Pathogenicity of turkey coronavirus in turkeys and chickens

Preparation of a new monoclonal antibody against nucleocapsid protein of swine acute diarrhea syndrome coronavirus and identification of its linear antigenic epitope

Swine acute diarrhea syndrome coronavirus (SADS-CoV), which causes severe diarrhea in newborn piglets, was first identified in Southern China in 2017. Since the Nucleocapsid (N) protein in SADS-CoV is highly conserved and plays a key role in virus replication, it is often used as a target protein in scientific research. In this study, the N protein of SADS-CoV was successfully expressed, and a new monoclonal antibody (mAb), 5G12, against the protein was generated successfully. The mAb 5G12 can be used to detect SADS-CoV strains by indirect immunofluorescence assay (IFA) and western blotting. The mAb 5G12 epitope was located to amino acids 11 EQAESRGRK 19 by evaluating the antibody for reactivity with a series of truncated N protein segments. The biological information analysis showed that the antigenic epitope had a high antigenic index and conservation. This study will help further understand the protein structure and function of SADS-CoV and in the establishment of specific SADS-CoV detection methods.

Diversity of gammacoronaviruses and deltacoronaviruses in wild birds and poultry in Russia

Coronaviruses of the genera Gammacoronavirus and Deltacoronavirus are globally widespread and circulate primarily in wild and domestic birds. Prior studies have established frequently occurring crossover events from avian to mammalian reservoirs. However, there is limited understanding of the diversity and geographical distribution of coronaviruses among birds. In this study, the surveillance of coronaviruses in birds in Russia during 2020 revealed the presence of coronaviruses in 12% of samples from birds. Targeted NGS approach was used for the evaluation of genetic diversity based on RdRp gene. While gammacoronviruses were found in both wild birds and poultry, deltacoronaviruses were found in wild birds only and represent the first detections for Russia. A number of cases with the simultaneous detection of gamma- and deltacoronaviruses in one bird was reported. The results of this study highlight the importance of further research concerning the spread and diversity of coronaviruses among birds within and migrating throughout the territory of Russia across the globe.

Targeted detection and molecular epidemiology of turkey coronavirus spike gene variants in turkeys and chickens

Turkey coronavirus (TCoV) is a member of the Avian coronavirus species with infectious bronchitis virus (IBV), which is considered to be the source of TCoV. These 2 viruses are highly similar in all regions of their genomes, except for the spike gene, which is necessary for virus attachment. Although TCoV causes severe enteric disease in turkey poults, it does not cause clinical disease in chickens. However, considering that TCoV can infect chickens, it is important to distinguish TCoV from IBV in chickens. This is particularly true for chickens that are housed near turkeys and thus might be infected with TCoV and serve as a silent source of TCoV for turkeys. We developed and validated a real-time PCR assay to detect the spike gene of TCoV and sequenced a portion of this gene to evaluate the molecular epidemiology of TCoV infections associated with a commercial turkey premises in the United States in 2020-2021. We identified natural infections of TCoV in chickens, and based on the molecular epidemiology of the viruses detected, these chickens may have served as a source of infection for the commercial turkey premises located nearby.

Effects of Plant Metabolites on the Growth of COVID-19 (Coronavirus Disease-19) Including Omicron Strain

According to recent reports out of India, a new strain of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) B1.1.529 Omicron virus has emerged. In comparison to the Wuhan (WHU) strain and the delta variant, this variant showed a far stronger effect on the angiotensin converting enzyme2 (ACE2) receptor. There are several medicinal compounds in plant metabolites, and their diverse chemical structures make them ideal for the treatment of serious illnesses. It's possible that some of these could be useful alternative pharmaceuticals, as well as a starting point for the repurposing of existing medications and new chemical discoveries. SARS-CoV-2 infection triggered a worldwide epidemic of the severe acute respiratory syndrome (SARS). There have been trials for different therapies for SARS-CoV-2 and so also there are recent announcements of extensive research into the development of viable medicines for this global health calamity. After a thorough examination of plant-derived treatments for COVID-19, investigators in the current study decided to focus on plant-derived secondary metabolites (PSMs). According to some researchers, new MDR (Multi-Drug Resistant) antibiotics may one day be developed due to the adaptability of secondary metabolites. Identifying plant metabolites that can treat a wide range of viral infections was one of the study's aims. Many natural medications that could be recommended for the treatment of COVID-19 were discovered as a result of this research, including remedies from plant families, viral candidates that are susceptible, antiviral assays, and mechanisms of therapeutic action. The findings of this study will inspire further research and speed up the development of new antiviral plant-based medications.

Recombinant Protein Technology in the Challenging Era of Coronaviruses

Coronaviruses have caused devastation in both human and animal populations, affecting both health and the economy. Amidst the emergence and re-emergence of coronaviruses, humans need to surmount the health and economic threat of coronaviruses through science and evidence-based approaches. One of these approaches is through biotechnology, particularly the heterologous production of biopharmaceutical proteins. This review article briefly describes the genome, general virion morphology, and key structural proteins of different coronaviruses affecting animals and humans. In addition, this review paper also presents the different systems in recombinant protein technology such as bacteria, yeasts, plants, mammalian cells, and insect/insect cells systems used to express key structural proteins in the development of countermeasures such as diagnostics, prophylaxis, and therapeutics in the challenging era of coronaviruses.

BDCNet: multi-classification convolutional neural network model for classification of COVID-19, pneumonia, and lung cancer from chest radiographs

Globally, coronavirus disease (COVID-19) has badly affected the medical system and economy. Sometimes, the deadly COVID-19 has the same symptoms as other chest diseases such as pneumonia and lungs cancer and can mislead the doctors in diagnosing coronavirus. Frontline doctors and researchers are working assiduously in finding the rapid and automatic process for the detection of COVID-19 at the initial stage, to save human lives. However, the clinical diagnosis of COVID-19 is highly subjective and variable. The objective of this study is to implement a multi-classification algorithm based on deep learning (DL) model for identifying the COVID-19, pneumonia, and lung cancer diseases from chest radiographs. In the present study, we have proposed a model with the combination of Vgg-19 and convolutional neural networks (CNN) named BDCNet and applied it on different publically available benchmark databases to diagnose the COVID-19 and other chest tract diseases. To the best of our knowledge, this is the first study to diagnose the three chest diseases in a single deep learning model. We also computed and compared the classification accuracy of our proposed model with four well-known pre-trained models such as ResNet-50, Vgg-16, Vgg-19, and inception v3. Our proposed model achieved an AUC of 0.9833 (with an accuracy of 99.10%, a recall of 98.31%, a precision of 99.9%, and an f1-score of 99.09%) in classifying the different chest diseases. Moreover, CNN-based pre-trained models VGG-16, VGG-19, ResNet-50, and Inception-v3 achieved an accuracy of classifying multi-diseases are 97.35%, 97.14%, 97.15%, and 95.10%, respectively. The results revealed that our proposed model produced a remarkable performance as compared to its competitor approaches, thus providing significant assistance to diagnostic radiographers and health experts.

Update on the Phylodynamics of SADS-CoV

Coronaviruses are known to be harmful and heterogeneous viruses, able to infect a large number of hosts. Among them, SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alphacoronavirus), or SeA-CoV (Swine Enteric Alphacoronavirus), is the most recent Alphacoronavirus discovered, and caused several outbreaks reported in Chinese swine herds between late 2016 and 2019. We performed an upgraded phylodinamic reconstruction of SADS-CoV based on all whole genomes available on 21 June 2021. Results showed a very close relationship between SADS-CoV and HKU2-like CoV, which may represent the evolutionary intermediate step towards the present SADS-CoV. The direct progenitor of SADS-CoV is so far unknown and, although it is well known that horseshoe bats are reservoirs for Rhinolophus bat coronavirus HKU2-like (HKU2-like CoVs), the transmission path from bats to pigs is still unclear. The discrepancies in the phylogenetic position of rodent CoV, when different molecular markers were considered, corroborate the recombination hypothesis, suggesting that wild rats, which are frequent in farms, may have played a key role. The failure of the attempt at molecular dating, due to the lack of a clock signal, also corroborates the occurrence of a recombination event hypothesis. Zoonotic infections originating in wildlife can easily become a significant threat for human health. In such a context, due to the high recombination and cross-species capabilities of Coronavirus, SADS-CoV represents a possible high-risk pathogen for humans which needs a constant molecular monitoring.

Poult Enteritis and Mortality Syndrome in Turkey Poults: Causes, Diagnosis and Preventive Measures

Simple Summary

The poult enteritis and mortality syndrome (PEMS) causes severe economic losses in turkeys. Several agents were described to be associated with the PEMS; however, a specific etiological agent(s) has not been identified. The diagnosis of PEMS is still a huge challenge for several reasons: (1) no specific clinical signs or pathognomonic lesions, (2) isolation of some enteric viruses still difficult, (3) the pathogenicity of several enteric viruses in turkeys is not fully understood, (4) PEMS is an interaction between several known and might be unknown agents and (5) opportunistic microorganisms also have a role in the pathogenesis of PEMS. Both electron microscopy and molecular techniques can be used for diagnosis of PEMS and might help to discover unknown causes. Until now, no specific vaccines against enteric viruses associated with PEMS. However, biosecurity, maintaining a healthy gut and strengthening the immune system of turkey poults using probiotics, prebiotics and/or phytogenic substances are crucial factors to prevent and/or reduce losses of PEMS in turkeys. This review is a call for scientists to perform further research to investigate the real cause(s) of PEMS and to develop a preventive strategy against it.

Abstract

Poult enteritis and mortality syndrome (PEMS) is one of the most significant problem affecting turkeys and continues to cause severe economic losses worldwide. Although the specific causes of PEMS remains unknown, this syndrome might involve an interaction between several causative agents such as enteropathogenic viruses (coronaviruses, rotavirus, astroviruses and adenoviruses) and bacteria and protozoa. Non-infectious causes such as feed and management are also interconnected factors. However, it is difficult to determine the specific cause of enteric disorders under field conditions. Additionally, similarities of clinical signs and lesions hamper the accurate diagnosis. The purpose of the present review is to discuss in detail the main viral possible causative agents of PEMS and challenges in diagnosis and control.

Pathogenic evaluation of a turkey coronavirus isolate (TCoV NC1743) in turkey poults for establishing a TCoV disease model

Turkey coronavirus (TCoV) can cause a highly contagious enteric disease in turkeys with severe economic losses in the global turkey industry. To date, no commercial vaccines are available for control of the disease. In the present study, we isolated a field strain (NC1743) of TCoV and evaluated its pathogenicity in specific-pathogen-free (SPF) turkey poults to establish a TCoV disease model. The results showed that the TCoV NC1743 isolate was pathogenic to turkey poults with a minimal infectious dose at 10⁶ EID₅₀/bird. About 50 % of one-day-old SPF turkeys infected with the virus's minimal infectious dose exhibited typical enteric disease signs and lesions from 6 days post-infection (dpi) to the end of the experiment (21 dpi). In contrast, fewer than 20 % of older turkeys (1- or 2-week-old) infected with the same amount of TCoV displayed enteric disease signs, which disappeared after 15-18 dpi. Although all infected turkeys, regardless of age, shed TCoV, the older turkeys shed less virus than the younger birds, and 50 % of the 2-week-old birds even cleared the virus at 21 dpi. Furthermore, the viral infection caused day-old turkeys more body-weight-gain reduction than older birds. The overall data demonstrated that the TCoV NC1743 isolate is a highly pathogenic strain and younger turkeys are more susceptible to TCoV infection than older birds. Thus, one-day-old turkeys infected with the minimal infectious dose of TCoV NC1743 could be used as a TCoV disease model to study the disease pathogenesis, and the TCoV NC1743 strain could be used as a challenge virus to evaluate a vaccine protective efficacy.

Virology features of a family cluster of SARS-CoV-2 infections in Shanghai, China

The global spread of SARS-CoV-2 is currently continuing, and the World Health Organization has announced the risk assessment of the viruses as high. In this study, we analyzed virology features of SARS-CoV-2 causing a family cluster outbreak. Among the six family members, five have been laboratory-confirmed infection of SARS-CoV-2 viruses. A total of five SARS-CoV-2 viruses have been isolated from the nasopharyngeal swabs. The complete genome of the viruses exhibited 100% nucleotide identity with each other. Only two nucleotide differences have been observed between genomes of the isolated viruses and the HCoV/Wuhan/ IVDC-HB-01/2019 strain. Therefore, SARS-CoV-2 has been confirmed as the causation of the family cluster infections.

A Computational Framework for Pattern Detection on Unaligned Sequences: An Application on SARS-CoV-2 Data

The exponential growth of genome sequences available has spurred research on pattern detection with the aim of extracting evolutionary signal. Traditional approaches, such as multiple sequence alignment, rely on positional homology in order to reconstruct the phylogenetic history of taxa. Yet, mining information from the plethora of biological data and delineating species on a genetic basis, still proves to be an extremely difficult problem to consider. Multiple algorithms and techniques have been developed in order to approach the problem multidimensionally. Here, we propose a computational framework for identifying potentially meaningful features based on k-mers retrieved from unaligned sequence data. Specifically, we have developed a process which makes use of unsupervised learning techniques in order to identify characteristic k-mers of the input dataset across a range of different k-values and within a reasonable time frame. We use these k-mers as features for clustering the input sequences and identifying differences between the distributions of k-mers across the dataset. The developed algorithm is part of an innovative and much promising approach both to the problem of grouping sequence data based on their inherent characteristic features, as well as for the study of changes in the distributions of k-mers, as the k-value is fluctuating within a range of values. Our framework is fully developed in Python language as an open source software licensed under the MIT License, and is freely available at https://github.com/BiodataAnalysisGroup/kmerAnalyzer.

COVID-19 and future pandemics: a global systems approach and relevance to SDGs

Background

The COVID-19 pandemic is adversely impacting modern human civilization. A global view using a systems science approach is necessary to recognize the close interactions between health of animals, humans and the environment.

Discussion

A model is developed initially by describing five sequential or parallel steps on how a RNA virus emerged from animals and became a pandemic: 1. Origins in the animal kingdom; 2. Transmission to domesticated animals; 3. Inter-species transmission to humans; 4. Local epidemics; 5. Global spread towards a pandemic. The next stage identifies global level determinants from the physical environments, the biosphere and social environment that influence these steps to derive a generic conceptual model. It identifies that future pandemics are likely to emerge from ecological processes (climate change, loss of biodiversity), anthropogenic social processes (i.e. corporate interests, culture and globalization) and world population growth. Intervention would therefore require modifications or dampening these generators and prevent future periodic pandemics that would reverse human development.

Addressing issues such as poorly planned urbanization, climate change and deforestation coincide with SDGs such as sustainable cities and communities (Goal 11), climate action (Goal 13) and preserving forests and other ecosystems (Goal 15). This will be an added justification to address them as global priorities. Some determinants in the model are poorly addressed by SDGs such as the case of population pressures, cultural factors, corporate interests and globalization. The overarching process of globalization will require modifications to the structures, processes and mechanisms of global governance. The defects in global governance are arguably due to historical reasons and the neo-liberal capitalist order. This became evident especially in the aftermath of the COVID-19 when the vaccination roll-out led to violations of universal values of equity and right to life by some of the powerful and affluent nations.

Summary

A systems approach leads us to a model that shows the need to tackle several factors, some of which are not adequately addressed by SDGs and require restructuring of global governance and political economy.

Phylo-geo-network and haplogroup analysis of 611 novel coronavirus (SARS-CoV-2) genomes from India

The novel coronavirus (SARS-CoV-2) from Wuhan China discovered in December 2019 has since developed into a global epidemic. Presently, we constructed and analyzed the phylo-geo-network of SARS-CoV-2 genomes from across India to understand the viral evolution in the country. A total of 611 full-length genomes from different states of India were extracted from the EpiCov repository of GISAID initiative on 6 June, 2020. Their alignment with the reference sequence (Wuhan, NCBI accession number NC_045512.2) uncovered 270 parsimony informative sites. Furthermore, 339 genomes were divided into 51 haplogroups. The network revealed the core haplogroup as that of reference sequence NC_045512.2 (Haplogroup A1) with 157 identical sequences present across 16 states. Remaining haplogroups had <10 identical sequences across a maximum of three states. Some states with fewer samples had more haplogroups. Forty-one haplogroups were localized exclusively to any one state. The two most common lineages are B6 and B1 (Pangolin) whereas clade A2a (Covidex) appears to be the most predominant in India. Because the pandemic is still emerging, the observations need to be monitored.

Fibrinogen Dysregulation is a Prominent Process in Fatal Conditions of COVID-19 Infection; a Proteomic Analysis

INTRODUCTION

Molecular pathophysiology of COVID-19 is not completely known. Expression changes in patients' plasma proteins have revealed new information about the disease. Introducing the key targeted plasma protein in fatal conditions of COVID-19 infection is the aim of this study.

METHODS

Significant differentially expressed proteins (DEPs) in the plasma of cases with a fatal condition of COVID-19 were extracted from an original article. These proteins were included in a network via STRING database along with 100 first neighbor proteins to determine central nodes of the network for analyzing.

RESULTS

Queried and added proteins were included in a scale free network. Three hub nodes were identified as critical target proteins. The top queried hub proteins were chains of fibrinogen; Fibrinogen Alpha chain (FGA), Fibrinogen gamma chain (FGG), and Fibrinogen beta chain (FGB), which are related to the coagulation process.

CONCLUSIONS

It seems that fibrinogen dysregulation has a deep impact on the fatality of COVID-19 infection.

Porcine Deltacoronavirus Infection and Transmission in Poultry, United States1

Coronaviruses cause respiratory and gastrointestinal diseases in diverse host species. Deltacoronaviruses (DCoVs) have been identified in various songbird species and in leopard cats in China. In 2009, porcine deltacoronavirus (PDCoV) was detected in fecal samples from pigs in Asia, but its etiologic role was not identified until 2014, when it caused major diarrhea outbreaks in swine in the United States. Studies have shown that PDCoV uses a conserved region of the aminopeptidase N protein to infect cell lines derived from multiple species, including humans, pigs, and chickens. Because PDCoV is a potential zoonotic pathogen, investigations of its prevalence in humans and its contribution to human disease continue. We report experimental PDCoV infection and subsequent transmission among poultry. In PDCoV-inoculated chicks and turkey poults, we observed diarrhea, persistent viral RNA titers from cloacal and tracheal samples, PDCoV-specific serum IgY antibody responses, and antigen-positive cells from intestines.

Pathology of Coronavirus Infections: A Review of Lesions in Animals in the One-Health Perspective

Coronaviruses (CoVs) are worldwide distributed RNA-viruses affecting several species, including humans, and causing a broad spectrum of diseases. Historically, they have not been considered a severe threat to public health until two outbreaks of COVs-related atypical human pneumonia derived from animal hosts appeared in 2002 and in 2012. The concern related to CoVs infection dramatically rose after the COVID-19 global outbreak, for which a spill-over from wild animals is also most likely. In light of this CoV zoonotic risk, and their ability to adapt to new species and dramatically spread, it appears pivotal to understand the pathophysiology and mechanisms of tissue injury of known CoVs within the "One-Health" concept. This review specifically describes all CoVs diseases in animals, schematically representing the tissue damage and summarizing the major lesions in an attempt to compare and put them in relation, also with human infections. Some information on pathogenesis and genetic diversity is also included. Investigating the lesions and distribution of CoVs can be crucial to understand and monitor the evolution of these viruses as well as of other pathogens and to further deepen the pathogenesis and transmission of this disease to help public health preventive measures and therapies.

Novel coronavirus (COVID-19) and its potential G.I. manifestation: A review

The outbreak of the new coronavirus in Wuhan, Chinese Hubei City (COV-2) was also known as COVID-19 and has spread to more than 213 countries, zones or territories worldwide, and is an emergency of international public health with no antiviral drugs or vaccines; and, also, the presencouragement of the disease has become a global public health emergency. This novel coronavirus is now the seventh member of the coronaviridae family, known for infecting humans and showing evidence of causing gastric symptoms, and has the potential to be transmitted through the fecal-oral route according to a new report published online by physicians at Shanghai Jiao Tong University (Gastroenterology. 2020 March 3. doi: 10.1053/j.gastro. 2020.02.054). Here we identify the efforts to compile and disseminate the COVID-19 epidemiological information on Its potential G.I. Demonstration of news media and social networks, and few newspapers recently published. Physicians should know, how GI manifestation discussed in different publications to suspect CORONA virus infection in that patients who does not have any upper and lower respiratory tract symptom and intervein to discuss the disease severity and duration. It will increase the threshold of suspicion of physician toward Covid-19 disease.

3D printing for development of medical equipment amidst coronavirus (COVID-19) pandemic—review and advancements

Background and aims

Coronavirus (COVID-19) has surfaced as a global pandemic and has created an unprecedented global demand for medical equipment. The shortage of onsite workforce, need for social distancing and less time available for sourcing have further made it difficult for the governments and the medical professionals to combat the pandemic. This study’s prime objective is to review the advancements in the area of 3D printing to develop medical equipment and explore the potential of 3D printing in addressing the shortage of medical equipment mainly the personal protective equipment (PPE) amidst COVID-19 pandemic.

Methods

3D printing or additive manufacturing has emerged as a new manufacturing process with tremendous potential to develop complex products in short time with minimal human interventions. The paper summarises 3D printing’s potential to serve the increasing need for medical equipment, mainly personal protective equipment (PPE) and ventilator equipment in the ongoing global COVID-19 pandemic.

Results

The minimum human interventions required to carry out production using 3D printing also make the technology an excellent option to deal with the current situation.

Conclusions

The recommendations and opinions presented in the paper shall act as a stimulant to develop components very critical for the pandemic and help save precious lives globally.

Potential Diagnostic Systems for Coronavirus Detection: a Critical Review

Abstract

Currently there are no effective anti-viral drugs for SARS-CoV-2, so the primary line of defense is to detect infected cases as soon as possible. The high rate of contagion for this virus and the highly nonspecific symptoms of the disease (Coronovirus disease 2019, (Covid-19)) that it causes, such as respiratory symptoms, cough, dyspnea, fever, and viral pneumonia, require the urgent establishment of precise and fast diagnostic tests to verify suspected cases, screen patients, and conduct virus surveillance. Nowadays, several virus detection methods are available for viral diseases, which act on specific properties of each virus or virus family, therefore, further investigations and trials are needed to find a highly efficient and accurate detection method to detect and prevent the outcomes of the disease. Hence, there is an urgent need for more and precise studies in this field. In this review, we discussed the properties of a new generation of coronaviruses (SARS-CoV-2) following routine virus detection methods and proposed new strategies and the use of potential samples for SARS-CoV-2 detection.

Graphical Abstract

Plants Metabolites: Possibility of Natural Therapeutics Against the COVID-19 Pandemic

COVID-19, a disease induced by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2), has been the cause of a worldwide pandemic. Though extensive research works have been reported in recent days on the development of effective therapeutics against this global health crisis, there is still no approved therapy against SARS-CoV-2. In the present study, plant-synthesized secondary metabolites (PSMs) have been prioritized to make a review focusing on the efficacy of plant-originated therapeutics for the treatment of COVID-19. Plant metabolites are a source of countless medicinal compounds, while the diversity of multidimensional chemical structures has made them superior to treat serious diseases. Some have already been reported as promising alternative medicines and lead compounds for drug repurposing and discovery. The versatility of secondary metabolites may provide novel antibiotics to tackle MDR (Multi-Drug Resistant) microbes too. This review attempted to find out plant metabolites that have the therapeutic potential to treat a wide range of viral pathogens. The study includes the search of remedies belonging to plant families, susceptible viral candidates, antiviral assays, and the mode of therapeutic action; this attempt resulted in the collection of an enormous number of natural therapeutics that might be suggested for the treatment of COVID-19. About 219 plants from 83 families were found to have antiviral activity. Among them, 149 plants from 71 families were screened for the identification of the major plant secondary metabolites (PSMs) that might be effective for this pandemic. Our investigation revealed that the proposed plant metabolites can serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development processes to combat COVID-19 and future pandemics caused by viruses. This review will stimulate further analysis by the scientific community and boost antiviral plant-based research followed by novel drug designing.

High throughput and comprehensive approach to develop multiepitope vaccine against minacious COVID-19

The ongoing enigmatic COVID-19 outbreak, first reported from Wuhan, China, on last day of the year 2019, which has spread to 213 countries, territories/areas till 28th April 2020, threatens hundreds of thousands human souls. This devastating viral infection has stimulated the urgent development of viable vaccine against COVID-19 across the research institutes around the globe. The World Health Organization (WHO) has also confirmed that the recent pandemic is causing Public Health Emergency of International apprehension. Moreover, the earlier two pathogenic SARS-CoV and MERS-CoV and many others yet to be identified pose a universal menace. Here, in this piece of work, we have utilized an in silico structural biology and advanced immunoinformatic strategies to devise a multi-epitope subunit vaccine against ongoing COVID-19 infection. The engineered vaccine sequence is adjuvanted with ß-3 defensin and comprised of B-cell epitopes, HTL epitopes and CTL epitopes. This is very likely that the vaccine will be able to elicit the strong immune response. Further, specific binding of the engineered vaccine and immune cell receptor TLR3 was estimated by molecular interaction studies. Strong interaction in the binding groove as well as good docking scores affirmed the stringency of engineered vaccine. The interaction is stable with minimal deviation in root-mean square deviation and root-mean-square fluctuation was confirmed by the molecular dynamics simulation experiment. The immune-simulation by C-ImmSim server, which mimics the natural immune environment, yielded more potent immune response data of B-cells, Th cells, Tc cells and IgG for vaccine. The encouraging data obtained from the various in-silico works indicated this vaccine as an effective therapeutic against COVID-19.

Coronavirus disease - COVID-19: new perceptives towards epidemic to pandemic

The sudden outbreak and uncontrolled spread of the novel coronavirus disease 2019 (COVID-19) has shocked the world to a degree never seen before. Due to the wide spread transmission of the virus, the number of infected cases worldwide has surpassed 16,421,958 and global death toll has spiked up to 6,52,308 from December 2019 to 27 July 2020. The virus has been labelled as a pandemic by the WHO. Virologists have found that this virus outbreak is similar to past outbreaks of viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome that caused severe respiratory syndrome and transmitted rapidly in humans. These single stranded RNA viruses come under the genera of β-coronaviruses which ultimately infect lungs and respiratory tract. Even though the origin, source and intermediate hosts of this virus is unknown, transmittance from human-to-human through various paths has been identified globally. As of today, there are no approved drugs and vaccines. Several clinical trials are being conducted today to evaluate vaccines against the virus. The aim of our present review is to furnish brief details about the statistics, diagnosis, epidemiology, pathogenesis, prevention and treatment of COVID-19 to assist researchers and the society at large to come to grip with the deadly disease.HighlightsCumbersome outbreak of the novel Coronavirus Disease 2019 (COVID-19) became a pandemicAt June 19, 2020, as per WHO report 8,618,787 infected cases and 457,275 dead were recorded globallyMajor spread was found to be human to human transmissionsPeople with positive COVID-19 were infected with severe respiratory syndromeMore animal and clinical studies have to be done to overcome this pandemic.

Potential Drugs and Remedies for the Treatment of COVID-19: a Critical Review

ABSTRACT

COVID-19 disease with a high rate of contagious and highly nonspecific symptoms, is an infectious disease caused by a newly discovered coronavirus. Most people who fall sick with COVID-19 will experience mild to moderate symptoms such as respiratory symptoms, cough, dyspnea, fever, and viral pneumonia and recover without any special cure. However, some others need special and emergency treatment to get rid of this widespread disease. Till now, there are numbers of proposed novel compounds as well as standards therapeutics agent existed for other conditions seems to have efficacy against the 2019-nCoV. Some which are being tested for MERS-CoV and SARS-CoV are validated that could be also efficient against this new coronavirus. However, there are currently no effective specific antivirals or drug combinations introduced for 2019-nCoV specifically that be supported by high-level evidence. The main purpose of this paper is to review typical and ongoing treatments for coronavirus disease including home remedies, herbal medicine, chemical drugs, plasma therapy, and also vaccinies. In this regards, famous herbal medicines and common chemical drugs which are routinely to be prescribed for patients are introduced. Moreover, a section is assigned to the drug interactions and some outdated drugs which have been proved to be inefficient. We hope that this work could pave the way for researchers to develop faster and more reliable methods for earlier treatment of patients and rescue more people.

GRAPHICAL ABSTRACT

Characterization of novel, pathogenic field strains of infectious bronchitis virus (IBV) in poultry in Trinidad and Tobago

Avian coronaviruses, including infectious bronchitis virus (IBV) and turkey coronavirus (TCoV), are economically important viruses affecting poultry worldwide. IBV is responsible for causing severe losses to the commercial poultry sector globally. The objectives of this study were to identify the viruses that were causing outbreaks of severe respiratory disease in chickens in Trinidad and Tobago (T&T) and to characterize the strains. Swab samples were collected from birds showing severe respiratory signs in five farms on the island of Trinidad. Samples were tested for the presence of IBV, as well as avian influenza virus (AIV), Newcastle disease virus (NDV) and avian metapneumovirus (aMPV) by real-time reverse transcription polymerase chain reaction (qRT-PCR). All samples from the five farms tested negative for AIV, NDV and aMPV; however, samples from clinically affected birds in all five of the farms tested positive for IBV. Genetic data revealed the presence of TCoV in chickens on two of the farms. Interestingly, these two farms had never reared turkeys. Phylogenetic analysis showed that IBV S1 sequences formed two distinct clusters. Two sequences grouped with vaccine strains within the GI-1 lineage, whereas three sequences grouped together, but separately from other defined lineages, forming a likely new lineage of IBV. Pairwise comparison revealed that the three unique variant strains within the distinct lineage of IBV were significantly different in their S1 nucleotide coding regions from viruses in the closest lineage (16% difference) and locally used vaccine strains (>20% difference). Results also suggested that one of the samples was a recombinant virus, generated from a recombination event between a Trinidad virus of the GI-1 lineage and a Trinidad virus of the newly defined lineage. Many amino acid differences were also observed between the S1 coding regions of the circulating field and vaccine strains, indicating that the IBV vaccines may not be protective. Vaccine-challenge studies are however needed to prove this.

More effective strategies are required to strengthen public awareness of COVID-19: Evidence from Google Trends

BACKGROUND

The outbreak of coronavirus disease 2019 (COVID-19) has posed stress on the health and well-being of both Chinese people and the public worldwide. Global public interest in this new issue largely reflects people's attention to COVID-19 and their willingness to take precautionary actions. This study aimed to examine global public awareness of COVID-19 using Google Trends.

METHODS

Using Google Trends, we retrieved public query data for terms of "2019-nCoV + SARS-CoV-2 + novel coronavirus + new coronavirus + COVID-19 + Corona Virus Disease 2019" between the 31st December 2019 and the 24th February 2020 in six major English-speaking countries, including the USA, the UK, Canada, Ireland, Australia, and New Zealand. Dynamic series analysis demonstrates the overall change trend of relative search volume (RSV) for the topic on COVID-19. We compared the top-ranking related queries and sub-regions distribution of RSV about COVID-19 across different countries. The correlation between daily search volumes on the topic related to COVID-19 and the daily number of people infected with SARS-CoV-2 was analyzed.

RESULTS

The overall search trend of RSV regarding COVID-19 increased during the early period of observing time and reached the first apex on 31st January 2020. A shorter response time and a longer duration of public attention to COVID-19 was observed in public from the USA, the UK, Australia, and Canada, than that in Ireland and New Zealand. A slightly positive correlation between daily RSV about COVID-19 and the daily number of confirmed cases was observed (P < 0.05). People across countries presented a various interest to the RSV on COVID-19, and public awareness of COVID-19 was different in various sub-regions within countries.

CONCLUSIONS

The results suggest that public response time to COVID-19 was different across countries, and the overall duration of public attention was short. The current study reminds us that governments should strengthen the publicity of COVID-19 nationally, strengthen the public's vigilance and sensitivity to COVID-19, inform public the importance of protecting themselves with enough precautionary measures, and finally control the spread of COVID-19 globally.

More effective strategies are required to strengthen public awareness of COVID-19: Evidence from Google Trends

BACKGROUND

The outbreak of coronavirus disease 2019 (COVID-19) has posed stress on the health and well-being of both Chinese people and the public worldwide. Global public interest in this new issue largely reflects people's attention to COVID-19 and their willingness to take precautionary actions. This study aimed to examine global public awareness of COVID-19 using Google Trends.

METHODS

Using Google Trends, we retrieved public query data for terms of "2019-nCoV + SARS-CoV-2 + novel coronavirus + new coronavirus + COVID-19 + Corona Virus Disease 2019" between the 31^st December 2019 and the 24^th February 2020 in six major English-speaking countries, including the USA, the UK, Canada, Ireland, Australia, and New Zealand. Dynamic series analysis demonstrates the overall change trend of relative search volume (RSV) for the topic on COVID-19. We compared the top-ranking related queries and sub-regions distribution of RSV about COVID-19 across different countries. The correlation between daily search volumes on the topic related to COVID-19 and the daily number of people infected with SARS-CoV-2 was analyzed.

RESULTS

The overall search trend of RSV regarding COVID-19 increased during the early period of observing time and reached the first apex on 31^st January 2020. A shorter response time and a longer duration of public attention to COVID-19 was observed in public from the USA, the UK, Australia, and Canada, than that in Ireland and New Zealand. A slightly positive correlation between daily RSV about COVID-19 and the daily number of confirmed cases was observed (P < 0.05). People across countries presented a various interest to the RSV on COVID-19, and public awareness of COVID-19 was different in various sub-regions within countries.

CONCLUSIONS

The results suggest that public response time to COVID-19 was different across countries, and the overall duration of public attention was short. The current study reminds us that governments should strengthen the publicity of COVID-19 nationally, strengthen the public's vigilance and sensitivity to COVID-19, inform public the importance of protecting themselves with enough precautionary measures, and finally control the spread of COVID-19 globally.

Coronavirus Disease 2019 (COVID-19) pandemic, lessons to be learned!

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported as a worldwide emergency. Due to the extensiveness of spread and death, it has been declared as a pandemic. This review focused on the current pandemic situation and understanding the prevention and control strategies of COVID-19. Data presented here was by April 3, 2020. A total of 1,016,399 cases of COVID-19 with 53,238 deaths was reported from 204 countries and territories including two international conveyances over the world. After China, most of the new cases were from Europe, particularly Italy acting as the source of importation to many of the other countries around the world. China has obtained success by ascribing control strategies against COVID-19. The implementation of China's strategy, as well as the development of a vaccine, may control the pandemic of COVID-19. Further robust studies are required for a clear understanding of transmission parameters, prevention, and control strategies of SARS-CoV-2. This review paper describes the nature of COVID-19 and the possible ways for the effective controlling of the COVID-19 or similar viral diseases that may come in the future.

Convalescent plasma in Covid-19: Possible mechanisms of action

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible of the coronavirus disease 2019 (COVID-19) pandemic. Therapeutic options including antimalarials, antivirals, and vaccines are under study. Meanwhile the current pandemic has called attention over old therapeutic tools to treat infectious diseases. Convalescent plasma (CP) constitutes the first option in the current situation, since it has been successfully used in other coronaviruses outbreaks. Herein, we discuss the possible mechanisms of action of CP and their repercussion in COVID-19 pathogenesis, including direct neutralization of the virus, control of an overactive immune system (i.e., cytokine storm, Th1/Th17 ratio, complement activation) and immunomodulation of a hypercoagulable state. All these benefits of CP are expected to be better achieved if used in non-critically hospitalized patients, in the hope of reducing morbidity and mortality.

Convalescent plasma in Covid-19: Possible mechanisms of action

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible of the coronavirus disease 2019 (COVID-19) pandemic. Therapeutic options including antimalarials, antivirals, and vaccines are under study. Meanwhile the current pandemic has called attention over old therapeutic tools to treat infectious diseases. Convalescent plasma (CP) constitutes the first option in the current situation, since it has been successfully used in other coronaviruses outbreaks. Herein, we discuss the possible mechanisms of action of CP and their repercussion in COVID-19 pathogenesis, including direct neutralization of the virus, control of an overactive immune system (i.e., cytokine storm, Th1/Th17 ratio, complement activation) and immunomodulation of a hypercoagulable state. All these benefits of CP are expected to be better achieved if used in non-critically hospitalized patients, in the hope of reducing morbidity and mortality.

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Coronavirus disease 19 (COVID-19) is an emerging viral threat with major repercussions for public health.

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There is not specific treatment for COVID-19.

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Convalescent plasma (CP) emerges as the first option of management for hospitalized patients with COVID-19.

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Transference of neutralizing antibodies helps to control COVID-19 infection and modulates inflammatory response.

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Other plasma components may enhance the antiviral and anti-inflammatory properties of CP.

Etiology and genetic evolution of canine coronavirus circulating in five provinces of China, during 2018-2019

As the outbreaks of COVID-19 in worldwide, coronavirus has once again caught the attention of people. Canine coronavirus is widespread among dog population, and sometimes causes even fatal cases. Here, to characterize the prevalence and evolution of current circulating canine coronavirus (CCoV) strains in China, we collected 213 fecal samples from diarrheic pet dogs between 2018 and 2019. Of the 213 samples, we found 51 (23.94%) were positive for CCoV. Co-infection with canine parvovirus (CPV), canine astrovirus (CaAstV), canine kobuvirus (CaKV), Torque teno canis virus (TTCaV) were ubiquitous existed. Mixed infection of different CCoV subtypes exists extensively. Considering the limited sequences data in recent years, we sequenced 7 nearly complete genomes and 10 complete spike gene. Phylogenetic analysis of spike gene revealed a new subtype CCoV-II Variant and CCoV-IIa was the most prevalent subtype currently circulating. Moreover, we identified strain B906_ZJ_2019 shared 93.24% nucleotide identifies with previous strain A76, and both of them clustered with CCoV-II Variant, which were not well clustered with the known subtypes. Recombination analysis of B906_ZJ_2019 indicated that strain B906_ZJ_2019 may a recombinant variant between CCoV–I and CCoV-II, which is consistent with strain A76. Furthermore, amino acid variations widely existed among current CCoV-IIa strains circulating in China and the classic CCoV-IIa strains, in spite of the unknown functions.

In a word, we report a useful information as to the etiology and evolution of canine coronavirus in China based on the available sequences, which is urgent for the devise of future effective disease prevention and control strategies.

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Phylogenetic analysis revealed a new subtype CCoV-II Variant and currently the most prevalent subtype CCoV-IIa.

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Strain B906_ZJ_2019 shared 93.24% nucleotide identify with strain A76, and both of them clustered with CCoV-II Variant.

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Amino acid variations widely existed among current CCoV-IIa strains circulating in China and the classic CCoV-IIa strains.

Practitioners specialized in oral health and coronavirus disease 2019: Professional guidelines from the French society of stomatology, maxillofacial surgery and oral surgery, to form a common front against the infectious risk

Medical as well as non-medical practitioners specialized in oral health are at high risk of infection with the Coronavirus-19 (Covid-19) because of the proximity with potentially infected biological fluids. This risk is permanent, especially during examination, care and transfer of patients. Regarding the pandemic progression of Covid-19, efficient protocols of prevention are urgently needed. Based on our experience and on the recently reported guidelines from the French National Agency for Public Health (ARS, March 5, 2020), the French Society of Hospital Hygiene (SFHH, March 4, 2020) and the Department of Infectious Risk Prevention of the Hospitals of Paris-Public Assistance (APHP, March 6, 2020), we provide several recommendations for practitioners specialized in oral health, to protect themselves from nosocomial infections, especially Covid-19.

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

BACKGROUND

In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed.

METHODS

We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus.

FINDINGS

The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues.

INTERPRETATION

2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin-converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation.

FUNDING

National Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, Chinese Academy of Sciences, Shandong First Medical University.

A Coronavirus Associated with Runting Stunting Syndrome in Broiler Chickens

Runting stunting syndrome (RSS) is a disease condition that affects broilers and causes impaired growth and poor feed conversion because of enteritis characterized by pale and distended small intestines with watery contents. The etiology of the disease is multifactorial, and a large variety of viral agents have been implicated. Here we describe the detection and isolation of an infectious bronchitis virus (IBV) -like coronavirus from the intestines of a flock of 60,000 14-day-old brown/red broiler chicks. The birds showed typical clinical signs of RSS including stunting and uneven growth. At necropsy, the small intestines were pale and distended with watery contents. Histopathology of the intestines revealed increased cellularity of the lamina propria, blunting of villi, and cystic changes in the crypts. Negative stain electron microscopy of the intestinal contents revealed coronavirus particles. Transmission electron microscopy of the intestine confirmed coronavirus in the cytoplasm of enterocytes. Using immunohistochemistry (IHC), IBV antigen was detected in the intestinal epithelial cells as well as in the proventriculus and pancreas. There were no lesions in the respiratory system, and no IBV antigen was detected in trachea, lung, air sac, conjunctiva, and cecal tonsils. A coronavirus was isolated from the intestine of chicken embryos but not from the allantoic sac inoculated with the intestinal contents of the broiler chicks. Sequencing of the S1 gene showed nucleic acid sequence identities of 93.8% to the corresponding region of IBV California 99 and of 85.7% to IBV Arkansas. Nucleic acid sequence identities to other IBV genotypes were lower. The histopathologic lesions in the intestines were reproduced after experimental infection of specific-pathogen-free chickens inoculated in the conjunctiva and nares. Five days after infection, six of nine investigated birds showed enteritis associated with IBV antigen as detected by IHC. In contrast to the field infection, birds in the experimental group showed clear respiratory signs and lesions in the upper respiratory tract. The results suggest a broader tissue tropism of this isolate, which might be related to the mutations in the S1 gene.

Global distributions and strain diversity of avian infectious bronchitis virus: a review

The poultry industry faces challenge amidst global food security crisis. Infectious bronchitis is one of the most important viral infections that cause huge economic loss to the poultry industry worldwide. The causative agent, infectious bronchitis virus (IBV) is an RNA virus with great ability for mutation and recombination; thus, capable of generating new virus strains that are difficult to control. There are many IBV strains found worldwide, including the Massachusetts, 4/91, D274, and QX-like strains that can be grouped under the classic or variant serotypes. Currently, information on the epidemiology, strain diversity, and global distribution of IBV has not been comprehensively reported. This review is an update of current knowledge on the distribution, genetic relationship, and diversity of the IBV strains found worldwide.

Cross-sectional survey of selected enteric viruses in Polish turkey flocks between 2008 and 2011

Background

Enteric diseases are an important health problem for the intensive poultry industry, resulting in considerable economic losses. Apart from such microbiological agents associated with enteritis as bacteria and parasites, a lot of research has been recently conducted on viral origin of enteric diseases. However, enteric viruses have been identified in intestinal tract of not only diseased but also healthy poultry, so their role in enteritis is still unclear. The present study aimed at determination of the prevalence of four enteric viruses, namely astrovirus, coronavirus, parvovirus and rotavirus in meat-type turkey flocks in Poland as well as at statistical evaluation of the occurrence of the studied viruses and their relationships with the health status and the age of birds. Two hundred and seven flocks of birds aged 1-20 weeks originating from different regions of the country were investigated between 2008 and 2011. Clinical samples (10 individual faecal swabs/flock) were duly processed and examined using molecular methods targeting the conservative regions of viral genomes: RNA-dependent RNA polymerase gene of astrovirus, non-structural 1 gene of parvovirus, non-structural protein 4 gene of rotavirus, and 5′ untranslated region fragment of turkey coronavirus. Different statistical methods (i.e. the independence chi-square test, the correspondence analysis and the logistic regression model) were used to establish any relationships between the analyzed data.

Results

Overall, 137 (66.2%, 95% CI: 59.3-72.6) of the 207 turkey flocks sampled were infected with one or more enteric viruses. Among the 137 flocks, 74 (54%, 95% CI: 45.3-62.6) were positive for one virus, whereas 54 (39.4%, 9 5% CI: 31.2-48.1) and 9 (6.6%, 95% CI: 3.1-12.1) were co-infected with two or three different enteric viruses, respectively. No flock was simultaneously infected with all four viruses studied. The prevalence of astrovirus infection was 44.9% (95% CI: 38.0-52.0), parvovirus 27.5% (95% CI: 21.6-34.2), rotavirus 18.8% (95% CI: 13.8-24.8), and coronavirus 9.7% (95% CI: 6.0-14.5). Young turkeys aged 1-4 weeks old had the highest (82.1%, 95% CI:71.7-89.8) prevalence of viral infection. Applied statistical methods have indicated the dependence of rotavirus infection as well as the co-infection with multiple viruses and the health status of turkeys. Furthermore, our results statistically confirm that especially young birds are susceptible to infection with rotavirus and astrovirus.

Conclusions

The study demonstrated the presence of astrovirus, coronavirus, parvovirus and rotavirus infections in Polish turkey farms. These viruses were detected in both healthy and diseased birds. However, the presented results provide valuable feedback which could help to evaluate the role of some enteric viruses in the etiology of enteritis in turkey.

Infectious Bronchitis Virus in Captured Free-Living, Free-Range and Intensively Reared Birds in Southwest Nigeria

Infectious bronchitis (IB) is an acute infectious viral disease causing severe economic losses in poultry production. In Nigeria, there has only been monitoring of the disease in chickens with little attention given to other bird species. For this study, blood samples were collected from 184 apparently healthy, unvaccinated birds which comprised of 61 captured free-living pigeons, 60 free range indigenous chickens and 63 intensively reared Japanese quails. Sera from these birds were screened for IB virus antibodies (IBV) using a commercial ELISA kit. The birds were from Oyo and Osun States, in southwest Nigeria. Overall, 63 (34.2 %) sera were positive for IBV with 3.3 % (2/61), 95.0 % (57/60) and 6.3 % (4/63) from pigeons, indigenous chickens and Japanese quails, respectively. These findings suggest that they were subclinically infected with either field or vaccine virus and could thus serve as possible reservoirs of this virus to domestic poultry. Thus, there is need for continuous surveillance of the disease in different bird species and their possible role in the spread of IBV in Nigeria.

Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

Human coronaviruses (HCoVs) were first described in the 1960s for patients with the common cold. Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. It was recently discovered that dromedary camels in Saudi Arabia harbor three different HCoV species, including a dominant MERS HCoV lineage that was responsible for the outbreaks in the Middle East and South Korea during 2015. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans.

High Prevalence and Putative Lineage Maintenance of Avian Coronaviruses in Scandinavian Waterfowl

Coronaviruses (CoVs) are found in a wide variety of wild and domestic animals, and constitute a risk for zoonotic and emerging infectious disease. In poultry, the genetic diversity, evolution, distribution and taxonomy of some coronaviruses have been well described, but little is known about the features of CoVs in wild birds. In this study we screened 764 samples from 22 avian species of the orders Anseriformes and Charadriiformes in Sweden collected in 2006/2007 for CoV, with an overall CoV prevalence of 18.7%, which is higher than many other wild bird surveys. The highest prevalence was found in the diving ducks--mainly Greater Scaup (Aythya marila; 51.5%)--and the dabbling duck Mallard (Anas platyrhynchos; 19.2%). Sequences from two of the Greater Scaup CoV fell into an infrequently detected lineage, shared only with a Tufted Duck (Aythya fuligula) CoV. Coronavirus sequences from Mallards in this study were highly similar to CoV sequences from the sample species and location in 2011, suggesting long-term maintenance in this population. A single Black-headed Gull represented the only positive sample from the order Charadriiformes. Globally, Anas species represent the largest fraction of avian CoV sequences, and there seems to be no host species, geographical or temporal structure. To better understand the eitiology, epidemiology and ecology of these viruses more systematic surveillance of wild birds and subsequent sequencing of detected CoV is imperative.

Investigating turkey enteric coronavirus circulating in the Southeastern United States and Arkansas during 2012 and 2013

Periodic monitoring of poultry flocks in the United States via molecular diagnostic methods has revealed a number of potential enteric viral pathogens in continuous circulation in turkeys and chickens. Recently turkey integrators in the Southeastern United States and Arkansas experienced an outbreak of moderate to severe enteritis associated with turkey enteric coronavirus (TCoV), and numerous enteric samples collected from turkey flocks in these areas tested positive for TCoV via real-time reverse-transcriptase PCR (RRT-PCR). This report details the subsequent sequence and phylogenetic analysis of the TCoV spike glycoprotein and the comparison of outbreak-associated isolates to sequences in the public database. TCoVs investigated during the present outbreak grouped geographically based upon state of origin, and the RRT-PCR assay was a good indicator of subsequent seroconversion by TCoV-positive turkey flocks.

Detection of enteric pathogens in Turkey flocks affected with severe enteritis, in Brazil

Twenty-two flocks of turkeys affected by enteric problems, with ages between 10 and 104 days and located in the Southern region of Brazil, were surveyed for turkey by PCR for turkey astrovirus type 2 (TAstV-2), turkey coronavirus (TCoV), hemorrhagic enteritis virus (HEV), rotavirus, reovirus, Salmonella spp., and Lawsonia intracellularis (Li) infections. Eleven profiles of pathogen combination were observed. The most frequently encountered pathogen combinations were TCoV-Li, followed by TCoV-TAstV-2-Li, TCoV-TastV-2. Only TCoV was detected as the sole pathogen in three flocks. Eight and 19 flocks of the 22 were positive for TAstV-2 and TCoV, respectively. Six were positive for Salmonella spp. and L. intracellularis was detected in 12 turkey flocks. Reovirus and HEV were not detected in this survey. These results throw new light on the multiple etiology of enteritis in turkeys. The implications of these findings and their correlation with the clinical signs are comprehensively discussed, illustrating the complexity of the enteric diseases.

Enteric viruses in turkey enteritis

Gut health is very important to get maximum returns in terms of weight gain and egg production. Enteric diseases such as poult enteritis complex (PEC) in turkeys do not allow their production potential to be achieved to its maximum. A number of viruses, bacteria, and protozoa have been implicated but the primary etiology has not been definitively established. Previously, electron microscopy was used to detect the presence of enteric viruses, which were identified solely on the basis of their morphology. With the advent of rapid molecular diagnostic methods and next generation nucleic acid sequencing, researchers have made long strides in identification and characterization of viruses associated with PEC. The molecular techniques have also helped us in identification of pathogens which were previously not known. Regional and national surveys have revealed the presence of several different enteric viruses in PEC including rotavirus, astrovirus, reovirus and coronavirus either alone or in combination. There may still be unknown pathogens that may directly or indirectly play a role in enteritis in turkeys. This review will focus on the role of turkey coronavirus, rotavirus, reovirus, and astrovirus in turkey enteritis.

Enteric viruses in Brazilian turkey flocks: single and multiple virus infection frequency according to age and clinical signs of intestinal disease

Poult enteritis complex has been associated with enteritis and reduction in growth rates in commercial turkeys worldwide. Intestinal samples from 76 turkey flocks from different Brazilian states affected or not with intestinal disorders were evaluated for the presence of adenovirus groups 1 and 2 (TAV), astrovirus types 1 and 2 (TAstV-1 and TAstV-2), turkey coronavirus (TCoV), reovirus, rotavirus, and avian nephritis virus (ANV) using PCR. The percentage of positive samples was categorized according to the geographic origin, age of the flocks, and presence of clinical signs of intestinal disease. The percentage of samples that were positive for at least one virus was 93.4%, whereas the percentage of samples that were positive for more than one virus was 69.7%. An average of 3.20 viruses per sample was detected in turkeys in the growing phase of the production cycle (1 to 4 wk of age). The TAstV-1 and TCoV were the most frequently observed viruses in growing phase turkeys and occurred simultaneously in 85% of these samples. In turkeys in the finishing phase of development (5 to 18 wk), a lower average number of viruses was observed (2.41), and the most frequent viruses isolated in these turkeys were TAstV-1 (57.1%) and rotavirus (51.8%). Overall, every virus was detected more frequently in growing phase turkeys than in finishing phase turkeys with the exception of TAV. Samples from flocks exhibiting clinical signs of intestinal disease showed a higher rate of positivity, and TAstV-1, TAstV-2, and TCoV were the most frequently occurring viruses in this cohort. Birds without clinical signs most frequently harbored TAstV-1 and rotavirus. Future studies should focus on the description and elucidation of the role of each virus, as well as the pathogenic and immunological implications of the different combinations of viruses in turkeys.

Infection with a pathogenic turkey coronavirus isolate negatively affects growth performance and intestinal morphology of young turkey poults in Canada

Turkey coronavirus (TCoV) is an important viral pathogen causing diarrhoea of young turkey poults that is associated with sizeable economic losses for the turkey industry. Using a field isolate that was found to be free from turkey astrovirus and avian reovirus we were able to reproduce the clinical disease associated with TCoV. Clinical signs and weight gain of poults during experimental infections were compared with age-matched, uninfected controls. Poults infected at 2 days of age had 100% morbidity and 10% mortality, and birds infected at 28 days of age showed 75% morbidity and no mortality. Diarrhoea was consistently seen in infected poults at 2 to 3 days post infection (d.p.i.) with a duration of about 3 to 5 days. Mean body weights of birds infected at 2 or 28 days of age were significantly reduced compared with uninfected birds by 7 d.p.i. and remained significantly lower for the duration of the study. At 44 days of age, poults infected at 2 or 28 days of age weighed only 68.1% or 77.7%, respectively, compared with uninfected turkeys of the same age on the same diet, a mean difference in body weights of 683 or 477g, respectively. Infected birds had profound villus atrophy with some compensatory crypt hyperplasia at 5 to 7 d.p.i. Villus heights in the duodenum were significantly reduced at 7 d.p.i. We were able to reproduce enteric disease using only a pathogenic field isolate (MG10) of TCoV that negatively affected growth performance and intestinal morphology of young turkey poults.