Clinical monitoring of infected chicks reveals at first, apparent respiratory symptoms beginning at day 2 post-inoculation (dpi). Respiratory clinical signs were predominant in all of the inoculated groups and were intense and more severe until 7 dpi, with no clear differences in the pathogenicity of the three strains. The most prominent clinical signs were characterized by gasping, depression, sneezing, difficulty in breathing, cough, pulmonary and tracheal rales, with high scores were reported for all the tested strains with clinical score of 108, 126 and 140 for IBV/RA, IBV/MN and IBV/TU strain respectively, (Tables 1, 2 and 3).

Nasal discharge and watery eyes were also observed but were transient in some of infected by IBV/RA and IBV/MN chicks. These clinical symptoms were persisted in all groups until 12dpi. The birds infected by IBV/MN and IBV/TU appeared lethargic, reluctant to move (Fig. 1), whereas, chicks infected with by IBV/RA were not as apathetic. At autopsy, all infected chicks that were killed at 5 dpi to prevent their suffering were examined for the macroscopic lesions in the trachea, lung and kidney. These gross lesions consisted in hemorrhagic tracheitis, mucosal congestion and catarrhal exudates that mainly progressed. For the three strains used, the signs were observed in the most infected chicks with dominance in the lungs that were hemorrhagic and sometimes cyanotic at one lobe. Therefore, samples were taken at 14 dpi just for a macroscopic examination of organs to confirm whether the absence of clinical signs is correlative with the gross lesions. Whereas, gross lesions of kidney, were not observed in all inoculated chicks. During the experiment, the non-infected control group stayed normally without clinical signs or gross lesions. The statistical analysis was not performed as the three tested strains are phylogentically related to each other and the difference in clinical and tissues scores is not very significant.

Infectious bronchitis virus (IBV) is, by definition, the coronavirus of the domestic fowl. Although it does indeed cause respiratory disease, it also replicates at many nonrespiratory epithelial surfaces, where it may cause pathology, for example, kidney and gonads [1, 2]. Strains of the virus vary in the extent to which they cause pathology in nonrespiratory organs. Replication at enteric surfaces is considered to not normally result in clinical disease, although it does result in faecal excretion of the virus. Infectious bronchitis (IB) is one of the most important diseases of chickens and continues to cause substantial economic losses to the industry. Infectious bronchitis is caused by IB virus (IBV), which is one of the primary agents of respiratory disease in chickens worldwide. All chickens are susceptible to IBV infection, and the respiratory signs include gasping, coughing, rales, and nasal discharge. Sick chicks usually huddle together and appear depressed. The severity of the symptoms in chickens is related to their age and immune status. Other signs of IB, such as wet droppings, are due to increased water consumption. The type of virus strain infecting a flock determines the pathogenesis of the disease, in other words, the degree and duration of lesions in different organs. The upper respiratory tract is the primary site of infection, but the virus can also replicate in the reproductive, renal, and digestive systems. The conventional diagnosis of the IBV is based on virus isolation in embryonated eggs, followed by immunological identification of isolates. Since two or three blind passages are often required for successful primary isolation of IBV, this procedure could be tedious and time consuming. Alternatively, IBV may be isolated by inoculation in chicken tracheal organ cultures. Furthermore, IBV may be detected directly in tissues of infected birds by means of immunohistochemistry [6, 7] or in situ hybridization. The reverse transcription-polymerase chain reaction (RT-PCR) has proved useful in the detection of several RNA viruses [9, 10]. Outbreaks of the disease can occur even in vaccinated flocks because there is little or no cross-protection between serotypes [2, 11]. The necessity of IB prevention in chicken regarding the nature of the virus with a high mutation rate in the S1 gene dictates the necessity to develop effective vaccines. The first step is to study the virus strains distributed in the geographical region and determine their antigenicity and pathogenicity in order to choose a suitable virus strain for vaccination. This virus was isolated from a flock suspected of IB suffering from severe respiratory distress and experiencing high mortality. The objective of the present study was to clarify some aspects of pathogenesis of the disease caused by IRFIBV32 (793/B serotype) in experimentally infected broilers. RT-PCR test was performed to detect the presence of the virus in body tissues and samples. The clinical signs, gross lesions, and antibody response of the affected chicks were also monitored.

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/).

Coronaviruses belong to the Coronaviridae family in the Nidovirales order. Corona represents crown-like spikes on the outer surface of the virus; thus, it was named as a coronavirus. Coronaviruses are minute in size (65–125 nm in diameter) and contain a single-stranded RNA as a nucleic material, size ranging from 26 to 32kbs in length (Fig. 1). The subgroups of coronaviruses family are alpha (α), beta (β), gamma (γ) and delta (δ) coronavirus. The severe acute respiratory syndrome coronavirus (SARS-CoV), H5N1 influenza A, H1N1 2009 and Middle East respiratory syndrome coronavirus (MERS-CoV) cause acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) which leads to pulmonary failure and result in fatality. These viruses were thought to infect only animals until the world witnessed a severe acute respiratory syndrome (SARS) outbreak caused by SARS-CoV, 2002 in Guangdong, China. Only a decade later, another pathogenic coronavirus, known as Middle East respiratory syndrome coronavirus (MERS-CoV) caused an endemic in Middle Eastern countries.

Recently at the end of 2019, Wuhan an emerging business hub of China experienced an outbreak of a novel coronavirus that killed more than eighteen hundred and infected over seventy thousand individuals within the first fifty days of the epidemic. This virus was reported to be a member of the β group of coronaviruses. The novel virus was named as Wuhan coronavirus or 2019 novel coronavirus (2019-nCov) by the Chinese researchers. The International Committee on Taxonomy of Viruses (ICTV) named the virus as SARS-CoV-2 and the disease as COVID-19,,. In the history, SRAS-CoV (2003) infected 8098 individuals with mortality rate of 9%, across 26 contries in the world, on the other hand, novel corona virus (2019) infected 120,000 induviduals with mortality rate of 2.9%, across 109 countries, till date of this writing. It shows that the transmission rate of SARS-CoV-2 is higher than SRAS-CoV and the reason could be genetic recombination event at S protein in the RBD region of SARS-CoV-2 may have enhanced its transmission ability. In this review article, we discuss the origination of human coronaviruses briefly. We further discuss the associated infectiousness and biological features of SARS and MERS with a special focus on COVID-19.

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–[3]. 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–[12], 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 host, initial infection occurs at epithelia of Harderian gland, trachea, lungs, and air sacs. The virus then moves to the kidney and urogenital tract, to establish systemic infection [33, 35]. In this regard, the severity and clinical features of IB depend on the organ or system involved. Infection of the respiratory system may result in clinical signs such as gasping, sneezing, tracheal rales, listlessness, and nasal discharges. Affected birds appeared listless and dull with ruffled feathers (Figure 1). Other signs may include weight loss and huddling of birds together under a common heat source.

Other clinical outcomes associated with IB infection include frothy conjunctivitis, profuse lacrimation, oedema, and cellulitis of periorbital tissues. Infected birds may also appear lethargic, with evidence of dyspnoea and reluctance to move. Nephropathogenic IBV strains are most described in broiler-type chickens. Clinical signs include depression, wet droppings, and excessive water intake. Infection of reproductive tract is associated with lesions of the oviduct, leading to decreased egg production and quality. Eggs may appear misshapen, rough-shelled, or soft with watery egg yolk (Figure 2). Unless effective measures are instituted, decline in egg production does not return to normal laying, thus contributing to high economic loss [1, 37].

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).

Avian coronavirus is the main representative of genus Gammacoronavirus, family Coronaviridae, and order Nidovirales. Within the avian coronavirus group, the infectious bronchitis virus (IBV) is among the most researched. This virus is known to cause an important disease that incurs a high economic loss in the poultry industry despite an ongoing vaccination program. It causes respiratory disease while also affecting the kidneys and reproductive tract through viremia with a severity that differs depending on serotypes. Mutations and recombination have produced a high genetic diversity of the virus. In addition, vaccinations performed in the farm setting can influence the evolution of the virus. Many serotypes of IBV are often not cross-protective. Mismatching between the circulating strain and the administered vaccine may contribute to vaccination failure. Ubiquitous IBV and IBV-like viruses have also been found in species other than chicken, such as in peafowl, guinea fowl, partridge, waterfowl, and teal. This finding strengthens the possibility that IBV may have a wider range of hosts than previously thought. Despite this, data relating to IBV in Indonesia is still limited to poultry. Studies of diseases on endemic species are valuable for the conservation effort, yet are rarely conducted.

The Eclectus parrot (Eclectus roratus) is a sexually dichromatic parrot native to a part of Eastern Indonesia and Northern Australia. It is classified as protected in Indonesia according to Government Decree Number 7, Year 1999 and Constitution Number 5, Year 1990. Visually captivating, with both male and female showing radically different plumage, the Eclectus parrot is naturally talkative and popular as a pet. However, there has been limited information about viral diseases among Eclectus parrots. The latest finding on coronavirus in parrots was in 2006 when a virus distinct from IBV was found in the green-cheeked Amazon parrot. Understanding viral diseases in Eclectus parrots may be beneficial for the conservation effort and may provide additional information about viral diseases in birds.

There is limited information as to whether avian coronaviruses cause diseases in Psittacine birds; therefore, information about the presence of this virus among parrots might be valuable for the conservation effort of endemic birds and the poultry industry, which is robust in Indonesia. This study aimed to determine the presence of and to characterize avian coronavirus isolated from Eclectus parrots reared by an Indonesian local bird breeder.

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.

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.

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.

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.

The influenza virus has been in existence for centuries and has been constantly infecting both humans and animals (including birds). The avian influenza (AI) virus (also called avian flu or bird flu virus) is a subtype that causes contagious respiratory disease mainly in birds. Wild waterfowls, especially ducks, are natural reservoirs and can carry the virus without manifesting symptoms of the disease and spread the virus over great distances. Domesticated poultry are also susceptible to avian flu and can cause varying symptoms ranging from reduced egg production to rapid death. The severe form of the disease is called "highly pathogenic avian influenza" (sometimes abbreviated as HPAI) and is associated with near 100% mortality rates among domesticated birds. AI has become endemic in several parts of Asia and it is believed that this is a result of unregulated poultry rearing practices in rural areas of developing countries. This is of concern because such birds often live in close proximity to humans and this increases the chance of genetic re-assortment between avian and human influenza viruses which may produce a mutant strain that is easily transmitted between humans.

In the past, avian influenza viruses have rarely caused severe disease in humans. However, in Hong Kong during 1997, a highly pathogenic strain of avian influenza of H5N1 subtype crossed from birds to humans who were in direct contact with diseased birds during an avian influenza outbreak among poultry. The cross-infection was confirmed by molecular studies which showed that the genetic makeup of the virus in humans were identical to those found in poultry. The H5N1 virus caused severe illness and high mortality among humans: among 18 persons who were infected, 6 died. The outbreak ended after authorities slaughtered Hong Kong's entire stock of 1.5 million poultry. Since then, AI among birds has been reported all over the world and one of the factors responsible for the spread is the trans-oceanic and trans-continental migration of wild birds. Most deaths from AI have occurred in Indonesia to date and nearly all of the human cases resulted from close contact with infected birds. However, there has been a reported cluster of plausible human-to-human transmission of the H5N1 virus within an extended family in the village of Kubu Sembelang in north Sumatra, Indonesia, in May 2006.

Strains of influenza virus are classified into subtypes by their protein coat antigens, namely haemagglutin (HA) and neuramidase (NA). Of the 15 HA subtypes known, H1, H2 and H3 are known to have circulated among humans in the past century and hence, most people have gained immunity to interrupt the transmission of the virus. However, the H5N1 strain is unfamiliar to most humans and our low herd immunity to it poses a pandemic threat. There are thought to be three pre-requisites for a viral pandemic to occur: (1) the infectious strain is a new virus subtype which the population has little or no herd immunity; (2) the virus is able to replicate and cause serious illness and (3) the virus has the ability to be transmitted efficiently from human to human. The H5N1 virus satisfies the first two pre-requisites of a pandemic but has not developed the ability to be transmitted easily from human to human, yet.

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.

In 2003, the Chinese population was infected with a virus causing Severe Acute Respiratory Syndrome (SARS) in Guangdong province. The virus was confirmed as a member of the Beta-coronavirus subgroup and was named SARS-CoV,. The infected patients exhibited pneumonia symptoms with a diffused alveolar injury which lead to acute respiratory distress syndrome (ARDS). SARS initially emerged in Guangdong, China and then spread rapidly around the globe with more than 8000 infected persons and 776 deceases. A decade later in 2012, a couple of Saudi Arabian nationals were diagnosed to be infected with another coronavirus. The detected virus was confirmed as a member of coronaviruses and named as the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The World health organization reported that MERS-coronavirus infected more than 2428 individuals and 838 deaths. MERS-CoV is a member beta-coronavirus subgroup and phylogenetically diverse from other human-CoV. The infection of MERS-CoV initiates from a mild upper respiratory injury while progression leads to severe respiratory disease. Similar to SARS-coronavirus, patients infected with MERS-coronavirus suffer pneumonia, followed by ARDS and renal failure.

Recently, by the end of 2019, WHO was informed by the Chinese government about several cases of pneumonia with unfamiliar etiology. The outbreak was initiated from the Hunan seafood market in Wuhan city of China and rapidly infected more than 50 peoples. The live animals are frequently sold at the Hunan seafood market such as bats, frogs, snakes, birds, marmots and rabbits. On 12 January 2020, the National Health Commission of China released further details about the epidemic, suggested viral pneumonia. From the sequence-based analysis of isolates from the patients, the virus was identified as a novel coronavirus. Moreover, the genetic sequence was also provided for the diagnosis of viral infection. Initially, it was suggested that the patients infected with Wuhan coronavirus induced pneumonia in China may have visited the seafood market where live animals were sold or may have used infected animals or birds as a source of food. However, further investigations revealed that some individuals contracted the infection even with no record of visiting the seafood market. These observations indicated a human to the human spreading capability of this virus, which was subsequently reported in more than 100 countries in the world. The human to the human spreading of the virus occurs due to close contact with an infected person, exposed to coughing, sneezing, respiratory droplets or aerosols. These aerosols can penetrate the human body (lungs) via inhalation through the nose or mouth (Fig. 2),,,.

Influenza A virus (IAV) has caused significant morbidity and mortality globally in humans, with an estimated 14 pandemics that have occurred since the 1500s.1 Wild aquatic birds are well known to be the natural reservoirs for IAV subtypes harbouring H1–H16 subtypes,2, 3, 4 with the exception of H17 and H18 subtypes that were recently discovered in bats.5, 6 The phylogenetic relationships of all IAV subtypes are displayed in Fig. 1. In addition to its natural reservoir species, influenza viruses infect a wide range of hosts including canids, equids, humans and swine.2 IAVs’ ability to generate novel gene constellations through reassortment between subtypes poses a risk for immune escape in these new hosts.7 Furthermore, IAV undergoes rapid genetic and antigenic evolution, which makes vaccination control difficult in humans and other domestic species.

In addition to human pandemics that have emerged from avian and swine hosts, there are also repeated spillover events from domesticated animals, primarily poultry and swine, that pose a significant threat to human health.8, 9, 10, 11, 12, 13, 14 Direct transmission of IAV from a wild avian source to humans is rare, as there has only been a single report of laboratory‐confirmed human infection with H5N1 contracted through close contact with dead and infected wild swan in Azerbaijan.15 However, there is serological evidence of H5N1 infection among Alaskan hunters who handled dead wild avian species,16 indicating that exposure to IAVs from wild birds through close contact can potentially cause infection. More notably, viral genes that are similar to the 1918‐like H1N1 avian virus were recently detected in the influenza gene pools of wild birds, raising the potential for the re‐emergence of a 1918‐like pandemic virus.17 Furthermore, due to increasing human encroachment of wildlife habitats, the potential of a wild‐source threat becomes more relevant, as is seen with the emergence of other pathogens such as human immunodeficiency virus (HIV), severe acute respiratory syndrome coronavirus and the more recent Zaire‐variant Ebola virus in Western Africa.18, 19, 20, 21

In this review, we discuss the current knowledge of ecological and molecular determinants responsible for interspecies transmission of IAV, with specific focus on avian‐derived influenza subtypes involved in zoonotic and epizootic transmission to other hosts (see Fig. 2).

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.

The virus isolate used in this study was IRFIBV32 (GenBank: HQ123359.1). It was obtained from Shiraz Veterinary University and was propagated two times in 9- to 11-day-old embryonated chicken eggs. The embryo lethal dose (ELD50) was calculated according to the Reed and Muench formula.

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.

Developing RT-PCR using vaccinal and reference strains of IBV and NDV. The specificity of duplex-RT-PCR was shown using IB88 and 793/B strains of IBV and two standard strains of NDV. The duplex-RT-PCR products visualize by gel electrophoresis was 433 bp for IBV and 121 bp for NDV (Fig. 1).

Application of developed duplex-RT-PCR for detection and differentiation of IBV and NDV in clinical samples. The applicability of developed duplex-RT-PCR assay for detection and differentiation of IBV and NDV in the diagnosis was validated examining 12 clinical samples as showed in Fig. 2. Among five positive clinical samples belonged to five different broiler farms, three farms were infected with only one virus and two farms were co-infected with IBV and NDV.

LPAIV H7N9 was identified as a newly emerging zoonotic pathogen in early 2013. It has caused since then a total of 680 cases of zoonotic infection, with a case-fatality rate of about 20%, principally in adult and elderly individuals. With an incubation time of 2–8 days, H7N9 virus infection can progress from initial symptoms of high fever and other influenza-like signs to more severe lower respiratory tract infection, respiratory distress and associated complications. Exposure to infected poultry is considered the primary risk factor for human infection. A total of 556 outbreaks have been reported in domestic poultry, including chickens, ducks, geese, pigeons and pheasants, largely concurrently to zoonotic cases of infection (Table 1). A few cases were reported in wild bird species. Because of their low pathogenic nature, H7N9 viruses typically cause asymptomatic or mild infections in birds.

Most animal outbreaks and zoonotic cases of low pathogenic avian influenza H7N9 virus infection occurred in mainland China, while imported zoonotic cases were identified in Canada and Malaysia (Fig. 1). The first epidemic of H7N9 virus infection in poultry peaked in April 2013 soon after the first identification of the virus as a cause of a zoonotic case of infection. Epidemics subsequently re-occurred in winter 2014 and 2015, with the highest reported numbers of animal outbreaks and zoonotic cases of infection during the months of January–February of each year.

LPAIV H7N9, in contrast to most other avian influenza viruses, can bind to the cellular receptors used by seasonal influenza viruses,. This ability is associated with one or two specific amino-acids in the hemagglutinin glycoprotein. Because seasonal influenza viruses and LPAIV H7N9 peak coincidentally during the winter months, they may co-infect an individual and subsequently reassort. This may give rise to a transmissible variant, against which the human population has little pre-existing immunity, and may be at the origin of a new influenza pandemic. Strict monitoring and isolation measures are therefore essential to limit the risk of seasonal influenza and reassortment in individuals with zoonotic H7N9 virus infection.

Coronaviruses (CoVs) comprise a family under the order Nidovirales (family Coronaviridae) and infect a wide variety of mammals and birds. The course of infection varies greatly from asymptomatic to severe disease, depending on the host and virus species in question. The genome of CoVs is one of the largest (25–32 kb) viral RNA-genomes. Based on phylogenetic analysis, the CoVs are divided into four different genera: Alpha-, Beta-, Gamma-, and Deltacoronavirus. The alpha- and betacoronaviruses are carried by mammals, whereas the gamma- and deltacoronaviruses mainly infect birds, with few exceptions. The large genomes, infidelity of the RNA-dependent RNA polymerase, and high frequency of homologous RNA recombination are the main factors contributing to the high genetic diversity of CoVs [4–6].

The first CoV, Infectious bronchitis virus (IBV), was identified in 1937. IBV mainly infects chickens, but may infect other bird species as well. IBV is highly contagious and affects the respiratory tract, gut, kidney, and reproductive systems, causing substantial economic losses in the poultry industry. Despite the global distribution of IBV, poultry in Finland remained free of clinical cases until April 2011 after which outbreaks involving several CoV genotypes have occurred in Southern Finland.

The first human CoVs were identified in 1960s [10–12]. The human CoVs cause generally mild to moderate upper respiratory tract infections [13–15]. In 2003, a novel highly pathogenic betacoronavirus emerged in China, causing severe disease characterized by acute respiratory distress and it became known as severe acute respiratory syndrome (SARS)-CoV. The emergence of SARS-CoV inspired virologists to more explore the highly divergent group of coronaviruses and their hosts, leading to the identification of a rapidly growing number of CoV species particularly in bats. More recently, another highly pathogenic betaCoV infecting humans, the Middle East Respiratory Syndrome (MERS) CoV emerged in 2012 with a case fatality rate of over 40%.

Migratory birds have the ability to facilitate the dispersion of microorganisms with zoonotic potential. Wild birds have been associated with the ecology and dispersal of at least West Nile virus, tick-borne encephalitis virus, influenza A virus (IAV) and Newcastle disease virus (NDV) [19–21]. Since the discovery of IBV in 1937, it remained the only known Gammacoronavirus for over 50 years, but the number has increased dramatically during the last 10 years. Thereafter, representatives of the genera Gamma- and Deltacoronavirus have been isolated from both wild and domestic birds including species from the order Anseriformes, Pelecaniformes, Ciconiiformes, Galliformes, Columbiformes, and Charadriiformes [22–24]. In this report we provide a description of CoV species circulating in wild birds in Finland. Altogether 939 samples representing 61 different bird species were collected during 2010–2013 and examined for the presence of CoV RNA.

Infectious bronchitis (IB) is an acute, highly contagious respiratory, and urogenital disease caused by infections bronchitis virus (IBV). The IBV genome consists of a positive-stranded RNA of 27.6 kb in length, and the virus belongs to the Gammacoronavirus genus (Coronaviridae family, Nidovirales order; Cavanagh et al., 1992). The disease, which affects chickens of all ages, poses a major economic threat to the worldwide poultry industry because of poor weight gain and lost feeding efficiency in broilers, and reduced egg numbers and quality in egg-laying birds (Yu et al., 2001; Xu et al., 2007; Jackwood, 2012).

Currently, the main method of protecting chickens from IB is vaccination with both live and inactivated vaccines (Zhao et al., 2015). However, effective vaccination is undermined by rapidly acquired genetic changes in IBV (e.g., gene insertion, mutation, deletion, and reconstruction; Dolz et al., 2008; Kuo et al., 2010). Additionally, immunity against IBV affords a low degree of cross protection between different IBV serotypes (Cowen and Hitchner, 1975), thus confirming the results of molecular epidemiology studies on IBV (Han et al., 2011; Li et al., 2012). Because of the inaccuracy of the coronavirus RNA-dependent RNA polymerase and high frequency of homologous RNA recombination, the emergence of new variant strains, genotypes, and serotypes of IBV is continuously reported (Cavanagh et al., 1986). Existing vaccines for IB no longer provide protection and they tend to be ineffective against the epidemic IBV strains when new variant IBV isolates emerge or when new serotypes appear (Sun et al., 2011). Therefore, screening new live-attenuated vaccine strains based on new isolates is necessary to protect chickens against the common epidemic IBV strains.

A predominant IBV type, QX-like IBV, has been circulating in China since 1998 when the first variant of this type was reported (Wang et al., 1998; Zhao et al., 2014). Over time, we have seen a sustained increase in the QX-like genotype in China (from 11.7 to nearly 70% at present; Zhao et al., 2016). Concurrently, there have been increasing reports of QX-like cases in many other countries (Thailand, Zimbabwe, Korea, Denmark, France, Germany, Russia, Spain, and UK), where the viruses involved share sequence similarities with QX-like viruses (Domanskablicharz et al., 2006; Worthington and Jones, 2006; Worthington et al., 2008; Valastro et al., 2010; Krapež et al., 2011; Abro et al., 2012; Amin et al., 2012; Mo et al., 2013). However, since the first TW-like domestic strain CK/CH/LSD/05I was isolated in the Shandong Province of China, an increasing number of TW-like strains have also been isolated in mainland China (Liu et al., 2008), as confirmed by our previous findings (Xu et al., 2016).

Here, we determined the pathogenicity of the TW-like IBV GD strain. We also evaluated the protective efficacy induced by QX-like strain JS against the TW-like field strain GD by observing the clinical signs and gross lesions, and by analysis of the virus distribution, virus shedding, and tracheal ciliary activity in experimental chickens. Our results suggest that TW-like IBV GD is highly virulent, and that QX-like JS may provide effective vaccine protection against TW-like IBV viruses.

Amplification was performed on original swab samples and allantoic fluids. None of these samples was positive for the 3’-UTR of the avian coronavirus (UTR11−/41+). Three out of 10 swab samples were positive for the N gene coronavirus, but none of them was positive for the S1 IBV gene. However, four out of 10 samples of allantoic fluid tested were positive for the coronavirus N gene. Of the two that tested positive for the S1 gene of IBV, only one of them, which was designated as parrot/Indonesia/BX9/16, was able to be further sequenced. These results are presented in Table-3.