Isolation of MERS coronavirus from a dromedary camel, Qatar, 2014

Binding affinity between coronavirus spike protein and human ACE2 receptor

Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.

Interspecies transmission of SARS CoV-2 with special emphasis on viral mutations and ACE-2 receptor homology roles

COVID-19 outbreak was first reported in 2019, Wuhan, China. The spillover of the disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to a wide range of pet, zoo, wild, and farm animals has emphasized potential zoonotic and reverse zoonotic viral transmission. Furthermore, it has evoked inquiries about susceptibility of different animal species to SARS-CoV-2 infection and role of these animals as viral reservoirs. Therefore, studying susceptible and non-susceptible hosts for SARS-CoV-2 infection could give a better understanding for the virus and will help in preventing further outbreaks. Here, we review structural aspects of SARS-CoV-2 spike protein, the effect of the different mutations observed in the spike protein, and the impact of ACE2 receptor variations in different animal hosts on inter-species transmission. Moreover, the SARS-CoV-2 spillover chain was reviewed. Combination of SARS-CoV-2 high mutation rate and homology of cellular ACE2 receptors enable the virus to transcend species barriers and facilitate its transmission between humans and animals.

Global patterns of Middle East respiratory syndrome coronavirus (MERS-CoV) prevalence and seroprevalence in camels: A systematic review and meta-analysis

The Middle East respiratory syndrome Coronavirus (MERS-CoV) is one of the human coronaviruses that causes severe respiratory infection. Bats are considered to be the natural reservoir, where dromedary camels (DC) are the intermediate hosts of the virus. The current study was undertaken to provide an update on global distribution of the virus in camels, and to investigate the pooled prevalence and camel-associated risk factors of infection. After registration of the review protocol in the Open Science Framework, data searches were conducted on 18 April 2023 through Embase, PubMed, Scopus, and Web of Science. Considering only natural MERS-CoV infection in camels, 94 articles were selected for data curation through blind screening by two authors. Meta-analysis was conducted to estimate the pooled prevalence and to evaluate camel-associated risk factors. Finally, the results were presented in forest plots. The reviewed articles tested 34 countries, of which camels of 24 countries were seropositive and in 15 countries they were positive by molecular method. Viral RNA was detected in DC. Non-DC, such as bactrian camels, alpaca, llama, and hybrid camels were only seropositive. The global estimated pooled seroprevalence and viral RNA prevalence in DC were 77.53% and 23.63%, respectively, with the highest prevalence in West Asia (86.04% and 32.37% respectively). In addition, 41.08% of non-DC were seropositive. The estimated pooled prevalence of MERS-CoV RNA significantly varied by sample types with the highest in oral (45.01%) and lowest in rectal (8.42%) samples; the estimated pooled prevalence in nasal (23.10%) and milk (21.21%) samples were comparable. The estimated pooled seroprevalence in <2 years, 2-5 years, and > 5 years age groups were 56.32%, 75.31%, and 86.31%, respectively, while viral RNA prevalence was 33.40%, 15.87%, and 13.74%, respectively. Seroprevalence and viral RNA prevalence were generally higher in females (75.28% and 19.70%, respectively) than in males (69.53% and 18.99%, respectively). Local camels had lower estimated pooled seroprevalence (63.34%) and viral RNA prevalence (17.78%) than those of imported camels (89.17% and 29.41%, respectively). The estimated pooled seroprevalence was higher in camels of free-herds (71.70%) than confined herds (47.77%). Furthermore, estimated pooled seroprevalence was higher in samples from livestock markets, followed by abattoirs, quarantine, and farms but viral RNA prevalence was the highest in samples from abattoirs, followed by livestock markets, quarantine, and farms. Risk factors, such as sample type, young age, female sex, imported camels, and camel management must be considered to control and prevent the spread and emergence of MERS-CoV.

Versatile use of bat ACE2 for cellular entry by MERS-CoV-like viruses

Cellular entry receptors for bat MERS-CoV-like viruses NeoCoV and PDF-2180 were unknown, leaving their zoonotic potential ambiguous. A recent study by Xiong et al. published in Nature identified bat ACE2 as the cellular entry receptor for both viruses, highlighting the ability of coronaviruses to utilize a range of entry receptors.

The COVID-19 pandemic - How many times were we warned before?

Infectious diseases are known to act in both predictable and unpredictable ways, which leads to the notions of emerging and reemerging infectious diseases. Emerging diseases with their disastrous consequences might be surprising and unpredictable, but they could be foreseen. For instance, some emerging diseases and recently the coronavirus disease 2019 (COVID-19) were the reason for papers published by the World Health Organization (WHO) and other researchers addressing the likely pathogens causing future outbreaks, according to the reports of the WHO in 2016 and 2018. Although it might seem like a wisdom in retrospect, several studies had already indicated possible future outbreaks caused by coronaviruses. Announcements, which may be viewed as "warnings," appeared since the emergence of the first coronavirus-related outbreak caused by severe acute respiratory syndrome coronavirus (SARS-CoV) in the winter of 2002-2003 and a later outbreak caused by the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012-2013. Therefore, we were curious to review the medical literature prior to the COVID-19 pandemic with an aim to enumerate and evaluate studies addressing and warning against future outbreaks, and surprisingly pandemics, of members of coronaviruses. Interestingly, we found numerous studies that correctly predicted the current pandemic of COVID-19. While this part is highly interesting, how authorities reacted and prepared for warnings, if any, and how will they get prepared for the next warnings are our main messages. Taking these points into serious consideration will certainly aid in analyzing reports regarding possible future outbreaks as well as in developing various strategies for prevention and coping with such epidemics.

Lessons from SARS-CoV, MERS-CoV, and SARS-CoV-2 Infections: What We Know So Far

Within past decades, human infections with emerging and reemerging zoonotic viral pathogens have raised the eminent public health concern. Since November 2002, three highly pathogenic and major deadly human coronaviruses of the βετα-genera (β-hCoVs), namely, severe acute respiratory distress syndrome-coronavirus (SARS-CoV), middle east respiratory syndrome-coronavirus (MERS-CoV), and SARS-CoV-2, have been globally emerged and culminated in the occurrence of SARS epidemic, MERS outbreak, and coronavirus disease 19 (COVID-19) pandemic, respectively. The global emergence and spread of these three major deadly β-hCoVs have extremely dreadful impacts on human health and become an economic burden. Unfortunately, clear specific and highly efficient medical countermeasures for these three β-hCoVs and their underlying fatal illnesses remain under development. Although they belong to the same family and share many features and convergent evolution, these three deadly β-hCoVs have some important and obvious differences. By utilizing their lessons and gaining a deeper understanding of these β-hCoVs, we can identify areas of improvement and provide preparedness plans for fighting and controlling the future reemerging human infections that might arise from them or from other potential pathogenic hCoVs. Therefore, this review summarizes the state-of-the-art information and compares the similarities and dissimilarities between SARS-CoV, MERS-CoV, and SARS-CoV-2, in terms of their evolution trait, genome organization, host cell entry mechanisms, tissue infectivity tropisms, transmission routes and contagiousness, and the clinical characteristics, laboratory features, and immunological abnormalities of their related illnesses. It also provides an overview of the emerging SARS-CoV-2 variants. Additionally, it discusses the challenges of the most proposed treatment options for SARS-CoV-2 infections.

Animal models for studying coronavirus infections and developing antiviral agents and vaccines

In addition to severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has become the third deadly coronavirus that infects humans and causes the new coronavirus disease (COVID-19). COVID-19 has already caused more than six million deaths worldwide and it is likely the biggest pandemic of this century faced by mankind. Although many studies on SARS-CoV-2 have been conducted, a detailed understanding of SARS-CoV-2 and COVID-19 is still lacking. Animal models are indispensable for studying its pathogenesis and developing vaccines and antivirals. In this review, we analyze animal models of coronavirus infections and explore their applications on antivirals and vaccines.

Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.

Analyzing the roles of some species of arthropods in the transmission of the Middle East respiratory syndrome coronavirus

BACKGROUND

The Middle East Respiratory Syndrome coronavirus (MERS-CoV) is still listed on the WHO Research and Development Blueprint of emerging pathogens. Dromedary camels remain the only known animal reservoir of the virus. The animal-to-animal as well as the animal-to-human transmission in the MERS-CoV cycles were reported. However, many aspects of these transmission chains are not well studied. One of these directions is the potential roles of various species of arthropods in the transmission of the virus.

OBJECTIVES

The main goal of the current work was to study the roles of several species of arthropods in the transmission of MERS-CoV.

METHODOLOGY

To achieve this goal, we identified some MERS-CoV naturally infected dromedary camel populations. We conducted a longitudinal study among these animals for more than 2 months. This was done by repeated testing of nasal swabs biweekly from some selected animals in this population for the presence of MERS-CoV-RNAs by real-time PCR. During the duration of this study, we collected several species of arthropods (Culicoides, Stomoxys, Musca domestica and some Culex species) that shared the habitat and were circulating in this farm during this longitudinal study.

RESULTS

Our results showing, despite the detection of the viral RNAs in some animals throughout this study, none of the examined species of arthropods tested positive for the viral RNA.

CONCLUSIONS

These results are suggesting that at least the tested species of arthropods may not play roles in the transmission of MERS-CoV. However, more large-scale studies are required to explore any potential roles of arthropods in the transmission cycle of MERS-CoV.

Vaccine efficacy and SARS-CoV-2 control in California and U.S. during the session 2020-2026: A modeling study

BACKGROUND

Besides maintaining health precautions, vaccination has been the only prevention from SARS-CoV-2, though no clinically proved 100% effective vaccine has been developed till date. At this stage, to withhold the debris of this pandemic-experts need to know the impact of the vaccine efficacy rates, the threshold level of vaccine effectiveness and how long this pandemic may extent with vaccines that have different efficacy rates. In this article, a mathematical model study has been done on the importance of vaccination and vaccine efficiency rate during an ongoing pandemic.

METHODS

We simulated a five compartment mathematical model to analyze the pandemic scenario in both California, and whole U.S. We considered four vaccines, Pfizer (95%), Moderna (94%), AstraZeneca (79%), and Johnson & Johnson (72%), which are being used rigorously to control the SARS-CoV-2 pandemic, in addition with two special cases: a vaccine with 100% efficacy rate and no vaccine under use. SARS-CoV-2 related data of California, and U.S. were used in this study.

FINDINGS

Both the infection and death rates are very high in California. Our model suggests that the pandemic situation in California will be under control in the last quartile of the year 2023 if vaccination program is continued with the Pfizer vaccine. During this time, six waves may happen from the beginning of the immunization where the case fatality and recovery rates will be 1.697% and 98.30%, respectively. However, according to the considered model, this period might be extended to the mid of 2024 when vaccines with lower efficacy rates are used. On the other hand, the daily cases and deaths in the U.S. will be under control at the end of 2026 with multiple waves. Although the number of susceptible people will fall down to none in the beginning of 2027, there is less chance to stop the vaccination program if vaccinated with a vaccine other than a 100% effective vaccine or Pfizer, and at that case vaccination program must run till the mid of 2028. According to this study, the unconfirmed-infectious and infected cases will be under control at the end of 2027 and at the mid of 2028, respectively.

INTERPRETATION

The more effective a vaccine is, the less people suffer from this malign infection. Vaccines which are less than 90% effective do not have notable contribution to control the pandemic besides hard immunity. Furthermore, specific groups of people are getting prioritized initially, mass vaccination and quick responses are required to control the spread of this disease.

An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking

β-Coronaviruses such as SARS-CoV-2 hijack coatomer protein-I (COPI) for spike protein retrograde trafficking to the progeny assembly site in endoplasmic reticulum-Golgi intermediate compartment (ERGIC). However, limited residue-level details are available into how the spike interacts with COPI. Here we identify an extended COPI binding motif in the spike that encompasses the canonical K-x-H dibasic sequence. This motif demonstrates selectivity for αCOPI subunit. Guided by an in silico analysis of dibasic motifs in the human proteome, we employ mutagenesis and binding assays to show that the spike motif terminal residues are critical modulators of complex dissociation, which is essential for spike release in ERGIC. αCOPI residues critical for spike motif binding are elucidated by mutagenesis and crystallography and found to be conserved in the zoonotic reservoirs, bats, pangolins, camels, and in humans. Collectively, our investigation on the spike motif identifies key COPI binding determinants with implications for retrograde trafficking.

The cytosolic tail of β-coronavirus spike proteins contains dibasic motifs that must be able to bind to the host’s coatomer protein-I (COPI) for trafficking and be released for viral assembly in the ER-Golgi intermediate compartment. The critical residues in both the spike cytosolic tail and COPI are identified that modulate the association-dissociation kinetics.

Monitoring of the Middle East Respiratory Syndrome Coronavirus Activity in a Secluded Herd of Camels Kept Under Field Conditions

Background: Camel-to-human transmission of the Middle East Respiratory Syndrome coronavirus (MERS-CoV) was confirmed as a cause of primary infection in humans. There is a dearth of information regarding the behavior of the virus in camels and the mode of spread among them under natural conditions. The aim of this study was to monitor exposure of camels to the MERS-CoV under field conditions. Methods: From January 1 to November 30, 2015, a secluded herd of 20 pregnant female camels and their neonate calves was established. Nasal and rectal swabs were collected from calves daily for 90 days after birth, then weekly until the end of the study. Nasal and rectal samples were collected from the dams at outset and then weekly until the end of the study. The samples were tested with rtRT-PCR to detect the MERS-CoV RNA. Results: All purchased pregnant camels were MERS-CoV RNA negative at outset. Nineteen dams and 15 calves completed the study. Seven (46.7%) of the 15 calves developed a rise in rectal temperature (39-40°C), shivering, rhinitis, anorexia, and general weakness at a mean ± standard deviation of 18.9 ± 4.9 days of age and their MERS-CoV RNA test was positive on the first day of illness. Three of the seven infected calves died 14 ± 9.1 days postonset of illness at age 17, 14, and 46 days, respectively. The remaining four infected calves fully recovered and they were MERS-CoV RNA positive for 17.5 ± 8.8 days. Four (21.1%) of the 19 dams had positive tests; three dams had no clinical signs, whereas the fourth dam exhibited signs not compatible with MERS-CoV infection and died three days after the positive test, 33 days after parturition. All MERS-CoV infections occurred within 22 days. Conclusions: This study has expanded our understanding of the MERS-CoV epidemiology among camels, which is an important step forward to device effective preventive measures.

Understanding the prevalence of SARS-CoV-2 (COVID-19) exposure in companion, captive, wild, and farmed animals

Several animal species, including ferrets, hamsters, monkeys, and raccoon dogs, have been shown to be susceptible to experimental infection by the human severe acute respiratory syndrome coronaviruses, such as SARS-CoV and SARS-CoV-2, which were responsible for the 2003 SARS outbreak and the 2019 coronavirus disease (COVID-19) pandemic, respectively. Emerging studies have shown that SARS-CoV-2 natural infection of pet dogs and cats is also possible, but its prevalence is not fully understood. Experimentally, it has been demonstrated that SARS-CoV-2 replicates more efficiently in cats than in dogs and that cats can transmit the virus through aerosols. With approximately 470 million pet dogs and 370 million pet cats cohabitating with their human owners worldwide, the finding of natural SARS-CoV-2 infection in these household pets has important implications for potential zoonotic transmission events during the COVID-19 pandemic as well as future SARS-related outbreaks. Here, we describe some of the ongoing worldwide surveillance efforts to assess the prevalence of SARS-CoV-2 exposure in companion, captive, wild, and farmed animals, as well as provide some perspectives on these efforts including the intra- and inter-species coronavirus transmissions, evolution, and their implications on the human-animal interface along with public health. Some ongoing efforts to develop and implement a new COVID-19 vaccine for animals are also discussed. Surveillance initiatives to track SARS-CoV-2 exposures in animals are necessary to accurately determine their impact on veterinary and human health, as well as define potential reservoir sources of the virus and its evolutionary and transmission dynamics.

Evolution, Interspecies Transmission, and Zoonotic Significance of Animal Coronaviruses

Coronaviruses are single-stranded RNA viruses that affect humans and a wide variety of animal species, including livestock, wild animals, birds, and pets. These viruses have an affinity for different tissues, such as those of the respiratory and gastrointestinal tract of most mammals and birds and the hepatic and nervous tissues of rodents and porcine. As coronaviruses target different host cell receptors and show divergence in the sequences and motifs of their structural and accessory proteins, they are classified into groups, which may explain the evolutionary relationship between them. The interspecies transmission, zoonotic potential, and ability to mutate at a higher rate and emerge into variants of concern highlight their importance in the medical and veterinary fields. The contribution of various factors that result in their evolution will provide better insight and may help to understand the complexity of coronaviruses in the face of pandemics. In this review, important aspects of coronaviruses infecting livestock, birds, and pets, in particular, their structure and genome organization having a bearing on evolutionary and zoonotic outcomes, have been discussed.

Genetic Insights into the Middle East Respiratory Syndrome Coronavirus Infection among Saudi People

BACKGROUND

The Middle East respiratory syndrome coronavirus (MERS-CoV) was isolated for the first time in Saudi Arabia from a patient suffering from atypical pneumonia. The Saudi Genome database was built by King Abdulaziz Medical City via the next-generation sequencing of 7000 candidates.

METHOD

A large list of point mutations were reported in the region of the dipeptidyl peptidase 4 (DPP4) gene. The DPP4 amino acid residues correlated to MERS-CoV entry and the site of activity of DPP4 inhibitors was investigated. We retrieved the SNPs (Single-Nucleotide Polymorphism) with a variation frequency of >0.05.

RESULTS

SNP 2:162,890,175 and SNP 2:162,891,848 in the intronic region were located within 50 bp of amino acid residues responsible for MERS-CoV entry, amino acids 259-296 and 205-258, respectively. The variation frequency of SNP 2:162,890,175 was 2321 out of 2379 screened individuals. Moreover, mutation of SNP 2:162,891,848, which is located near amino acid residues E205 and E206 (crucial for the activity of DPP4 inhibitors), occurred in 76 out of 2379 screened individuals.

CONCLUSIONS

Our study shows high variation frequency in the DPP4 region reported in the Saudi Genome database. The identified SNPs are of high significance for MERS-CoV infection in better understanding disease pathogenesis.

Biofilms and Coronavirus Reservoirs: a Perspective Review

Bats are a key reservoir of coronaviruses (CoVs), including the agent of the severe acute respiratory syndrome, SARS-CoV-2, responsible for the recent deadly viral pneumonia pandemic. However, understanding how bats can harbor several microorganisms without developing illnesses is still a matter under discussion. Viruses and other pathogens are often studied as stand-alone entities, despite that, in nature, they mostly live in multispecies associations called biofilms—both externally and within the host. Microorganisms in biofilms are enclosed by an extracellular matrix that confers protection and improves survival. Previous studies have shown that viruses can secondarily colonize preexisting biofilms, and viral biofilms have also been described. In this review, we raise the perspective that CoVs can persistently infect bats due to their association with biofilm structures. This phenomenon potentially provides an optimal environment for nonpathogenic and well-adapted viruses to interact with the host, as well as for viral recombination. Biofilms can also enhance virion viability in extracellular environments, such as on fomites and in aquatic sediments, allowing viral persistence and dissemination. Moreover, understanding the biofilm lifestyle of CoVs in reservoirs might contribute to explaining several burning questions as to persistence and transmissibility of highly pathogenic emerging CoVs.

Coronavirus, the King Who Wanted More Than a Crown: From Common to the Highly Pathogenic SARS-CoV-2, Is the Key in the Accessory Genes?

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that emerged in late 2019, is the etiologic agent of the current "coronavirus disease 2019" (COVID-19) pandemic, which has serious health implications and a significant global economic impact. Of the seven human coronaviruses, all of which have a zoonotic origin, the pandemic SARS-CoV-2, is the third emerging coronavirus, in the 21st century, highly pathogenic to the human population. Previous human coronavirus outbreaks (SARS-CoV-1 and MERS-CoV) have already provided several valuable information on some of the common molecular and cellular mechanisms of coronavirus infections as well as their origin. However, to meet the new challenge caused by the SARS-CoV-2, a detailed understanding of the biological specificities, as well as knowledge of the origin are crucial to provide information on viral pathogenicity, transmission and epidemiology, and to enable strategies for therapeutic interventions and drug discovery. Therefore, in this review, we summarize the current advances in SARS-CoV-2 knowledges, in light of pre-existing information of other recently emerging coronaviruses. We depict the specificity of the immune response of wild bats and discuss current knowledge of the genetic diversity of bat-hosted coronaviruses that promotes viral genome expansion (accessory gene acquisition). In addition, we describe the basic virology of coronaviruses with a special focus SARS-CoV-2. Finally, we highlight, in detail, the current knowledge of genes and accessory proteins which we postulate to be the major keys to promote virus adaptation to specific hosts (bat and human), to contribute to the suppression of immune responses, as well as to pathogenicity.

Zoonotic and Reverse Zoonotic Transmissibility of SARS-CoV-2

The Coronavirus Disease 2019 (COVID-19) is the first known pandemic caused by a coronavirus. Its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appears to be capable of infecting different mammalian species. Recent detections of this virus in pet, zoo, wild, and farm animals have compelled inquiry regarding the zoonotic (animal-to-human) and reverse zoonotic (human-to-animal) transmissibility of SARS-CoV-2 with the potential of COVID-19 pandemic evolving into a panzootic.

It is important to monitor the global spread of disease and to assess the significance of genomic changes to support prevention and control efforts during a pandemic. An understanding of the SARS-CoV-2 epidemiology provides opportunities to prevent the risk of repeated re-infection of humans and requires a robust One Health-based investigation. This review paper describes the known properties and the existing gaps in scientific knowledge about the zoonotic and reverse zoonotic transmissibility of the novel virus SARS-CoV-2 and the COVID-19 disease it causes.

Monitoring Coronavirus Disease 2019: A Review of Available Diagnostic Tools

Coronavirus disease 2019 (COVID-19) pneumonia is caused by the virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has rapidly become a global public health concern. As the new type of betacoronavirus, SARS-CoV-2 can spread across species and between populations and has a greater risk of transmission than other coronaviruses. To control the spread of SARS-CoV-2, it is vital to have a rapid and effective means of diagnosing asymptomatic SARS-CoV-2-positive individuals and patients with COVID-19, an early isolation protocol for infected individuals, and effective treatments for patients with COVID-19 pneumonia. In this review, we will summarize the novel diagnostic tools that are currently available for coronavirus, including imaging examinations and laboratory medicine by next-generation sequencing (NGS), real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) analysis, immunoassay for COVID-19, cytokine and T cell immunoassays, biochemistry and microbiology laboratory parameters in the blood of the patients with COVID-19, and a field-effect transistor-based biosensor of COVID-19. Specifically, we will discuss the effective detection rate and assay time for the rRT-PCR analysis of SARS-CoV-2 and the sensitivity and specificity of different antibody detection methods, such as colloidal gold and ELISA using specimen sources obtained from the respiratory tract, peripheral serum or plasma, and other bodily fluids. Such diagnostics will help scientists and clinicians develop appropriate strategies to combat COVID-19.

Where do we stand to oversee the coronaviruses in aqueous and aerosol environment? Characteristics of transmission and possible curb strategies

By 17 October 2020, the severe acute respiratory syndrome coronavirus (SARS-CoV-2) has caused confirmed infection of more than 39,000,000 people in 217 countries and territories globally and still continues to grow. As environmental professionals, understanding how SARS-CoV-2 can be transmitted via water and air environment is a concern. We have to be ready for focusing our attention to the prompt diagnosis and potential infection control procedures of the virus in integrated water and air system. This paper reviews the state-of-the-art information from available sources of published papers, newsletters and large number of scientific websites aimed to provide a comprehensive profile on the transmission characteristics of the coronaviruses in water, sludge, and air environment, especially the water and wastewater treatment systems. The review also focused on proposing the possible curb strategies to monitor and eventually cut off the coronaviruses under the authors' knowledge and understanding.

SARS-CoV-2 transmission via aquatic food animal species or their products: A review

Outbreaks of COVID-19 (coronavirus disease 2019) have been reported in workers in fish farms and fish processing plants arising from person-to-person transmission, raising concerns about aquatic animal food products' safety. A better understanding of such incidents is important for the aquaculture industry's sustainability, particularly with the global trade in fresh and frozen aquatic animal food products where contaminating virus could survive for some time. Despite a plethora of COVID-19-related scientific publications, there is a lack of reports on the risk of contact with aquatic food animal species or their products. This review aimed to examine the potential for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) contamination and the potential transmission via aquatic food animals or their products and wastewater effluents. The extracellular viability of SARS-CoV-2 and how the virus is spread are reviewed, supporting the understanding that contaminated cold-chain food sources may introduce SAR-CoV-2 via food imports although the virus is unlikely to infect humans through consumption of aquatic food animals or their products or drinking water; i.e., SARS-CoV-2 is not a foodborne virus and should not be managed as such but instead through strong, multifaceted public health interventions including physical distancing, rapid contact tracing, and testing, enhanced hand and respiratory hygiene, frequent disinfection of high-touch surfaces, isolation of infected workers and their contacts, as well as enhanced screening protocols for international seafood trade.

Updated and Validated Pan-Coronavirus PCR Assay to Detect All Coronavirus Genera

Coronavirus (CoV) spillover events from wildlife reservoirs can result in mild to severe human respiratory illness. These spillover events underlie the importance of detecting known and novel CoVs circulating in reservoir host species and determining CoV prevalence and distribution, allowing improved prediction of spillover events or where a human-reservoir interface should be closely monitored. To increase the likelihood of detecting all circulating genera and strains, we have modified primers published by Watanabe et al. in 2010 to generate a semi-nested pan-CoV PCR assay. Representatives from the four coronavirus genera (α-CoVs, β-CoVs, γ-CoVs and δ-CoVs) were tested and all of the in-house CoVs were detected using this assay. After comparing both assays, we found that the updated assay reliably detected viruses in all genera of CoVs with high sensitivity, whereas the sensitivity of the original assay was lower. Our updated PCR assay is an important tool to detect, monitor and track CoVs to enhance viral surveillance in reservoir hosts.

An Overview of Current Knowledge of Deadly CoVs and Their Interface with Innate Immunity

Coronaviruses are a large family of zoonotic RNA viruses, whose infection can lead to mild or lethal respiratory tract disease. Severe Acute Respiratory Syndrome-Coronavirus-1 (SARS-CoV-1) first emerged in Guangdong, China in 2002 and spread to 29 countries, infecting 8089 individuals and causing 774 deaths. In 2012, Middle East Respiratory Syndrome-Coronavirus (MERS-CoV) emerged in Saudi Arabia and has spread to 27 countries, with a mortality rate of ~34%. In 2019, SARS-CoV-2 emerged and has spread to 220 countries, infecting over 100,000,000 people and causing more than 2,000,000 deaths to date. These three human coronaviruses cause diseases of varying severity. Most people develop mild, common cold-like symptoms, while some develop acute respiratory distress syndrome (ARDS). The success of all viruses, including coronaviruses, relies on their evolved abilities to evade and modulate the host anti-viral and pro-inflammatory immune responses. However, we still do not fully understand the transmission, phylogeny, epidemiology, and pathogenesis of MERS-CoV and SARS-CoV-1 and -2. Despite the rapid application of a range of therapies for SARS-CoV-2, such as convalescent plasma, remdesivir, hydroxychloroquine and type I interferon, no fully effective treatment has been determined. Remarkably, COVID-19 vaccine research and development have produced several offerings that are now been administered worldwide. Here, we summarise an up-to-date understanding of epidemiology, immunomodulation and ongoing anti-viral and immunosuppressive treatment strategies. Indeed, understanding the interplay between coronaviruses and the anti-viral immune response is crucial to identifying novel targets for therapeutic intervention, which may even prove invaluable for the control of future emerging coronavirus.

Challenges and Opportunities in the Use of High and Maximum Biocontainment Facilities in Developing and Licensing Risk Group 3 and Risk Group 4 Agent Veterinary Vaccines

New solutions are necessary for the singular global health security threat formed by endemic, epidemic, and emerging/re-emerging zoonoses, coupled with epizootic and enzootic transboundary animal diseases (TADs). This One Health issue is related to the daily interactions between wildlife, domesticated and indigenous livestock, and humans primarily associated with global trade, transboundary co-movement of humans and diverse livestock/livestock products, and agriculture production intensification and penetration into previously uninhabited areas. The World Health Organization defines Risk Group 3 (RG-3) and RG-4 pathogens as mainly viruses but also bacteria that serve as the foundation for approximately 60% of emerging infectious diseases that are zoonoses. The World Organisation for Animal Health defines trade-notifiable TADs, and subsets of these are zoonotic. Livestock vaccination policies mainly focus on TADs that are promulgated by the United Nations Food and Agriculture Organization and government agriculture agencies. The development, licensure, and product manufacturing of next-generation molecular-based RG-3 and RG-4 veterinary vaccines largely ignored by the global animal health biopharmaceutical sector can have an important positive impact on food security and One Health. There have been sharp increases in the global demand for livestock meat and milk products, especially in low- and middle-income countries in Africa and Asia. This relatively recent market driver-coupled with scientific advances in human EID and zoonotic disease vaccine platform technologies and increases in the number of high (US biosafety level 3 agriculture) and maximum (US animal biosafety level 4) biocontainment facilities with supporting workforce capabilities-offers new investment opportunities to the animal health biopharmaceutical sector. Moreover, a growing number of One Health public-private partnerships have moved the net present value calculus in favor of the financial feasibility of RG-3 and RG-4 veterinary vaccine product development and licensure. This article highlights the challenges and opportunities in the use of high and maximum biocontainment facilities in developing and licensing RG-3 and RG-4 veterinary vaccines that are safe and effective against epizootic and enzootic TADs and zoonotic diseases.

Lack of detection of the Middle East respiratory syndrome coronavirus (MERS-CoV) nucleic acids in some Hyalomma dromedarii infesting some Camelus dromedary naturally infected with MERS-CoV

Objective

The Middle East respiratory syndrome coronavirus (MERS-CoV) is one of the zoonotic coronaviruses [Hemida Peer J 7:e7556, 2019; Hemida et al. One Health 8:100102, 2019]. The dromedary camels remained the only known animal reservoir for this virus. Several aspects of the transmission cycle of the virus between animals, including arthropod-borne infection, is still largely unknown. The main objective of the current work was to study the possibility of MERS-CoV transmission through some arthropod vectors, particularly the hard ticks. To achieve this objective, we identified a positive MERS-CoV dromedary camel herd using the commercial available real-time PCR kits. We collected some arthropods, particularly the ticks from these positive animals as well as from the animal habitats. We tested these arthropods for the presence of MERS-CoV viral RNAs.

Results

Our results showing the absence of any detectable MERS-CoV-RNAs in these arthropods despite these animals were actively shedding the virus in their nasal secretions. Our results are confirming for the first the failure of detection of the MERS-CoV in ticks infesting dromedary camels. Failure of the detection of MERS-CoV in ticks infesting positive naturally infected MERS-CoV camels is strongly suggesting that ticks do not play roles in the transmission of the virus among the animals and close contact humans.

Coronaviruses in farm animals: Epidemiology and public health implications

Coronaviruses (CoVs) are documented in a wide range of animal species, including terrestrial and aquatic, domestic and wild. The geographic distribution of animal CoVs is worldwide and prevalences were reported in several countries across the five continents. The viruses are known to cause mainly gastrointestinal and respiratory diseases with different severity levels. In certain cases, CoV infections are responsible of huge economic losses associated or not to highly public health impact. Despite being enveloped, CoVs are relatively resistant pathogens in the environment. Coronaviruses are characterized by a high mutation and recombination rate, which makes host jumping and cross-species transmission easy. In fact, increasing contact between different animal species fosters cross-species transmission, while agriculture intensification, animal trade and herd management are key drivers at the human-animal interface. If contacts with wild animals are still limited, humans have much more contact with farm animals, during breeding, transport, slaughter and food process, making CoVs a persistent threat to both humans and animals. A global network should be established for the surveillance and monitoring of animal CoVs.

SARS-CoV-2, SARS and MERS: Three formidable coronaviruses which have originated from bats

The recent continuously emerging rampancy of novel coronavirus (SARS-CoV-2) that started in Wuhan in late December 2019 has become an international public health emergency and is still spreading rapidly in the world. Up to October 11, 2020, 37.109.6851 confirmed cases of COVID-19 have been announced with 2.8 percent death, which means 1.070.355 confirmed death cases. At the moment, a specific vaccine or drug for the new coronavirus is not available; thus, the development of a drug with far-reaching HCoV inhibitory activity is an urgent medical need. It is, however, vital to first comprehend the nature of this family and other coronaviruses that have caused the outbreak. Here, we relate the epidemiological and virological characteristics of the COVID-19, SARS, and MERS rampancy.

The history of the emergence and transmission of human coronaviruses

Human coronaviruses are known respiratory pathogens associated with a range of respiratory illnesses, and there are considerable morbidity and hospitalisation amongst immune-compromised individuals of all age groups. The emergence of a highly pathogenic human coronavirus in China in 2019 has confirmed the long-held opinion that these viruses are important emerging and re-emerging pathogens. In this review article, we trace the discovery and emergence of coronaviruses (CoVs) over time since they were first reported. The review article will enrich our understanding on the host range, diversity and evolution, transmission of human CoVs and the threat posed by these viruses circulating in animal populations but overtime have spilled over to humans because of the increased proximity between humans and animals.

Host Diversity and Potential Transmission Pathways of SARS-CoV-2 at the Human-Animal Interface

Emerging infectious diseases present great risks to public health. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), has become an urgent public health issue of global concern. It is speculated that the virus first emerged through a zoonotic spillover. Basic research studies have suggested that bats are likely the ancestral reservoir host. Nonetheless, the evolutionary history and host susceptibility of SARS-CoV-2 remains unclear as a multitude of animals has been proposed as potential intermediate or dead-end hosts. SARS-CoV-2 has been isolated from domestic animals, both companion and livestock, as well as in captive wildlife that were in close contact with human COVID-19 cases. Currently, domestic mink is the only known animal that is susceptible to a natural infection, develop severe illness, and can also transmit SARS-CoV-2 to other minks and humans. To improve foundational knowledge of SARS-CoV-2, we are conducting a synthesis review of its host diversity and transmission pathways. To mitigate this COVID-19 pandemic, we strongly advocate for a systems-oriented scientific approach that comprehensively evaluates the transmission of SARS-CoV-2 at the human and animal interface.

Coronavirus Infections of Animals: Future Risks to Humans

Coronaviruses have tremendous evolutionary potential, and three major outbreaks of new human coronavirus infections have occurred in the recent history of humankind. In this paper, the patterns of occurrence of new zoonotic coronavirus infections and the role of bioveterinary control in preventing their potential outbreaks in the future are determined. The possibility of SARS-CoV-2 infection in companion animals is considered. Diverse human activities may trigger various interactions between animal species and their viruses, sometimes causing the emergence of new viral pathogens. In addition, the possibility of using probiotics for the control of viral infections in animals is discussed.

The zoonotic potential of bat-borne coronaviruses

Seven zoonoses - human infections of animal origin - have emerged from the Coronaviridae family in the past century, including three viruses responsible for significant human mortality (SARS-CoV, MERS-CoV, and SARS-CoV-2) in the past twenty years alone. These three viruses, in addition to two older CoV zoonoses (HCoV-229E and HCoV-NL63) are believed to be originally derived from wild bat reservoir species. We review the molecular biology of the bat-derived Alpha- and Betacoronavirus genera, highlighting features that contribute to their potential for cross-species emergence, including the use of well-conserved mammalian host cell machinery for cell entry and a unique capacity for adaptation to novel host environments after host switching. The adaptive capacity of coronaviruses largely results from their large genomes, which reduce the risk of deleterious mutational errors and facilitate range-expanding recombination events by offering heightened redundancy in essential genetic material. Large CoV genomes are made possible by the unique proofreading capacity encoded for their RNA-dependent polymerase. We find that bat-borne SARS-related coronaviruses in the subgenus Sarbecovirus, the source clade for SARS-CoV and SARS-CoV-2, present a particularly poignant pandemic threat, due to the extraordinary viral genetic diversity represented among several sympatric species of their horseshoe bat hosts. To date, Sarbecovirus surveillance has been almost entirely restricted to China. More vigorous field research efforts tracking the circulation of Sarbecoviruses specifically and Betacoronaviruses more generally is needed across a broader global range if we are to avoid future repeats of the COVID-19 pandemic.

Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged to cause widespread infections in humans. SARS-CoV-2 infections have been reported in the Kingdom of Saudi Arabia, where Middle East respiratory syndrome coronavirus (MERS-CoV) causes seasonal outbreaks with a case fatality rate of ~37 %. Here we show that there exists a theoretical possibility of future recombination events between SARS-CoV-2 and MERS-CoV RNA. Through computational analyses, we have identified homologous genomic regions within the ORF1ab and S genes that could facilitate recombination, and have analysed co-expression patterns of the cellular receptors for SARS-CoV-2 and MERS-CoV, ACE2 and DPP4, respectively, to identify human anatomical sites that could facilitate co-infection. Furthermore, we have investigated the likely susceptibility of various animal species to MERS-CoV and SARS-CoV-2 infection by comparing known virus spike protein-receptor interacting residues. In conclusion, we suggest that a recombination between SARS-CoV-2 and MERS-CoV RNA is possible and urge public health laboratories in high-risk areas to develop diagnostic capability for the detection of recombined coronaviruses in patient samples.

An update on COVID-19: SARS-CoV-2 life cycle, immunopathology, and BCG vaccination

The causative agent of novel coronavirus disease (COVID-19) is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 possesses RNA as a genetic material with 79% of the match with the bat SARS-CoV genome, which became epidemic in 2002. The SARS-CoV-2 peripheral Spike-Fc protein binds specifically to the ACE2 receptors present on bronchial epithelial cells and alveolar pneumocytes to downmodulates its expression which leads to severe acute respiratory failure. The disease is super infectious from human to human and the symptoms are similar to flu. The old aged and immunocompromised population are severely affected, and healthcare providers globally applied various strategies for treatment including the repurposing of drugs including antimalarial drug, hydroxychloroquine and anti-viral drugs.Herein, we described the SARS-CoV-2 pandemic, immune responses, possible drug targets, vaccines under the trials and correlated the possibility of trained immunity induced by BCG vaccination over control of SARS-CoV-2 infection. The countries with constraint BCG vaccination policy are struggling badly compared to countries with BCG vaccination policy. The BCG vaccination policy supports either lowering the total number of COVID-19 cases or the increasing recovery rate.

From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses

Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) - diseases termed as COVID-19. Current SARS-CoV-2 outbreak have fueled ongoing efforts to exploit various viral target proteins for therapy, but strategies aimed at blocking the viral proteins as in drug and vaccine development have largely failed. In fact, evidence has now shown that coronaviruses undergoes rapid recombination to generate new strains of altered virulence; additionally, escaped the host antiviral defense system and target humoral immune system which further results in severe deterioration of the body such as by cytokine storm. This demands the understanding of phenotypic and genotypic classification, and pathogenesis of SARS-CoV-2 for the production of potential therapy. In lack of clear clinical evidences for the pathogenesis of COVID-19, comparative analysis of previous pandemic HCoVs associated immunological responses can provide insights into COVID-19 pathogenesis. In this review, we summarize the possible origin and transmission mode of CoVs and the current understanding on the viral genome integrity of known pandemic virus against SARS-CoV-2. We also consider the host immune response and viral evasion based on available clinical evidences which would be helpful to remodel COVID-19 pathogenesis; and hence, development of therapeutics against broad spectrum of coronaviruses.

Middle East Respiratory Syndrome Coronavirus Transmission

Middle East respiratory syndrome coronavirus (MERS-CoV) infection causes a spectrum of respiratory illness, from asymptomatic to mild to fatal. MERS-CoV is transmitted sporadically from dromedary camels to humans and occasionally through human-to-human contact. Current epidemiologic evidence supports a major role in transmission for direct contact with live camels or humans with symptomatic MERS, but little evidence suggests the possibility of transmission from camel products or asymptomatic MERS cases. Because a proportion of case-patients do not report direct contact with camels or with persons who have symptomatic MERS, further research is needed to conclusively determine additional mechanisms of transmission, to inform public health practice, and to refine current precautionary recommendations.

Molecular Basis of Pathogenesis of Coronaviruses: A Comparative Genomics Approach to Planetary Health to Prevent Zoonotic Outbreaks in the 21st Century

In the first quarter of the 21st century, we are already facing the third emergence of a coronavirus outbreak, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the coronavirus disease 2019 (COVID-19) pandemic. Comparative genomics can inform a deeper understanding of the pathogenesis of COVID-19. Previous strains of coronavirus, SARS-CoV, and Middle-East respiratory syndrome-coronavirus (MERS-CoV), have been known to cause acute lung injuries in humans. SARS-CoV-2 shares genetic similarity with SARS-CoV with some modification in the S protein leading to their enhanced binding affinity toward the angiotensin-converting enzyme 2 (ACE2) receptors of human lung cells. This expert review examines the features of all three coronaviruses through a conceptual lens of comparative genomics. In particular, the life cycle of SARS-CoV-2 that enables its survival within the host is highlighted. Susceptibility of humans to coronavirus outbreaks in the 21st century calls for comparisons of the transmission history, hosts, reservoirs, and fatality rates of these viruses so that evidence-based and effective planetary health interventions can be devised to prevent future zoonotic outbreaks. Comparative genomics offers new insights on putative and novel viral targets with an eye to both therapeutic innovation and prevention. We conclude the expert review by (1) articulating the lessons learned so far, whereas the research is still being actively sought after in the field, and (2) the challenges and prospects in deciphering the linkages among multiomics biological variability and COVID-19 pathogenesis.

Zoonotic Diseases: Etiology, Impact, and Control

Most humans are in contact with animals in a way or another. A zoonotic disease is a disease or infection that can be transmitted naturally from vertebrate animals to humans or from humans to vertebrate animals. More than 60% of human pathogens are zoonotic in origin. This includes a wide variety of bacteria, viruses, fungi, protozoa, parasites, and other pathogens. Factors such as climate change, urbanization, animal migration and trade, travel and tourism, vector biology, anthropogenic factors, and natural factors have greatly influenced the emergence, re-emergence, distribution, and patterns of zoonoses. As time goes on, there are more emerging and re-emerging zoonotic diseases. In this review, we reviewed the etiology of major zoonotic diseases, their impact on human health, and control measures for better management. We also highlighted COVID-19, a newly emerging zoonotic disease of likely bat origin that has affected millions of humans along with devastating global consequences. The implementation of One Health measures is highly recommended for the effective prevention and control of possible zoonosis.

Comparative Review of SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza A Respiratory Viruses

The 2019 novel coronavirus (SARS-CoV-2) pandemic has caused a global health emergency. The outbreak of this virus has raised a number of questions: What is SARS-CoV-2? How transmissible is SARS-CoV-2? How severely affected are patients infected with SARS-CoV-2? What are the risk factors for viral infection? What are the differences between this novel coronavirus and other coronaviruses? To answer these questions, we performed a comparative study of four pathogenic viruses that primarily attack the respiratory system and may cause death, namely, SARS-CoV-2, severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV), and influenza A viruses (H1N1 and H3N2 strains). This comparative study provides a critical evaluation of the origin, genomic features, transmission, and pathogenicity of these viruses. Because the coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 is ongoing, this evaluation may inform public health administrators and medical experts to aid in curbing the pandemic's progression.

From SARS and MERS to COVID-19: a brief summary and comparison of severe acute respiratory infections caused by three highly pathogenic human coronaviruses

Within two decades, there have emerged three highly pathogenic and deadly human coronaviruses, namely SARS-CoV, MERS-CoV and SARS-CoV-2. The economic burden and health threats caused by these coronaviruses are extremely dreadful and getting more serious as the increasing number of global infections and attributed deaths of SARS-CoV-2 and MERS-CoV. Unfortunately, specific medical countermeasures for these hCoVs remain absent. Moreover, the fast spread of misinformation about the ongoing SARS-CoV-2 pandemic uniquely places the virus alongside an annoying infodemic and causes unnecessary worldwide panic. SARS-CoV-2 shares many similarities with SARS-CoV and MERS-CoV, certainly, obvious differences exist as well. Lessons learnt from SARS-CoV and MERS-CoV, timely updated information of SARS-CoV-2 and MERS-CoV, and summarized specific knowledge of these hCoVs are extremely invaluable for effectively and efficiently contain the outbreak of SARS-CoV-2 and MERS-CoV. By gaining a deeper understanding of hCoVs and the illnesses caused by them, we can bridge knowledge gaps, provide cultural weapons for fighting and controling the spread of MERS-CoV and SARS-CoV-2, and prepare effective and robust defense lines against hCoVs that may emerge or reemerge in the future. To this end, the state-of-the-art knowledge and comparing the biological features of these lethal hCoVs and the clinical characteristics of illnesses caused by them are systematically summarized in the review.

From SARS and MERS to COVID-19: a brief summary and comparison of severe acute respiratory infections caused by three highly pathogenic human coronaviruses

Within two decades, there have emerged three highly pathogenic and deadly human coronaviruses, namely SARS-CoV, MERS-CoV and SARS-CoV-2. The economic burden and health threats caused by these coronaviruses are extremely dreadful and getting more serious as the increasing number of global infections and attributed deaths of SARS-CoV-2 and MERS-CoV. Unfortunately, specific medical countermeasures for these hCoVs remain absent. Moreover, the fast spread of misinformation about the ongoing SARS-CoV-2 pandemic uniquely places the virus alongside an annoying infodemic and causes unnecessary worldwide panic. SARS-CoV-2 shares many similarities with SARS-CoV and MERS-CoV, certainly, obvious differences exist as well. Lessons learnt from SARS-CoV and MERS-CoV, timely updated information of SARS-CoV-2 and MERS-CoV, and summarized specific knowledge of these hCoVs are extremely invaluable for effectively and efficiently contain the outbreak of SARS-CoV-2 and MERS-CoV. By gaining a deeper understanding of hCoVs and the illnesses caused by them, we can bridge knowledge gaps, provide cultural weapons for fighting and controling the spread of MERS-CoV and SARS-CoV-2, and prepare effective and robust defense lines against hCoVs that may emerge or reemerge in the future. To this end, the state-of-the-art knowledge and comparing the biological features of these lethal hCoVs and the clinical characteristics of illnesses caused by them are systematically summarized in the review.

Middle East Respiratory Syndrome Coronavirus (MERS-CoV): State of the Science

Coronaviruses belong to a large family of viruses that can cause disease outbreaks ranging from the common cold to acute respiratory syndrome. Since 2003, three zoonotic members of this family evolved to cross species barriers infecting humans and resulting in relatively high case fatality rates (CFR). Compared to Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV, CFR = 10%) and pandemic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, CFR = 6%), the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) has scored the highest CFR (approximately 35%). In this review, we systematically summarize the current state of scientific knowledge about MERS-CoV, including virology and origin, epidemiology, zoonotic mode of transmission, and potential therapeutic or prophylactic intervention modalities.

Potential Zoonotic Origins of SARS-CoV-2 and Insights for Preventing Future Pandemics Through One Health Approach

Coronavirus disease 2019 (COVID-19) is an emerging infectious disease that has resulted in a global pandemic and is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Zoonotic diseases are infections that are transmitted from animals to humans. COVID-19 caused by SARS-CoV-2 most likely originated in bats and transmitted to humans through a possible intermediate host. Based on published research so far, pangolins are considered the most likely intermediate hosts. Further studies are needed on different wild animal species, including pangolins that are sold at the same wet market or similar wet markets before concluding pangolins as definitive intermediate hosts. SARS-CoV-2 is capable of reverse zoonosis as well. Additional research is needed to understand the pathogenicity of the virus, especially in companion animals, modes of transmission, incubation period, contagious period, and zoonotic potential. Interdisciplinary one health approach handles these mosaic issues of emerging threats by integrating professionals from multiple disciplines like human medicine, veterinary medicine, environmental health, and social sciences. Given that the future outbreak of zoonotic diseases is inevitable, importance must be given for swift identification of the pathogen, source, and transmission methods. Countries should invest in identifying the hot spots for the origin of zoonotic diseases, enhance diagnostic capabilities, and rapid containment measures at local, regional, and national levels. The threat posed by emerging infectious diseases in modern-days also needs combined efforts internationally where a single discipline or nation cannot handle the burden alone.

Potential Zoonotic Origins of SARS-CoV-2 and Insights for Preventing Future Pandemics Through One Health Approach

Coronavirus disease 2019 (COVID-19) is an emerging infectious disease that has resulted in a global pandemic and is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Zoonotic diseases are infections that are transmitted from animals to humans. COVID-19 caused by SARS-CoV-2 most likely originated in bats and transmitted to humans through a possible intermediate host. Based on published research so far, pangolins are considered the most likely intermediate hosts. Further studies are needed on different wild animal species, including pangolins that are sold at the same wet market or similar wet markets before concluding pangolins as definitive intermediate hosts. SARS-CoV-2 is capable of reverse zoonosis as well. Additional research is needed to understand the pathogenicity of the virus, especially in companion animals, modes of transmission, incubation period, contagious period, and zoonotic potential. Interdisciplinary one health approach handles these mosaic issues of emerging threats by integrating professionals from multiple disciplines like human medicine, veterinary medicine, environmental health, and social sciences. Given that the future outbreak of zoonotic diseases is inevitable, importance must be given for swift identification of the pathogen, source, and transmission methods. Countries should invest in identifying the hot spots for the origin of zoonotic diseases, enhance diagnostic capabilities, and rapid containment measures at local, regional, and national levels. The threat posed by emerging infectious diseases in modern-days also needs combined efforts internationally where a single discipline or nation cannot handle the burden alone.

Betacoronavirus Genomes: How Genomic Information has been Used to Deal with Past Outbreaks and the COVID-19 Pandemic

In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of coronaviruses in the aftermath of the 2002-2003 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-2020 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2. We focus on shared genomic features of the betacoronaviruses and the application of genomic information to phylogenetic analysis, molecular epidemiology and the design of diagnostic systems, potential drugs and vaccine candidates.

[Source of the COVID-19 pandemic: ecology and genetics of coronaviruses (Betacoronavirus: Coronaviridae) SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS-CoV (subgenus Merbecovirus).]

Since the early 2000s, three novel zooanthroponous coronaviruses (Betacoronavirus) have emerged. The first outbreak of infection (SARS) caused by SARS-CoV virus occurred in the fall of 2002 in China (Guangdong Province). A second outbreak (MERS) associated with the new MERS-CoV virus appeared in Saudi Arabia in autumn 2012. The third epidemic, which turned into a COVID-19 pandemic caused by SARS-CoV-2 virus, emerged in China (Hubei Province) in the autumn 2019. This review focuses on ecological and genetic aspects that lead to the emergence of new human zoanthroponous coronaviruses. The main mechanism of adaptation of zoonotic betacoronaviruses to humans is to changes in the receptor-binding domain of surface protein (S), as a result of which it gains the ability to bind human cellular receptors of epithelial cells in respiratory and gastrointestinal tract. This process is caused by the high genetic diversity and variability combined with frequent recombination, during virus circulation in their natural reservoir - bats (Microchiroptera, Chiroptera). Appearance of SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS (subgenus Merbecovirus) viruses is a result of evolutionary events occurring in bat populations with further transfer of viruses to the human directly or through the intermediate vertebrate hosts, ecologically connected with bats. This review is based on the report at the meeting «Coronavirus - a global challenge to science» of the Scientific Council «Life Science» of the Russian Academy of Science: Lvov D.K., Alkhovsky S.V., Burtseva E.I. COVID-19 pandemic sources: origin, biology and genetics of coronaviruses of SARS-CoV, SARS-CoV-2, MERS-CoV (Conference hall of Presidium of RAS, 14 Leninsky Prospect, Moscow, Russia. April 16, 2020).

The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia

This study compared the phylogeography of MERS-CoV between hospital outbreak-associated cases and sporadic cases in Saudi Arabia. We collected complete genome sequences from human samples in Saudi Arabia and data on the multiple risk factors of human MERS-CoV in Saudi Arabia reported from 2012 to 2018. By matching each sequence to human cases, we identified isolates as hospital outbreak-associated cases or sporadic cases. We used Bayesian phylogenetic methods including temporal, discrete trait analysis and phylogeography to uncover transmission routes of MERS-CoV isolates between hospital outbreaks and sporadic cases. Of the 120 sequences collected between 19 June 2012 and 23 January 2017, there were 64 isolates from hospital outbreak-associated cases and 56 from sporadic cases. Overall, MERS-CoV is fast evolving at 7.43 × 10-4 substitutions per site per year. Isolates from hospital outbreaks showed unusually fast evolutionary speed in a shorter time-frame than sporadic cases. Multiple introductions of different MERS-CoV strains occurred in three separate hospital outbreaks. MERS-CoV appears to be mutating in humans. The impact of mutations on viruses transmissibility in humans is unknown.