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.

Human adenovirus (HAdV) is the most common cause of infection to the ocular surface, accounting for up to 75% of conjunctivitis cases.1 The most common presentation is pharyngoconjunctival fever (PCF), which often occurs in children and manifests clinically with fever, pharyngitis, rhinitis, follicular conjunctivitis, and regional lymphoid hyperplasia.2 Epidemic keratoconjunctivitis (EKC) is the most severe ocular form and is distinguished by its ability to invade the corneal epithelium, ranging in presentation from a keratitis to persistent and recurrent subepithelial infiltrates (SEIs). HAdV is highly contagious due to its unique structure and ability to evade the normal host’s immune system. It is distinguished from other types of conjunctivitis in that it often involves the cornea, with potentially devastating visual complications. These features contribute to a heavy economic burden and necessitate the establishment of a standard treatment protocol.1 In addition to the potential ocular manifestations of this virus, HAdV infections have the propensity to manifest systemically, in cases such as respiratory, urinary, and gastrointestinal tract (GIT) infections. This variety of presentations can infect a normal, healthy host, and also have an increased risk in immunocompromised individuals. Despite the detrimental effect that HAdV infections pose, there has yet to be an FDA-approved drug to treat these conditions, making management difficult. Even following the active phase of the disease, viral persistence and reactivation may occur. Oral and topical antivirals have been considered as off-label management solutions, but problems with efficacy, bioavailability, and therapeutic profiles have limited their use. With regards to EKC, topical disinfection during active cases as well as treatment of corneal sequelae using corticosteroids and immunosuppressive agents show promise. This review will focus on how persistence and dissemination of HAdV poses a significant challenge to the management of adenoviral keratoconjunctivitis. Furthermore, current and future trends in prophylactic and therapeutic modalities for adenoviral keratoconjunctivitis will be discussed.

The clinical picture of PRRS can vary tremendously from one herd to another, from not recognisable to severe disease. When the virus first enters the breeding herd disease is seen in dry sows, lactating sows, sucking piglets and growers. Clinical signs in dry sows during the first month of infection are inappetence, fever and late term abortions at 1–6% level. These are often the first signs to be noted. Other signs can be discoloration (blueing) of the ears, reproduction problems, coughing and respiratory signs, agalactia and mastitis, mummified piglets (10–15% may die in the last 3–4 weeks of pregnancy), stillbirth (level may increase up to 30%) and birth of very weak piglets. In piglets, more diarrhoea, less viable piglets and increase in respiratory infections can bee seen. Adult animals shed virus for much shorter periods of time (14 days) compared to growing pigs which can excrete for 1–2 months.

Depending upon the involvement of etiological agent, the infectious respiratory diseases of small ruminants can be categorized as follows [9, 14]:bacterial: Pasteurellosis, Ovine progressive pneumonia, mycoplasmosis, enzootic pneumonia, and caseous lymphadenitis,viral: PPR, parainfluenza, caprine arthritis encephalitis virus, and bluetongue,fungal: fungal pneumonia,parasitic: nasal myiasis and verminous pneumonia,others: enzootic nasal tumors and ovine pulmonary adenomatosis (Jaagsiekte).

Manytimes due to environmental stress, immunosuppression, and deficient managemental practices, secondary invaders more severely affect the diseased individuals; moreover, mixed infections with multiple aetiology are also common phenomena [5, 8, 13, 15].

These conditions involve respiratory tract as primary target and lesions remain confined to either upper or lower respiratory tract [7, 16]. Thus, these diseases can be grouped as follows [5, 8, 14, 17].Diseases of upper respiratory tract, namely, nasal myiasis and enzootic nasal tumors, mainly remain confined to sinus, nostrils, and nasal cavity. Various tumors like nasal polyps (adenopapillomas), squamous cell carcinomas, adenocarcinomas, lymphosarcomas, and adenomas are common in upper respiratory tracts of sheep and goats. However, the incidence rate is very low and only sporadic cases are reported.Diseases of lower respiratory tract, namely, PPR, parainfluenza, Pasteurellosis, Ovine progressive pneumonia, mycoplasmosis, caprine arthritis encephalitis virus, caseous lymphadenitis, verminous pneumonia, and many others which involve lungs and lesions, are observed in alveoli and bronchioles.

Depending upon the severity of the diseases and physical status of the infected animals, high morbidity and mortality can be recorded in animals of all age groups. These diseases alone or in combination with other associated conditions may have acute or chronic onset and are a significant cause of losses to the sheep industry [3, 10]. Thus, the respiratory diseases can also be classified on the basis of onset and duration of disease as mentioned below [3, 9, 14, 18]:acute: bluetongue, PPR, Pasteurellosis, and parainfluenza,chronic: mycoplasmosis, verminous pneumonia, nasal myiasis, and enzootic nasal tumors,progressive: Ovine progressive pneumonia, caprine arthritis encephalitis virus, caseous lymphadenitis, and pulmonary adenomatosis.

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.

Small ruminants particularly sheep and goats contribute significantly to the economy of farmers in Mediterranean as well as African and Southeast Asian countries. These small ruminants are valuable assets because of their significant contribution to meat, milk, and wool production, and potential to replicate and grow rapidly. The great Indian leader and freedom fighter M. K. Gandhi “father of the nation” designated goats as “poor man's cow,” emphasizing the importance of small ruminants in poor countries. In India, sheep and goats play a vital role in the economy of poor, deprived, backward classes, and landless labours. To make this small ruminant based economy viable and sustainable, development of techniques for early and accurate diagnosis holds prime importance. Respiratory diseases of small ruminants are multifactorial and there are multiple etiological agents responsible for the respiratory disease complex. Out of them, bacterial diseases have drawn attention due to variable clinical manifestations, severity of diseases, and reemergence of strains resistant to a number of chemotherapeutic agents. However, sheep and goat suffer from numerous viral diseases, namely, foot-and-mouth disease, bluetongue disease, maedi-visna, orf, Tick-borne encephalomyelitis, peste des petits ruminants, sheep pox, and goat pox, as well as bacterial diseases, namely, blackleg, foot rot, caprine pleuropneumonia, contagious bovine pleuropneumonia, Pasteurellosis, mycoplasmosis, streptococcal infections, chlamydiosis, haemophilosis, Johne's disease, listeriosis, and fleece rot [3–10].

The respiratory diseases represent 5.6 per cent of all these diseases in small ruminants. Small ruminants are especially sensitive to respiratory infections, namely, viruses, bacteria, and fungi, mostly as a result of deficient management practices that make these animals more susceptible to infectious agents. The tendency of these animals to huddle and group rearing practices further predispose small ruminants to infectious and contagious diseases [6, 9]. In both sheep and goat flocks, respiratory diseases may be encountered affecting individuals or groups, resulting in poor live weight gain and high rate of mortality. This causes considerable financial losses to shepherds and goat keepers in the form of decreased meat, milk, and wool production along with reduced number of offspring. Adverse weather conditions leading to stress often contribute to onset and progression of such diseases. The condition becomes adverse when bacterial as well as viral infections are combined particularly under adverse weather conditions. Moreover, under stress, immunocompromised, pregnant, lactating, and older animals easily fall prey to respiratory habitats, namely, Streptococcus pneumoniae, Mannheimia haemolytica, Bordetella parapertussis, Mycoplasma species, Arcanobacterium pyogenes, and Pasteurella species [2, 4, 7–9, 12, 13]. Such infections pose a major obstacle to the intensive rearing of sheep and goat and diseases like PPR, bluetongue, and ovine pulmonary adenomatosis (Jaagsiekte) adversely affect international trade [2, 9, 10, 13], ultimately hampering the economy.

Hand, foot, and mouth disease (HFMD) is an infectious disease that usually affects infants and young children under 5 years of age worldwide. HFMD typically causes self-limiting illness, but development of severe cardiopulmonary and neurologic complications have also been reported [1, 2]. The clinical manifestations are typically ulcerations in the oral cavity, buccal mucosa (enanthema) and tongue with peripherally distributed cutaneous lesions and vesicular rash (exanthema) on the palms of hands and soles of feet. Other parts of the limbs including knees, elbows and buttocks may also be affected. Transmission occurs via person-to-person through direct contact with respiratory secretion, saliva, fluid from blisters, and feces from infected individuals. A number of enteroviruses belonging to the family Picornaviridae cause HFMD, although human enterovirus 71 (EV71) and coxsackievirus (CV) type A16 are two of the most important enteroviruses implicated in many large-scale outbreaks in Asian-Pacific countries including Japan, Taiwan, Malaysia, Singapore, and China [2–4]. Additional enterovirus species including CV-A6, CV-A10 and CV-A4 also cause HFMD [5–9]. Clinical symptoms resulting from CV-A16 as well as other enteroviruses are usually relatively mild and indistinguishable with low incidence of severe complications. In contrast, serious complications such as encephalitis, myocarditis, and poliomyelitis-like illness were observed when EV71 were reported as the causative pathogen [10–12].

HFMD has been continuously present and remains a major cause of morbidity and mortality of young children particularly in Asia. Typically, HFMD exhibits cyclical pattern of outbreaks every two to three years. Factors underlying the prevalence of HFMD remain controversial. Data from countries with long history of HFMD outbreaks suggest that dissemination is associated with socio-economic status, population ethnicity, regional climate [14–16], and attendance in school or care centers of school-age children. The magnitude of HFMD outbreaks appears to fluctuate [3, 18, 19]. HFMD in tropical climate countries, such as Malaysia, Singapore and Thailand, typically showed years-round activity with no discrete epidemic periods although peaks during the rainy and winter seasons were also detected depending on season, year, and geographic regions [20, 21]. At present, no specific treatment for HFMD exists. Vaccines or antiviral drug against EV71 are currently being developed in Taiwan, China and Singapore but are not yet commercially available [22–24]. Prompted by geographically widespread outbreaks, careful monitoring of the spatial and temporal epidemiology is considered to be of great importance to control the spread of HFMD according to the different regional characteristics. As reported by the Bureau of Epidemiology, Ministry of Public Health of Thailand, HFMD has shown an upward trend in the last five to six years. In June 2012, the largest recorded outbreak of HFMD occurred throughout the country. This outbreak affected more than 39,000 individuals, including three deaths, over a period of four to five months with hot spots in Chiang Rai and Mae Hong Son provinces. In our previous study, we monitored HFMD activity in Thailand between 2008 and 2012. Our results revealed that the HFMD epidemic in 2012 was significantly different from previous ones in Thailand including the size of the epidemic and the viruses detected [26, 27]. During the 2012 epidemic, beside a high prevalence of EV71 and CV-A16, multiple EV types such as CV-A6 were also detected. Even though the standardized 5' untranslated region (5'UTR) pan-enterovirus PCR and viral capsid protein 1 (VP1) gene typing PCR assays were used, approximately one third of the suspected cases, mostly young children, were negative for enterovirus by these assays. These findings raised questions regarding the sensitivity of the current assay in identifying causative viruses other than EV71 and CV-A16 that may be present below the limit of detection by conventional PCR. In recent years, metagenomic has become an important strategy for virus discovery in human and animal diseases [28–30]. This technique, based on recognition of sequence similarities following non-specific nucleic acid amplification, circumvents some of the limitations of virus isolation, serology, and the amplification of only known conserved genomic regions. To evaluate circulating enterovirus and previously uncharacterized viruses associated with HFMD, we describe here the virus community (virome) in fecal samples negative by RT-PCR for EV71 and CV-A16/A6 obtained from 29 pediatric patients with HFMD during the outbreak in Thailand in 2012.

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.

Adenoviruses are ubiquitous, non-enveloped, double-stranded DNA viruses. Human adenoviruses (HAdVs) are classified into 7 species (Human mastadenovirus A to G) and at least 69 recognized genotypes based on serology, whole-genome sequencing, and phylogenetic analyses. The prevalence of different HAdV types varies among different geographical regions. HAdVs have been recognised as pathogens that cause a broad spectrum of diseases [1, 2], including acute respiratory infection (ARI), gastroenteritis, conjunctivitis, cystitis, and meningoencephalitis. ARI is prevalent in children, and is one of the most common causes of morbidity and mortality in the paediatric population in developing countries [3, 4]. Numerous outbreaks of ARI caused by HAdV have been reported during the last decade in many countries including China [5–14]. The HAdV types most commonly found in respiratory samples belong to HAdV-C (HAdV-1, -2, -5, -6) and HAdV-B (HAdV-3, -7) [2, 10–15]; however, severe or even fatal disease outbreaks are predominantly caused by only a few types (such as HAdV-14, -21 and -55) [2, 5–9]. The molecular typing by HAdV hexon sequences can help to accelerate the discrimination of types, resulting in timely epidemiological examinations and improved patient care [16–20]. Several studies have shown the association between severe respiratory infections in adult and HAdV species [7–9]; however, reports among children with severe acute respiratory infection (SARI) in China are limited.

The purpose of this study was to determine the prevalence and genotype (sequencing of the hexon gene after polymerase chain reaction [PCR] screening) of HAdVs among children with SARI in different areas of China from 2007 to 2010. HAdV infections are often associated with the co-infection of bacterial or viral agents, frequently leading to severe clinical consequences in hospital patients. Thus, co-infection with other respiratory viruses of HAdV was also investigated.

Bovine herpesvirus 1 (BoHV-1) is an α-herpesvirinae subfamily member that causes significant economical losses to the cattle industry (1). Three well-defined subtypes exist, BoHV-1.1, BoHV-1.2a, and BoHV-1.2b (2b) (2). Subtype 1 virus isolates are prevalent in Europe, North America, and South America: these subtypes are frequently detected in cattle suffering from infectious bovine rhinotracheitis (IBR) and the respiratory tract of aborted fetuses. Subtype 2a strains are prevalent in Brazil and are associated with respiratory and genital tract infections, including IBR, infectious pustular vulvovaginitis (IPV), balanopostitis (IPV), and abortions (3). Subtype 2b strains, which are frequently isolated in Australia or Europe (4), are associated with respiratory disease and IPV/IPB, but not abortion (3, 5). The seroprevelance of BoHV-1 ranges from 14 to 90% depending on the age of cattle and geographical location (6, 7). Serological testing and removal of infected animals has eliminated BoHV-1 from Denmark, Switzerland, and Austria (8).

BoHV-1 is the most frequently diagnosed cause of viral abortion in North American cattle (9). Exposure of a susceptible herd to BoHV-1 can result in abortion storms ranging from 25 to 60% of cows undergoing abortion. Commercially available modified live vaccines also induce abortions in pregnant cows. Furthermore, several studies concluded that naïve heifers vaccinated with an inactivated BoHV-1 vaccine are more likely to have a normal estrous cycle and significantly higher pregnancy rates relative to heifers vaccinated with a modified live (MLV) vaccine (9–13).

The incubation period for the genital forms of BoHV-1 is 2–6 day and initial clinical signs are frequent urination and a mild vaginal infection (14). It is also common to observe swollen vulva or small papules followed by erosions and ulcers on the mucosal surface. In bulls, similar lesions occur on the penis and prepuce. If secondary bacterial infections occur, inflammation of the uterus and transient infertility with purulent vaginal discharge occurs for several weeks. BoHV-1 infection, virulent field strains or modified live vaccines, of sero-negative heifers can target the ovary and corpus luteum during estrus and early in gestation (9).

Bovine respiratory disease complex (BRDC), a poly-microbial disease initiated by stress and/or virus infection, is the most economically important disease that affects beef and dairy cattle. Annual BRDC losses in the U.S. are ~$1 billion (15–18). A gram negative bacterium, Mannheimia haemolytica (MH), exists in the upper respiratory tract of healthy ruminants (19, 20). Following stressful stimuli or co-infections with other viruses (21), this commensal relationship is disrupted and MH becomes the predominant organism that causes life threatening bronchopneumonia in many BRDC cases (22–25). BoHV-1 infection frequently causes upper respiratory tract disease (26, 27), high fever, conjunctivitis, and erodes mucosal surfaces of the upper respiratory tract. Consequently, colonization of MH occurs in the lower respiratory tract (22, 23, 25), thus enhancing interactions between the MH leukotoxin, bovine peripheral blood mononuclear cells, and neutrophils (28, 29). Co-infection of calves with BoHV-1 and MH consistently leads to pneumonia (30). Finally, a BoHV-1 protein that is required for virus entry was identified as a significant BRDC susceptibility gene in Holsteins (31) confirming BoHV-1 is an important BRDC cofactor.

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.

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.

Over the past decades, the global bovine production has been subjected to intensification, in order to improve efficiency of production because of the demand from a growing human population. The intensification of bovine production involved the application of confinement methods characterized by the concentration of animals in large outdoor feedlots or in specialized indoor environments. In confinement, the potential for transfer of pathogens among animals is higher, as there are more animals in a smaller space (1–3).

Severe gastrointestinal infectious diseases causing malabsorption and diarrhea are important causes of discomfort and death in young calves, resulting in important economic losses to bovine producers. Gastrointestinal infectious diseases are able to cause significant economic losses to the cattle industry in big cattle-producing countries and can impair the development of cattle industry in small cattle-producing countries (1–3). In particular, the neonatal gastroenteritis in the bovine host is a multifactorial disease. This disorder can be caused by different bacterial or viral pathogens, including bovine coronavirus (BCV), bovine rotavirus (BRV), and bovine viral diarrhea viruses (BVDV) (4, 5). Although these viral pathogens belong to distinct families and possess different physical characteristics, they are all able to infect intestinal epithelial cells (IECs), generate villous atrophy, and cause inflammatory intestinal tissue damage and diarrhea.

Probiotics are defined as live microorganisms with the capacity to confer a health benefit on the host when administered in adequate amounts. Among them, those that are able to impact on human and animal health by modulating the mucosal and systemic immune systems have been called immunobiotics. It has been reported that immunobiotic lactic acid bacteria are able to generate protection against viral pathogens by differentially modulating antiviral immune responses in humans and livestock animals like pigs (6, 7). It is also believed that immunobiotics could be used in cattle feeds to improve bovine health and produce safe animals (8–10).

The purpose of this review is to provide an update of the status of the modulation of intestinal antiviral innate immunity in the bovine host by immunobiotics, and their beneficial impact on viral infections. The results of our group, which demonstrate the capacity of immunobiotic strains to advantageously modulate Toll-like receptor (TLR)-3-triggered immune responses in bovine IECs and improve the resistance to viral infections, are particularly highlighted.

Mycoplasma alkalescens is a bovine mycoplasma species, which was originally isolated from the nasal cavity of cattle in Australia. Like many other mycoplasmas, M. alkalescens is a normal inhabitant of the upper respiratory tract, but it has also been associated with disease. M. alkalescens has mostly been implicated in mastitis in cattle. It has been isolated from bulk tank milk samples, as well as from outbreaks and sporadic cases of clinical mastitis. Furthermore, M. alkalescens has been isolated from cases of severe arthritis, and its ability to induce joint lesions has been confirmed under experimental conditions. Rosenfeld & Hill isolated M. alkalescens in pure culture from abomasum and lung of an aborted bovine foetus, while Lamm et al. found M. alkalescens in association with otitis in calves. Finally, M. alkalescens has occasionally been found in association with disorders of the respiratory tract.

Recently, 17 bronchoalveolar lavage samples from calves suffering from pneumonia in a single herd in Denmark were submitted, on two occasions, to the National Veterinary Institute for laboratory examinations. The samples were examined for the presence of bacterial pathogens, bovine respiratory mycoplasmas, as well as for the presence of bovine respiratory syncytial virus (BRSV), bovine coronavirus and parainfluenza-3 virus (PI-3). The samples were not examined for infectious bovine rhinotracheitis virus, as Denmark is considered free of this infection. Thereby, eight arginine-metabolizing mycoplasmas were isolated. In the present study the identification of the isolates as M. alkalescens is presented. This is the first report of isolation of this species in Denmark.

Bacteriological examination was performed according to standard laboratory procedures. Examination for BRSV, bovine coronavirus and PI-3 was performed using an indirect sandwich-ELISA assay. Isolation of mycoplasmas was performed according to standard laboratory procedures using a Hayflick's type of medium enriched with arginine, with and without addition of 5% of rabbit hyperimmune antiserum against Mycoplasma bovirhinis. The isolates were filtered through 0.45 μm membrane filters (Millipore), cloned and submitted to serologic identification, which was performed by the disc growth inhibition test (DGI) with 6 mm filter paper discs prepared with rabbit hyperimmune antisera against M. alkalescens PG51T (ATCC 29103; NCTC 10135), Mycoplasma arginini G230T (ATCC 23838; NCTC 10129) and Mycoplasma canadense 275CT (ATCC 29418; NCTC 10152), as well as by the indirect epi-immunofluorescence test (IF) on colonies on solid medium. Molecular identification of the isolates was performed by amplification and sequencing of their 16S rRNA genes by using universal primers.

Laboratory examinations revealed the presence of several bacterial pathogens in 15 of the 17 bronchoalveolar lavage samples, while no pathogenic bacteria were detected in the two remaining samples. Pasteurella multocida, Mannheimia haemolytica, Histophilus somni and Salmonella Dublin were found in three, three, one and one samples, respectively. Mycoplasma bovirhinis was found in five samples, while arginin-metabolizing mycoplasmas were found in eight samples. Two P. multocida, three M. bovirhinis and five arginin-metabolizing mycoplasma isolates were found as sole bacteriological findings in 10 respective samples. From five samples multiple bacterial species were isolated: M. bovirhinis was found once in combination with P. multocida and once in combination with M. haemolytica, while arginin-metabolizing mycoplasmas were found once in combination with M. haemolytica, once in combination with S. Dublin and once in combination with M. haemolytica and H. somni. No viral pathogens were detected in any of the analysed samples.

Further examinations on arginin-metabolizing mycoplasmas showed that all eight isolates could be serologically identified as M. alkalescens and that they were clearly different from the two other arginine-degrading species that are commonly found in cattle, M. canadense and M. arginini (Table 1). The reactions were clear-cut for the DGI tests showing approximately 3–5 mm broad zones of total or nearly total inhibition around the disc. In the IF test some minor cross reactions were noted when three of the isolates and the type strain of M. alkalescens PG51T were tested with anti-M. canadense 275CT hyperimmune serum. The 16S rDNA sequences of the analysed isolates were identical to each other and to the 16S rDNA sequence of the type strain M. alkalescens PG51T (GenBank accession no. U44764;), which corroborated the serological identification of the isolates as M. alkalescens.

Previous studies have shown that H. somni, M. haemolytica and P. multocida are the bacteria that are most commonly associated with bronchopneumonia in calves in Denmark, although they are also part of the normal bacterial flora of the respiratory tract. Also, S. Dublin, which is predominantly found in cattle, is capable of causing pneumonia in calves. Isolation of these bacterial species in the submitted samples most likely indicate their role as the primary cause of respiratory disease in the herd, probably in combination with unidentified environmental factors. In addition to the bacteria, M. bovirhinis and M. alkalescens were also isolated. M. bovirhinis is commonly found as a part of the normal respiratory tract microflora of cattle and is not considered to be pathogenic. M. alkalescens, however, has been found in association with disorders of the respiratory tract but its role as a respiratory pathogen remains equivocal. Experimental infections have demonstrated that M. alkalescens has the ability to colonize lung tissue, but the two strains used in the study apparently failed to produce pneumonia. In the present study, we found M. alkalescens in pure culture in five of the analysed bronchoalveolar lavage samples. This finding is, however, not sufficient to warrant a role of M. alkalescens as a cause of bronchopneumonia, since we also found two samples containing only a non-pathogenic M. bovirhinis, and two samples without any bacterial or viral pathogens, despite the fact that they derived from calves with clinical signs of a respiratory disease. The failure to detect respiratory tract pathogens in these samples may be due to i.e., their absence in a particular disease stadium when sampling took a place or due to antibiotic treatment. Taking into the consideration the overall bacteriological findings of this study, it seems likely that M. alkalescens may have had a role either as a secondary invader or as an opportunistic pathogen rather than suggesting a causal role of the organism in the pneumonia complex.

M. alkalescens is regarded as one of the most common causative agents of mastitis. So, with demonstration of the organism in a Danish cattle herd, a further member of Mycoplasma is added to the group of bovine mastitis-inducing microorganisms in Denmark. The only mycoplasma species isolated from clinical outbreaks of mastitis in Denmark so far has been Mycoplasma bovis, while other mastitis-inducing species, Mycoplasma bovigenitalium and M. canadense, have been isolated only from the respiratory and the genital tract and semen samples. Further investigations are needed in order to determine the prevalence of M. alkalescens in the Danish cattle population and, indeed, to draw a firm conclusions on its importance in disease conditions other than mastitis.

Group A rotaviruses (RVA) are a member of the family Reoviridae, genus Rotavirus. RVA infect both animals and humans, and cause an acute gastroenteritis (AGE) accompanied by abdominal pain, fever, nausea, and vomiting. The genome of these viruses is composed of 11 segments of dsRNA and is surrounded by three concentric layers of proteins. The outermost layer is formed by two proteins, VP4 and VP7. Dimers of VP4 form spikes that extend from the virus surface and have essential functions in the virus life-cycle, including receptor binding and cell penetration.

The diagnosis of RVA was initially based on electron microscopy, ELISA, RNA electrophoresis, nucleic acid hybridization, immunofluorescence (IF), the conventional reverse transcription-polymerase chain reaction (RT-PCR), or recently the quantitative real time RT-PCR (qRT-PCR). These tests while faster, highly sensitive and specific present some limits. They require subsequent virus isolation for the evaluation of agent infectivity. Indeed, virus isolation remains the gold standard test to recover the viral particles from clinical fecal samples, to determine their behavior in tissue culture and to measure their infectivity. In addition, isolation remains the basic assay to provide antigens that can be used as successful immunogenics to raise prominent antibodies which can be useful for the construction and development of a wide variety of immunoassays (rapid immunochromatographic strip test, microneutralization assays (SNT), ELISA, IF or qRT-PCR standards). Thus, the direct cultivation method would be necessary when large numbers of samples need to be analyzed during epidemiological surveys, vaccine trials or when further sensitivity is required. Moreover, efficient and accurate isolation of RVA is of primary importance for pathogenesis, vaccine development and academic research.

In Morocco, no report is available regarding isolation and cultivation of RVA in clinical samples from domestic animals or children with AGE and burden due this infection in animals remain unknown. Hence, this study aims at the isolation and virus characterization of bovine RVA strains from suspected diarrheal clinical cases to support RVA disease control in Morocco. Consequently, this will provide RVA isolates that could be utilized in future vaccine development.

Infectious diseases cause significant financial losses for the cattle industry through their detrimental effects on animal health and performance. As such, researchers are continually developing more sophisticated epidemiological models to better understand how disease control resources can be applied more cost-effectively across the large population of cattle herds. Cattle movements have received particular attention in recent years both because of their central role in the epidemiology of many economically important cattle diseases and because the movements of individual cattle have been explicitly recorded in databases across the European Union since 1998. The latter has provided researchers with an unprecedented opportunity to study the dynamics of directly transmissible infectious diseases. Using network analysis based approaches, it has been consistently shown that targeting control measures at the small number of herds or movements that are highly connected in the trade network can lead to significantly greater reductions in disease prevalence than targeting the same number of herds or movements at random.

From a practical perspective, these findings must be interpreted with some caution as most models assume that purchased cattle all carry the same risk of generating disease outbreaks in the destination herd. As numerous empirical studies have shown, the probability of any individual animal being infected or transmitting disease to susceptible cattle is strongly influenced by factors such as age, production type, and on-farm management practices. For example, contagious mastitis pathogens are highly unlikely to spread through the movements of male cattle or store calves purchased for fattening, whereas older lactating dams are predicted to have a significantly increased risk based on the higher prevalence of disease and greater opportunity to spread disease through contaminated milking equipment. Identifying cattle movements that are associated with the greatest risk of infectious disease transmission has important implications for refining future epidemiological models and disease control strategies. In this analysis, we use data on bovine viral diarrhoea virus (BVDV) in Scotland as a case example to illustrate that not all cows in the movement network are epidemiologically equal.

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.

This is a detailed description of the use of MALDI‐TOF for identification of Nocardia veterana in a dog in North America. It also describes successful treatment of Nocardia veterana bacteremia in a dog with antimicrobial drugs and discontinuation of immunosuppressive drug treatment. Nocardia are filamentous branching gram‐positive bacteria found in soil and plant matter. Disseminated nocardiosis is a relatively uncommon disease in dogs and cats and is most often reported in immunocompromised animals or in individuals on immunosuppressive medications such as cyclosporine.2, 3 With the more widespread application of gene sequencing and MALDI‐TOF MS for bacterial identification, novel species of Nocardia have been identified, including N. veterana, which was first discovered in 2001 in human bronchoalveolar lavage fluid.4 Initially, the role of N. veterana in clinical disease was poorly understood, but it was subsequently isolated from a mycetoma in a woman with systemic lupus erythematous (SLE).5 Phylogenetically, N. veterana is closely related to N. nova, N. africana, and N. vaccinii and until recently had been indistinguishable from these species based on antimicrobial susceptibility testing and restriction fragment length polymorphism (RFLP) analysis.6, 7

Historically, 16S rRNA gene sequencing has been used most commonly for identification as the 16S rRNA gene is highly conserved among Nocardia species.8 However, in the case of a newer Nocardia spp., N. kruczakiae, and N. veterana, 16S rRNA gene sequencing could not differentiate between these 2 distinct species.9 New techniques using secA1 gene were able to discriminate between different Nocardia spp. better than 16S rRNA gene and therefore may be more clinically useful for Nocardia spp. identification.1 These techniques, however, are not readily available at most clinical laboratories, and with results taking up to several days to return, implementation of appropriate treatment can be delayed. MALDI‐TOF MS has recently emerged as a rapid and reliable method of species identification.10 Within minutes, MALDI‐TOF MS analyzes the protein composition of a bacterial or fungal isolate and compares it to a library of mass spectrometry profiles, which is unique for each species. The ability of this technology to rapidly determine the identity of a bacterial isolate makes this technology particularly useful for identification of slow‐growing, fastidious organisms such as Nocardia.11 Some of the isolates made from the dog reported here had low identity score values. Recently, it has been shown that repeat extraction, duplicate spotting on the target plate, and addition of other libraries can increase genus‐level and species‐level identification significantly.12

Since it was first isolated, fewer than 20 cases of N. veterana infection have been reported in the human literature.5, 7, 13, 14, 15, 16, 17, 18 Inhalation is thought to be the most common route of transmission, and in the few reported cases of human N. veterana infections, pulmonary manifestations predominate.6, 7, 13 However, a wide variety of other clinical manifestations of N. veterana infection have been reported in humans including urinary tract infections, brain and bowel abscesses, endogenous endophthalmitis, nodular lymphangitis, mycetomas, and bacteremia.5, 14, 15, 16, 17, 18, 19 In veterinary medicine, reports of N. veterana infection have been limited to bovine mastitis resulting from direct inoculation, and a puppy from Germany with disseminated N. veterana infection and concurrent canine distemper virus infection.20, 21 In the latter case, diagnosis was made at necropsy and as in the study reported here, bacterial isolates from lung tissue were identified by MALDI‐TOF MS and confirmed with 16S rRNA gene sequencing.

In this dog, it is unclear whether disseminated N. veterana infection led to a secondary IMPA or whether the immunosuppressive drugs used to treat primary IMPA predisposed the dog to nocardiosis. In people with disseminated nocardiosis, approximately 65% have underlying immunodeficiency, so it may be more likely in this case that combination immunosuppressive drug treatment was responsible.22 In addition, the dog was clinically stable for 3 months after initiation of immunosuppressive drug treatment, so it seemed unlikely that nocardiosis contributed to the clinical signs of IMPA. However, after treatment for Nocardia and discontinuation of immunosuppressive drug treatment, there has been no relapse in clinical signs for IMPA. In this case, cyclosporine treatment was instituted despite clinical improvement because of persistent mild neutrophilic joint inflammation. More evidence is required to determine whether decisions about immunosuppressive drug treatment should be based on serial monitoring of synovial fluid. In light of the risks of opportunistic infections, perhaps treatment with multidrug immunosuppressive treatment should be reconsidered in dogs that develop clinical resolution of IMPA despite cytologic evidence of persistent joint inflammation.

Infection with N. veterana might have followed inhalation in this dog, or alternatively, it might have followed ingestion of a contaminated penetrating foreign body, especially as the dog had a history of chewing sticks. The latter could also have explained the gagging behavior that was initially observed, which was otherwise unexplained. Additionally, culture of the focal jejunal mass grew Lactobacillus acidophilus as well as Candida, suggesting the possibility of perforation secondary to direct trauma or the inflammatory lesion itself. Histopathology of the jejunal mass revealed no evidence of plant or foreign material. Finally, it is possible that the organism was introduced by direct cutaneous inoculation, such as from a plant awn or other penetrating organic matter.

Identification of the Nocardia species involved is important because it can predict susceptibility to antimicrobials, which differs among Nocardia species, and can be difficult to determine accurately through in vitro susceptibility testing.23

Nocardia veterana tends to be resistant to many antimicrobial drugs.24 In this case, the N. veterana isolate was susceptible to TMS, imipenem, amikacin, and clarithromycin. The TMS was chosen because of its recognized activity against Nocardia spp., low cost, and oral formulation, despite the breed predisposition to keratoconjunctivitis sicca and the history of IMPA. No adverse effects of TMS were noted during treatment, although there was concern that the profound hypercholesterolemia that developed after discontinuation of prednisone could have resulted from sulfonamide‐induced hypothyroidism. When nocardiosis is severe or refractory to monotherapy, combination antimicrobial treatment can be instituted.8 The optimal duration of treatment is not known but is generally recommended for at least 6 months in people with disseminated nocardiosis, and recurrence of disease is common.25 In this case, treatment with TMS was only for 3 months, but the granulomatous masses in the small intestinal tract were surgically excised and the underlying immunosuppression was reversible, which likely also facilitated elimination of the pathogen. Additionally, early intervention with appropriate antimicrobial treatment with the aid of MALDI‐TOF MS may have played a role in the successful treatment of this dog. In this case, identification of Nocardia spp. by MALDI‐TOF MS occurred 7 days before results of secA1 gene sequencing were available. The decision to discontinue treatment early was due to resolution of skin lesions, lameness, and hematologic abnormalities within about 6–8 weeks. The absence of clinical relapse 1 year after discontinuing antimicrobial treatment suggests infection was eliminated.

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.

The ocular manifestations of viral infections in neonates and children vary greatly and can range from innocuous to vision threatening (73). The majority of viral conjunctivitis in children are caused by adenovirus, a DNA virus, which can cause a range of human diseases, including upper respiratory tract infection. Viral conjunctivitis is associated with epidemic keratoconjunctivitis, pharyngoconjunctival fever and acute haemorrhagic conjunctivitis (74). Signs include eyelid oedema and tender pre-auricular lymphadenopathy, prominent conjunctival hyperaemia, follicles and punctate epithelial keratitis. In viral infections in children, the involvement of the anterior segment is mild and self-limited; spontaneous resolution usually occurs within 2–3 weeks, except in cases of congenital infection, which are often associated with significant alterations in ocular structures.

Neonatal conjunctivitis (also known as ophthalmia neonatorum) is defined as conjunctival inflammation developing within the first month of life. It is the most common type of infection in neonates, occurring in up to 10% of neonates. It is often identified as a specific entity distinct from conjunctivitis in older infants as it is often the result of infection transmitted from the mother to the infant during delivery (74). Molluscum contagiosum ocular infection in children is caused by a specific double-stranded DNA poxvirus, which typically affects otherwise healthy children with a peak incidence between the ages of two and four. Transmission occurs through contact, with subsequent autoinoculation. Presentation is with chronic unilateral ocular irritation and mild discharge, while lesions are usually self-limiting. Primary infection with herpes simplex virus (HSV) is usually associated with eyelid and periorbital vesicles, papillary conjunctivitis, discharge and lid swelling. Dendritic corneal ulcers can also be present, particularly in patients with atopic infection can lead to eczema herpeticum, which can be very severe (75–77). Varicella-zoster virus (VZV) is a serious, but rare, viral infection in children, in which prolonged inflammation may lead to corneal thinning or perforation, glaucoma and cataract formation (74).

Involvement of the posterior structures mostly related to HSV and VZV is potentially sight-threatening. Retinal or optic nerve involvement should be suspected in any child, who complains of an acute onset of blurred vision in the absence of anterior segment inflammation or opacities in the ocular media. Optic neuropathy may occur as an isolated sign, although it is more often associated with a more generalised involvement of the central nervous system (77,78). While specific therapy is not always available, the early diagnosis of ocular viral disease in children should aid in the amelioration of acute symptoms and in the prevention of long-term complications.

HSV-1 is an enveloped, linear double-stranded DNA virus which is highly prevalent in most part of the world. Approximately 50–90% of the world’s population is seropositive for this virus (Smith and Robinson, 2002; Fatahzadeh and Schwartz, 2007). Diseases caused by herpes simplex virus include cold sores, keratoconjunctivitis, genital herpes and encephalitis (Fatahzadeh and Schwartz, 2007; Burcea et al., 2015; Sauerbrei, 2016). Treatments currently directed against HSV infections are nucleoside analogs such as acyclovir, valacyclovir, penciclovir, and famciclovir that target viral DNA polymerase (Vadlapudi et al., 2013). However, extensive use of these drugs has led to clinical problems with the emergence of drug-resistant virus strains, particularly in immunocompromised patients (Jiang et al., 2016). The discovery of new drugs to treat HSV infection has become an important goal of drug development.

Rhubarb is the rhizomes of plants that belong to the genus Rheum in the family Polygonaceae. Chinese Rhubarb includes Rheum tanguticum (R. palmatum var. tanguticum), Rheum palmatum, Rheum officinale, etc. The rhubarb contains several main chemical compositions such as anthraquinones, anthrones, stilbenes, tannins, polysaccharides, etc. (Cao et al., 2017). These compositions show a wide range of pharmacological activities, including antioxidant, anti-tumor, anti-microbial and anti-inflammatory activities (Lai et al., 2015; Cao et al., 2017). Moreover, anthraquinones derivatives like aloe-emodin, rhein, emodin, and chrysophanol, reportedly demonstrated antiviral effects (Semple et al., 2001; Lin et al., 2008; Schwarz et al., 2011; Wang et al., 2018). However, as with most Chinese herbal medicines, the application of rhubarb is limited due to its poor bioavailability and hydrophobicity. Therefore, it is necessary to find new ways for the usage of rhubarb in order to make better use of it. The field of nanotechnology is an advanced approach in modern materials science. Nanoparticles might resolve the biopharmaceutical problems related to improving the uptake of poorly soluble drugs, reducing toxicity and increasing the drug bioavailability (Onoue et al., 2014; Marella and Tollamadugu, 2018). Moreover, it is well documented that the unique properties of nanoparticles, such as small particle size, large surface area to volume ratios, and tunable surface charge, make nanoparticles attractive tools for viral treatment (Singh et al., 2017). In recent years, several nanoparticles have been reported for the treatment of viral infections, among them silver nanoparticles have proven to be active against several types of viruses (Galdiero et al., 2011; Singh et al., 2017).

Given the importance of antiviral effect of rhubarb and advantages of nanoparticles, we designed some assays to investigate the activity of R. tanguticum nanoparticles against herpes simplex virus type I. We first conducted plaque reduction assays using HEp-2 cells to test the capacity of these nanoparticles to inactivate the HSV-1 virions and block the viral attachment and entry into cells, following the evaluation of inhibitory effect on viral replication using real-time quantitative PCR, Western blot, and immunofluorescence methods. Furthermore, the in vivo efficacies of these nanoparticles were investigated with a mouse model of HSV-1 encephalitis. The positive results offer a novel promising way for the usage of Chinese herbal medicine to control the HSV-1 infection.

As can be seen by a graph depicting the number of PubMed citations per year, advances in virology and prion studies are accelerating at a pace that makes it difficult for any individual to remain informed in areas outside one’s specialty (Figure 1). In addition, scientific meetings are continuing to focus on specific areas to maximize dissemination of information to select groups while general meetings that cover multiple fields are typically too large to permit prolonged informal discussion, especially with students and early-stage investigators. With these facts in mind, the Rocky Mountain Virology Association (RMVA) was formed to provide a venue that permitted formal presentations of current research in multiple areas of virology and prion biology in a venue that is sufficiently removed from major cities to ensure extended informal discussions and opportunities to establish/strengthen collaborations. Professional child daycare was provided to help enable attendance by individuals with young children, which provided an educational opportunity through the children’s participation in a virus and prion themed performance during the formal poster session. Taken together, the 17th annual RMVA meeting (Figure 2) upheld the tradition of presenting novel findings, summarized below, that spanned the fields of bio-informatics, host-pathogen interactions, immunology, therapeutics, replication of DNA and RNA viruses along with prion detection and disease propagation.

BK carried out bacteriological examination of samples, isolation and cloning of mycoplasmas and drafted the manuscript.

NFF carried out identification of mycoplasma isolates by DGI test and epi-immunofluorescence.

PA carried out molecular identification of mycoplasma isolates.

All authors read and approved the final manuscript.

Clinical (e.g., age, vaccination record, and clinical signs) and farm history should be provided to clinicians for determining the cause of diarrhea. Once the specimens are submitted to a veterinary diagnostic laboratory, the diagnostician sorts the samples to ensure proper delivery to testing laboratories based on the history and sample type. Generally, fecal sample are examined by microscopy (for C. parvum and Coccidia), bacterial culturing (for Salmonella spp., E. coli, and C. perfringens), and PCR (for BRV and BCoV). In contrast, intestinal tissues are subjected to immunohistochemistry or bacterial culturing. More recently, nucleic acid-based techniques such as PCR and an antigen-capturing enzyme-linked immunosorbent assay (Ag-ELISA) have been more commonly used for the rapid detection of various bacterial and viral pathogens in clinical specimens from diarrheic calves. When the laboratory test results are available, clinicians should consider the overall farm and clinical history in conjunction with lab results before identifying the causative pathogen.