with symptoms of fever, nasal discharge, and cough. Betancur et al. reported a statistical association between seroprevalence values for BPI-3V and age groups.

Aguachica, Rio de Oro, and La Gloria municipalities are located in Cesar department, which, in turn, is located in the Northeast of Colombia, and is very important agricultural and fish raising region, being the dual-purpose cattle husbandry one of the most important agricultural components of the regional economy, with a participation of 8% in the cattle national inventory. According to the National Agricultural Institute, the state has a population of 1,305,984 heads of cattle, being 30% located in the three municipalities.

Information about the prevalence of these viral pathogens is available from several countries in which these diseases have been reported. Nevertheless, there is very little epidemiological information on viral pathogens in cattle, mainly in the Northeast region of Colombia. Therefore, the present study was conducted to estimate the seroprevalence of respiratory viral pathogens in dual-purpose cattle and evaluate risk factors in the municipalities of Aguachica, Rio de Oro, and La Gloria in the department of Cesar.

Alpaca (Vicugna pacos, also known as Lama guanicoe pacos) are domesticated members of the New World camelid species (Lamini), which also include guanaco (Lama guanicoe), vicuna (Vicugna vicugna), and llama (Lama glama). The natural habitat for alpaca is at high altitude (3500–5000 m) in South America (Peru, Ecuador, Bolivia, and Chile) where they are kept as livestock in herds and their fiber is used much like wool. Approximately 300,000 animals are in the U.S. Compared to other livestock, e.g., about 96 million cattle, their number is still relatively small.

Previously reported viral infections in domestic alpaca include adenovirus, equine viral arteritis virus, rabies, bluetongue virus, foot-and-mouth disease virus, bovine respiratory syncytial virus, influenza A virus, rotavirus, orf virus, bovine papillomavirus, vesicular stomatitis virus, coronavirus, bovine parainfluenza-3 virus, West Nile virus, equine herpesvirus-1,, and bovine viral diarrhea virus–[13]. Bovine enteroviruses (BEV) have not previously been reported to infect alpaca. The bovine enterovirus species previously contained two types, BEV-A and BEV-B, although a new classification structure was ratified recently, redesignating these as species Enterovirus E (EV-E) and Enterovirus F (EV-F), respectively,. Each of the new BEV species includes multiple serotypes, with EV-E comprising four described serotypes (previously A1–4, renamed E1–E4), and EV-F containing six reported serotypes (previously B1–6, renamed F1–F6).

Recently developed approaches to virus detection have the potential to further expand understanding of viral disease in animals, including alpaca. Many of these approaches are based on non-specific PCR amplification used in conjunction with standard or high-throughput sequencing to identify PCR products.

We utilized such a method–[19] to investigate an outbreak of a respiratory infection in alpaca, identifying a bovine enterovirus (EV-F), named Enterovirus F, strain IL/Alpaca, after other techniques had failed to detect any pathogen.

Bovine respiratory disease (BRD) incorporates all possible respiratory diseases in cattle and is characterised by abnormal clinical signs of the respiratory tract. Bovine respiratory disease refers to bacterial bronchopneumonia that may be complicated by previous, or concurrent, viral or Mycoplasma infection. The principal viruses involved in BRD include bovine herpesvirus 1 (BHV-1), bovine respiratory syncytial virus (BRSV), bovine parainfluenza virus type 3 (PI-3) and bovine viral diarrhoea virus (BVDV). Despite advances in veterinary medicine, animal husbandry, and animal welfare, respiratory disease among dairy cattle continues to be a major problem in the dairy industry. In addition to enzootic calf pneumonia, outbreaks of respiratory disease in adult animals can have devastating economic outcomes for dairy owners.

Many studies have been performed to detect animal-level risk factors for respiratory disease in young calves, whereas the literature concerning BRD in adult dairy cattle is deficient. In adult dairy cattle, respiratory disease is less important than mastitis, lameness, or reproductive disorders as a cause of morbidity. According to the Annual Report of the Estonian Animal Recording Centre (EARC, 2009), BRD was the reason for culling dairy cows in 0.7% of cases. According to our experience, in most herds BRD occurs as a sporadic disease in adult dairy cattle. However, epidemic outbreaks occur with high morbidity accompanied with dramatic economic losses due to medication use and discarded milk, as well as cow fatalities.

The subclinical course of BHV-1 infection has been observed after the introduction of the virus to a naive herd, however high morbidity of BHV-1 outbreaks involving respiratory disease symptoms (lethargy, coughing, conjunctivitis and oculonasal discharge) was seen on a number of occasions. Outbreaks of severe respiratory disease due to bovine respiratory syncytial virus (BRSV) have been observed in dairy herds throughout Sweden, where adult cattle were most severely affected. Risk factors associated with acute bovine respiratory disease, especially with BRSV outbreaks, were larger herd size, as well as the type of the production with a higher risk in dairy herds compared to beef herds. Acute BRD has been found to occur mainly during cold months, with an epidemic peak in December. Despite the multifactorial nature of BRD, only limited research data is available on herd management-related risk factors for respiratory disease in adult dairy cattle.

Poor fertility is the leading cause of culling cows in Estonia (EACR, 2009). Problems associated with reduced fertility in dairy cattle are related to: diseases of the reproductive tract of the cow, bull fertility, breeding management, and the environment, as well as nutrition. Several infectious diseases are related to abortion in cattle, and BHV-1, BVDV and Neospora caninum are often diagnosed as causes of abortion in cattle world-wide. However, field studies estimating the effect of BHV-1 on herd level reproductive performance have given contrary results. Previous studies found no association between the proportion of calves with antibodies against BVDV or BHV-1 virus and reproductive performance in beef herds. A somewhat higher mean open days period was found in cows that were serologically positive for BHV-1 than in seronegative dairy cows, however no decrease in reproduction performance was found to occur during an outbreak of BHV-1 in a dairy herd. To our knowledge no epidemiological studies have been published to identify and quantify the association between herd BHV-1 seroprevalence and farm-level reproductive performance in dairy cattle.

The objective of this study was to ascertain the associations between herd BHV-1 seroprevalence and the occurrence of acute respiratory disease and reproductive performance in adult dairy cattle. The association between management-related factors and higher BRD occurrence was also estimated.

Actinobacillus pleuropneumoniae Possesses an Antiviral Activity against Porcine Reproductive and Respiratory Syndrome Virus

In 2005, Allander et al., reported the discovery of a previously undescribed human parvovirus in respiratory secretions from children with respiratory tract disease in Sweden. Phylogenetic analysis showed that this virus belonged to the genus Bocavirus (subfamily, Parvovirinae; family, Parvoviridae) and was most closely related to bovine parvovirus (BP) and minute virus of canines (MVC). The virus was thus named "human bocavirus" (HBoV).

Human bocaviruses (HBoV) contain 3 open reading frames (ORFs) encoding a nonstructural protein (NS1, NP1) and two capsid proteins VP1 and VP2, respectively. The genomic organization of HBoV closely resembles that of bovine parvovirus type 1.

HBoV has been reported in respiratory samples from children with acute respiratory tract disease in various parts of the world (including Australia, North America, Europe, Asia, and Africa), suggesting that the virus is circulating worldwide. Pneumonia, acute bronchitis, bronchiolitis, are the main manifestations of HBoV infection.

HBoV seems to be a new member of the community-acquired respiratory viruses such as respiratory syncytial virus, adenovirus, influenza virus, parainfluenza virus, and rhinovirus, which cause common respiratory tract infections in the community. Because of its very high copy numbers in respiratory tract secretions, aerosol and contact transmission are likely effective, as they are for other respiratory viruses.

HBoV has been detected also in nasopharyngeal, serum, fecal and urine samples obtained mainly from young children around the age of 2 years predominantly during the winter season. HBoV was detected in two pediatric patients after organ transplantation, in human immunodeficiency virus-infected pediatric patients, and immunosuppressed adult patients.

Diagnosis of HBoV infection is based on the PCR amplification of viral genome fragments present in human respiratory, serum, stool and urine samples. A great number of different PCR techniques employing varying sets of primers specific for the viral genes NP1[10], NS1, and VP1, VP2 have been described. In addition to the detection of viral genomes by PCR, recent reports describe the detection of HBoV-specific IgG and IgM-antibodies against HBoV VP2 in serum samples using western blot or immunofluorescence assays. Furthermore, a standardized ELISA for the quantitative determination of HBoV-specific antibodies has been established by. The aim of the work was determination of HBoV in respiratory specimens (NPA) of infants by qualitative PCR and determination of acute HBoV infection by estimation of IgM antibodies in serum by ELISA.

Bovine respiratory syncytial virus (BRSV) is an economically significant pathogen in cattle production, as it is one of the most important causes of lower respiratory tract infections in calves. In dairy cattle, BRSV infection usually occurs in young calves aged between 2 weeks and 9 months. Adult animals with subclinical infection are the main source of infection, since reinfections are common in the herds [1, 4, 5].

BRSV, bovine herpesvirus 1 (BoHV-1), bovine viral diarrhea virus (BVDV) and bovine parainfluenza type-3 (PI-3) are considered primary agents involved in the bovine respiratory complex. Additionally, secondary infection by Pasteurella multocida, Histophilus somni and mycoplasmas contribute to the aggravation of the disease. Clinical signs are characterized by respiratory symptoms, initially with moderated intensity, such as nasal and ocular discharges which can be aggravated leading to pneumonia. However, mainly in calves, an acute and severe onset is also observed, due to maternal antibodies not effectively protect against BRSV infection.

Considering the high prevalence of the disease, several studies determined risk factors involved in the epidemiology of BRSV. In Europe, risk factors were mainly attributed to herd size, herd density, purchasing of new animals, geographic location of the farms, herd type and concomitant BVDV infection [7–11]. Similar studies have also been performed in some Latin American countries and they showed that most of the animals probably have already been exposed to the virus with consequent high BRSV prevalence in cattle herds. In these countries, herd size, age group, presence of bordering farms, herd type and geographic location of the farms were the main risk factors associated with BRSV infection [12–16].

In Brazil, BRSV was first diagnosed in calves in the state of Rio Grande do Sul and some studies have shown that BRSV infection is widespread in Southern and Southeastern Brazil, with high serological prevalence rates [18–20]. Nevertheless, research has not been conducted in order to verify possible risk factors involved in BRSV epidemiology. Due to this, the current study aimed to determine antibody prevalence against BRSV and investigate some risk factors associated with BRSV seroprevalence in herds of an important milk producing region in São Paulo State, Brazil.

Along with equine rhinitis virus (ERV) and foot and mouth disease virus (FMDV), bovine rhinitis A and B viruses (BRAV and BRBV, respectively) are species in the genus Aphthovirus, family Picornaviridae. Two serotypes of BRAV have been identified, BRAV1 and BRAV2, while BRBV consists of a single serotype. The BRAV1 strain SD-1 was isolated in Germany in 1962 from nasal secretions from a calf with rhinitis. Additional BRAV1 strains were subsequently isolated from both healthy and diseased bovines in England, Japan, Italy and the U.S. and shown to cross react in serum neutralization assays [3–6]. The sole BRBV isolate EC-11 was isolated in England in 1964 by Reed from the lung of a specific pathogen free calf with respiratory disease. Likewise, BRAV2 consists of a single specimen, strain H-1, isolated from an outbreak of respiratory disease in cattle in 1984. Despite numerous studies on bovine rhinitis viruses (BRV) in the 1960’s through mid-1980’s, little work has been published on their epidemiology and ecology the past several decades.

Bovine respiratory disease complex (BRDC) is the most economically significant disease of the cattle industry, leading to losses due to mortality, morbidity, treatment costs and feed inefficiency in excess of $750 million dollars per year in the U.S. alone. BRDC has a multifactorial etiology involving a variety of bacteria and viruses in addition to host and environmental factors. Numerous commercial vaccines including both killed and attenuated live bacteria are available. Viruses commonly included in commercial vaccine include bovine viral diarrhea virus (BVDV), bovine herpes virus 1 (BHV1), parainfluenza virus 3 (PI3) and bovine respiratory syncytial virus (BRSV). Despite their widespread use, BRDC incidence has increased over the past 20 years. BRDC pathogenesis often involves a primary viral infection which damages respiratory mucosa and alters host immune responses leading to secondary bacterial pneumonia caused by commensal bacteria already present in the respiratory tract.

Both BRAV and BRBV are established but rarely studied etiologic agents of BRDC. Experimental inoculation of calves with BRAV1 via intranasal (IN) or intratracheal (IT) routes, either singly or in combination, resulted in variable clinical signs of respiratory disease and histologic lesions consistent with pneumonia. BRAV1 was also recovered from nasal swabs of IN inoculated animals and all animals inoculated or exposed by contact seroconverted to BRAV1 by day seven post inoculation. A similar experiment using a different BRAV1 strain (RS 3x) and colostrum deprived calves failed to reproduce clinical disease but was successful in isolating BRAV1 from nasal swabs post inoculation and found histological lesions of focal rhinitis and a neutralizing antibody response in all inoculated calves. BRBV pathogenesis was investigated using intranasal inoculation of gnotobiotic calves. Clinical signs including fever, nasal discharge and increased respiration rate were observed. Foci of epithelial necrosis were observed histologically in the turbinates and trachea and interstitial pneumonia was evident in the lungs. Virus was isolated from multiple tissues and was neutralized by convalescent antiserum. In addition to controlled studies, numerous investigations of acute respiratory disease in cattle resulted in the isolation of bovine rhinitis viruses where paired acute and convalescent sera suggested a causative role for bovine rhinitis virus.

Metagenomic sequencing on nasal swabs obtained from BRDC diagnostic submissions were performed to survey viruses present. Contigs with high identity to BRAV2 and BRBV were identified in one swab. To further our understanding of the epidemiology and ecology of bovine rhinitis viruses in BRDC, a more comprehensive survey was performed.

Bovine respiratory disease complex (BRDC) is a global problem causing severe economic losses to the cattle farming industry through mortality, loss of production, and treatment costs [1, 2]. It has a complex etiology that involves various pathogens, host factors, and environmental factors. Viruses such as bovine herpes 1 virus (BoHV-1, parainfluenza virus 3 (PBIV-3), bovine respiratory syncytial Virus (BRSV), respiratory bovine coronavirus (BoCoV) and bovine viral diarrhoea virus (BVDV) in conjunction with stress factors have been implicated as causes of respiratory tract infections of cattle by immunosuppression and damage to the respiratory epithelium. A primary viral infection can be followed by an opportunistic secondary infection with bacteria like Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, or Trueperella pyogenes [2, 4, 5], but these bacteria could also act as primary pathogen. In addition it has become increasingly clear that Mycoplasmas are important contributors to BRD, either as primary pathogens or in co-infection [2, 6–9]. M. bovis is the best known Mycoplasma species causing respiratory disease [4, 7], but also M. dispar and M. bovirhinis have been associated with BRD [2, 9–11]. M. bovis has not only been identified as a primary or opportunistic pathogen in BRD in beef cattle worldwide, but it has also been implicated in other clinical manifestations in cattle, such as mastitis, otitis, arthritis, and reproductive disorders. M. bovirhinis and M. dispar are regularly isolated from the nasal cavity of cattle with respiratory disease and are usually regarded as an opportunistic pathogen in respiratory diseases [7, 12].

Bacteriological, serological and histopathological examinations are important tools to detect particular animal-carriers of Mycoplasma, however, these assays are time-consuming, insensitive and can give false positive results. Bronchoalveolar lavage fluid (BALF) from calves with BRD may contain various potential pathogens, but additional antibiotic use in the affected herds can inhibit cultivation and thereby can cause false-negative test results. In BRD, differential diagnosis of these pathogens with rapid turnaround time procedure is essential to implement appropriate treatment and intervention measures in a timely manner. Rapid detection of these pathogens at the early stage of outbreak can contribute substantially to minimize the spread of infection and increase treatment efficiency. Today quick, highly sensitive and species-specific PCRs are used in the diagnosis of Mycoplasma-associated diseases for M. dispar [14, 15], M. bovis [4, 16] and M. bovirhinis in BALF or nasal swabs. Combining a 16S Ribosomal DNA PCR with denaturing gradient gel electrophoresis fingerprinting (PCR/DGGE) enabled the simultaneous detection of mixed Mycoplasma populations, however information about the detection limit in clinical samples is limited. Additionally, a DNA microarray assay was developed for the parallel detection of 37 Mycoplasma species, in which species-specific probes derived from the 23S rRNA and tuf genes were used for species differentiation.

Multiplex real-time PCR could be a promising and practical approach to speed up the differential diagnosis from 1 to 2 weeks for traditional culture to 24 h, with limited expenses. This will make diagnostic testing more accessible for veterinary practitioners and thereby improve BRD diagnosis. This report describes the RespoCheck triplex PCR developed by Central Veterinary Institute (CVI, Lelystad, The Netherlands) for detection of three Mycoplasma species.

Bovine respiratory disease complex (BRDC), a multi-factorial disease, is an economically important health problem of cattle worldwide. The disease is commonly referred to as “Shipping fever” and causes an increase in morbidity mortality rates. The multiple factors that cause BRDC include stress, infectious agents, immunity, and housing conditions. The infectious agents associated with BRDC include viruses, bacteria, and mycoplasmas. While most acute infections with uncomplicated infectious agents are sub-clinical, they can cause respiratory disease characterized by a cough, fever, and nasal discharge. Mixed infections with two or more infectious agents are thought to contribute to BRDC. The primary viral infectious pathogens that cause BRDC are bovine parainfluenza virus 3 (BPIV3), bovine respiratory syncytial virus (BRSV), bovine viral diarrhea virus (BVDV), bovine alphaherpesvirus 1 (BHV-1), bovine coronavirus (BCV), and so forth.

Bovine parainfluenza virus type 3 (BPIV3) was one of the most important viruses associated with BRDC in cattle. It was first isolated in 1959 and first identified in cases of BRDC. BPIV3 is an enveloped, non-segmented negative-strand RNA virus within the genus Respirovirus. BPIV3 induces respiratory tract damage and immunosuppression. More severe secondary bacterial and mycoplasma infections are caused in susceptible animals in instances of high stress, such as transportation and feedlot situations.

Up to now, based on phylogenetic analysis, BPIV3 has been divided into three genotypes: Genotype A, genotype B, and genotype C. Multiple BPIV3 genotype A strains have been isolated in USA, China, Argentina, and Japan. Genotype B was initially identified in Australia. Isolation of BPIV3 genotype C, first identified in China, has also been conducted in South Korea, Japan, Argentina, and USA. A high seropositivity rate for BPIV3 in dairy cattle indicated that a high level of BPIV3 infections occurs. Many efforts have been made focusing on the prevention and control of BRDC in order to reduce production losses in the livestock industry.

Here, we describe the cell culture isolation and genomic sequencing of a BPIV3 genotype A strain isolated from cattle in China. Although BPIV3 is endemic in cattle, little is known about the pathogenesis of this virus and information regarding antigenic variation owing to the genetic variability is rare. The phylogenetic comparison of our isolated strain with strains previously characterized in China indicated the presence of divergent strains of genotype A circulating in the country. The diversity of BPIV3 in China seems to mirror the diversity of this virus, which is observed in the USA. In addition, the full characterization of our BPIV3 genotype A strain will lend support to molecular diagnoses and to future studies aimed at developing an efficient vaccine against multiple viral lineages.

Bovine respiratory disease (BRD) affects the lower respiratory tract of cattle, causing high mortality and carcasses of lower quality. The syndrome has a multifactorial etiology, including infectious agents, host and environmental factors, with particular emphasis on transport stress. The latter is indeed responsible for physiological changes that favor pathogen proliferation and invasion of tissues by opportunistic pathogens. Viruses and stress-related behavior interfere with the mucociliary clearance of the respiratory tract and dysregulate the tracheal antimicrobial peptides of the innate defenses, allowing opportunistic bacteria to cause pulmonary infections. Infectious agents of BRD include both viral and bacterial agents such as bovine herpesvirus type 1 (BoHV-1), bovine adenovirus (BAdV), bovine viral diarrhea virus (BVDV), bovine coronavirus (BCoV), bovine respiratory syncytial virus (BRSV), bovine parainfluenza virus (BPiV), Pasteurella multocida, Mannheimia haemolytica, Histophilus somni and Mycoplasma bovis.

It has been shown that, to minimize the incidence of transport-related respiratory disease, antibiotics and vaccines are widely used both before and after transport. However, the data on the effectiveness of these preventative methods are conflicting. The hypothesis of this work was that there would be a change in the nasal microbiota, with an increase in the prevalence of bacteria and virus involved in BRD, in beef steers subjected to long distance transportation and not treated before the journey.

Despite the high number of trucks transporting livestock from North Europe to Italy, to the authors’ knowledge, there are no data available in Italy regarding the potential associations between long-distance transport and the onset of BRD after feedlot arrival. Consequently, the aim of this pilot study was to document the prevalence of the multiple pathogens involved in BRD after a long-distance travel from France to southern Italy through investigation of the nasal microbiota.

Cultures of nasopharyngeal aspirates from 100 patients were positive in 67% of patients. Cultures yielded growth of one or more pathogen among upper respiratory tract normal flora. Gram positive cocci were isolated from 57/90 (63.3%) of specimens including: Streptococcus pneumoniae 25/90 (27.7%), Staphylococcus aureus 32/90 (35.5%). Gram negative bacilli were detected in 33/90(36.6%) of specimens including, Klebsiella pneumoniae 15/90 (16.6%), Escherichia coli 10/90 (11.1%), Pseudomonas aeruginosa 8/90 (8.8%), while Cultures of the control group showed growth of upper respiratory tract normal flora (table 1).

Bovine respiratory disease complex (BRDC) is a major problem for cattle breeders worldwide, causing serious economic losses. BRDC is associated with infection by certain viruses, bacteria, and parasites (33). In addition to these infectious agents, stress factors such as transport, gestation, and poor management conditions play an important role in the onset of the disease (30). Bovine herpes virus 1 (BHV-1), bovine respiratory syncytial virus (BRSV), and bovine parainfluenza virus-3 (BPIV3) are the most common viral agents of the respiratory system. Some opportunistic agents (Mannheimia haemolytica, Pasteurella multocida, Haemophilus somnus, and Mycoplasma spp.) contribute to the appearance of clinical signs and thus increase mortality and cause losses in the herds (18). Suppressed immunity also has an important role in the prognosis. Diseases such as bovine leucosis and bovine viral diarrhoea suppress immunity and lead to more animal loss by worsening clinical symptoms.

BPIV3 (the new name of which is bovine respirovirus 3) is an RNA virus assigned to the Paramyxoviridae family under the Respirovirus genus. BRSV (the new name of which is bovine orthopneumovirus) is in the Pneumoviridae family under the Orthopneumovirus genus. To date, three genotypes of BPIV3 have been described. These genotypes, termed A, B, and C, were differentiated based on phylogenetic analysis. Genotype A strains have been isolated in North America, China, and Japan. Genotype B was originally found in Australia. Isolations of genotype C were in China, South Korea, and Japan. In addition, all three genotypes have been reported in Argentina (23).

Initially BRSV subgroups were identified (A, B, and AB or intermediary) based on monoclonal antibody and polyclonal sera analyses against F and G proteins (31). Additionally, Valarcher et al. (36) proposed that six genetic subgroups may be found in BRSV strains, when F, G, and nucleoprotein sequences are phylogenetically analysed by maximum-likelihood algorithms. Therefore, six subgroups were detected in BRSV. These subgroups termed I (the subgroup B prior to the recommendation of Valarcher et al. (36)), III (subgroup A), and II, IV, V, and VI (subgroup AB) were differentiated based on phylogenetic analysis. Subgroup I consists of European strains (UK and Switzerland). Subgroup III includes viruses exclusively from the USA. Subgroup II aggregates strains from the Netherlands, Belgium, France, Denmark, Sweden, and Japan. Subgroup IV is of European and USA strains while subgroups V and VI are found only in French and Belgian isolates (29, 36). Subgroup VII was detected in later years (9) and some strains are known which are still not classified (these are regarded as untyped) (10).

BPIV3 and BRSV can cause mild symptoms or subclinical disease when present alone. However, when there is a co-infection, they may cause bronchopneumonia, severe cough, high fever, and nasal discharge and contribute to a more serious clinical course of infection (33). Regardless of the infecting agent in BRDC, clinical symptoms may be similar and the process of detecting the underlying primal agent may be hindered due to mixed bacterial infections. This situation makes viral diagnosis difficult and decreases the specificity and sensitivity of the molecular methods (when compared to immunofluorescence antibody tests) (15).

Data on virological detection of these agents in Turkey is limited (2, 6), but there are more studies on seroprevalence of these viruses among cattle herds. The studies reported lowest and highest seropositivity of 11% (1) and 92.8% (13) for BPIV3 and 28% (1) and 94% (13) for BRSV. Serological studies on BRSV and BPIV3 were previously conducted in different geographic regions of our country. In these studies the following percentage values for BRSV and BPIV3 prevalence were determined respectively: Alpay et al. (5) 26.6% and 44.6%, Alkan et al. (3) 62.0% and 44.6%, Avci et al. (7) 78.2% and 85.6%, Çabalar and Can Sahna (11) 67.3% and 18%, Yavru et al. (40) 46% and 53.9%, and Yesilbag and Gungor (41) 73.0% and 43%. These studies were conducted either countrywide (3) or in selected regions (40, 41).

The aim of this study was the detection and molecular characterisation of BPIV3 and BRSV strains retrieved from nasal swabs and lung samples of cows in the eastern region of Turkey. The determination of BRSV and BPIV3 types and associated co-infections for respiratory system infections was conducted.

Bovine corona virus (BCV) and bovine respiratory syncytial virus (BRSV) are two worldwide distributed viruses. BCV causes diarrhoea in calves, winter dysentery in adults and various degrees of respiratory symptoms. BRSV is regarded as one of the most important causes of respiratory tract disease, especially in young calves. An infection can cause respiratory distress, fever, anorexia and subcutaneous emphysema and can lead to secondary bacterial pneumonia and death. Outbreaks of BCV and BRSV occur mainly in autumn and winter. These infections are common in dairy herds; in a nationwide survey in England and Wales the prevalence of antibodies to these viruses in bulk tank milk (BTM) was 100%. Swedish studies have shown a prevalence of 70-100% for BCV and 41-89% for BRSV, with the higher prevalence in southern parts. In a more recent study in a high animal-density area in south-west Sweden, the prevalence in BTM was 100% for both BCV and BRSV.

Previous studies have shown that BRSV and BCV infections are effectively spread within the herd. It has also been shown that acquired antibodies remain detectable for years, even without reinfection, whereas maternal antibodies are only detectable for a few months. Spot samples from a few young animals can thus be used to reflect recent infections of BRSV and BCV in a herd, whereas bulk tank milk samples mirror the long-term history. Spot sampling has previously been described for bovine virus diarrea virus (BVDV).

Despite the importance of these viruses and the fact that they are widely spread, little is known about transmission routes and management risk factors. Introduction of new animals and indirect spread via people and equipment are believed to be important and airborne transmission has been shown to occur for BRSV, at least under experimental conditions. Studies have been carried out to determine the relationship between herd health, reproduction efficiency and milk production and seropositivity to other viruses, for example bovine viral diarrhoea virus and bovine leukemia virus. Similar studies for BRSV and BCV have, as far as we know, not been conducted and it is therefore difficult to quantify their effect on the farm efficiency and economy. The purpose of this study was to explore if there were any associations between antibody status to BCV and BRSV and disease incidence, reproduction and some herd characteristics in dairy herds. A secondary aim was to investigate if there were any difference in proportion antibody positive herds between two neighbouring areas.

Bovine Respiratory Disease (BRD) is a multifactorial disease characteristic of a viral-bacterial synergistic infection with predisposition from environmental stressors. The disease constitutes a major source of economic loss through mortality, clinical disease and the associated treatments and long lasting reduced growth performance of infected young stock [2, 3]. The annual cost of BRD is estimated at $1billion in the USA, with preventative measures contributing a further $3billion [4, 5]. Vaccines are commonly used for controlling BRD viral pathogens, but despite seasonal vaccination, animals can become infected with each new outbreak, maintaining the infection within the population. The viral pathogens associated with BRD [Bovine Parainfluenza Virus type-3 (BPI3V), Bovine Respiratory Syncytial Virus, Bovine Viral Diarrhoea Virus and Bovine Herpes Virus-1] impair immune responses in infected animals and damage the respiratory tract allowing the establishment of secondary infections, that may develop further into bacterial pneumonia. However, vaccinated animals can successfully clear viral infections faster than non-vaccinated animals through immune memory response, reducing the associated viral tissue damage or impairment of immune functions preventing the establishment of secondary bacterial and mycoplasma infections. During disease outbreaks, identification of unvaccinated animals at the early stages of infection could provide a window for effective treatment and facilitate the removal of animals that pose a greater risk of becoming infected and transmitting the infection to more susceptible juvenile stock. Furthermore, halting viral disease progression to more severe and costly secondary bacterial infections through the identification of vaccine failure animals during infection outbreaks would reduce the level of antibiotic use in the agricultural industry.

The only definitive method for successfully identifying vaccinated animals in the presence of an active viral infection is to determine the rate of viral shedding by virus isolation, cytokine/interleukin profiling or virus neutralization assay. These types of analysis require repeated sampling, a period for seroconversion and are expensive compared to serology based ELISA, and are therefore not routinely employed during endemic viral infection outbreaks. Differentiating infected from vaccinated animals (DIVA) marker vaccines (e.g. a modified wild type virus with a gene deletion resulting in the absence of a particular diagnostic antigen) can be employed to differentiate vaccine antibody responses from that of wild type virus. Companion serology based tests rely on seroconversion, and upon exposure to wild type virus the antibody response to DIVA vaccines will be masked by that of the wild type virus. Vaccine DIVA functionality is often limited to large viruses with increased potential for gene deletion and removal of redundant expressed antigens. Therefore, for viruses with small genomes such as paramyxoviruses (e.g. BPI3V and Bovine Respiratory Syncytial Virus of the BRD complex) where gene deletion of neutralizing antigens may reduce vaccine efficacy, alternative approaches are required to provide DIVA functionality. One approach is to design molecular DIVA vaccines that contain a marker nucleotide sequence differing from the wild type virus that can be employed in combination with PCR-based molecular diagnostics to differentiate between vaccine and wild virus strains [10, 11]. Successful differentiation of vaccinated from non-vaccinated animals using this technique requires concurrent vaccination and infection [12, 13], with a narrow diagnostic window post-infection for detection of DIVA vaccine and viral genetic material. Furthermore, detection of vaccine genetic material only demonstrates exposure to the vaccine and not the successful generation of immune protection, limiting functionality in assessment of herd level immunity. Consequently, there is a clear need for alternative diagnostic methods that can assess efficacy of vaccines and vaccination status of animals exposed to BRD viral pathogens at the early stages of infection prior to seroconversion and which do not require repeated sampling. Additionally, the lower initial exposure rates to viral infections in field settings combined with variation in strain nucleotide sequences and short periods of virus secretion highlights the requirement for a DIVA approach with a long diagnostic window which is not strain specific.

A potential approach that can meet these needs is based on the application of metabolomics to identify metabolites or ‘small molecules’ in biological samples that are signatures that correlate or provide some evidence of immune protection. These metabolites are often the end stage products of biological processes and therefore provide an accurate representation of an organism’s homeostatic status at time of sampling [14, 15]. Metabolomic analysis of bio-fluids has provided new insights to the understanding of the patho-physiological processes involved in disease establishment, development and diagnosis [16–19]. Whilst metabolomics has had limited application in the field of veterinary research, several studies have demonstrated the potential of this technique in the prediction of BRD disease outcome, differentiation of stress from viral infection responses, and characteristic of immune responses following vaccination. This study focuses specifically on BPI3V due to its endemnicity within cattle populations and absence of clinical symptoms which still predispose animals to more severe bacterial infections. Due to its small genome and absence of non-redundant proteins suitable for removal in DIVA vaccines, BPI3V is an excellent model for assessing the potential of metabolomics to establish vaccination status in infected animals. The aims of the current study were therefore to assess the performance of Reverse Phase (RP) and Hydrophobic Interaction Liquid Chromatography (HILIC) separation methods for Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) metabolomic profiling of bovine plasma and identify plasma metabolomic markers capable of differentiating between vaccinated and non-vaccinated calves following intranasal challenge with BPI3V. This work for the first time reports the metabolomic responses following challenge with BPI3V and demonstrates how the application of metabolomic profiling may help overcome current limitations in DIVA diagnostics by identifying markers capable of differentiating between vaccinated and non-vaccinated animals, and importantly allow the development of better tools to assess the performance of vaccines.

Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality for all production classes of cattle and calves in the U.S., causing losses to the cattle industry in excess of $1 billion dollars annually [1, 2]. Multiple etiologies, including both viral and bacterial, contribute to BRD. Those generally accepted to be important contributors to BRD include the viral pathogens bovine herpesvirus-1 (BHV-1), bovine viral diarrhea virus types 1 and 2 (BVDV), bovine respiratory syncytial virus (BRSV) and parainfluenza-3 virus (PI3); and the bacteria Mannheimia haemolytica, Pasteurella multocida, Histophilus somni and Mycoplasma bovis [2, 4]. BRD is frequently initiated by a viral infection that disrupts local defenses and/or causes immune suppression, allowing opportunistic bacterial pathogens that are in healthy animals as normal nasophayngeal commensals to proliferate and infect the lungs [2, 4]. Superimposed environmental or management related stress (such as adverse weather, shipping, and commingling) can further suppress the host immune system, increase pathogen exposure, and may be important co-requisites in many BRD outbreaks. Although vaccines and antibiotic treatments are readily available to prevent and treat infection caused by common BRD pathogens, the incidence of disease remains high.

In recent years, bovine coronavirus (BCV) has been implicated as an important contributor to BRD. Although initially described as being associated with calf diarrhea, BCV has been found to infect the upper and lower respiratory tract and has been isolated from pneumonic lungs alone or in combination with other respiratory pathogens [7–12]. In addition, results of multiple studies indicate that groups of cattle with high titers of serum antibodies to BCV at the time of feedlot entry are less likely to shed BCV and develop BRD than those with low anti-BCV serum antibody titers [7, 13–15]. Taken together, it appears that BCV contributes to feedlot BRD, and high titers of serum anti-BCV antibodies associate with reduced risk of BCV infection and disease. However, it remains unknown whether the serum antibodies themselves are immune correlates of protection, or whether they simply reflect prior exposure to the virus.

The relationship between BCV and BRD in pre-weaned beef calves has not been comprehensively evaluated. Though BCV is frequently detected in nasal swabs from nursing calves with BRD, subclinical BCV infections are also common in young dairy calves, even in the presence of relatively high anti-BCV antibody titers [16, 17]. These results raise questions about the association between anti-BCV antibody titers and BCV shedding with the risk of developing BRD in nursing dairy calves. Similarly, in a 2014 study, our group sampled four research herds (n = 890) at predefined times from birth through their fifth week in the feedlot. This study revealed that the herds in which BCV was detected in nasal sections during the pre-weaning period also had the highest incidence of pre-weaning BRD; however, nasal swabs were not collected at the time of treatment to diagnose the pathogens associated with those pre-weaning BRD cases. This study also reported that serum anti-BCV antibody abundance did not correlate with BCV shedding prior to weaning. Thus, while mounting evidence suggests that anti-BCV antibodies protect weaned feedlot cattle from BRD associated with BCV infection, the relationship between humoral immunity to BCV, virus shedding, and the risk for developing BRD in nursing calves remains unclear. This represents a major obstacle in the development of effective control strategies to reduce the impact of BCV-related respiratory disease in cattle, which is significant given that there are currently no licensed BCV vaccines in the United States to aid in the prevention of BRD.

To address this knowledge gap, the present study serially sampled 817 calves from three herds of beef cattle from birth through weaning to determine whether shedding of BCV is associated with BRD and whether levels of anti-BCV serum antibodies associate with BCV shedding or BRD incidence in pre-weaned beef calves. Sequence analysis of the virus strain(s) circulating in each herd and the prevalence of common opportunistic bacterial pathogens (M. haemolytica, P. multocida, H. somni and Mycoplasma bovis) in the upper respiratory tract of sick and apparently healthy cattle were also evaluated to account for potentially confounding factors that could influence BRD development in these populations.

Coronaviruses (CoV, family Coronaviridae) are large enveloped viral particles containing a positive sense single stranded RNA genome (26–30 kb), coding for several structural proteins, including polymerase (Pol), nucleocapsid (N), membrane (M), hemagglutinin-esterase (HE), spike (S) proteins and several non-structural proteins (NSPs). Coronaviruses have been associated with respiratory and enteric infections in humans and ruminants.

Enteric Bovine coronavirus (BCoV) replicates in the epithelial cells of the gut, destroying villi, resulting in severe, often bloody diarrhea in calves, which can be life threatening, due to loss of electrolytes and malnutrition. Disease in calves usually occurs within the first month of life, with respiratory and enteric infections being the most common conditions diagnosed. In adult cows, as a result of close confinement during transport or housing, BCoV is associated with winter dysentery and shipping fever. The spike proteins of BCoV play an important role in immune response, eliciting both cellular immune responses and neutralizing antibodies.

BCoV has been detected in Ireland using molecular or immunological techniques [4–6], but it has not been characterized or compared to other global BCoV strains. Enteric pathogens frequently isolated from neonatal calves with enteritis in Ireland are rotavirus, cryptosporidium and much less frequently, coronavirus. Currently in Ireland, a trivalent vaccine is licensed for the immunization of pregnant cows against rotavirus, coronavirus and Escherichia coli, confering passive immunity to calves, the coronavirus aspect of the vaccine is based on an inactivated Mebus strain. In this study we aimed to: (i) characterize bovine coronavirus in the South of Ireland via analysis of the Spike gene, and (ii) compare Irish BCoV to global and vaccine isolates to identify variations in the hyper-variable region of the spike gene.

Clinical signs of classical swine fever usually appear 5–10 days after infection (occasionally longer). An individual pig may show one of four types of clinical effect; Peracute (sudden death, especially at the beginning of a farm outbreak), Acute (fever, depression, weakness, anorexia, conjunctivitis, diarrhoea or vomiting, purple discoloration of abdominal skin, or necrosis of the tips of extremities, and neurological signs), Chronic (weight loss, hair loss, dermatitis, discoloration of abdomen or ears) and subclinical. Affected pigs may recover or relapse, depending on the severity of the disease. Reproductive effects is also common; abortions, stillbirths, mummifications and also congenital tremor of piglets.

Respiratory syncytial virus (RSV) infection is a major cause of death in the first year of life, with especially high mortality rates in African and Asian countries,,. Upper respiratory tract infections (URTI) with RSV generally cause relatively mild disease that does not require treatment. These infections can progress, however, into lower respiratory tract infections (LRTI) and cause severe disease, especially in pre-mature infants. RSV can also cause recurrent infection of the upper respiratory tract.

An important complication of upper respiratory infections is middle ear inflammation and-related deafness,, and RSV infections are associated with the development of asthma at a later age,,.

Other common causes for respiratory tract infections are Haemophilus influenzae type b (Hib), parainfluenza virus, rhinovirus and influenza virus

[9],,.

Protective immunity against respiratory pathogens like influenza and RSV is mediated by IgG and IgA,,,,. RSV-specific serum IgG levels in neonates are inversely associated with increased prevalence of RSV infections,, and breastfeeding reduces the incidence and severity of RSV infection,. In addition, the levels of anti-influenza IgA in breast milk correlates with decreased frequency of respiratory illness with fever. These findings indicate that pathogen-specific antibodies are crucial for protection against respiratory infections, and that orally ingested immunoglobulins (like breastmilk-derived IgA) may contribute to immunity to airway infections.

Human and bovine milk contain high levels of immunoglobulins, which are important for protecting the infant from infections with bacteria and viruses,. Cross-species activity between human and bovine immune-related milk proteins has been reported before,, and cow’s milk contains bovine IgG (bIgG) that binds to gastrointestinal pathogens that also infect humans, such as Shigella flexneri, Escherichia coli, Clostridium difficile, Streptococcus mutants, Cryptosporidium parvum, Helicobacter pylori, and rotavirus.

At present there is, however, no information on binding of bovine IgG to human respiratory viruses.

Most infant nutrition is bovine milk-based, but lacks intact bIgG as a result of heat treatment during processing. To investigate if bIgG would be a useful ingredient in these formulas, the aim of the present study was to investigate the specificity and functional relevance of bIgG against RSV and other human respiratory pathogens, the ability of bIgG to bind to human Fcγ receptors, and the induction of effector functions in human myeloid cells.

Bovine respiratory disease is amongst the most significant causes of health problems and reduced welfare and profitability in the cattle industry. Decreases in production and profitability are associated with factors such as reduced growth rate, treatment costs and increased mortality. In dairy herds, one may also observe reduced milk production, milk quality and reproductive performance [1–5].

Bovine respiratory syncytial virus (BRSV) is an important etiological agent in bovine respiratory disease. The infection can be subclinical, or result in mild to severe clinical signs. Disease might be caused by BRSV directly or in combination with secondary bacterial infections which occurs frequently [7, 8]. The morbidity in a BRSV outbreak is reported to be between 60 and 80 %, and the mortality between 0 and 20 %.

Many experimental studies have been conducted to describe the clinical and pathological consequences of BRSV infection [7, 9–13]. However, experimental infection usually results in less severe disease compared to natural outbreaks, fewer animals are usually included, and the animals are monitored for a relatively short period after virus exposure. Studies on natural BRSV outbreaks [14–19] often lack relevant information on the situation prior to the outbreak, and suitable control groups are usually not available. Furthermore, such studies often provide little information on the production after the outbreak.

Large scale epidemiological studies from data records investigating production losses and economic impact of bovine respiratory disease are usually based on clinical diagnosis, without specific information about the etiological agent [1, 2, 4]. For BRSV specifically, reduced milk yield [5, 20] and reduced semen quality are amongst the reported effects. Studies on negative consequences of this infection, relevant for rearing of young stock, are scarce and represent an important knowledge gap in the estimation of the total consequences of BRSV.

The Norwegian cattle population is currently free from several globally important respiratory pathogens such as bovine herpes virus type 1 and bovine viral diarrhoea virus, and Mycoplasma bovis has never been detected. This makes the Norwegian cattle population a suitable population for studying the impact of BRSV. The prevalence on herd level is estimated to be between 34 and 41 %. BRSV has been found to be the main cause of outbreaks of respiratory disease, either acting as a single agent or in combination with other pathogens. Other viral pathogens known to cause respiratory disease in Norwegian cattle, are bovine corona virus (BCoV) and bovine parainfluenza virus type 3 (BPIV3).

To calculate the cost-efficiency of preventive strategies for BRSV, accurate estimates of the potential losses are essential. The aim of the present study was to provide robust estimates of such losses by analysing the association between exposure to BRSV, weight gain and feed conversion rate, quantify any reduction in these parameters, and estimate the duration of decreased production. Furthermore, it was an objective to illustrate a method for estimating the effect of disease outbreaks in beef herds by employing intra-herd comparisons based on health and production records.

Infectious bovine rhinotracheitis virus (IBRV), often referred to as bovine herpesvirus 1 (BoHV-1), is responsible for infectious bovine rhinotracheitis (IBR). IBR is highly contagious, and can cause a diverse range of clinical manifestations from upper respiratory disease, rhinitis, vulvovaginitis, traeheitis, enteritis, conjunctivitis, abortion and encephalitis, to fatal systemic infection in neonatal calves. IBRV can also induce immune suppression that contributes to the severity of disease manifestation. In addition, IBRV is one of the bovine respiratory disease complex pathogens, which is the leading cause of cattle death around the world [2–4]. Taken together, it is a major disease of cattle leading to significant economic losses to the dairy industry worldwide [5, 6]. Several developed countries such as Germany, have adopted immunization and eradication of pathogen-positive animals for IBR control. Therefore, early identification of IBRV positive animals is critical for disease control and elimination programs to diminish its burden on the dairy industry.

At present, IBRV can be routinely detected using cell culture, polymerase chain reaction (PCR), immune-histopathology, and enzyme-linked immunosorbent assay (ELISA) as well as the virus neutralization test [8–10]. However, currently available diagnostic tests remain laboratory-based and require sophisticated instruments operated by specially trained personnel. Although isothermal amplification techniques such as the loop-mediated isothermal amplification (LAMP) have been offered as a simple, rapid and alternative molecular pathogen diagnostic tool for point-of-care testing in the field [11, 12], the LAMP assay needs four to six primers, leading to longer amplicons and possibly more difficult to design in the case of highly variable viruses.

Recombinase polymerase amplification (RPA), is a novel isothermal alternative to PCR, which targets and amplifies DNA from clinical samples with high sensitivity and specificity. The technology takes advantage of three major proteins, including recombinase proteins, single-strand binding proteins (SSB), and polymerases, and relies on two specific oligonucleotide primers and a probe, and can specifically amplify nucleic acid sequences ranging from trace levels to detectable amounts of product in an isothermal format in less than 30 min. RPA products can be detected by gel electrophoresis, probe-based fluorescence monitoring or lateral flow dipsticks depending on the specific primers and/or probe configuration. Although RPA technology has been widely used for detection of various pathogens since its initial development [14–19], to date, there is no RPA assay developed for IBRV detection.

In this study, RPA primer and probe combinations were designed, and screened to permit LFD-RPA detection of IBRV. The development of a combination of LFD-RPA detection for IBRV was described. Finally, the performance of the RPA assay on acute phase fever clinical samples was evaluated and the results compared with SYBR Green I real time PCR.

In 2011, a new influenza virus was isolated from pigs with influenza-like symptoms and shared only 50% overall homology to human influenza C virus. This virus was considered as a new genus and named thereafter influenza D virus (IDV). IDV circulates widely and has been detected in America, Europe, Asia and Africa. Several studies demonstrated that IDV has a large host range and a higher prevalence in cattle than in swine and other species, suggesting that bovine could be a main host for IDV. The virus or its specific antibodies were also detected in horses, small ruminants, camels or feral swine. However, the zoonotic potential of IDV is still unclear. The circulation of IDV in Europe is not fully understood but data is available in Luxembourg and Italy with small cohorts tested: 80% and 93% of the tested cattle sera were positive in Luxembourg and Italy, respectively (n = 480 and 420 sera tested in each country).

Here, we performed a large scale seroprevalence study of IDV in large and small domestic ruminants at a country level. As we aimed to detect IDV antibodies with an individual prevalence limit of 0.1% for cattle and 0.5% for small ruminants with 95% confidence, at least 3000 and 600 sera were needed, respectively.

Influenza viruses are known to constantly evolve and cross species barriers. The genetic diversity of influenza viruses is ever increasing with more novel influenza subtypes being discovered periodically. The purpose of this review is to provide an up-to-date overview of ecology and evolution of influenza viruses including the novel influenza viruses in bats and cattle. In addition, we discussed the growing complexity of influenza virus–host interactions and highlighted the key research questions that need to be answered for a better understanding of the emergence of pandemic influenza viruses.

Many different infectious agents, viruses, bacteria, parasites and fungi, can lead to perinatal diseases in animals. Some infectious agents have the genital system as their primary target; they will mainly lead to infertility, abortion, stillbirth or weak newborns. Other agents give a more generalised infection and reproductive problems are only a small part of the picture. This lecture will focus on some important infectious agents that infect the animals during late gestation leading to abortion, stillbirth or foetus anomalies. Infections of the newborn animals the first few days after birth will also be considered.

Ureaplasmas, also belong to the same family as the Mycoplasmas, and are pathogenic bacteria which were initially associated with urogenital tract infections but have also been isolated from pneumonic bovine lungs [10, 68, 75]. The species Ureaplasma diversum has been associated with clinical respiratory disease [75, 76]. As Ureaplasma was found to be present in pneumonic lung tissue samples from calves which died from BRD, this genus may be an important contributor to BRD which is often overlooked.