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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)
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Initially, interferons-α nebulization, broad-spectrum antibiotics, and anti-viral drugs were used to reduce the viral load,,, however, only remdesivir has shown promising impact against the virus. Remdesivir only and in combination with chloroquine or interferon beta significantly blocked the SARS-CoV-2 replication and patients were declared as clinically recovered,,. Various other anti-virals are currently being evaluated against infection. Nafamostat, Nitazoxanide, Ribavirin, Penciclovir, Favipiravir, Ritonavir, AAK1, Baricitinib, and Arbidol exhibited moderate results when tested against infection in patients and in-vitro clinical isolates,,,. Several other combinations, such as combining the antiviral or antibiotics with traditional Chinese medicines were also evaluated against SARS-CoV-2 induced infection in humans and mice. Recently in Shanghai, doctors isolated the blood plasma from clinically recovered patients of COVID-19 and injected it in the infected patients who showed positive results with rapid recovery. In a recent study, it was identified that monoclonal antibody (CR3022) binds with the spike RBD of SARS-CoV-2. This is likely due to the antibody’s epitope not overlapping with the divergent ACE2 receptor-binding motif. CR3022 has the potential to be developed as a therapeutic candidate, alone or in combination with other neutralizing antibodies for the prevention and treatment of COVID-19 infection.
There is no available vaccine against COVID-19, while previous vaccines or strategies used to develop a vaccine against SARS-CoV can be effective. Recombinant protein from the Urbani (AY278741) strain of SARS-CoV was administered to mice and hamsters, resulted in the production of neutralizing antibodies and protection against SARS-CoV,. The DNA fragment, inactivated whole virus or live-vectored strain of SARS-CoV (AY278741), significantly reduced the viral infection in various animal models,,,,,. Different other strains of SARS-CoV were also used to produce inactivated or live-vectored vaccines which efficiently reduced the viral load in animal models. These strains include, Tor2 (AY274119),, Utah (AY714217), FRA (AY310120), HKU-39849 (AY278491),, BJ01 (AY278488),, NS1 (AY508724), ZJ01 (AY297028), GD01 (AY278489) and GZ50 (AY304495). However, there are few vaccines in the pipeline against SARS-CoV-2. The mRNA based vaccine prepared by the US National Institute of Allergy and Infectious Diseases against SARS-CoV-2 is under phase 1 trial. INO-4800-DNA based vaccine will be soon available for human testing. Chinese Centre for Disease Control and Prevention (CDC) working on the development of an inactivated virus vaccine,. Soon mRNA based vaccine’s sample (prepared by Stermirna Therapeutics) will be available. GeoVax-BravoVax is working to develop a Modified Vaccina Ankara (MVA) based vaccine. While Clover Biopharmaceuticals is developing a recombinant 2019-nCoV S protein subunit-trimer based vaccine.
Although research teams all over the world are working to investigate the key features, pathogenesis and treatment options, it is deemed necessary to focus on competitive therapeutic options and cross-resistance of other vaccines. For instance, there is a possibility that vaccines for other diseases such as rubella or measles can create cross-resistance for SARS-CoV-2. This statement of cross-resistance is based on the observations that children in china were found less vulnerable to infection as compared to the elder population, while children are being largely vaccinated for measles in China.
Anti-viral drugs are thought to be backbone of a management plan of an avian flu pandemic. Only two anti-viral drugs have shown promise in treating avian influenza: oseltamivir (Tamiflu®) and zanamivir (Relenza®). A treatment of Tamiflu® includes 10 pills taken over five days while Relenza® is administered by oral inhalation. The US Food and Drug Administration has approved both anti-viral drugs for treating influenza but only Tamiflu® has been approved to prevent influenza infection. Because antivirals can be stored without refrigeration and for longer periods than vaccines, developing a stockpile of antivirals has advantages as part of an overall strategy to control a flu epidemic. However, there are limitations to the use of antivirals: Tamiflu® needs to be taken within 2 days of initial flu symptoms for it to be effective, but many people may not be aware that they have the flu early in the disease. Some research in animals and recent experience in the use of the drug to treat human cases have also found that Tamiflu may be less effective against the recent strains for the current H5N1 virus than the 1997 strain. Improper compliance to antivirals by irresponsible individuals during an outbreak may results in the emergence of a drug-resistant strain. Lastly, there are current concerns about the safety of Tamiflu® which has been associated with increased psychiatric symptoms among Japanese adolescents.
The HACCP framework enables the identification of risks within a system and the design of control methods. It does not contain the scope for monitoring or ensuring compliance of the control points identified; such control should be applied via other means. Given that EIDs are appearing with increasing frequency, often in countries where they place additional strain on already over-burdened public health and healthcare systems, being able to rapidly identify and design strategies for control has valuable application in responding to emerging health threats such as the Middle East Respiratory Syndrome (MERS) virus which first appeared in Saudi Arabia in late 2012 or the rapidly spreading outbreak of a novel avian influenza A H7H9 in China since March 2013. Conducting detailed, timely and comprehensive field investigations into HPAI H5N1 outbreaks is hampered by the majority of cases occurring in developing countries. Advantages to such a framework are that it requires minimal resources and can be implemented by local health officials and international expertise, if required, can be provided remotely. It also complements recently developed diagnostic statistical models for known pathogens. Subsequent detailed and time-consuming experimental analyses can then be conducted if required. Whereas in-depth epidemiological studies can take weeks or months to produce results and recommendations the HACCP framework may provide a means of producing a response within days of an outbreak occurring.
The route of administration and delivery method used in vaccination may affect vaccine-induced immune responses, antigen presentation, and type of MHC molecule involved in the resultant response. Live attenuated IB vaccines have gained wide application via injection orally and through aeronasal spray. Killed or inactivated DNA vaccines and peptide-based vaccines are commonly used via injection routes. Some improved methods have been used to deliver recombinant proteins, plasmid DNA, and peptide vaccine. For example, an IBV-DNA vaccine carrying S1- and/or N-protein of IBV has been delivered orally using attenuated Salmonella enterica serovar Typhimurium strain. Interestingly, both humoral and mucosal immune responses were shown to significantly increase following oral and intranasal immunization. Vaccinated chickens were protected against homologous challenge. Other approaches recorded success using a Lactococcus lactis bacterial system to deliver IBV vaccine, and this approach led to an efficient mucosal immune response [99, 100].
Virus-like particle (VLP) has been a new focus of interest in vaccine development. This technology utilizes the immunogenic properties of a live virus without potential to retain pathogenic effects. A VLP-based IBV vaccine has been developed using the IBV-M- and IBV-S-genes. Immunization of mice with the candidate vaccines demonstrated high levels of cell-mediated immunity, comparable with the results obtained using H120 live attenuated virus vaccine. Similarly, a chimeric VLP vaccine has been synthesized using M1 protein of avian influenza H5N1 virus and fusion protein “NA/S1” derived from IBV-S1 protein and the cytoplasmic and transmembrane domains of H5N1 avian influenza NA protein. The chimeric vaccine induced significant S1-specific antibodies in mice and chickens, neutralizing antibody in chickens, and increased IL-4 secretion in immunized mice. Putting together these findings, there is a huge potential for VLP-based vaccines as innovative candidate and their use may provide a delivery system for the newer IBV vaccine.
Only one isolate, defined as parrot/Indonesia/BX9/16, was sequenced for the partial S1 gene of IBV using XCE2+/XCE2− primers (Table-1). Nucleotide sequencing of 323 nucleotides from the partial S1 gene showed that there was no difference in the nucleotide sequence of the parrot/Indonesia/BX9/16 gene when compared with IBV 4/91 Israel variant 1 (AF093794.1) and the 4/91 vaccine strain (KF377577.1) (Figure-1). The nucleotide and amino acid pairwise distance also showed 100% homology with the IBV 4/91 Israel variant 1 (AF093794.1) and the 4/91 vaccine strain (KF377577.1). However, differences were observed between the sequenced gene, the H120 (FJ888351) positive control, and the non-chicken IBV-like peafowl/GD/KQ6/2003 virus (AY641576) (Table-4). A phylogenetic tree (Figure-2) of the aligned nucleotide sequence of the partial S1 gene was constructed using the maximum likelihood method with Mega 7 software with 1000 bootstrap value. The tree showed a close relatedness of viral isolate, parrot/Indonesia/BX9/16, to the IBV strain 4/91 variant 1 Israel (AF093794.1), the 4/91 vaccine strain (KF377577.1), CK/CH/YN/SL 1301-1 (KX107779.1), chicken/Attock/NARC-786/2013 (KU145467.1), and gammaCoV/Ck/Poland/G193/2015 (MK576138.1), whereas there were differences observed when compared with the H120 vaccine (FJ888351.1) positive control.
All tissue samples were immediately stored at −70°C until used. RNA of the samples was extracted using the Accuzol Userś Manual (BioNeer Corporation, Republic of Korea) according to the manufacturer's protocol. Briefly, appropriate tissue (50–100 mg of tissue) was homogenized with 1 mL of Accuzol, and then 200 μL chloroform was added into the mixture and the mixture was centrifuged at 12000 rpm at 4°C for 15 min. The upper phase was added to an equal volume of isopropyl alcohol and stored at −20°C for 10 min then centrifuged at 12000 rpm at 4°C for 10 min. After the washing step, by using 80% ethanol and centrifuging at 12000 rpm at 4°C for 5 min, the pellet was dissolved in a final volume of 50 μL distilled water (DW) and stored at −70°C until used.
In recombinant or subunit vaccines, consideration is given to the presence or absence of posttranslational modification associated with the vaccine antigen. However, thorough knowledge of the chemistry and biology of the immunodominant antigen is needed to guide selection of a suitable expression system, since outcomes may differ from bacteria, yeast, mammalian, baculovirus, and plant expression systems. Different expression systems have been used to generate recombinant protein antigen. An attempt, using a vaccinia virus-based IBV vaccine, failed to produce antigen enough to induce significant antibody responses in mice. It was proposed that the use of vaccinia virus-based vaccines may be hindered by issues of safety regarding vaccinia virus itself, as well as its poor replication ability in avian cells. In another study, a baculovirus-based vector was used to express the S1-glycoprotein of Korean nephropathogenic KM91 strain. Immunization of chickens with the KM91 vaccine resulted in 50% kidney protection following a homologous challenge. Similarly, an S1-glycoprotein of IBV has been expressed in a transgenic potato under the control of a cauliflower mosaic virus (35S) promoter gene. This success could be useful in designing food-based oral IB vaccines for use in poultry.
An improved “BacMam” virus surface display technology, a modified strategy from baculovirus vectoring, was used recently to display the S1-glycoprotein of IBV-M41 serotype. Subsequent experimental trials with the vaccine resulted in significant humoral and cell-mediated immune responses. About 83% of the challenged birds were shown to be protected, which is comparable to 89% protection obtained in birds immunized with commercial inactivated vaccine.
Frequent human-animal contact is the major cause for viral cross-species transmission. Next-generation sequencing is a highly efficient method for rapid identification of microorganisms and for surveillance of pathogens for infectious diseases. Animal models and other laboratory tests would be needed to pinpoint the causative agents. The novel coronaviruses in Wuhan likely had a bat origin, but how the human-infecting viruses evolved from bats requires further study. The human-infecting virus may become more infectious but less virulent as it continues to (co-)evolve and adapt to human hosts. Since Wuhan is one of the largest inland transportation hubs in China and the city has been closed off, it is urgently necessary to step up molecular surveillance and restrict the movement of people in and out of the affected areas promptly, in addition to closing the seafood markets. To prevent human-to-human transmission events, close monitoring of at-risk humans, including medical professionals in contact with infected patients, should also be enforced. Finally, virome projects should be encouraged to help identify animal viral threats before viral spillover or becoming pandemics.
Ninety-one-day-old commercial broiler chicks were divided randomly into two groups (seventy chicks in the experimental and twenty chicks in the control group). They were reared separately in the Animal Research Unit of the Veterinary School of Shiraz University and received feed and water ad libitum during the experiment. All experiments were conducted after institutional approval of the animal use committee of Shiraz University. Prior to challenge, all birds were serologically tested using enzyme-linked immunosorbent assay (ELISA) and they were negative for antibodies to infectious bronchitis virus antigens. Furthermore, five birds from the experimental group were killed and their organs were investigated for virus detection. At the age of 20 days, all birds in the experimental group were challenged intranasally and with allantoic fluid containing 105 ELD50/0.1 mL of the virus. The remaining 20 birds were left as unchallenged control. All the chickens were monitored daily for 20 days for clinical signs, antibody responses to IBV, and mortality. On days 1, 2, 3, 5, 7, 11, 13, 15, and 20 postinoculation (PI), four chickens from the experimental group and two chickens from the control group were randomly selected and used for sample collection. All were bled before humanly euthanasia. Gross lesions were recorded, and their trachea, lungs, kidneys, caecal tonsil, testes, and oviduct were aseptically collected for virus detection using RT-PCR assay (Table 1). Sera of the birds were collected on 0, 5, 11, 15, and 20 days PI for ELISA test.
The methods performed in this research have been approved by the Ethical Committee of the Faculty of Veterinary Medicine, Bogor Agricultural University, Indonesia, which were validated with the certificate number 058/KEH/SKE/IV/2017.
Since the highly pathogenic H5N1 avian influenza virus (AIV) was first transmitted from birds to humans in Hong Kong in 1997, other pathogenic AIVs, including H7N2, H7N3, H7N7, and H9N2 have been reported in China and other parts of the world.1,2,3,4 However, no human infections with the novel H7N9 virus have been reported until now from China. Here we report a fatal case caused by H7N9 AIV in the very early stage of this endemic.
A 52-year-old retired female resident in Shanghai was admitted to Fudan University affiliated Huashan Hospital due to 7-day history of pyrexia, accompanied by cough, chest stuffiness and dyspnea for the past two days. The patient had a sudden onset on March 27th, 2013 with rigors, and the highest temperature reached 40.6 °C but with no obvious symptoms of cough, pharyngalgia, stuffiness, dyspnea, nausea, vomiting, abdominal pain or diarrhea, and did not receive medication. The next day the patient visited emergency room and chest auscultation demonstrated rough breath sounds, absence of rales. Laboratory tests showed a leukocyte count of 5300/mm3, with 72% of neutrophils, and C reactive protein (CRP) of 26.8 mg/L. The patient was given antibiotics. On the third day, the patient took chest radiography and showed small patchy shadows in lower lobe of the right lung. The patient was given antibiotics intravenously for three consecutive days, still without cough, expectoration or shortness of breath, although her temperature was not resolved. On day 7 after onset of fever, due to quick progression of the symptoms, including cough, chest stuffiness and shortness of breath, the patient visited the emergency department of Fudan University affiliated Huashan Hospital again. Unfortunately, the arterial blood gas analysis showed severe hypoxemia, pH 7.54, PaCO2 4.33 kPa, PaO2 3.66 kPa, and saturation of oxygen 61.3% on room air. In the meantime, chest computed tomography (CT) demonstrated diffuse bilateral consolidation with right pleural effusion (Figure 1). Laboratory findings indicated a leukocyte count of 3290/mm3, with 92% of neutrophils and 5.5% of lymphocytes; platelets of 155 000/mm3; increased myocardial enzymes, prolonged prothrombin time and abnormal serum electrolytes. The patient was suspected severe flu with acute respiratory distress syndrome and thereafter was given endotracheal intubation and placed on a mechanical ventilator. Intravenous injection of methylprednisolone 40 mg was administered to inhibit inflammation and alleviate edema in the lung. On April 3rd (day 8), antimicrobial regimen as well as immune globulin therapy and the methylprednisolone were maintained. However, the patient's condition worsened and died of acute respiratory distress syndrome.
On April 4th, the throat swab was sent to the laboratory of Chinese Center for Disease Control and Prevention and the result revealed the presence of H7N9 avian influenza A virus. Meanwhile laboratory tests for pathogens, including respiratory syncytial virus, influenza B virus, human metapneumovirus, cytomegalovirus, herpes simplex virus 2, human immunodeficiency virus, and severe acute respiratory syndrome coronavirus (SARS-CoV), were all negative. This is one of the six laboratory confirmed fatal cases of H7N9 infection reported to World Health Organization.
To date (April 7th, 2013), a total of 21 cases have been laboratory confirmed with influenza A (H7N9) virus in China, including 6 deaths, 12 severe cases and 3 mild cases.5 An inter-government task force has been formally established, the animal health sector has intensified investigations into the possible sources and reservoirs of the virus. However no definite history of contact with livestock was found in this case. The patient also did not feed or eat poultry at households. Some other confirmed cases had close contact with poultry or with associated environment. It is interesting to note that the virus has also been found in a pigeon in a market in Shanghai. It is unclear how this case was infected by H7N9 AIV, similar to some other cases without known recent close contact with birds or poultry. However, influenza A H7 viruses are a group of influenza viruses that normally circulate among birds and the influenza A (H7N9) virus is one subgroup among the larger group of H7 viruses.6 Although the patient denied close contact with poultry, H7N9 virus was detected among poultry at local market. The most likely source of the virus in this case seems to be from the environment or food contaminated with this novel virus. The emergence of H7N9 AIV infections in humans suggests the avian influenza virus evolves to achieve adaptations including the ability to bind to mammalian cells and to break the species barrier. Fortunately, among close contacts of this case, the patient's husband was pyretic with a temperature of 38 °C, but negative for H7N9 AIV detection and recovered soon, indicating no evidence of human-to-human transmission up to this point. At this time there is no evidence of ongoing human-to-human transmission. The possibility of animal-to-human transmission is being investigated, as is the possibility of person-to-person transmission.
To date, the overall proportion of fatal cases among those reported 21 cases was 28.6% (6/21), lower than that in H5N1 AIV infection in humans (average 59%).7 According to the experience from H5N1 AIV treatment, cases with a fatal outcome were admitted to hospital later (median, 5 days) than those who survived (median, 1 day).7 All fatal cases in Shanghai including this patient were admitted to hospital very late until the symptom of shortness of breath developed. Meanwhile, due to unclear cause of the disease, fatal cases, including this patient, had not been given the anti-influenza drugs such as neuraminidase inhibitors (oseltamivir) as soon as possible and within 2∼4 days of disease onset, leading to loss of valuable salvage time for the severe cases. Since the laboratory testing conducted in China has shown that the influenza A (H7N9) viruses are sensitive to oseltamivir and zanamivir, and if these drugs are given early in the course of illness and the patients are hospitalized earlier, the survival rate of this new emerging infectious disease might be significantly improved. Future strategies to prevent fatal cases should include prompt laboratory diagnosis and early antiviral and steroid treatment, and good supportive care.
Clinical signs observed including gasping, coughing or depression started to appear from three days post-challenge with APEC or a mixed APEC and IBV infection. Bacteriophage treatment delayed the onset of the clinical signs to 6 days post-challenge (dpc) and in addition markedly reduced their severity in both groups (Figure 3). Regarding IBV infection, clinical signs were observed from four-days post-challenge, with bacteriophage treatment leading to a reduction of their severity, but not delaying their onset (Figure 3).
Bacteriophage treatment was not associated with mortality in single APEC or mixed APEC and IBV infected groups. In contrast, birds challenged with APEC alone and mixed APEC and IBV infection without bacteriophage treatment showed a 16% and 29% mortality rate at 8 and 7 days post-infection respectively (Figure 4). Bacteriophage treatment in combination with single IBV infection did not reduce the mortality of 26% (Figure 4).
Bacteriophage treatment significantly reduced APEC shedding after single APEC or mixed APEC and IBV challenge, with a gradual decrease of bacterial loads in lung tissues over time. In contrast, a non-treated and challenged group showed a significantly higher APEC load with a gradual increase over time especially at 9 and 15 dpc (Figure 5). Interestingly, bacteriophage treatment significantly reduced IBV shedding in the mixed infected group but not in the IBV alone infected group comparing to the mixed infected group without bacteriophage treatment. The bacteriophage treated group infected with IBV showed relatively comparable results to the infected non-treated group. Groups with single IBV infection and mixed APEC and IBV infection with bacteriophage treatment showed a reduction, but not statistically significant, of IBV comparing to single IBV infection without bacteriophage treatment, with the reduction only becoming statistically significant at 15 dpc (Figure 6).
The main objective is to prevent economic losses caused by viral immunosuppressive infection. Strategy control is based on different approaches including, good management, application of biosecurity standards, immunization of birds, and genetic selection.
The good management has an important role in optimizing turkey’s performances and in maintaining bird health and welfare. Delivering constantly a good quality air, a high quality water and feed is essential and required at all stages of growth. Control of mycotoxins, as an immunosuppressive agent, must be continually performed. Litter management is a key of the pathogens control.
Application of strict biosecurity measures is fundamental to prevent exposition to immunosuppressive viruses. Increasing bird’s resistance is a complement but essential tool through good vaccination, as the best tool inducing specific protection. Vaccines must be administrated properly for all animals in the same flock, in order to achieve uniform immune response. However, vaccines are not available for the main viral diseases in turkeys. The control of other immunosuppressive agents (bacteria, mycotoxins, parasites, and stress) must be considered to prevent vaccination failures.
Currently, turkeys can be vaccinated against few immunosuppressive viral diseases, such as HE, ND, aMPV, and Reoviruses. Live vaccines used against HE are effective in preventing disease outbreaks. However, they are immunosuppressive, predisposing young animals to opportunistic infections and vaccination failures.
Control of ND is based on different types of vaccines. Lives vaccines, worldwide used in poultry industry, can stimulate local protection. Inactivated vaccines required for a long lasting immunity. Currently, vectored vaccines, using glycoprotein F and administered in ovo or to 1-day old poults, are effective and safety
Vaccination against aMPV is performed to prevent lesions in the upper respiratory tract and the decrease in egg production. Live vaccines are used in young poults, while inactivated vaccines are reserved to adults.
The development of vaccination against Reoviruses interest chickens. In general, strain vaccine protected against viral arthritis with partial protection against RSS.
Although TCoV was identified as the causative agent of Bluecomb disease of turkey poults over 50 years ago (28), vaccines are not available to control the disease. Recent assays of vaccination using protein spike are performed with promoted results (Chen et al., 2018).
The MD is well controlled by vaccination in chickens. Despite the appearance of natural disease in commercial turkeys flocks, vaccination is not performed. However, possible immunization of poults at the hatchery with Rispens strain is suggested (Blake-Dyke and Baigent, 2013).
Cytokines may be used as therapeutic agents for viral diseases and for vaccines adjuvants (Wigley and Kaiser, 2003). IFN-α induces increase of antibody titer in turkeys immunized by NDV DNA vaccine (Rautenschlein et al., 2000a). While, addition of IFN-γ to NDV DNA vaccine, is accompanied by more rapid humoral response and increased protection to NDV challenge in turkeys and chickens vaccinated in ovo (Rautenschlein et al., 1999; Cardenas-Garcia et al., 2016).
Given the limitations associated with vaccination, several assays of genetic selection have been performed. Genetic resistance to MD is well documented, with a special focus on major histocompatibility complex. Notable correlation is demonstrated between resistance of chickens to MD and B21 allele, which is accompanied by reduction of infected T-cells. Mapping genes suggested the presence of a resistance gene in the natural killer region within chromosome 1 (Bumstead, 1998), whereas birds with a B-19 haplotype suffer 100% mortality (Briles et al., 1977). Certain types of artificial selection, as higher growth rates, influence negatively immune competence in turkeys (Husby et al., 2011).
Recently, insertion of transgenes that target AIV into the genomes of chickens allowed to limit virus spread, but this approach is incapable de prevent emergence of disease (Looi et al., 2018).
Genetic selection birds for optimal immune response to used vaccines may complete optimizing natural resistance to viral diseases. Selection for enhanced innate immunity is possible because of the existence of toll-like receptors in chickens and turkeys. Possible interactions between adjuvants and immunogenetics may lead to develop novel vaccines.
A case was defined as a staff member working at the NTNAMC who was hospitalized for respiratory tract infection between November 1 and November 30, 2012, and confirmed to have C. psittaci infection by polymerase chain reaction (PCR) and/or a four-fold rise in serum microimmunofluorescent antibody titer against C. psittaci (Focus Diagnostics, Cypress, California, USA).
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/).
About 70% of microbial agents causing outbreaks of emerging infectious diseases in humans originate directly from animals. Among respiratory virus infections, the influenza A viruses H5N1 and H7N9 from avian species, and the severe acute respiratory syndrome coronavirus from bats have caused large epidemics–. Atypical bacterial pathogens causing community-acquired pneumonia include Chlamydophila psittaci from psittacine birds and Coxiella burnetti from livestock and other animals. However, human outbreaks due to zoonotic bacteria associated with the emergence of a novel animal virus in the animal host were not previously documented.
In November 2012, an outbreak of human psittacosis affecting six staff members occurred at the New Territories North Animal Management Centre (NTNAMC) in Hong Kong. The human outbreak was preceded by an outbreak of avian chlamydiosis among the detained Mealy Parrots (Amazona farinose). Although birds in the tropical and sub-tropical areas are commonly infected with C. psittaci, most infected birds are asymptomatic,. Large human outbreaks are rare even among bird handlers. Although co-infection of C. psittaci and viruses has been reported in outbreaks of avian species–, no virus-bacterium co-infection of implicated avian species has ever been reported in outbreaks of human psittacosis. In this study, we sought to investigate viruses that cause avian co-infection, which may have led to this outbreak of psittacosis.
In the words of the late Director General of World Health Organization, Dr Lee Jong Wook, '"it is only a matter of time before an avian flu virus acquires the ability to be transmitted from human to human, sparking the outbreak of human pandemic influenza...we don't know when this will happen but we do know that it will happen". Factors that suggest that an AI pandemic would be less severe than past influenza pandemics include advances in medicine such as the availability of antiviral medications and vaccines, and international surveillance systems. However, there are also factors that suggest than an avian influenza pandemic could be worse than the 1918 pandemic, such as a more densely populated world, a larger immunocompromised population of elderly and AIDS patients, and faster air travel and interconnections between countries and continents which will accelerate the spread of disease. Nevertheless, unlike the past, we have the prior knowledge of a possible impending pandemic and the knowledge of how to contain and control it. Preparedness, vigilance and cooperation, on local, national and international levels, are our best weapons against a deadly bird flu pandemic.
Vaccination against respiratory viral disease is standard practice in commercial poultry operations. Both live and killed vaccines are administered to poultry, and live vaccines are commonly used for a variety of pathogens because they are effective when mass applied and are relatively economical. In general, live vaccines induce local and cell-mediated immunity and provide a broader protective response than killed vaccines, whereas killed vaccines primarily induce humoral immunity and tend to be antigen-specific. The duration of immunity achieved following live vaccine administration depends on the age and type of bird, levels of maternal immunity, disease targeted by the vaccine, immunogenicity of the vaccine, method of vaccine application, number of and interval between boosters, virulence and similarity of the field challenge virus, interval between vaccination and challenge, and immunocompetency of the host.
Avian coronavirus infectious bronchitis virus (IBV) is an upper respiratory tract viral pathogen of poultry and leads to reduced weight gain and feed efficiency, drops in egg production and egg quality, stunted growth, and secondary bacterial infection resulting in airsacculitis. The virus initially replicates in the upper respiratory tract, followed by systemic replication in the reproductive tract and some strains can cause lesions in the kidney. Infected birds may exhibit nasal discharge, coughing, sneezing, and tracheal rales. The disease is prevented by vaccination, and live vaccines are commonly used to induce local immunity and protection. Live vaccines are generally administered to young birds to achieve early protection, and layers and breeders are also boosted with either live or inactivated vaccines, which vary based on their similarity to the circulating field viruses.
Newcastle disease (ND) is caused by virulent strains of avian paramyxovirus type 1, which has recently been reclassified as avian avulavirus 1 (AAvV-1). Depending on the strain of the virus, clinical signs of ND infection may be absent or may involve depression, inappetence, respiratory signs (nasal discharge, sneezing, coughing), reduced egg production and egg quality, and neurological signs (torticollis, circling, paralysis). Strains of Newcastle disease virus (NDV) are characterized as lentogenic, mesogenic, and velogenic, according to their mean death time in embryos. Lentogenic strains are of low pathogenicity causing mild respiratory or enteric infections, followed by mesogenic strains, while velogenic isolates are highly pathogenic often causing neurological signs and mortality. Vaccination regimes against NDV vary and may utilize a combination of live, inactivated, and virus-vectored vaccines. In the United States, the most widely used traditional vaccine strains comprise lentogenic B1 (or virus clones of the B1 strain) and LaSota strains.
Infectious laryngotracheitis (ILT) is a respiratory disease of poultry caused by gallid alphaherpesvirus I, and is economically important worldwide. Clinical manifestations of ILT include increased mortality, reduced egg production, decreased body weight gain, conjunctivitis, tracheitis with expectoration of bloody mucus in severe cases, depression, severe dyspnea and susceptibility to other respiratory pathogens. Live vaccines against ILT virus (ILTV) may be of chicken embryo origin (CEO) or tissue culture origin (TCO), in which they are passaged multiple times in eggs or tissue culture, respectively. Although recombinant vaccines for ILT are commercially available, the CEO vaccine is the most widely used vaccine against ILTV worldwide.
Because of the need to protect chickens against different viral pathogens from an early age, vaccination programs typically include multiple vaccines against a variety of pathogens. Sample vaccination regimes in different poultry sectors are reviewed in the Merck Veterinary Manual (www.merckvetmanual.com), in which the interval between vaccinations is often only a matter of weeks. However, there is little information showing that the intervals between vaccinations are sufficient for the birds to develop adequate immune protection against challenge for each virus. The literature shows that sequential viral infections may result in viral interference, in which one virus blocks the subsequent infection and/or replication of another virus in the host, but until now it is unknown whether this phenomenon results in reduced protection from serially administered attenuated live vaccines in chickens. Interestingly, it has been reported that simultaneous administration of viruses to chickens or turkeys does not result in viral interference. In this study, we investigate how a typical commercial vaccination schedule consisting of a combination of serially administered, live attenuated viral respiratory disease vaccines affects the development and longevity of immunity and protection against homologous challenge.
Globally, environmental and anthropogenic changes are impacting ecosystems, and perturbing plant and animal demographics and behaviors. These changes contribute to the increasing pace of infectious disease emergence worldwide, largely driven by increasing contacts between and among species,. Drivers of disease emergence include mobility and trade, encroachment of natural habitats and climate change, as well as intrinsic characteristics of pathogens, such as wide host range for animal pathogens and the ability of plant pathogens to hybridize.
The vast majority of emerging infectious diseases in humans are zoonotic in nature,. Often, they escape their natural wildlife reservoirs and infect captive or domestic animals and humans upon cross-species transmission. While the majority of zoonotic pathogens spread limitedly among humans, occasionally some do evolve the ability to efficiently transmit. These may cause devastating epidemics, if not pandemics, and may establish as novel human pathogens. Emerging infectious diseases of animals likewise have typically the ability to cross species barriers and invade new host species. In contrast, introduction of pathogens into new geographical areas and climate change play an essential role in the emergence of plant diseases, and the hybridization of plant pathogens that are not naturally sympatric is repeatedly reported to be involved in plant disease emergence events. The consequences of emerging pathogens in newly infected species, be it wild or domestic, or in new geographical areas, can have dire repercussions on human welfare, for example, through the disruption of ecosystem services or from large agricultural economic losses,. As such, emerging infectious diseases are One Health threats to the global community.
Despite progress in our understanding of the mechanisms and drivers of pathogen emergence and adaptation, infectious disease emergence and associated health and economic burdens remain essentially unpredictable. They continue to impose heavy burdens on the global community, as most recently painfully demonstrated by the emergence of MERS coronavirus in the Middle East and Ebola virus in West Africa. Because the nature, time and location of the next One Health threat cannot be forecasted, preparedness and responsiveness are essential to curb future emerging infectious disease burdens.
Surveillance is key to preparedness by identifying and monitoring new threats to plant, animal and human health, and raising early-warning flags upon changing epidemiology. Major global initiatives have profoundly revolutionized the scope of infectious disease surveillance in plants, animals and humans. These include the World Animal Health Information Database (WAHID) Interface of the OIE, the Global Animal Disease Information system EMPRES-i of the FAO, the situation assessments and reports of the WHO, and the internet-based Program for Monitoring Emerging Diseases (ProMED) of the International Society for Infectious Diseases.
Using the data collected from these different sources, we present the current status of major One Health threats. In this update, the current status of low pathogenic avian influenza virus (LPAIV) H7N9, highly pathogenic avian influenza viruses (HPAIVs) of the H5 subtype, MERS coronavirus and Ebola virus are summarized. The present report will be updated every three months, with newly acquired data on the diseases listed above, as well as with data on any new One Health threat that would have emerged during that period.
Generally the short incubation period for IBV varies with infective dose and route of infection. For example, while infection via the tracheal route may take a course as short as 18 hours, ocular inoculation leads to an incubation period of 36 hours.
Infectious bronchitis (IB) causes significant economic losses to the poultry industry worldwide [1, 2]. The disease was first identified in North Dakota, USA, when Schalk and Hawn reported a new respiratory disease in young chickens. Since then, IBV has been recognized widely, especially in countries with large commercial poultry populations. Apart from respiratory infections, IB affects the kidney and reproductive tract, causing renal dysfunction and decreased egg production, respectively. Although the disease first was believed to occur primarily in young chickens, however, chickens of all age are also susceptible.
Respiratory diseases are among the most devastating diseases in poultry industry because of their major economic losses. In most cases, there are more than one pathogen involving in the pathogenesis of the respiratory diseases.1 Among several avian viruses with predilection for the respiratory tract, infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) are the most important viruses of poultry worldwide. Similar respiratory signs of infectious bronchitis (IB) and Newcastle disease (ND) making differential diagnosis of these two diseases difficult.2
In broilers, IBV affects weight gain and feed efficiency, and, when complicated with bacterial infections like E. coli or S. aureus, it causes high mortality and increased condemnations.3-5 IBV, the causative agent of IB is a coronavirus readily undergoes mutation in chickens resulting in the emergence of new variant serotypes and genotypes.6 As new strains of IBV emerge, rapid detection of IBV is useful for implementation of control measures, research purposes, and understanding the epidemiology and evolution of IBVs.7
Newcastle disease classified as a list A disease by the Office Internationale des Epizooties (OIE), is caused by avian paramyxovirus 1 (APMV-1) or NDV.8 The virus is enveloped with a negative-sense, single stranded RNA genome of approximately 15 kb encoding six proteins (nucleoprotein, phosphorprotein, matrix protein, fusion protein, hemagglutinin-neuraminidase protein, and large protein, respectively).9
Several laboratory methods such as virus isolation in embryonated eggs and organ cultures and serological tests are available for detecting and differentiating avian viral respiratory infections. However, these methods are time consuming and laborious.10-12 Molecular techniques such as reverse transcription-polymerase chain reaction (RT-PCR), sequencing and real time PCR, have been used for rapid and sensitive detection of IBV and NDV separately.13-17 However, those techniques detect only one specific pathogen at a time. The duplex PCR has the ability to amplify and differentiate multiple specific nucleic acids.18 The aim of the present study was to detect and differentiate two common avian viral pathogens using duplex RT-PCR for clinical diagnosis.
Avian infectious bronchitis (IB) is an acute, highly contagious respiratory disease of chickens, causes major economic losses in poultry industry worldwide. The IB virus (IBV) is a member of Gammacoronavirus genus, previously Group 3, within the Coronaviridae and it is the type species of the avian Coronavirus of the domestic chicken (Gallus Gallus)).
It is generally accepted that chickens are the most important natural host of IBV and epithelial cells of the upper respiratory tract are the primary target, and intensive virus replication, predominantly in the trachea, results in respiratory signs, which are the most frequent clinical manifestation of this disease.
Chickens of all ages are susceptible, but the severity is great in younger ages, and the clinical signs include depression, coughing, dyspnea, sneezing, nasal discharge, and death. However, some strains of IBV can also replicates in the ciliated epithelial cells of organs, such as the kidney, reproductive and enteric tracts, producing severe nephritis, reproductive disorders in males and females, a drop in egg production and quality in laying flocks and deep pectoral myopathy in broiler breeder may occure.
The transmission of IBV is mainly horizontal by direct contact via the respiratory tract from infected chickens. Infection takes place via inhalation of droplets containing the air born virus. Or indirect by contaminated feed and drinking water, including human beings, probably contribute to more local spread. In addition, it has been demonstrate that certain strains of IBV may persist in small amounts in the cecal tonsils of the intestinal tract by asymptomatic way during long time.
IBV is an enveloped, non segmented, positive sense, single stranded RNA virus. Its genome consists of about 27.6 kb and codes for four structural proteins: the membrane (M), small membrane (E), nucleoprotein (N) and spike (S). The multimeric coiled-coil S protein is post-translationally cleaved into smaller proteins namely S1 and S2. The S1 gene contains the hypervariable regions that are responsible for the induction of neutralizing, serotype specific antibodies and protective immunity. Many IBV genotypes and serotypes have been identified and have complicated efforts at control through vaccination, due to the frequent point mutations in S1 gene that can be partially or poorly neutralised by existing vaccine serotypes. For this reason, the sequencing of this gene is the most useful strategy for the molecular characterization of virus isolates existing in the field and the selection of appropriate vaccines.
In Morocco, IBV was identified for the first time in 1983 by El Houadfi & Jones. Subsequently, several reports confirmed the IBV strains related to the Massachusetts and to 4/91 genotypes [13, 14].
Recently, between 2010-2014, an epidemiological survey showed the emergence of a novel strain of Italy02 serotype with a prevalence of 32 %, co-circulating with two serotypes; Massachusetts and 4/91, with a prevalence of 66 % and 2 % respectively, that are isolated from vaccinated and unvaccinated chicken flocks.
Mass vaccination in Morocco is conducted using a vaccine against Massachusetts, which is the most dominant serotype, however no information about pathogenesis and tissue distribution of Italy 02 serotype, hence the objective of this present study which is reported for the first time in Morocco, aims to evaluate the pathogenicity and the tissue distribution of the three isolated Moroccan strains of IBV Italy 02 genotype in one day old experimentally infected SPF chickens. The clinical signs, tracheal ciliary activity, gross and microscopic lesions were evaluated. Serological response by the detection of IBV antibodies of the affected chicks was also checked. Re-isolation of the virus from the affected organs and RT-PCR test was used to detect virus in several tissues of infected birds.
Avian infectious bronchitis virus (IBV) is a highly contagious pathogen of chickens that replicates primarily in the respiratory tract and also in some epithelial cells of the gut, kidney and oviduct. IBV is a virus member of genus Coronavirus, family Coronaviridae, order Nidovirales. The virus possesses a positive stranded RNA genome that encodes phosphorylated nucleocapsid protein (N), membrane glycoprotein (M), spike glycoprotein (S) and small membrane protein (E). The spike glycoprotein is post-translationally cleaved into two subunits, S1 and S2. The S1 protein forms the N-terminal portion of the peplomer and contains antigenic epitopes mainly within three HVRs. Neutralizing and serotype specific epitopes are associated within the defined HVRs.
Variation in S1 sequences, has been recently used for distinguishing between different IBV serotypes. Diversity in S1 probably results from mutation, recombination and strong positive selection in vivo. Antigenically different serotypes and newly emerged variants from field chicken flocks sometimes cause vaccine breaks. The generation of genetic variants is thought to be resulted from few amino acid changes in the spike (S) glycoprotein of IBV.
In Egypt, isolates related to Massachusetts, D3128, D274, D-08880, 4/91 and the novel genotype; Egypt/Beni-Suef/01 were isolated from different poultry farms. The commonly used IBV attenuated vaccine is H120 while the Mass 41 (M41) strain is commonly used in inactivated vaccines.
In the present study, Egypt/F/03 was isolated from 25-day-old broiler chickens in Fayoum Governorate, identified by Dot-ELISA, RT-PCR and sequenced to determine its serotype. Pathogenicity test to 1-day-old chickens and protection afforded by the commonly used H120 live attenuated vaccine were also performed.