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
Since the identification of the first coronavirus – infectious bronchitis virus (IBV) isolated from birds – many coronaviruses have been discovered from such animals as bats, camels, cats, dogs, pigs, and whales. They may cause respiratory, enteric, hepatic, or neurologic diseases with different levels of severity in a variety of hosts, including humans. Coronaviruses have positive-sense single-stranded RNAs, their genomic size are 26 to 32 kilobases, the largest for an RNA virus. And the viruses themselves appear crown-shaped under electron microscopy. Coronaviruses belong to the subfamily Coronavirinae in the family Coronaviridae in the order Nidovirales. Coronavirinae is further divided into four genera, Alpha-, Beta-, Gamma-, and Deltacoronavirus, based on their phylogenetic relationships and genomic structures.
Coronaviruses occasionally jump across host barriers, often with lethal consequences. The alpha- and betacoronaviruses only infect mammals and usually cause respiratory illness in humans and gastroenteritis in animals. Gamma- and deltacoronaviruses mainly infect birds, and no human infection has been reported. Six coronaviruses known to infect humans are 229E, NL63 (genus Alpha-), OC43, HKU1, SARS-CoV, and MERS-CoV (Beta-), whereas only SARS- and MERS-CoV have caused large worldwide outbreaks with fatality, others usually cause mild upper-respiratory tract illnesses. A novel coronavirus was identified in a pneumonia patient in Wuhan on January 9 of this year represents the seventh human-infecting coronaviruses.
Severe acute respiratory syndrome (SARS, induced by SARS-CoV) first emerged in Guangdong province, China in 2002 and quickly spread around the world, with more than 8000 people infected and nearly 800 died. The MERS-CoV is a new member of Betacoronavirus and caused the first confirmed case of Middle East Respiratory Syndrome (MERS) in Saudi Arabia in 2012. Over 2000 MERS-related infections have been reported as of 2019 with a ∼34% fatality rate (https://www.who.int/).
The porcine hemagglutinating encephalomyelitis virus (PHEV) is the causative agent of neurological and/or digestive disease in pigs. PHEV was one of the first swine coronaviruses identified and isolated, and the only known neurotropic virus that affects pigs. However, PHEV remains among the least studied of the swine coronaviruses because of its low clinical prevalence reported in the swine industry worldwide. PHEV can infect naïve pigs of any age, but clinical disease is age-dependent. Clinical manifestations, including vomiting and wasting and/or neurological signs, are age-related, and generally reported only in piglets under 4 weeks old. Subclinical circulation of PHEV has been reported nearly worldwide in association with a high seroprevalence in swine herds. Protection from the disease could be provided through lactogenic immunity transferred from PHEV seropositive sows to their offspring in enzootically infected herds. However, PHEV still constitutes a potential threat to herds of high-health gilts, as evidenced by different outbreaks of vomiting and wasting syndrome and encephalomyelitis reported in neonatal pigs born from naïve sows, with mortality rates reaching 100%. In absence of effective vaccine, the best practice for preventing clinical disease in suckling piglets could be ensuring that gilts and sows are PHEV seropositive prior to farrowing.
Avian infectious bronchitis virus (IBV) belongs to the genus Gammacoronavirus of the Coronaviridae family and is the etiologic agent of infectious bronchitis (IB), which is a major, highly complex infectious disease of poultry caused by multiple serotypes of IBV (1). IBV possesses a single-stranded positive-sense RNA genome (approximately 27.6 kb) encoding 4 structure proteins (phosphorylated nucleocapsid (N) protein, small envelope protein (E), integral membrane glycoprotein (M), and spike glycoprotein (S)) in the order of 5′-Pol-S-3a-3b-E-M-5a-5b-N-UTR-3′ (2). The S glycoprotein is cleaved into S1 and S2 subunits posttranslationally. S1 protein involves in infectivity, contains serotype-specific sequences, hemagglutinin activity, and virus neutralizing epitopes. The mutations, deletions, insertions, and recombination events that have been observed in multiple structural genes, especially in the S1 gene, of IBV isolates recovered from natural infections have been considered to contribute to the genetic diversity and evolution of IBV, and consequently, to the development of a number of IBV serotypes (3, 4). IB affects chickens of all ages, and IBV replicates primarily in the respiratory tract and in some epithelial cells of the kidney, gut and oviduct, resulting in reduced performance, reduced egg quality and quantity, increased susceptibility to infections with other pathogens, and condemnations at processing. IBV is a major poultry pathogen that is endemic worldwide and leads to serious economic losses (5, 6). IB has been reported in peafowl, teal, partridge, turkey, pheasant, racing pigeon and guinea fowl (7). Therefore, serological and molecular characterization of the field isolates of the IBV is highly important. IB was firstly described in North Dakota, USA, in 1930 (8). The first isolation of IBV in Iran was reported by Aghakhan et al. in 1994. The isolate showed the antigenic relationship to the mass serotype (9). IB is still a serious problem in Iran. Some newly emerging IBV isolates have recently been found. Backyard chicken is considered an important source of spread and persistence of different diseases (IB, Newcastle disease and avian influenza) among the chickens in poultry farms, playing a major role in the epidemiology of avian infectious diseases. Most household flocks are small and of mixed age and feed mainly by scavenging. Chickens from different households may mix, potentially exposing them to different diseases.
Moreover, no preventive and controlling strategy has been undertaken against IB in backyard chickens in Iran (10–12).
Recent scientific and clinical evidence has indicated that the virus is found during upper and lower respiratory tract infections, causing symptoms and signs that do not differ greatly from the symptoms described for the 'old' viruses HCoV-229E and HCoV-OC43. Other systems involvement is still controversial.
Table 1 shows that patients diagnosed with the virus have presented with mild symptoms, indicating upper respiratory tract infection such as fever, cough and rhinorrhoea. On the other hand, the disease is also known to cause significant more alarming lower respiratory tract infection. One of the most alarming symptoms is bronchiolitis, an inflammation of the membranes lining the bronchioles. This symptom was reported by several research groups [25, 50, 64], and although a population-based study in China did not report an association of HCoV-NL63 with bronchiolitis, it is still believed to be one of the presenting symptoms. Several research groups have linked HCoV-NL63 to croup [26, 53]. Croup children present with pharangitis, sore throat and hoarseness of voice, and are considered for hospitalization. Of the rare findings, a group has reported the association between HCoV-NL63 and Kawasaki disease, a form of childhood vasculitis that is presented as fever, polymorphic exanthema, oropharyngeal erythema and bilateral conjuctivitis. However, others fail to report on this association [66, 67].
It is noteworthy to say that the report of symptoms in young children, who represent the majority of patients, is based mainly on parental observations, where other possible subjective signs and symptoms fail to be recognized by the parents. Moreover, most of the studies were conducted on patients reporting to hospitals suffering from acute respiratory tract infection. To date, there are only few population-based studies and the question arises whether larger numbers of such studies might reveal the involvement of other body systems.
Coronaviruses (CoVs) are large, enveloped, single-stranded, positive-sense RNA viruses that belong to the Coronaviridae family. Although the first two human CoVs—CoV-229E and CoV-OC43—had already been discovered in the 1960s, no special attention was given to them because infections were primarily self-limiting and were only associated with symptoms of the mild common cold. Since 2000, several new CoV types have emerged. In 2003, the World Health Organization issued a global alert about a deadly new infectious disease, severe acute respiratory syndrome, which turned out to be caused by a CoV. In late 2004 a novel CoV, NL63, was isolated from two children with respiratory symptoms in the Netherlands, followed by the discovery of CoV-HKU1 in a patient with pneumonia. In 2012, the Middle East respiratory syndrome CoV was identified and was acknowledged to be one of the most dangerous respiratory viruses for humans,.
As a result, CoVs are increasingly recognized as important pathogens associated with a broad range of clinical diseases. Previous studies have reported CoV-OC43 to be the most prevalent CoV in many countries,. Virus isolation in cell culture and more recently molecular techniques, specifically PCR, have been the method of choice for diagnosing CoV infections, but they have several disadvantages,. Commercial PCR-based methods are often relatively expensive, they require technical expertise and the presence of viral RNA or DNA does not always reflect acute disease. Moreover, using PCR, CoVs are frequently codetected with other respiratory viruses, and the contribution of positive CoV PCR results to disease severity is not always clear,.
Despite the high morbidity and mortality associated with infections caused by some specific CoVs and the frequent detection of CoV in patients with respiratory infections, there is no rapid method available that can detect clinically relevant CoVs in humans. The aim of this study was to increase our insight in clinically relevant CoV infections by monitoring antigen concentrations in confirmed CoV patients using a newly developed assay for the rapid detection of CoV-OC43 infections.
An assay to detect species-specific CoV-OC43 nucleoprotein antigens was introduced to the mariPOC respi test in 2017. mariPOC (ArcDia Int. Ltd., Turku, Finland) is an automated and multianalyte antigen detection test system that enables rapid detection of acute infections,,. Besides the recently added CoV-OC43, the mariPOC respi test is able to detect nine respiratory viruses (influenza A and B viruses, respiratory syncytial virus, adenovirus, human metapneumovirus, parainfluenzavirus type 1–3, human bocavirus) and Streptococcus pneumoniae from one nasopharyngeal sample at the point of care. The new CoV antigen test has an analytical sensitivity of 2 ng/mL for OC43 recombinant antigen. The test cross-reacts with neither HKU1, NL63, and 229E nor with other common respiratory pathogens or microbiota. It is therefore unlikely to cross-react either with Middle East respiratory syndrome CoV or severe acute respiratory syndrome CoV. According to the manufacturers' specification, the clinical specificity of the test is 99.4% (n = 160) compared to PCR.
For this study, we used the semiquantitative property of the mariPOC analysis to obtain CoV antigen levels by extrapolation from a standard concentration curve. For verification of the results, samples were sent to two laboratories (Laboratory of Clinical Virology, Academic Medical Center (AMC), The Netherlands; and the National Institute for Health and Welfare (THL), Finland) for PCR testing with a multiplex RT-PCR and a CoV-species–specific RT-PCR, respectively.
Interest in the virome, or the entire population of viruses present in a biological sample, has increased recently due to improved availability of high throughput sequencing or next generation sequencing (NGS) technologies, and improved metagenomic analytical methods [1, 2]. The virome comprises all types of viruses, including those that infect prokaryotic and eukaryotic organisms, DNA or RNA viruses, and viruses that cause acute or chronic infections. Many of these viruses are difficult or impossible to propagate in cell culture, and molecular detection is difficult as no common gene such as the ribosomal 16S gene that is present in bacterial species exists in viruses. These limitations have hindered the identification and characterisation of uncultured viruses [3, 4]. Recently, due to the advent of molecular enrichment protocols, high throughput sequencing and new metagenomic analytical methods we are now able to explore, identify and characterise viruses from different biological and environmental samples with a greater capacity [2, 5–11]
In studies of human faeces, the virome has been shown to include viruses that infect eukaryotic organisms and viruses that infect prokaryotes (bacteriophages) [2, 5, 12–18]. Bacteriophages have been reported in many studies to be the most frequently detected viral constituent in the gut of humans [1, 2, 5, 8, 16, 19, 20]. The faecal virome has been characterised for several animal species including pigs, bats, cats, pigeons, horses and ferrets [2, 6, 7, 9–11, 21–31]. In dogs, the presence of enteric viral pathogens such as canine parvovirus, coronavirus, rotavirus and distemper virus (Paramyxoviridae) have been identified only through targeted studies [32–35]. To date, only one published study has used high throughput sequencing to investigate the faecal viral population in diarrhoeic dogs. These investigators analysed faeces from dogs with acute diarrhoea and detected two new virus species, canine sapovirus and canine kobuvirus; known canine enteric viruses such as canine coronavirus, canine parvovirus, canine rotavirus as well as plant and insect viruses were also reported.
The aim of this study was to describe the faecal virome of samples collected from healthy dogs, and compare these findings to the faecal virome of dogs with acute diarrhoea in Australia, using an Illumina MiSeq shotgun metagenomic sequencing approach.
The order Nidovirales encompasses a diverse group of viruses that includes significant veterinary and human pathogens (1–6). These viruses cause a variety of diseases that range from mild enteric infection to severe respiratory disease or hemorrhagic fever (7, 8). Examples of disease-causing nidoviruses include the severe acute respiratory syndrome (SARS) coronavirus, a number of other coronaviruses that cause typically mild respiratory disease in humans, and agriculturally important animal pathogens, such as equine arteritis virus, porcine reproductive and respiratory syndrome virus, and yellow head virus. Nidoviruses are characterized by their overall genome architecture, distinct pattern of gene expression, and presence of a conserved set of functional domains in their nonstructural polyproteins. The nidoviruses cluster into five major groups, which have been taxonomically categorized into four families: Arteriviridae, Roniviridae, Mesoniviridae, and Coronaviridae. Viruses in the Coronaviridae family (subfamilies Torovirinae and Coronavirinae) have the largest known RNA genomes, an attribute thought possible because of a virally encoded proofreading exonuclease (ExoN) that increases replication fidelity (9–12). Although nidoviruses are known to infect mammals, birds, fish, and crustaceans, no nonavian reptile nidovirus has been previously described.
Ball pythons (Python regius) have become one of the most popular types of reptiles sold and kept as pets (13). Native to West Africa, these snakes make popular pets because of their relatively modest size (≤1.5 m), docile behavior, and ease of care. Selective captive breeding has resulted in a tremendous variety of colors and patterns (morphs), many of which command high prices. Since the late 1990s, veterinarians have been aware of respiratory tract disease as a common syndrome affecting ball pythons. This syndrome is often characterized by pharyngitis, sinusitis, stomatitis, tracheitis, and a proliferative interstitial pneumonia. The clinical and epidemiological characteristics suggested an infectious etiology.
In this study, we investigated the pathology and etiology of this disease. We obtained case samples from 7 collections around the United States, performed necropsies, and collected multiple tissues for light microscopy and samples of lung for transmission electron microscopy (TEM). Although TEM of the lung suggested a viral etiology, traditional molecular diagnostic methods did not identify an agent. Metagenomic sequencing was used to identify and assemble the genome of a novel virus in the order Nidovirales. Here we describe clinical and pathological manifestations of this disease, ultrastructural findings, tissue tropism, disease association, and subgenomic RNA expression and analyze the genome of this virus in the context of related viruses.
Infectious bronchitis (IB) is an acute contagious viral infection with low mortality and a significant reduction in performance in chicken. The causative agent of IB is infectious bronchitis virus (IBV) which is an enveloped, single-stranded, positive sense and RNA virus belonging to the family Coronaviridae, the genus gamma Coronavirus. The virus consists of three important structural proteins: the nucleocapsid (N), the membrane (M), and the spike (S1 and S2) glycoproteins. The nucleotide sequence of the S1 gene is highly variable, which makes it prone to mutation and emergence of new variants of the virus. For this reason, the molecular classification of IBVs is based on the investigation of the S1 gene.1 Vaccination is one of the best ways of immunization of susceptible birds. However, vaccinated flocks may experience disease involvement because there is almost no cross-protection among serotypes.2 Consequently, the viral strains that exist in a different geographical area must first be identified and their pathogenicity should be determined in order to select an appropriate virus strain for vaccination.
In Iran, Aghakhan et al. identified IBV by virus isolation and serological techniques. This isolate belonged to the Mass serotype.3 In previous studies conducted to identify IBV serotypes in Iran, the presence of 4/91 and Massachusetts serotypes have been reported.4,5 Recently, a new isolate of IBV (IRFIBV32) was identified by Boroomand et al. which had 95.00% similarity to 793/B strains.5 The other IBV serotypes also exist in Iran neighboring countries such as Dutch strains in Pakistan.6
In Ahvaz (southwest Iran), IBV vaccines including H120 and 4/91 are used in the vaccination program in broiler chicken flocks. However, IB continues to be responsible for the economic losses of the poultry industry in the region. The purpose of this study was to evaluate the role of IBV in broiler chicken respiratory complexes in Ahvaz, and also to study the partial S1 sequences among field isolates of IBVs.
Infectious bronchitis (IB) is primarily a respiratory disease of chickens but with potential to cause more widespread infection in the urinary and reproductive tracts in chicken leading to significant production losses in commercial broiler and layer flocks worldwide. The causative infectious bronchitis virus (IBV) belongs to the family Coronaviridae. The disease is usually characterized by high morbidity and low mortality in mature birds, whereas in naive young birds (2–3 weeks of age), mortality up to 100% can be observed. Being an RNA virus with the ability to mutate and recombine, IBV persist as numerous serotypes and strains. The control of IB relies on vaccination. Vaccines are available for commonly occurring serotypes and strains but they are not necessarily antigenically similar to the wild-type viral strains circulating in poultry barns. Although, these vaccine strains may provide some degree of protection for some related strains known as protectotypes, the commonly available vaccines may not elicit protective immune responses in a flock if the field strains are antigenically very different from the vaccine strains. Owing to this reason, vaccination against IBV is not currently considered to be a very effective control method and other biosecurity measures are necessary to prevent the introduction of IBV into poultry production facilities.
IBV is known to replicate in the respiratory tract leading to changes in the muco-cilliary clearance mechanism, as such, expose the IBV infected birds to secondary bacterial infections. Additionally, IBV has tropisms for a variety of tissues. However, the mode of dissemination from the common route of entry, i.e. the respiratory route, to the rest of the body systems could potentially be due to the initial viremia. Once disseminated, IBV infects epithelial cells of the reproductive and urinary systems, particularly the oviduct and kidney depending on the infecting strain. Recently, it has been shown that a nephro-pathogenic strain of IBV (B1648) could replicate in peripheral blood monocytes leading to viremia. The infection of circulating monocytes could potentially disseminate IBV to the urinary tract, liver and spleen.
Macrophages play roles in innate immune responses, as well as in mounting adaptive immune responses by functioning as antigen presenting cells, as such they are critical in protecting animals from microbial infections. Although it is known that macrophage numbers are elevated in the respiratory tract in response to IBV infection, the role played by macrophages in IBV infection, particularly if they serve as a target cell for viral replication is not known. Macrophages have been implicated to play in an important role in the pathogenesis of some animal and human viruses including Marek’s disease virus in birds, feline corona virus in cats, and human immunodeficiency virus (HIV). It was also shown that coronaviruses such as severe acute respiratory syndrome (SARS)-coronavirus (CoV) can replicate within human macrophages thereby interfering with macrophage functions leading to severe pathology. However, a single report based on in vitro studies indicated that IBV, particularly nonpathogenic Beaudette and Massachusetts type 82822 strains do not replicate in avian macrophages.
Therefore, in this study we investigated the interaction of IBV with macrophages in lungs and trachea in vivo and macrophage cell cultures in vitro using two IBV strains, Connecticut A5968 (Conn A5968) and Massachusetts-type 41 (M41) which are known to induce clinical disease and pathological lesions in chickens. As implicated in some other viruses, we hypothesized that these two strains of IBV replicate within avian macrophages leading to productive replication and interfering with selected macrophage functions in the process.
Viruses belonging to the Coronaviridae family have a single stranded positive sense RNA genome of 26–31 kb. Members of this family include both human pathogens, such as severe acute respiratory syndrome virus (SARS-CoV)1, and animal pathogens, such as porcine epidemic diarrhea virus2. Currently, the International Committee on the Taxonomy of Viruses (ICTV) recognizes four genera in the Coronaviridae family: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. While the reservoirs of the Alphacoronavirus and Betacoronavirus genera are believed to be bats, the Gammacoronavirus and Deltacoronavirus genera have been shown to spread primarily through birds3. The first three species of the Deltacoronavirus genus were discovered in 20094 and recent work has vastly expanded the Deltacoronavirus genus, adding seven additional species3.
By contrast relatively few species within the Gammacoronavirus genus have been identified. There are currently two recognized species in the Gammacoronavirus genus: avian coronavirus (ACoV) and beluga whale coronavirus SW1 (SW1). ACoVs infect multiple avian hosts and include several important poultry pathogens, such as infectious bronchitis virus (IBV) and turkey coronavirus (TCoV)5. IBV was first described in the United States6 but has since been described around the globe7. Turkey Coronavirus is the cause of acute enteritis in domestic turkeys8. The second species in the Gammacornavirus genus SW1 was first discovered in beluga whales9 but has since been detected in other cetaceans, such as Indo-Pacific bottlenose dolphins10. Despite IBV being the first discovered coronavirus and the impact it has on the poultry industry11, the number of identified species within the Gammacoronavirus genus remains small in comparison to the other coronavirus genera. Coronaviruses from several other avian hosts for which partial sequences are available suggest relatedness to IBV and TCoV. These viruses, which include goose coronavirus (GCoV), were tentatively classified as part of the ACoV species. An approximately 3 kb region, including the nucleocapsid gene and several accessory genes, of GCoV were previously sequenced from a greylag goose in Norway12.
Here we present the full genome of Canada goose coronavirus (CGCoV) sequenced directly from the cloacal swab of a Canada goose, which expired in a mass die-off in a remote region near the arctic in Nunavut, Canada. Our analyses demonstrate that it should be classified as a novel species in the Gammacoronavirus genus.
PHEV can infect naïve pigs of any age, but clinical disease is variable and dependent on age, possible differences in virus virulence (74), and the course of viral pathogenesis. In growing pigs and adults, PHEV infection is subclinical, and animals develop a robust humoral immune response against the virus (66, 75). Exceptionally, transient anorexia (1–2 days) was reported in PHEV-infected sows in absence of other clinical signs (55). An experimental study performed on 7 weeks old pigs reported transient mild neuromotor signs, including tremor and generalized muscle fasciculation in 17% (2/12) of pigs between 4 and 6 days after oronasal inoculation (75). Acute outbreaks of VWD and encephalomyelitis have been reported in piglets under 3–4 weeks of age born from naïve sows, with mortality rates reaching 100%. The first signs of infection are generally non-specific and may include sneezing and/or coughing because of virus replication primarily occur in the upper respiratory tract; followed by transient fever that may last for 1–2 days. More specific clinical manifestations may appear between 4 and 7 days after infection and are characterized by (1) VWD and (2) neurological signs including tremor, recumbency, padding opisthotonus, and finally death. Both clinical forms can be observed concurrently in the same herd during an acute outbreak. More recently, PHEV was associated with a case of influenza-like respiratory illness in a swine exhibition in Michigan, USA, in 2015 (76). Although PEHV can replicate in the respiratory epithelium, the role of PHEV as respiratory pathogen has not yet been confirmed and needs further investigation.
The VWD was experimentally reproduced and reported for the first time in 1974 (59) in colostrum-deprived (CD) pigs by oronasal and intracranial inoculation. Mengeling et al. (74) experimentally reproduced both clinical forms of the disease in neonatal pigs inoculated with a field virus isolate. Later, Andries et al. (77) evaluated the clinical and pathogenic outcomes with different routes of inoculation. In this experiment, all piglets inoculated oronasally or via the infraorbital nerve showed signs of VWD 5 days after the inoculation. However, a high percentage of animals inoculated through the stomach wall, intramuscularly, and intracerebrally showed VWD signs 3 days after inoculation. Pigs inoculated intravenously, intraperitoneal or in the stomach lumen did not show PHEV-associated VDW signs.
Suckling piglets experiencing PHEV-associated VWD show repeated retching and vomiting, which could be centrally induced (4, 49, 59, 73). The persistent vomiting and decreased food intake result in dehydration, constipation, and therefore a rapid loss of body condition. PHEV-infected neonates become severely dehydrated after few days, exhibit dyspnea, cyanosis, lapse into a coma, and die. During the acute stage of VWD outbreaks, some pigs may also display neurologic signs, including muscle tremors, hyperesthesia, excess physical sensitivity, incoordination, paddling, paralysis, and dullness (68). When the infection occurs in older pigs, there is anorexia followed by emaciation (Figure 1). They continue to vomit, although less frequently than in the acute stage. After the acute stage, animals start showing emaciation (“wasting disease”) and often present distension of the cranial abdomen. This “wasting” state may persist for several weeks after weaning, which in most cases requires euthanasia.
Pre-weaning morbidity varies depending on the immune status of neonatal litters at the time of PHEV infection (4, 74). In piglets without lactogenic immunity against PHEV, morbidity is litter-dependent and may approach 100% when the infection occurs near birth. Overall, morbidity decreases markedly as the pig's age increases at the time of PHEV infection. Mortality is variable, reaching up to 100% in neonatal litters born from PHEV naïve dams. However, a different epidemiological picture was observed in the outbreak reported during the winter of 2006 in Argentina (66) where only suckling pigs born from an isolated pool of non-immune gilts were affected. The severity of the main clinical signs reported, including vomiting, emaciation, wasting, and death was unexpected according to previous reports in the field (73). The morbidity was 27.6% in 1 week old pigs and declined to 1.6% in 3 weeks old pigs. After weaning, 15–40% of the pigs coming from affected farrowing units showed wasting disease. An estimated 12.6% (3,683) pigs died or were euthanized (66).
The first clinical signs observed during neurological PHEV outbreaks include sneezing, coughing, and vomiting 4–7 days after birth, with a morbidity rate of approximately 100% (4, 78, 79). Mild vomiting may continue intermittently for 1–2 days. In some outbreaks, the first sign is acute depression and huddling. After 1–3 days, pigs exhibit various combinations of neurological disorders. Generalized muscle tremors and hyperesthesia are common. Pigs may have a jerky gait and walk backwards, ending in a dog-sitting position. They become weak and unable to rise, and they paddle their limbs. Blindness, opisthotonus, and nystagmus may also occur. Finally, the animals become dyspneic and lie in lateral recumbency. In most cases, coma precedes death, with a mortality rate of 100% in neonatal pigs (4). Older pigs show mild transient neurological signs, including generalized muscle fasciculation and posterior paralysis. Outbreaks described in Taiwan (65) in 30–50 days old pigs were characterized by fever, constipation, hyperesthesia, muscular tremor, progressive anterior paresis, posterior paresis, prostration, recumbency, and paddling movements with a morbidity of 4% and a mortality of 100% at 4–5 days after the onset of clinical signs.
In non-swine species, PHEV-related disease only has been induced experimentally. It was also demonstrated that suckling mice (3 days old) were susceptible in a dose- and age-dependent manner to PHEV infection through intracranial inoculation, showing neurological signs and dying (80).
Infectious bronchitis (IB) is a serious and highly contagious disease of chickens, accompanied by decreased egg production and poor egg quality in laying flocks. Avian infectious bronchitis virus (IBV) was first reported in the USA, replicating in the respiratory tract and some epithelial cells of gut, kidney, and oviduct. IBV commonly predisposed the birds to secondary infection with some bacterium, such as Escherichia coli and Mycoplasma gallisepticum, resulting in complicated disease process and increased mortality. The clinical disease and production problems frequently cause catastrophic economic losses to the poultry industry all over the world. IBV belongs to the genus Coronaviridae, family Coronaviridae, order Nidovirales, and possesses a single stranded positive-sense RNA genome encoding four structure proteins, phosphorylated nucleocapsid (N) protein, small envelope protein (E), integral membrane glycoprotein (M), and spike glycoprotein (S). The S glycoprotein on the outside of the virus contains epitopes associated with serotype differences, and is cleaved post-translationally by cellular proteases into the S1 and S2 subunits. The globular S1 subunit forms the tip of a spike, extending outward, plays a role in attachment and entry into the host cell, which has relation to induce virus neutralizing antibody and hemagglutination inhibition antibody, whereas the S2 subunit anchors the S1 moiety to the viral membrane. Coding for the heavily glycosylated spike glycoprotein, the error-prone nature of RNA polymerase made the S1 gene could easily generate nucleotide insertions, deletions, point mutations, and RNA recombination under vaccine pressure, to bring about new variation strain and change of tissue tropism. It is documented that only a few amino acid differences amongst S proteins are sufficient to have a detrimental impact on cross-protection. Antigenically different serotypes and newly emerged variants of field chicken flocks lead to vaccine breaks.
Recently, more than 20 serotypes within IBV have been identified worldwide. The complex epidemiology characterize of IB raised the control difficulty. In China, since IBV strains were first isolated and identified in 1982, various live-attenuated and inactivated vaccines derived from Massachusetts (Mass) serotype strains have been widely and extensively used in chicken farms to reduce the adverse effect of the IBV. However, the disease continues to emerge and cause serious production problems, even occurred in routinely vaccinated layer and breeder flocks in China, and the situation gets worse as time progressed.
It was documented that nephropathogenic type IB has become more and more prevalent in China. The unprecedented economic losses caused by the nephropathogenic IB suggested that selecting the appropriate vaccine strain against the IB outbreaks is of great importance. However, the integrated natures of novel circulating IBV strains in mainland China were not well-learned.
The previous study by other researchers has been revealed that the variation in S1 sequences was closely confirmed relative to the emergence of novel strains, and S1 gene sequence was a good predictor of challenge of immunity in chickens. This study was conducted to identify the IBV strains that have escaped immune defenses conferred by vaccination in China. The genetic characterization of recent IBV field isolates in China was performed by sequencing the whole S1 genes, sequence alignment and phylogenetic analysis compared with other reference strains.
a Ferret Infected by Coronavirus in Japan
We prospectively followed six otherwise healthy immunocompetent Finnish volunteers who developed respiratory illness symptoms and tested positive for CoV-OC43 in the mariPOC assay between December 2015 and December 2016. Informed consent was obtained from patients or their parents before enrolment. After verification of symptoms, nasopharyngeal swabs were collected daily from onset of disease until disappearance of the symptoms. The patients were negative for all other ten pathogens covered by the mariPOC respi test. After mariPOC analysis, all samples were frozen at −20°C, and aliquots were sent to the AMC and THL for confirmation of the results. Antigen measurement results from (almost) daily collected samples are shown in Fig. 1. Antigen secretion correlated relatively well with symptom severity. The clinical characteristics of the CoV-positive patients are provided in Table 1. All samples with measurable CoV antigen levels in mariPOC were also positive by both PCRs.
Due to its high specificity and sensitivity, reverse transcription polymerase chain reaction (RT-PCR) and other nucleic acid tests are the preferred methods for diagnosis of coronavirus infections, such as SARS-CoV. The majority of nucleic acid amplification tests is designed with the ORF1a/1b, which is genetically stable in coronaviruses, and the nucleocapsid (N) or spike (S) genes (Table 1) [25, 26, 28, 30, 45, 46, 64, 67, 71-73]. Based on in vitro coronavirus expression studies, the N gene has the theoretical advantage of being more abundant in infected cells and therefore of higher sensitivity for PCR assays, but this has not been clearly proven in clinical studies. RT-PCR of nasopharyngeal samples, both frozen and fresh, is the most popular choice for detection of HCoV-NL63 (Table 1) and viral culture is frequently used for confirmation of infection [67, 73].
Fixed and frozen samples from affected snakes from collections in Wisconsin, Texas, Florida, Oklahoma, and Pennsylvania were collected between 2006 and 2013 (see Materials and Methods and Table 1). Necropsies were performed on 9 snakes with clinical signs of respiratory disease, and multiple tissues were collected for histopathology; samples of lung from two snakes were collected for TEM.
Lesions were evident in the upper and lower respiratory tracts of all diseased animals (Table 1 and Fig. 1). Four snakes had stomatitis/pharyngitis, with one having caseous material in the choanae (sinusitis) (Fig. 1A). Three snakes had pulmonary hemorrhage, three had either mucoid or caseous material in air passageways, and four snakes had moderately to severely thickened lungs (Fig. 1B). At a microscopic level, four snakes had mild to severe stomatitis (see Fig. S1A in the supplemental material). Eight of nine snakes had tracheitis, with multifocal mild to severe changes, including infiltrates of heterophils, macrophages, and lymphocytes in the lamina propria, and in four of these cases, there was hyperplasia in the tracheal epithelium (see Fig. S1B).
In comparison to the histology of normal snake lung, all nine snakes had a proliferative interstitial pneumonia of various severities (Table 1). In some cases, inflammatory cells were primarily around the terminal smooth muscle bundle of each septum that projected into the central lumen of the lung (Fig. 2A and B). Hyperplastic alveolar cells completely proliferated over capillary beds that are normally distributed at the surface of the primitive faveoli (Fig. 2C and D). Epithelial cells were tall and columnar with abundant apical mucus production (mucous metaplasia). Periodic acid-Schiff (PAS) and alcian blue staining were positive, consistent with the presence of mucopolysaccharides. Heterophils, lymphocytes, and in some cases macrophages infiltrated the interstitium of the pulmonary septa (Fig. 2D) and often were seen in air passageways along with sloughed epithelial cells. In deeper areas of the faveolar spaces, the lung was histologically normal. In more severe cases, the proliferative changes occurred diffusely throughout the lung and were seen from the proximal to distal surfaces lining faveolar structures.
Three snakes had mild to marked bronchial epithelial hyperplasia, with mild to moderate smooth muscle hypertrophy of the terminal muscle bundles. In these cases, the bronchus-associated lymphoid tissue was mildly to moderately hyperplastic. Sections of lungs of two cases were stained with Warthin-Starry stain and Brown-Hopps Gram stain; there was no positive staining for bacteria between cilia and microvilli of pneumocytes overlying muscle bundles. Three of five nasal cavities that were examined revealed mild subacute rhinitis/sinusitis. The vomeronasal organ in one snake was almost obliterated by foamy macrophages. Ziehl-Neelsen acid-fast staining was negative for acid-fast bacteria, and methenamine silver staining was negative for yeast and hyphae. Three cases had mild to moderate stomatitis/pharyngitis. The changes seen in the respiratory tract were consistent with a viral infection.
Of the 9 necropsied snakes, lesions were also observed in other areas of the body. These included mild nonsuppurative encephalitis characterized by periventricular perivascular lymphocytic cuffing (in 1 of 9 snakes examined), mild to moderate acute nephritis (1/9), mild nephrosis (1/9), mild to moderate multifocal subacute dermatitis (1/9), mild acute salpingitis (1/9), and hepatic lipidosis (5/9). In the eye of one snake, there was moderate necrotizing conjunctivitis, with diffuse corneal ulceration, mild superficial keratitis, and mild inflammation and necrosis of the inner layer of the spectacle. One snake had mild bacterial colitis. It is unclear whether these other lesions were related to the observed lung pathology.
For many years, FCoVs have been classified into different biotypes on the basis of their pathobiology. Avirulent strains, which usually induce mild or subclinical symptoms, are referred to as feline enteric coronavirus (FECV). Virulent strains cause feline infectious peritonitis and are called feline infectious peritonitis viruses (FIPV). Until 2005, CCoVs were considered to be mild enteropathogens. In 2005, a virulent variant causing systemic disease in pups and mortality was first recognized in Italy. This virulent biotype has been named canine pantropic coronavirus in reference to its systemic distribution in internal organs [39, 40]. Interestingly, ferret coronaviruses are also classified according to their virulence. The ferret enteric coronavirus (FRECV), which is widely distributed, causes an enteric disease called epizootic catarrhal enteritis, whose overall mortality rate is low. By contrast, the highly pathogenic ferret systemic coronavirus (FRSCV) induces FIP-like disease [42, 43].
Both feline genotypes may be responsible for mild enteric or FIP diseases. FIP remains a rare event, and only a minority of FCoV-infected cats (up to 10%) develop the illness [24, 44]. Two forms of FIP are recognized: the wet/effusive form with accumulation of a characteristic viscous yellow fluid in body cavities and the dry/noneffusive form with pyogranulomatous lesions affecting several organs. Both forms are progressive and ultimately fatal. FIP is often observed in young cats [47, 48]. In ferrets infected with FRSCV, the gross lesions resemble those described in cats with the dry form of FIP. Again, histologic lesions are characterized by severe pyogranulomas commonly observed in the mesentery and the peritoneal surface.
Both canine genotypes have been associated with enteric CCoV. By contrast, pantropic CCoVs identified so far all belong to the CCoV-IIa genetic cluster. Enteric CCoV infection does not prevent subsequent infection with the pantropic variant. Dogs seropositive for enteric CCoVs are still susceptible to pantropic viruses, but the clinical signs are moderate by comparison with those in seronegative dogs, probably owing to partial cross-protection induced by antibodies against enteric CCoV. During infection with the enteric CCoV, the virus remains restricted to the gastrointestinal tract. Conversely, the highly virulent pantropic CCoV is detected at high titres in lungs, spleen, liver, kidney, and brain. Clinical signs consist of fever, lethargy, haemorrhagic diarrhoea, severe lymphopenia, and neurological signs followed by death [39, 49]. The prevalence of the canine pantropic coronavirus is yet unknown, and further epidemiological studies are required to determine its distribution in dog populations. A pantropic strain (CB/05) has been successfully isolated from the lungs of a dead pup. CB/05 has subsequently been used to reproduce the disease experimentally, thereby improving understanding of this new illness. Infection with the CB/05 strain has demonstrated that disease outcome depends on the age at infection. Puppies over 6 months old may recover, whereas younger puppies (2-3 months) develop the most severe symptoms. Lymphopenia is one of the main features of pantropic CCoV infection under natural and experimental infections. While a transient reduction in T and B cell populations is observed during the first week after infection, the CD4+ T cell population remains depleted for 30 days postinfection, which could cause dysfunction of the immune system and favour opportunistic infections.
Avian infectious bronchitis (IB) is an economically important poultry disease affecting the respiratory, renal, and reproductive systems of chickens. Although IB was first identified in North Dakota, USA, epidemiological evidences confirmed the circulation of several IBV serotypes in different parts of the world. Currently, both classic and variant IBV serotypes have been identified in most countries, thus making IB control and prevention a global challenge [2, 3]. The disease is associated with huge economic losses resulting from decreased egg production, poor carcass weight, and high morbidity. Mortality rate could be high in young chickens especially with other secondary complications such as viral and bacterial infections.
Vaccination has been considered to be the most cost effective approach to controlling IBV infection. However, this approach has been challenged by several factors including the emergence of new IBV serotypes (currently over 50 variants) that show little or no cross protection. Importantly, some IBV strains to which vaccines become available might disappear as new variants emerged and thus necessitate the development of new vaccines. Until recently, most IBV vaccines are based on live attenuated or killed vaccines derived from classical or variant serotypes. These vaccines are developed from strains originating from the USA such as M41, Ma5, Ark, and Conn and Netherlands, for example, H52 and H120, as well as European strains such as 793/B, CR88, and D274. However, studies have shown that vaccines against these strains often lead to poor immune response especially against local strains. Live attenuated IB vaccines have also been shown to contribute to the emergence of new pathogenic IBV variants [7, 8]. Notably, changes in geographical distribution and tissue tropism have been observed in QX-like strains that initially emerged in China and spread to cause great economic loss to poultry farmers in Asia, Russia, and Europe [11–14]. This review is aimed at describing progress and challenges associated with IBV vaccine development. Some aspects of viral-induced immune responses are discussed.
Mazandaran province is one of the 31 provinces of Iran and is located along the Caspian Sea in Iran’s Region 3, just east of Gilan province, west of Golestan province, and north of Tehran and Semnan provinces (36.5656°N 53.0588°E). Mazandaran is a major producer of poultry, and poultry farmers in this region provide an important economic addition to the traditional dominance of agriculture. For serology, we collected 460 sera from backyard chickens (9 cities, Table 1) during October to December 2014; and for molecular detection and characterization, we collected cecal tonsils from 75 chickens.
Bats are notorious for carrying many emerging or re-emerging viruses. Epidemiological investigations have shown that almost all SARS patients have a history of animal exposure prior to the disease. SARS-CoV and anti-SARS-CoV antibodies were first found in the masked palm civet (Paguma larvata). However, coronaviruses related to human SARS-CoV were found in horseshoe bats (genus Rhinolophus) in 2005, pointing to a bat origin of SARS-CoV. This virus was named as SARS-related coronavirus (SARSr-CoV). Later, scientists reported two bat SARSr-CoVs could bind to both human and civet ACE2 receptors, suggesting that the Chinese horseshoe bats could serve as the natural reservoir of SARS-CoVs. Additionally a five-year surveillance found highly diverse SARSr-CoVs in bats in one cave of Yunnan province, China, and these viral strains in this location contain all genetic building blocks needed to form a human SARS-CoV, further supporting a direct bat origin for human SARS-CoVs.
Viruses isolated from MERS patients were found to have close contact with dromedary camels, suggesting the animal origin. Phylogenetic analysis indicated humans and camels were infected with the same source of MERS-CoV within a short time period. More than 10 bat species have been found to harbor MERS-related coronaviruses (MERSr-CoVs), but structural divergence in viral proteins (such as spike proteins) exists between bat MERSr-CoVs and human/camel MERS-CoVs, with MERSr-CoVs at the base of phylogenetic tree, suggesting MERS-CoVs likely to originate from bats.
It is worthy of notice that in 2016 swine acute diarrhea syndrome was found in Guangdong province, China, with a mortality up to 90% for piglets. The causative pathogen was identified as a new coronavirus, called swine acute diarrhea syndrome coronavirus (SADS-CoV), shared 95% genomic identity with bat alphacoronavirus HKU2, suggesting a bat spillover into pigs.
The results showed that 12 flocks (48.00%) were positive for IBV (Fig. 1). The nucleotide sequences of four isolates were submitted to the GenBank sequence database and were given the accession numbers IRIBVb: KP751243, IRIBVc: KP751244, IRIBVe: KP751245 and IRIBVf: KP751246. A phylogenetic tree (Fig. 2), based on the hypervariable region of S1 gene sequences of four IBV isolates from the present study and other strains of IBV retrieved from GenBank, was generated. Based on the Phylogenetic analysis, these four isolates were clustered with QX-like viruses. The results demonstrated the occurrence of QX-like serotype/genotype in Ahvaz, Iran. The IBV isolates were closely correlated to PCRLab/06/ 2012 (Iran), QX, HC9, HC10, CK/CH/GX/NN11-1, CK/CH/ JS/YC11-1, CK/CH/JS/2010/13, CK /CH/JS/2011/2 (China), QX/SGK-21, QX/SGK-11 (Iraq) with nucleotide homology up to 99.00%.
Nidovirales is an order of enveloped, single-stranded positive genomic RNA viruses. They have the largest known viral RNA genomes and infect a broad range of hosts. The order of Nidovirales includes four virus families: Roniviridae, Arterividae, Mesoniviridae, and Coronaviridae (Figure 1). This classification is principally based on the organization of their viral genome, the closeness in genome sequences, the antigenic properties of the viral proteins, the replication strategy, the structure and physicochemical properties of the virions, the natural host range, the cell and tissue tropism, the pathogenicity, the cytopathology, and the mode of transmission. The name of Nidovirales, from the Latin word “nidus” for nest, refers to a nested set of viral subgenomic messenger RNAs that is produced during infection. Within the Coronaviridae family, the subfamily Coronavirinae is the one encompassing the larger number of viruses. Species in this subfamily, which include several human pathogens, can be grouped into four main subgroups on the basis of serological and genetic properties: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (Figure 1). Torovirinae is also a subfamily of Coronaviridae and four Torovirus species have been identified so far: the equine, bovine, porcine, and human Toroviruses (Figure 1). The Mesoniviridae subfamily has one genus, which contains one species, the Alphamesonivirus. Alphamesonivirus are mosquito-specific viruses with extensive geographic distribution and host range. Their virions are 60–80 nm in diameter, with club-shaped surface spikes and consist of eight major structural proteins, including a nucleocapsid protein, four differentially glycosylated forms of the membrane protein, and the spike S protein. Roniviridae contain the genus Okavirus and although still little is known about them, the yellow head virus (YHV) can cause significant economic losses to the shrimp industry and is listed as a notifiable disease by the World Organization for Animal Health. In recent years, veterinarians have also become very concerned about Arterividae, in particular the porcine reproductive and respiratory syndrome virus (PRRSV), which is causing economic losses to the USA swine industry that are estimated to US$560 million per year.
Nidoviruses rank among the most complex RNA viruses and their molecular genetics clearly discriminates them from other RNA virus orders. Still, our knowledge about their life cycle, mostly unveiled with studies on Coronaviruses (CoVs), is very limited. To enter cells, Nidoviruses bind to cell surface receptors, an event that precedes the fusion of the viral and cellular membranes (Figure 2, step 1), which is presumably mediated by one of the surface glycoproteins. The fusion takes place either at the plasma membrane or in the endosomes and releases the nucleocapsid into the host cell cytoplasm (Figure 2, step 1). After genomic RNA uncoating from the nucleocapsid, two large replicase open reading frames (ORFs), ORF1a and ORF1b, are translated by host ribosomes to yield two large polyprotein precursors that undergo autoproteolytic processing to eventually produce the non-structural (nsp) proteins. The nsp proteins interfere with the host defenses but also induce the formation of double-membrane vesicles (DMVs) and convoluted membranes, on which they collectively form the replication-transcription complexes (RTCs) (Figure 2, steps 2, 3, and 4). These complexes mediate the synthesis of the genomic RNA and a nested set of subgenomic RNAs that directs the translation of the structural proteins (the nucleocapsid N protein, the membrane M protein, the envelope E protein and the spike S protein) and some accessory proteins, like the hemagglutinin esterase in the case of Severe Acute Respiratory Syndrome (SARS)-CoV or Mouse Hepatitis Virus (MHV) (Figure 2, steps 5 and 6). Newly synthesized genomic RNAs associate with the cytoplasmic nucleocapsid proteins to generate the so-called ribonucleoprotein complexes. The viral structural envelope proteins are inserted into endoplasmic reticulum (ER) and targeted to the site of virus assembly, the ER, or the Golgi, where they interact with the ribonucleoprotein complex to initiate the budding of virus particles into the lumen of the membrane compartment (Figure 2, steps 7, 8 and 9). Newly formed virions then egress the host cell through secretion via the exocytic pathway (Figure 2, step 10).
Coronaviruses are enveloped viruses with a large (27–32 kb) single-stranded, positive-sense RNA. The genome includes at least 6 open reading frames (ORFs) flanked by 5′ and 3′ untranslated regions. The viral RNA is packaged by the nucleocapsid protein (N), which are themselves enclosed in an envelope containing at least three virally-encoded membrane proteins: the spike (S) glycoprotein, transmembrane protein (M), and small membrane protein (E) [2, 3]. Some coronaviruses have an additional membrane glycoprotein, hemagglutinin esterase.
The trimeric S protein forms characteristic viral peplomers that are involved in virus attachment to cell receptors and in virus-cell fusion [5, 6]. The M protein, the most abundant structural component, is a type III glycoprotein consisting of a short amino-terminal ectodomain, a triple-spanning transmembrane domain, and a carboxyl-terminal inner domain. The E protein has been found to be important for viral envelope assembly.
Coronaviruses infect many animals species, including cats and dogs. Feline infectious peritonitis (FIP) was first recognized in 1963 at the Angell Memorial Animal Hospital in Boston by Holzworth. A few years later, Ward discovered that the etiologic agent of this disease was a virus of the family Coronaviridae, that is, the feline coronavirus (FCoV). The first observation of canine coronavirus (CCoV) infection was reported in 1971, when Binn and colleagues isolated a coronavirus (strain 1-71) from dogs with acute enteritis in a military canine unit in Germany. Since these discoveries, much knowledge has been gained as regarding the molecular biology and pathobiology of these viruses. This paper describes recent advances in knowledge of their genetic diversity, the determinants of pathogenesis, and their ability to cross the species barrier. Differences and similarities between these viruses have been highlighted. The paper focuses on feline and canine coronaviruses of the Alphacoronavirus genus, and leaves the canine respiratory coronavirus, which belongs to the Betacoronavirus genus, aside (see below).
Infectious bronchitis virus (IBV) is a single stranded, enveloped RNA virus belonging to the family Coronaviridae, order Nidovirales. The virus causes infectious bronchitis (IB), a contagious disease associated with huge economic loses in poultry industry worldwide. Of major concern in the control of IB is the continued emergence of variant IBV strains that differ in terms of their tissue tropism, pathogenicity, and cross protection. Over the years, serological and molecular studies have been carried out extensively to determine the epidemiology of local IBV strains. Remarkably, both classical and variants IBV strains have been reported in different countries. Among the widely identified IBV strains are IBV M41 (classical strain), originally recognized in USA [4, 5], and CR88 (variant strain otherwise known as 793/B or 4/91) which was first reported in Europe [3, 6, 7].
Over the years, control of IBV infection largely depends on vaccination using live attenuated and killed vaccines. However, one of the challenges with live attenuated IB vaccines is that such vaccines are reported to encourage mutation and recombination, thus leading to the emergence of new variant strains. Live attenuated vaccines have also been linked with reversion to virulence, severe disease, and increased mortality rate [8–10]. On the other hand, killed vaccines induce humoral but not cell mediated immune (CMI) response and in most cases require adjuvants as well as repeated boosting especially in laying chickens and breeder flocks. These challenges therefore necessitate the needs for novel broad vaccines for the control of IB in poultry. To achieve this, stimulation of both humoral (B-cell) and cell mediated immune (CMI) responses is considered very essential for any candidate vaccine. Neutralizing antibodies are important in removing freely circulating IB virus, whereas cytotoxic T- lymphocytes (CTL) response is crucial for the control and clearance of virally infected cells. The latter is achieved through MHCI immune surveillance as well as antigen presentations which is the function of MHCI molecule and both have been associated with the epitope within the S1 glycoprotein [13, 14]. While much has been documented on MHC restricted allele in human and mouse models, little information is available on the biological functions of these molecules in poultry. A large binding groove of BF2∗2101 MHCI molecule identified in B21 chicken line is thought to confer conformational flexibility to the crucial Arg9 residue which allows remodeling of key peptide-binding sites and play a role in the resistance against poultry viral infections. Chicken MHC B–F molecules have been structurally and functionally linked to mammalian MHC class I molecules and involved in antigen presentation to the CD8+ T lymphocytes, which is crucial in antiviral immune response. Interestingly, the S1 glycoprotein of IBV (520 aa) contains different immune epitopes responsible for both antibodies and CTL-based immune responses, thus playing major protective role as viral antigenic determinant.
Currently, the use of peptide based DNA vaccines represents a novel strategy for addressing challenges associated with the control of viral infections [19, 20]. This technology may employ the use of in silico analysis to predict novel B-cells and T-cells immune epitopes for further use in their in vivo applications. One of the innovations in using this technology is the ability to incorporate several epitope peptides directed against different viruses and/or multiple virus strains into one single delivery system with the view to induce broad and specific immune response in single administration. To date, only few epitope based peptide vaccines have been developed and evaluated against IB [20, 21]. The objective of this study therefore is to identify novel B-cells and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. The antigenicity of the predicted peptides was also evaluated.
The coronaviruses are a group of enveloped viruses iruses. The putative membranous envelopes have a mosaic structure. This structure is composed of a lipid bilayer membrane that is derived from the endoplasmic reticulum (ER) and Golgi complex of the host cell and viral gene-encoded proteins (1).
As a small structural protein, the E (envelope) protein is so-named because it has generally been regarded as the main component of the viral envelope since its first identification in RNA viruses. In addition to the pivotal role that it purportedly plays in the assembly of the viral envelope and/or the host-derived membrane, there is accumulating evidence from research on known coronaviruses that the expression of the E protein also results in the production and release of membrane vesicles or virus-like particles (VLPs) 2., 3., 4., induction of apoptosis (3), and synthesis of α-interferon (5). Its involvement in RNA replication has also been reported 6., 7.. Induced mutation or recombination of the E protein may result in lethal or temperature-sensitive phenotypes and aberrant morphology (8).
Herein we examine the role of the E protein as a multifunctional membrane protein in SARS-CoV. We conducted comparative and phylogenetic analyses of the structure and function of the E protein in sixteen genome sequences of SARS-CoV published by Beijing Genomics Institute (BGI; ref. 9) and other laboratories 10., 11., 12., and in genome sequences of all other members of Coronaviridae published in Genbank.