Dataset: 11.1K articles from the COVID-19 Open Research Dataset (PMC Open Access subset)
All articles are made available under a Creative Commons or similar license. Specific licensing information for individual articles can be found in the PMC source and CORD-19 metadata.
More datasets: Wikipedia | CORD-19
Deep Learning Technology: Sebastian Arnold, Betty van Aken, Paul Grundmann, Felix A. Gers and Alexander Löser. Learning Contextualized Document Representations for Healthcare Answer Retrieval. The Web Conference 2020 (WWW'20)
Funded by The Federal Ministry for Economic Affairs and Energy; Grant: 01MD19013D, Smart-MD Project, Digital Technologies
The majority of emerging infectious diseases that affect humans originate from animal reservoirs, predominantly wild life, including bats, rodents and birds. Norovirus is one of five genera of the family Caliciviridae and the most common non-bacterial cause of foodborne gastroenteritis worldwide. Noroviruses are currently categorized into at least seven genogroups (GI–GVII) that are further divided into more than 40 genotypes. The virus contains three open reading frames (ORFs), ORF1 encoding the polyprotein that includes the viral polymerase, and ORF2 and ORF3 encoding the major- and minor capsid protein (VP1, VP2), respectively. Recombination between ORF1 and ORF2 frequently occurs and therefore a dual nomenclature describing both the polymerase and capsid genotype is used. Viruses from genogroups GI, GII and GIV are known to infect humans. Animal noroviruses including viruses found in pigs, dogs, and cats are closely related to human strains and cluster within GII (porcine norovirus) and GIV (feline and canine norovirus), respectively. Noroviruses belonging to the other genogroups infect a broad range of hosts that includes livestock animals such as cows and sheep but also marine mammals and rodents. In the past years, an increasing number of metagenomic studies have led to the discovery of additional noroviruses in new animal hosts and it seems evident that we lack understanding of the full diversity of noroviruses and their host range. Most human infections and outbreaks are caused by viruses belonging to GI and GII. The GII.4 genotype viruses have been particularly prevalent in the past two decades, and evolve through accumulation of mutations but also by recombination. Such recombinants and other new genotypes emerge regularly but the origin of these new viruses is not well understood. This regular detection of novel strains and the reporting of human-like norovirus genotypes in stool samples of symptomatic and asymptomatic farm animals have sparked interest in the possible role of animals as potential zoonotic reservoir for these emerging strains. Antibodies directed against bovine and canine norovirus have been detected in humans suggesting some level of exposure of humans to animal norovirus. For other viruses of the Caliciviridae family, interspecies transmission has been reported including some case reports of zoonotic events between marine mammals and humans (reviewed in).
This systematic review summarizes the literature on the known animal reservoir for norovirus, the virus diversity, prevalence, and geographic distribution, as well as pathological findings associated with norovirus infections in animals. We will further discuss the existing evidence and probability of interspecies transmission including susceptibility of animals used as models in norovirus research. There are several reviews that focus exclusively on the role of mice in norovirus research; therefore, we will discuss murine norovirus only in context of surveillance of wild animals. Molluscs are an important vehicle of foodborne norovirus transmission, but do not support norovirus replication and have been reviewed elsewhere.
HAstVs are a classic cause of viral diarrhea in children, along with rotavirus, norovirus, sapovirus and adenovirus. Seroprevalence studies indicate that most children in Europe encounter astrovirus before the age of two. Astrovirus-associated diarrhea is not reported in immunocompetent adults, as infection in childhood is considered to confer protective immunity. Additionally, humoral immunity is considered to play a major protective role, along with cellular adaptive immunity. Therefore, immunosuppressed patients and the elderly can also develop astrovirus-associated diarrhea.
In non-immunocompromised individuals, after an incubation period of 4–5 days, an astrovirus infection will induce a mild disease, characterized by mild and short watery diarrhea for two to three days, followed by nausea, vomiting, and abdominal pain, which usually resolves spontaneously. These symptoms are most often milder than a rotavirus infection. Recent seroprevalence studies have indicated that some infections can be asymptomatic as well. As reported for rotavirus and norovirus, astrovirus has also been associated with intussusception in infants. Although virological diagnosis of astrovirus-associated diarrhea is not routinely used in medical practice, it is sometimes used in epidemiological studies in the context of diarrheal outbreaks and surveillance of diarrheal diseases.
An astrovirus infection in immunocompromised individuals may induce gastroenteritis, but it can also lead to severe and sometimes fatal systemic and central nervous system (CNS) infections, as seen in multiple cases of astrovirus-associated encephalitis and meningitis. These reports are associated with newly identified HAstVs that belong to novel species (MAstV 6 and 9). Studies are under way to assess the actual disease burden associated with these novel neurotropic astroviruses in humans. These novel astroviruses are enteric viruses, associated with diarrhea and fecal carriage, but their pathogenicity in the non-immunosuppressed host has not yet been precisely determined, although a case of meningitis in an apparently healthy adult has recently been reported. Therefore, these newly-discovered viruses seem to share some clinical characteristics with enteroviruses, due to their association with diarrhea, but may also induce meningitis and encephalitis in the immunosuppressed patients. For this reason, their detection should now be part of the laboratory diagnostic work-up in patients, in particular those who are immunosuppressed and are diagnosed with meningitis or encephalitis of unknown cause.
In mammals, astroviruses have been reported in piglets, minks and dogs with preweaning diarrhea, but accurate diagnosis is complicated due to the prevalence of fecal shedding in healthy animals, which complicates the interpretation of the results. Therefore, etiological diagnostic is not a routine practice. In mink presenting with the so called “shaking mink syndrome”, and cattle with encephalitis, astroviruses can be tested in necropsy brain samples. Additionally, astroviruses have been associated with severe avian diseases (i.e., chicken diarrhea, duck hepatitis, turkey enteritis, and avian nephritis), and diagnosis can be made in severely affected flocks by reverse transcription polymerase chain reaction (RT-PCR), using necropsy samples in specialized laboratories.
Porcine epidemic diarrhea virus (PEDV) is an enveloped, single-stranded, positive-sense RNA virus that is taxonomically classified within the family Coronaviridae, genus Alphacoronavirus. PEDV is the main causative agent of porcine epidemic diarrhea (PED), a devastating enteric disease that is characterized by watery diarrhea, vomiting, dehydration and significant mortality in piglets. Approximately 80 to 100% of PEDV-infected piglets die within 24 h of being infected with virulent PEDV strains, resulting in tremendous economic losses to the swine industry [1, 2].
Since December 2010, a large-scale outbreak of diarrhea, characterized by watery stool, dehydration, and vomiting, with 80 to 100 % morbidity and 50 to 90 % mortality in suckling piglets, has been observed in swine farms in China [3, 4]. Accumulated evidence indicates that this large-scale outbreak of diarrhea may be caused by highly virulent PEDV variants [5, 6]. In the present study, a PEDV strain, YC2014, was isolated from intestinal samples of suckling piglets with acute diarrhea in 2014, the evolutionary characteristics and the immune protective efficiency of YC2014 were also determined.
Astroviruses were first discovered in 2008 by electron microscopy (EM) examination of stool samples from children with diarrhea. The virus name was given due to the star-shaped morphology of the virus, which is observed on the surface of some of the particles. Before the development of molecular techniques, EM was the only tool for laboratory diagnostics, as no cell line permissive for a broad range of strains was identified, precluding routine virus isolation. EM, and later polymerase chain reaction (PCR), increasingly demonstrated the role of astroviruses in diarrheal human disease in babies and infants (as well as in numerous animal species such as birds and mammals), and most of the population has demonstrated exposure to the virus, as is evidenced by antibody detection. Recently, unbiased high throughput sequencing (HTS) has identified the unexpected role of astroviruses from a specific clade in human and bovine encephalitis. This paper summarizes the current tools available for the identification of astroviruses in diagnostic or research applications.
The MAstV-1 species is comprised of HAstV-1–8, and surveillance has revealed that HAstV-1 is the most commonly detected type in children, followed by HAstV-2–5, whereas HAstV-6–8 have been rarely detected. HAstV-4 and HAstV-8 have been associated with infection of older children and longer duration of diarrhea (>7 days). A HAstV-4 strain was also isolated from an infant with fatal meningoencephalitis. Based upon the phylogenetic analysis of the ORF2 region, different lineages within each HAstV type have been proposed; HAstV-1 (HAstV-1a–d) and HAstV-2 (HAstV-2a–d) have been divided into four lineages, whereas HAstV-3 (HAstV-3a–b) and HAstV-4 (HAstV-4a–c) have been classified into two and three lineages, respectively.
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–. 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– 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.
Astroviruses are classified within the unassigned Astroviridae family and are non-enveloped viruses characterized by a positive sense, single-stranded RNA (ssRNA) genome 6.4–7.9 kb long comprised of a 5′-untranslated region (UTR), three open reading frames (ORFs)—ORF1a, ORF1b, and ORF2, a 3′-UTR, and a poly A tail. The ORF1a region encodes a non-structural polyprotein (serine protease), ORF1b encodes a polyprotein including the RNA-dependent RNA polymerase (RdRp), and ORF2 encodes the viral capsid protein. A further ORF, termed ORFX, has been observed in classic HAstVs and some mammalian astroviurses, overlapping the 5′ end of ORF2 which may be translated through a leaking scanning mechanism. Astroviruses exhibit several distinctive features in addition to a distinctive morphology. The viruses lack a RNA-helicase domain encoded within the genome and utilize a ribosomal frameshifting mechanism to translate the RdRp, which distinguishes the Astroviridae family from other non-enveloped ssRNA virus families such as Picornaviridae and Caliciviridae. The greatest diversity in the genome is within the ORF2 region, which is characterized by a highly-conserved N-terminal domain (amino acids (aa) 1–424), a hypervariable domain (aa 425–688) which is believed to form the capsid spike and contribute to receptor binding, and a highly acidic C-terminal domain.
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.
PDCoV is an enveloped, positive-sense, single-stranded RNA virus that belongs to the subfamily Coronavirinae in the family Coronaviridae within the order Nidovirales. This novel virus was initially reported in Hong Kong in 2012, and then outbreak of PDCoV in pig herds was announced in the United States in early 2014. Since then, the detection of PDCoV was reported subsequently in many countries, such as South Korea, Canada, China, Vietnam and Japan [5–9]. PDCoV could cause acute diarrhea, vomiting, dehydration and even lead to death in nursing piglets, with the main lesion of villous atrophy in intestines [10–13]. The prevalence of PDCoV in Henan province of China was about 23.49%, and up to 36.43% in suckling piglets. Infected sows usually did not show obviously clinical signs so that the PDCoV detection in sows was often ignored.
Besides PDCoV, there are several main viral pathogens, which cause porcine diarrhea that endanger the healthy development of swine industry. Transmissible gastroenteritis virus (TGEV), the re-emerged porcine epidemic diarrhea virus (PEDV), and the novel swine acute diarrhoea syndrome coronavirus (SADS-CoV), which all belong to genus Alphacoronavirus, have similar clinical symptoms with watery diarrhea, vomiting and dehydration, and similar pathological features with small intestinal enterocyte necrosis and villous atrophy in neonatal piglets. The co-infection of PDCoV with these viruses is common in clinic. However, PEDV could cause severe diarrhea and high mortality (up to 100%) in piglets worldwide. The prevalence of PEDV infection was higher in cold season, especially in January and February, compared with that in warm seasons. With TGEV infection, the mortality rate of neonatal piglets comes up to 100%, especially in piglets no more than 2 weeks of age. SADS-CoV mainly infected newborn pigs which are less than 5 days of age, and the mortality rate was 90%.
During June of 2017, March of 2018 and January of 2019, three swine farms in different cities (Zhumadian, Zhoukou, Nanyang) of Henan Province, China, broke out diarrhea diseases in different ages of pigs with high mortality in suckling piglets. The diarrhea disease in the three farms all first broke out at sows with vomiting and mild diarrhea, and then the newborn piglets developed acute, watery diarrhea, anorexia, rough hair and vigorous prostration with high mortality rate about 60%. Fattening pigs developed diarrhea with growth retardation and anorexia. However, some sows with vomiting and diarrhea recovered 1 day later, which showed transient diarrhea.
In the present study, the fecal samples of pigs with different ages were collected and identified by RT-PCR of viruses which cause diarrhea. After the pathogen causing diarrhea in the three swine farms was determined, virus distribution in tissues of the infected piglets was assessed by Taqman real-time RT-PCR, and the histopathological changes and antigen were observed by Hematoxylin and Eosin (H.E) staining and IHC.
Toroviruses are enveloped, positive-stranded polyadenylated RNA viruses, which belong to the family Coronaviridae and also toroviruses are potential gastroenteritis causing agents affecting humans, calves, pigs, and horses [1–6]. In 1982, bovine torovirus (BToV) was first isolated from a case of neonatal calf diarrhea in the United States and BToV was reported to be related to calf diarrhea in experimentally infected gnotobiotic calves and under field conditions. Porcine torovirus is a member of the genus Torovirus (family Coronaviridae, order Nidovirales), and its genome organization is similar to other toroviruses, consisting of ~28000 nucleotides organized into five ORFs expressing a replicase polyprotein and four structural proteins: spike (S), membrane (M), hemagglutinin-esterase (HE) and nucleocapsid (N) [6–8]. Porcine torovirus has been reported in Canada, South Africa and European countries, Italy, Hungary, and in recent years also in Spain [5, 9, 10]. However, to our knowledge, detection of PToV in China has not been reported. In 2011 winter, there were epidemic outbreaks of diarrhea that occurred with high morbidity and mortality in China, which has caused great economic losses. Diarrhea samples were collected for examination of enteric pathogens, in which PToV was included. In this study, we reported the first detection of PToV in southwest China and analyzed the phylogenetic relationships between the Chinese PToV and PToV reference strains as well as other representative toroviruses. A survey for other enteric pathogens was also conducted and statistical analysis of the epidemiological study with regard to clinical signs (diarrhea) was performed to reveal any association of PToV infection with diarrhea in piglets.
Rotavirus, a double-stranded RNA virus, is a member of the family Reoviridae. Rotaviruses are classified into six, or possibly seven serogroups. Rotavirus infections with group A are the major cause of acute diarrhea among newborn animals and humans leading to death. Identification of infected calves, in combination with a proper vaccination program, is essential to control BRV successfully. The current methods for the detection and characterization of BRV, which include virus isolation, immunoassay, electron microscopy, and nucleic acid hybridization, are time consuming and laborious. On the other hand, the polymerase chain reaction (PCR) has been used successfully for the detection and characterization of BRV. Unfortunately, PCR assays require sophisticated equipment, which is costly to maintain, and must be performed in specialized laboratories (Additional file 1: Figure S1 and S2).
The recently described loop-mediated isothermal amplification (LAMP) can amplify specific target DNA sequences with high sensitivity and can be completed within 60 minutes under isothermal conditions without the need of a thermal cycler and specialized laboratory. This technique eliminates the heat denaturation step for DNA synthesis used in conventional PCR, and relies instead on auto-cycling strand displacement DNA synthesis achieved by a DNA polymerase with high strand displacement activity and a set of two specially designed inner and two outer primers. Another important feature of LAMP is a resulting color change following the addition of a fluorescent dye, making it visible to the naked eye. The LAMP assay has been used successfully to detect many pathogens and in using reverse transcriptase, it has been further adapted for the detection of RNA viruses. The objective of the study reported here was to develop and optimize the reverse transcription LAMP (RT-LAMP) assay for the detection of group A BRV in calves.
Infectious viral diseases, both emerging and re-emerging, pose a continuous health threat and disease burden to humans. Many important human pathogens are zoonotic or originated as zoonoses before adapting to humans–. This is exemplified by recently emerged diseases in which mortality ranged from a few hundred people due to infection with H5N1 avian influenza A virus to millions of HIV-infected people from acquired immunodeficiency syndrome–. Severe acute respiratory syndrome (SARS) coronavirus and the pandemic influenza A/H1N1(2009) virus in humans were linked to transmission from animal to human hosts as well and have highlighted this problem–. An ongoing systematic global effort to monitor for emerging and re-emerging pathogens in animals, especially those in key reservoir species that have previously shown to represent an imminent health threat to humans, is crucial in countering the potential public health threat caused by these viruses.
Relatively few studies have been conducted on diseases of non-domestic carnivores, especially regarding diseases of small carnivores (e.g. mustelids). Ferrets (Mustela putorius furo) can carry bacteria and parasites such as Campylobacter, Giardia, and Cryptosporidium in their intestinal tract and potentially spread them to people,. In addition, they can transmit influenza A virus to humans and possibly on rare occasions rabies virus as well–. Because of their susceptibility to several human respiratory viruses, including human and avian influenza viruses, SARS coronavirus, nipah virus, and morbilliviruses–, ferrets have been used as small animal model for these viruses. To further characterize this important animal model and to obtain epidemiological baseline information about pathogens in ferrets, the fecal viral flora of ferrets was studied using a metagenomics approach. Both known and new viruses were identified.
The impact of diarrhea is primarily felt in the developing world, where approximately 2 million deaths result from diarrhea annually. In developed countries, where diarrhea related mortality is relatively rare, there is still nonetheless a tremendous disease burden. For example, in the United States, approximately 9% of all hospitalizations for children under age 5 years are due to diarrhea episodes. While rotaviruses, caliciviruses, adenoviruses, and astroviruses are responsible for the greatest proportion of cases, approximately 40% of diarrhea cases are of unknown etiology.
Many picornaviruses can be detected in human stool such as enteroviruses, polio, Aichi virus, and cardioviruses. Some of these viruses, such as Aichi virus, are associated with diarrheal disease while others such as polio are shed fecally, but manifest pathogenicity in other organ systems. Picornaviruses are non-enveloped viruses with a single stranded positive-sense RNA genome that encodes a single polyprotein. The picornavirus family currently consists of 14 proposed genera associated with a diverse range of diseases. Viruses in six of these genera potentially infect humans (Enterovirus, Hepatovirus, Parechovirus, Kobuvirus, Cosavirus, and Cardiovirus). With the advent of culture independent molecular methods, many diverse new members of the picornavirus family have been identified in recent years. These include novel cardioviruses, rhinoviruses, parechoviruses and the novel genus of cosaviruses. These studies have demonstrated that significant viral diversity exists in the human gut that remains unexplored.
We have previously described a mass sequencing strategy based on high throughput Sanger sequencing to analyze human stool for previously undescribed viruses. In this study, we used a similar strategy but incorporated a next-generation pyrosequencing platform (Roche Genome Sequencer) in place of traditional Sanger sequencing. This resulted in the identification of a highly divergent picornavirus in a stool sample collected in 1984 from a child in Australia with acute diarrhea. Sequencing and phylogenetic analysis demonstrated that this virus is a novel member of the family Picornaviridae. We propose that this virus be named klassevirus 1 (kobu-like virus associated with stool and sewage).
Astroviruses were first discovered in stool samples of infants suffering from diarrhea in 1975. Since then, our knowledge about the molecular and phenotypic characteristics of these viruses, on the viral pathogenesis and on the spectrum of susceptible hosts has been considerably expanded. Astroviruses belong to the Astroviridae family which is, according to the International Committee on Taxonomy of Viruses (ICTV), divided into two genera: Mamastrovirus, including 19 species, designated Mamastrovirus 1–19; and Avastrovirus including three species, formerly assigned as turkey, chicken and duck astrovirus. This virus family comprises a diverse group of small, non-enveloped single-stranded RNA viruses of positive polarity with a characteristic star-like appearance. The genome consists of 6.17 to 7.72 kb with a 5′untranslated region (UTR) that is followed by three open reading frames (ORFs), a 3′UTR and eventually a poly-A tail. ORF1a and ORF1b encode non-structural polyproteins 1a and 1b that include a protease and the conserved RNA-dependent RNA polymerase (RdRp) whereas ORF 2 encodes a more divergent structural capsid protein. Altogether 19 species of mamastroviruses, have been identified with a wide geographic distribution in a great number of domestic animals, in wildlife including bats, as well as in humans. Most of the infections caused by astroviruses are assumed to be asymptomatic but, depending on the affected species, the age and immunological status of the affected host, an infection can also be associated with diarrhea, hepatitis, nephritis or, more recently, even encephalitis. In bats, astroviruses were mostly found in apparently healthy animals. Since 2008, a growing number of bat species have been found to carry astroviruses with a noticeable prevalence and diversity.
Bats are frequently considered the reservoir host for a broad variety of newly emerging viruses, especially in the tropics, although their general role in the epidemiology and spillover of zoonotic viral diseases is still not fully understood. Some of these newly emerged viruses such as corona-, henipa- and filoviruses are zoonotic and show high pathogenic potential in humans. As generally assumed for the reservoir hosts, bats do not develop severe clinical symptoms upon these viral infections. The reasons are still not fully understood and little is known about the immune system of bats and its interaction with pathogens. As the only flying mammals, bats have evolved special anatomical and physiological characteristics. Several of them appear to be relevant for their role as reservoir hosts of viral agents. As opposed to the reduced body temperature when resting, the body temperature of bats may increase during flight to above 40 °C, which is thought to mimic a fever. On the other hand, the reduced body temperature and low metabolic rate during hibernation or torpor have been discussed to negatively affect the efficient immune response to infections. This may impair viral clearance, and therefore, by transmission to juvenile bats born after hibernation, may even cause virus persistence in the affected colony. The roosting of certain bat species in gatherings of thousands if not millions of individuals is thought to facilitate high intra- and interspecies contact rates that might allow efficient virus transmission. Deforestation, growing urbanization and environmental changes have not only destroyed great parts of the bats’ habitats, but have also increased their interactions with humans and livestock. To analyze the potential health risk for humans, it has become important to study the ecology and the zoonotic potential of viruses found in bats. This review gives an overview on what is known about astroviruses in bats and their potential to cross species barriers to humans and/or livestock.
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.
Calf diarrhea (also known as calf scouring) is a commonly reported disease and a major cause of economic loss to cattle producers. The 2007 National Animal Health Monitoring System (NAHMS) for U.S. dairy reported that 57% of weaning calf mortality was due to diarrhea and most cases occurred in calves less than 1 month old. A similar mortality rate (53.4%) for dairy calves due to calf diarrhea was recently reported in Korea. The economic loss associated with calf death in Norway where calf production is 280,000 heads per year was estimated to be approximately 10 million US dollars in 2006.
Calf diarrhea is attributed to both infectious and non-infectious factors. Multiple enteric pathogens (e.g., viruses, bacteria, and protozoa) are involved in the development of this disease. Co-infection is frequently observed in diarrheic calves although a single primary pathogen can be the cause in some cases. The prevalence of each of pathogen and disease incidence can vary by geographical location of the farms, farm management practices, and herd size.
Although the cattle industry has made great improvements with herd management, animal facilities and care, feeding and nutrition, and timely use of bio-pharmaceutics, calf diarrhea is still problematic due to the multi-factorial nature of the disease. Prevention and control of calf diarrhea should be based on a good understanding of the disease complexities such as multiple pathogens, co-infection, environmental factors, and feeding and management during the calving period before disease outbreaks. In this overview, infectious agents involved in calf diarrhea, appropriate application of diagnostic methods for identifying these pathogens, and intervention strategies for managing calf diarrhea are described. The article consists of three sections. The first section presents the characteristics of major enteric pathogens known to cause calf diarrhea (i.e., bovine rotavirus (BRV), bovine coronavirus (BCoV), bovine viral diarrhea virus (BVDV), Salmonella (S.) enterica, Escherichia (E.) coli, Clostridium (C.) perfringens, and Cryptosporidium (C.) parvum) along with newly emerging enteric pathogens such as bovine torovirus (BToV) and caliciviruses (bovine norovirus [BNoV] and Nebovirus). In the second section, proper sampling and handling techniques (e.g., sample collection and delivery to a diagnostic laboratory) as well as various laboratory diagnostic methods are reviewed along with their advantages and disadvantages. The last section includes a discussion of prevention and control strategies for calf diarrhea that involve multiple factors such as peripartum calving management, calf immunity, and environmental stress and contamination.
The search yielded 6702 papers of which a total of 182 were included in the review. An additional nine papers were later included (see methods).
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.
Porcine epidemic diarrhea virus (PEDV) is an enveloped, positive-stranded RNA virus which readily infects pigs, resulting in highly contagious porcine epidemic diarrhea. PEDV belongs to family Coronaviridae, subfamily Coronavirinae and genus Alphacoronavirus. Some viruses of the Coronaviridae family cause severe disease in humans such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) [3, 4]. Coronaviruses of veterinary significance include avian infectious bronchitis virus infecting chickens, transmissible gastroenteritis virus (TGEV) infecting pigs, bovine coronavirus, feline coronaviruses, canine coronavirus and turkey coronavirus.
Porcine epidemic diarrhea (PED) was first observed in Europe in the early 1970s, and PEDV was first isolated in Belgium in 1978. Subsequently, PED has become an endemic disease in Asian pig farming countries. Severe PED outbreaks were reported in China in 2010–2012 [7, 8]. From April 2013 to the present, major PEDV outbreaks have been reported in the USA, Canada, Taiwan and Europian countries [12, 13]. The PED is characterized by the presence of watery diarrhea in the infected piglets in first few weeks of their life, dehydration, vomiting and anorexia resulting in high morbidity and mortality. PEDV infection of older pigs results in considerably lower morbidity and mortality. The symptoms of the disease are similar to transmissible gastroenteritis of pigs and hence only laboratory tests can aid in differencial diagnosis. Although, some efforts have been made to create the vaccine against PEDV with varied success, no effective vaccine is available in the market to protect the newborn piglets [14, 15].
The size of PEDV genomic RNA is about 28 kb, and contains seven open reading frames (ORFs) encoding viral proteins: 1A, 1B, spike (S), ORF3, envelope (E), membrane (M) and nucleocapsid (N). The S protein is present at the outer surface of the virion and is 1386 amino acid long. The spike protein of coronaviruses forms trimers and plays an important role in the virus attachment and in virus-cell membrane fusion. Porcine aminopeptidase N has been demonstrated to be a functional receptor for the PEDV coronavirus. The S protein of PEDV is a class I membrane glycoprotein consisting of two subunits: the N-terminal S1 and the C-terminal S2. Cleavage of spike protein into S1 and S2 is an essential event in the cellular entry for wild-type PEDV virus but not for cell culture adapted PEDV. Proteolytic cleavage of spike protein in PEDV needs trypsin [19, 20]. Several neutralizing epitopes have been identified on the S protein sequence [21–23], and the recombinant S1 protein was previously shown to have protective activity in piglets.
Advances in the enteric microbiology research have improved the understanding of etiology of infectious gastroenteritis, as well as the involvement and transmission modes of enteric pathogens. This has enabled the design of specific control strategies limiting the losses due to consequent severe infections. Although, bacteria and viruses are both responsible for gastroenteritis, the latter have had more impact on public health (Gunn et al., 2015). As of date, non-bacterial acute gastroenteritis, and respiratory infections are the leading causes of global deaths in both humans (mainly children) and animals (Dominguez et al., 2009; Bok and Green, 2012; Dhama et al., 2015). Since the identification of the first enteric virus, Norovirus (Caliciviridae), in 1972 using electron microscopy, a range of viruses, such as Rotavirus (Reoviridae), Picobirnavirus (Picobirnaviridae), Astrovirus (Astroviridae), enteric Adenovirus (Adenoviridae), Sapovirus (Calciviridae), Torovirus (Coronaviridae), Parechovirus, Bocavirus, and Aichivirus (Picornaviridae), and many more, have been found to be associated with gastroenteritis infections (Cheng et al., 2008; Dhama et al., 2009, 2014; Malik et al., 2011, 2014; Ahmed et al., 2014; Yip et al., 2014; Sidoti et al., 2015; Kattoor et al., 2017; Delmas et al., 2018; Kattoor et al., 2019). The enteric viruses known as of now along with their respective advanced diagnostic methods are tallied in Table 1. Although acute viral gastroenteritis is more common in immune-compromised and young individuals (Krones and Högenauer, 2012), it is also seen in the aged individuals, which may be due to changes in physiology and the waning of immunity with time (Estes and Kapikian, 2007).
New viruses are emerging at a faster pace, apparently as a feature of their rapidly changing genetic makeup due to the accumulation of point mutations, reassortments or recombinations (Malik et al., 2016; Kattoor et al., 2017). For an example, a new porcine coronavirus, has emerged through recombination between the transmissible gastroenteritis virus and a porcine epidemic diarrhea virus (Boniotti et al., 2016). Enteric viral diseases are diagnosed by identifying the causative viral agents in feces/body fluids or viral antigens and/or antibodies in the serum of patients. Conventional methods to achieve this, however, are either inefficient, cumbersome or time consuming, because of the pace of change of the virome. There were not much significant approaches available in the past, and in the recent time various techniques have come up offering a modern field for advances in bio-techniques for the easy, quick and reliable diagnosis and discovery of new viruses. In clinical laboratories, polymerase chain reaction (PCR)-based assays are considered as gold-standard for the detection of viruses, but when it comes to multiple detections of similar types of viruses simultaneously, variations in the properties of viral nucleic acids make the amplification difficult (Fout et al., 2003; Fong and Lipp, 2005). Among different techniques used to explore new viruses, such as conventional and next-generation sequencing, metagenomics has been a promising approach to study the unrevealed viral genomes since more than a decade (Garza and Dutilh, 2015; Martinez-Hernandez et al., 2017). This allows researchers to study the genetic material directly from pooled samples and bypass the need for culturing the virus in vitro as well. Virome capture sequencing is another approach for vertebrate viruses, in which several million probes covering the genomes of several viral taxonomies are used to enrich virus targets (Briese et al., 2015). A new metagenomic sequencing method, ViroCap, based on the target nucleic acid capture and enrichment detects viral sequences with up to 58% variation from the references used to select capture probes (Wylie et al., 2015).
Nevertheless, several diagnostic methods have been developed over the last two decades, seeing the constant evolution of viruses, newer, sensitive, efficient, and rapid diagnostics are still warranted for the effective diagnosis (Liu et al., 2007; Saminathan et al., 2016). This paper systematically describes and discusses the features, advantages and limitations primarily of advanced diagnostic tools devised for the sensitive and quick detection of enteric viruses worldwide (Figure 1).
Porcine epidemic diarrhea (PED), which is caused by the porcine epidemic diarrhea virus (PEDV), is an acute and highly contagious enteric viral disease in nursing pigs. PED is characterized by vomiting and lethal watery diarrhea; and is a global problem, especially in many swine-producing countries. PED was first reported in feeder pigs and fattening swine in the United Kingdom in 1971; since then, it has emerged in numerous European and Asian countries, resulting in tremendous economic losses to the pork industry worldwide. In 2013, the first PED outbreak was reported in the U.S.; subsequently, the outbreak spread rapidly across the country, and similar outbreaks were also reported in Canada and Mexico. In China, PED outbreaks have occurred infrequently with only sporadic incidents. However, in late 2010, a remarkable increase in PED outbreaks was reported in the pork-producing provinces. In 2014, an outbreak of severe acute diarrhea, with high morbidity and mortality, occurred in sucking piglets in Nanjing, China. Herds vaccinated with the CV777-inactivated vaccine were also infected.
During this period, the effectiveness of the CV777-based vaccine was questioned as PED outbreaks also occurred in vaccinated herds. PED has since become one of the most significant epidemics affecting pig farming in China. PEDV is an enveloped, single-stranded, positive-sense RNA virus belonging to the genus Alphacoronavirus, family Coronaviridae, and order Nidovirales. The size of its genome is approximately 28 kb, with 5′- and 3′- untranslated regions (UTRs) and seven open reading frames (ORFs) that encode four structural proteins, i.e., spike (S), envelope (E), membrane (M), and nucleocapsid (N), and three nonstructural proteins. The S protein of PEDV is the major enveloped protein of the virion, associated with growth adaptation in vitro and attenuation in vivo. In addition, the S glycoprotein is used to determine the genetic relatedness among PEDV isolates and for developing diagnostic assays and effective vaccines.
The ability to propagate the virus is critical for the diagnosis and molecular analysis of PEDV, particularly the development of inactivated or attenuated vaccine. However, propagation of PEDV in vitro is challenging. Even though PEDV may be isolated from clinical samples, it gradually loses its infectivity during further passages in cell culture. Therefore, it is necessary to evaluate the disinfection efficiency in vitro viral isolates using a cell culture system that promotes growth of PEDV. Currently, several PEDV strains, such as CV777, KPEDV-9, and 83P-5, have been successfully propagated in Vero cells using media with added trypsin. In recent years, new variants of PEDV have emerged that are difficult to isolate and propagate in Vero cells with trypsin. Researchers have attempted to use pig bladder and kidney cells to isolate PEDV, with the addition of trypsin to the medium; this is the first report of isolation of PED virus in porcine cell culture. PEDV infects the epithelium of the small intestine, which is a protease-rich environment, and causes atrophy of the villi resulting in diarrhea and dehydration; this indicates that porcine intestinal epithelial cells are the target cells of this virus. In 2014, Wang et al. established a porcine intestinal epithelial cell line (ZYM-SIEC02) by introducing the human telomerase reverse transcriptase (hTERT) gene into small intestinal epithelial cells derived from a neonatal, unsuckled piglet. Several studies have used this established porcine intestinal epithelial cell (IEC) line; however, the characteristics of PEDV cultured in this cell line have not been reported.
The present study aimed to confirm and identify PEDV in samples collected from piglets with suggestive clinical signs, using the IEC line established by Wang et al.. A PEDV isolate, named PEDV strain NJ, was successfully isolated. Our results show that the PEDV strain NJ is adapted to growth in IECs with media containing trypsin, suggesting a new approach for the propagation of PEDV. Furthermore, the phylogeny and mutations of the S gene during serial passages were analyzed to determine its genetic homology and molecular variability. A virulence experiment for IEC-adapted NJ also confirmed that the virus had a tendency towards attenuation at 45 passages.
In the PEDV isolation and propagation experiment, the partial gene of nucleocapsid protein was analyzed by RT-PCR using primers N1/N2, which amplified an approximately 1 kb nucleocapsid gene fragment present in the isolated YC2014 infected Vero cells, but not in the blank control Vero cells (Fig. 1a). The isolated YC2014 PEDV strain was detected in the cytoplasm of infected Vero cells by an anti-PEDV N protein polyclonal antibody. Red fluorescence could be observed in the YC2014 strain-infected Vero cells (Fig. 1b). The isolated YC2014 PEDV strain was confirmed to be negative for other porcine enteric viruses, such as rotavirus groups A, B and C, TGEV, PRCV, calicivirus and porcine deltacoronavirus by RT-PCR. The growth kinetics study showed that YC2014 replicated rapidly and efficiently in Vero cells, reaching a maximum titer >107 TCID50/ml by 48 hpi (Fig. 2).
Porcine epidemic diarrhea virus (PEDV) was discovered in 1976 in the feces of young pigs with diarrhea, and subsequently demonstrated to induce diarrhea in pigs. Retrospectively, this virus was determined to be the cause of an enteric disease in feeder/fattening pigs that was first described in England in 1971, and characterized by severe watery diarrhea with low mortality. Although endemic PEDV infections have persisted in Europe until the present, the economic impact of the virus is considered to be minor. PEDV was first detected in Asia in 1982 when the virus was isolated in Japan. Within a few years it was recognized in other Southeast Asian countries. In contrast to Europe, the clinical impact of PEDV in Asia was much higher leading to the commercialization of both killed and attenuated vaccines in the late 1990s. Vaccine use may have led to a reduction in prevalence of the disease; however, in 2010 severe PEDV outbreaks with high morbidity and mortality in suckling piglets were reported in China and were subsequently attributed to vaccine failure against new viral PEDV strains.
PEDV is a member of the Coronaviridae family and is an enveloped, single-stranded, positive-sense RNA virus with a 28 kb genome encoding non-structural proteins and four major structural proteins including spike, envelope, membrane, and nucleocapsid proteins. The main method of PEDV transmission is fecal-oral; however the ability of the virus to aerosolize and be transported over large distances by air is being considered as an additional important route of virus transmission.
PEDV was first identified in the United States in April 2013 in sporadic outbreaks of severe diarrhea in young piglets with high mortality. Within one year the disease spread to 31 states and associated with a 5-7% loss in pig production nationwide. The first isolates identified in the United States had over 99% nucleotide identity to a Chinese isolate from the Anhui province suggesting a Chinese origin of infection, but the primary mode of entry into the United States is still under investigation. In January 2014, a variant strain of PEDV with genetic evidence of a Chinese origin was identified in the U.S. Although there is physical evidence for contaminated feed as a mode of transmission in a series of Canadian PEDV cases, such evidence does not exist for the initial introduction of PEDV in North America. Swine are susceptible to PEDV infection at all stages of production with mild diarrhea and vomiting in adults, and severe diarrhea in neonatal pigs causing up to 100% mortality in this age group.
Although the clinical disease during an acute outbreak in a breeding herd is well chronicled, little information is available on endemic PEDV infection. The goals of this study were to assess PEDV transmission among pigs, evaluate the duration of shedding of infectious virus, and demonstrate protective immunity of nursery-aged pigs.
Bovine coronavirus (BCoV) is an important livestock pathogen with a high prevalence worldwide. The virus causes respiratory disease and diarrhea in calves and winter dysentery in adult cattle. These diseases result in substantial economic losses and reduced animal welfare. One way of reducing the negative consequences of this virus is to prevent virus transmission between herds. Inter-herd transmission is possible either directly via transfer of live animals [2, 3], or indirectly via contaminated personnel or equipment. Measures to prevent virus spread between herds must be based upon knowledge of viral shedding, the potential for transmission to susceptible animals and the role of protective immunity. Several observational studies have been published on BCoV shedding in feces of diarrheic calves and after transportation to feedlots [3, 5–10]. However, relatively few studies on BCoV pathogenesis with emphasis on transmission potential under controlled conditions have been published.
BCoV belongs to the genus Betacoronavirus within the family Coronaviridae, also including the closely related HCoV-OC43, which causes respiratory infections in humans, and the human pathogens SARS-CoV and MERS-CoV [11–13].
BCoV consists of one serotype with some antigenic variation between different strains [14, 15]. Acutely infected animals develop antibodies that persist for a long period, possibly for several years [16–18]. However, the protective immunity is shorter and incomplete. In two experimental studies, infected calves were not protected against reinfection with a different BCoV strain three weeks after the first challenge, but did not develop clinical signs [19, 20].
BCoV is transmitted via the fecal-oral or respiratory route. It infects epithelial cells in the respiratory tract and the intestines; the nasal turbinates, trachea and lungs and the villi and crypts of the small and large intestine, respectively [21, 22]. Replication leads to shedding of virus in nasal secretions and in feces. Important factors for the pathogenesis are still not fully explored, such as how the virus infects enterocytes shortly after introduction to an animal. Viremia has been detected in one study by Park et al.. Clinical signs range from none to severe, and include fever, respiratory signs and diarrhea with or without blood [1, 15]. As the time of infection is usually unknown and laboratory diagnostics are usually not performed, occurrence of clinical signs is the most relevant parameter to relate to viral shedding. The majority of experimental studies have used BCoV inoculation as challenge procedure, which may influence clinical signs and viral shedding, and thereby the transmission potential compared to natural infection. It has been hypothesized that BCoV can cause chronic subclinical infections which could be an important virus source. Kapil et al. documented viral antigen in the small and large intestines of infected calves three weeks post inoculation. Crouch et al. found that ten cows were shedding BCoV-immune complexes in the feces for 12 weeks. It is, however, difficult to establish whether there is true persistence of virus, or reinfection of partially immune animals and whether these animals represent a risk to other animals. There is a lack of experimental studies investigating viral shedding pattern for longer periods than two weeks, with sensitive detection methods. Viral load and infectivity also needs to be determined. This is of high practical relevance, since the farmers need guidance on biosecurity in trade and transport of live animals.
The current study was conducted to fill prevailing gaps in the knowledge on fundamental aspects of BCoV infection. The specific aims were to:study the duration and quantity of BCoV shedding in feces and nasal secretions, related to clinical signs in calves.study the presence of viremia and persistence of virus in lymphatic, intestinal and lung tissue.test the hypothesis that seropositive calves are not infectious to naïve in-contact calves three weeks after BCoV infection.
isolated from calves with diarrhea