Laboratory diagnosis of four recent sporadic cases of community-acquired SARS, Guangdong Province, China

Pandemic origins and a One Health approach to preparedness and prevention: Solutions based on SARS-CoV-2 and other RNA viruses

COVID-19 is the latest zoonotic RNA virus epidemic of concern. Learning how it began and spread will help to determine how to reduce the risk of future events. We review major RNA virus outbreaks since 1967 to identify common features and opportunities to prevent emergence, including ancestral viral origins in birds, bats, and other mammals; animal reservoirs and intermediate hosts; and pathways for zoonotic spillover and community spread, leading to local, regional, or international outbreaks. The increasing scientific evidence concerning the origins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is most consistent with a zoonotic origin and a spillover pathway from wildlife to people via wildlife farming and the wildlife trade. We apply what we know about these outbreaks to identify relevant, feasible, and implementable interventions. We identify three primary targets for pandemic prevention and preparedness: first, smart surveillance coupled with epidemiological risk assessment across wildlife–livestock–human (One Health) spillover interfaces; second, research to enhance pandemic preparedness and expedite development of vaccines and therapeutics; and third, strategies to reduce underlying drivers of spillover risk and spread and reduce the influence of misinformation. For all three, continued efforts to improve and integrate biosafety and biosecurity with the implementation of a One Health approach are essential. We discuss new models to address the challenges of creating an inclusive and effective governance structure, with the necessary stable funding for cross-disciplinary collaborative research. Finally, we offer recommendations for feasible actions to close the knowledge gaps across the One Health continuum and improve preparedness and response in the future.

System analysis of the fast global coronavirus disease 2019 (COVID-19) spread. Can we avoid future pandemics under global climate change?

The recent fast global spread of COVID-19 caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) questions why and how the disease managed to be so effective against existing health protection measures. These measures, developed by many countries over centuries and strengthened over the last decades, proved to be ineffective against COVID-19. The sharp increase in human longevity and current transport systems in economically developing countries with the background of persisting cultural frameworks and stable local pools of high bacterial and viral mutations generated the wide gap between the established health protection systems and the new emerging diseases. SARS-CoV-2 targets human populations over the world with long incubation periods, often without symptoms, and serious outcomes. Hence, novel strategies are necessary to meet the demands of developing economic and social environments. Moreover, the ongoing climate change adds extra challenges while altering the existing system of interactions in biological populations and in human society. Climate change may lead to new sources of viral and microbial mutations, new ways of zoonotic disease transmission and to huge social and economic transformations in many countries. The present short Opinion applies a system approach linking biomedical, climate change, social and economic aspects and, accordingly, discusses the measures and more efficient means to avoid future pandemics.

Serum cytokine/chemokine profile and clinical/paraclinical data in COVID-19 deceased and recovered patients

Objectives: The induction of an intense immune response and cytokine storm is proposed to be central in the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The study evaluated serum cytokine/chemokine profiles, and clinical and paraclinical data of COVID-19 deceased and recovered patients in Iran. Methods: The severity of disease, clinical data, and routine laboratory and inflammatory cytokine/chemokine responses were retrospectively explored in 60 in-hospital patients in northern Iran. Characteristics of those who deceased (n = 30) were compared to recovered (n = 30), and associations with serum levels of potential disease regulating pro- and anti-inflammatory mediators were studied. Results: The serum levels of IFN-γ, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, IL-17, IP-10, MIP1-α, MCP1, RANTES, and TNF-α were upregulated in all COVID-19 patients when compared to healthy and gender-matched individuals (n = 30). Although with no significant difference between deceased and recovered cases, the serum levels of all cytokines/chemokines tended to be higher in the severely diseased non-surviving patients. Association analyses revealed that all cytokine/chemokine levels (except IL-10) significantly affect the disease outcome. Conclusion: This study provides more evidence for the association of cytokine/chemokine levels with the clinical course and outcome of COVID-19. More studies are needed to consider this measurement as an indicator of disease stage and strategy for treatment.

Role of Hypertension on the Severity of COVID-19: A Review

ABSTRACT

The novel coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved into a global pandemic. The substantial morbidity and mortality associated with the infection has prompted us to understand potential risk factors that can predict patient outcomes. Hypertension has been identified as the most prevalent cardiovascular comorbidity in patients infected with COVID-19 that demonstrably increases the risk of hospitalization and death. Initial studies implied that renin-angiotensin-aldosterone system inhibitors might increase the risk of viral infection and aggravate disease severity, thereby causing panic given the high global prevalence of hypertension. Nonetheless, subsequent evidence supported the administration of antihypertensive drugs and noted that they do not increase the severity of COVID-19 infection in patients with hypertension, rather may have a beneficial effect. To date, the precise mechanism by which hypertension predisposes to unfavorable outcomes in patients infected with COVID-19 remains unknown. In this mini review, we elaborate on the pathology of SARS-CoV-2 infection coexisting with hypertension and summarize potential mechanisms, focusing on the dual roles of angiotensin-converting enzyme 2 and the disorders of renin-angiotensin-aldosterone system in COVID-19 and hypertension. The effects of proinflammatory factors released because of immune response and gastrointestinal dysfunction in COVID-19 are also discussed.

Interspecies Jumping of Bat Coronaviruses

In the last two decades, several coronavirus (CoV) interspecies jumping events have occurred between bats and other animals/humans, leading to major epidemics/pandemics and high fatalities. The SARS epidemic in 2002/2003 had a ~10% fatality. The discovery of SARS-related CoVs in horseshoe bats and civets and genomic studies have confirmed bat-to-civet-to-human transmission. The MERS epidemic that emerged in 2012 had a ~35% mortality, with dromedaries as the reservoir. Although CoVs with the same genome organization (e.g., Tylonycteris BatCoV HKU4 and Pipistrellus BatCoV HKU5) were also detected in bats, there is still a phylogenetic gap between these bat CoVs and MERS-CoV. In 2016, 10 years after the discovery of Rhinolophus BatCoV HKU2 in Chinese horseshoe bats, fatal swine disease outbreaks caused by this virus were reported in southern China. In late 2019, an outbreak of pneumonia emerged in Wuhan, China, and rapidly spread globally, leading to >4,000,000 fatalities so far. Although the genome of SARS-CoV-2 is highly similar to that of SARS-CoV, patient zero and the original source of the pandemic are still unknown. To protect humans from future public health threats, measures should be taken to monitor and reduce the chance of interspecies jumping events, either occurring naturally or through recombineering experiments.

Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif

The spike protein is the main protein component of the SARS-CoV-2 virion surface. The spike receptor-binding motif mediates recognition of the human angiotensin-converting enzyme 2 receptor, a critical step in infection, and is the preferential target for spike-neutralizing antibodies. Posttranslational modifications of the spike receptor-binding motif have been shown to modulate viral infectivity and host immune response, but these modifications are still being explored. Here we studied asparagine deamidation of the spike protein, a spontaneous event that leads to the appearance of aspartic and isoaspartic residues, which affect both the protein backbone and its charge. We used computational prediction and biochemical experiments to identify five deamidation hotspots in the SARS-CoV-2 spike protein. Asparagine residues 481 and 501 in the receptor-binding motif deamidate with a half-life of 16.5 and 123 days at 37 °C, respectively. Deamidation is significantly slowed at 4 °C, indicating a strong dependence of spike protein molecular aging on environmental conditions. Deamidation of the spike receptor-binding motif decreases the equilibrium constant for binding to the human angiotensin-converting enzyme 2 receptor more than 3.5-fold, yet its high conservation pattern suggests some positive effect on viral fitness. We propose a model for deamidation of the full SARS-CoV-2 virion illustrating how deamidation of the spike receptor-binding motif could lead to the accumulation on the virion surface of a nonnegligible chemically diverse spike population in a timescale of days. Our findings provide a potential mechanism for molecular aging of the spike protein with significant consequences for understanding virus infectivity and vaccine development.

Generation and Characterization of a Nanobody Against SARS-CoV

The sudden emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) has caused global panic in 2003, and the risk of SARS-CoV outbreak still exists. However, no specific antiviral drug or vaccine is available; thus, the development of therapeutic antibodies against SARS-CoV is needed. In this study, a nanobody phage-displayed library was constructed from peripheral blood mononuclear cells of alpacas immunized with the recombinant receptor-binding domain (RBD) of SARS-CoV. Four positive clones were selected after four rounds of bio-panning and subjected to recombinant expression in E. coli. Further biological identification demonstrated that one of the nanobodies, S14, showed high affinity to SARS-CoV RBD and potent neutralization activity at the picomole level against SARS-CoV pseudovirus. A competitive inhibition assay showed that S14 blocked the binding of SARS-CoV RBD to either soluble or cell-expressed angiotensin-converting enzyme 2 (ACE2). In summary, we developed a novel nanobody targeting SARS-CoV RBD, which might be useful for the development of therapeutics against SARS.

Nanotechnology based solutions to combat zoonotic viruses with special attention to SARS, MERS, and COVID 19: Detection, protection and medication

Zoonotic viruses originate from birds or animal sources and responsible for disease transmission from animals to people through zoonotic spill over and presents a significant global health concern due to lack of rapid diagnostics and therapeutics. The Corona viruses (CoV) were known to be transmitted in mammals. Early this year, SARS-CoV-2, a novel strain of corona virus, was identified as the causative pathogen of an outbreak of viral pneumonia in Wuhan, China. The disease later named corona virus disease 2019 (COVID-19), subsequently spread across the globe rapidly. Nano-particles and viruses are comparable in size, which serves to be a major advantage of using nano-material in clinical strategy to combat viruses. Nanotechnology provides novel solutions against zoonotic viruses by providing cheap and efficient detection methods, novel, and new effective rapid diagnostics and therapeutics. The prospective of nanotechnology in COVID 19 is exceptionally high due to their small size, large surface-to-volume ratio, susceptibility to modification, intrinsic viricidal activity. The nano-based strategies address the COVID 19 by extending their role in i) designing nano-materials for drug/vaccine delivery, ii) developing nano-based diagnostic approaches like nano-sensors iii) novel nano-based personal protection equipment to be used in prevention strategies.This review aims to bring attention to the significant contribution of nanotechnology to mitigate against zoonotic viral pandemics by prevention, faster diagnosis and medication point of view.

Peptide-Based Inhibitors for SARS-CoV-2 and SARS-CoV

The COVID‐19 (coronavirus disease) global pandemic, caused by the spread of the SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus 2) virus, currently has limited treatment options which include vaccines, anti‐virals, and repurposed therapeutics. With their high specificity, tunability, and biocompatibility, small molecules like peptides are positioned to act as key players in combating SARS‐CoV‐2, and can be readily modified to match viral mutation rate. A recent expansion of the understanding of the viral structure and entry mechanisms has led to the proliferation of therapeutic viral entry inhibitors. In this comprehensive review, inhibitors of SARS and SARS‐CoV‐2 are investigated and discussed based on therapeutic design, inhibitory mechanistic approaches, and common targets. Peptide therapeutics are highlighted, which have demonstrated in vitro or in vivo efficacy, discuss advantages of peptide therapeutics, and common strategies in identifying targets for viral inhibition.

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.

The threat of zoonotic coronaviruses

Since 2002, three zoonotic coronaviruses (CoV), SARS-CoV, MERS-CoV and SARS-CoV-2 have emerged in humans, establishing that emergence of coronaviruses from animal reservoirs represents a significant pandemic threat. SARS-CoV and MERS-CoV led to smaller epidemics with very high case fatality rates while SARS-CoV-2 resulted in a global pandemic. These zoonotic coronaviruses have their likely origins in bat species and they transmit to humans through intermediate hosts. Coronaviruses can occasionally jump between host species due to their high rate of recombination. Pandemic preparedness requires surveillance in animals and occupationally exposed humans and prevention and treatment strategies that have broad activity against coronaviruses.

SARS-CoV, MERS-CoV, and 2019-nCoV viruses: an overview of origin, evolution, and genetic variations

Coronaviruses are single stranded RNA viruses usually present in bats (reservoir hosts), and are generally lethal, highly transmissible, and pathogenic viruses causing sever morbidity and mortality rates in human. Several animals including civets, camels, etc. have been identified as intermediate hosts enabling effective recombination of these viruses to emerge as new virulent and pathogenic strains. Among the seven known human coronaviruses SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV) have evolved as severe pathogenic forms infecting the human respiratory tract. About 8096 cases and 774 deaths were reported worldwide with the SARS-CoV infection during year 2002; 2229 cases and 791 deaths were reported for the MERS-CoV that emerged during 2012. Recently ~ 33,849,737 cases and 1,012,742 deaths (data as on 30 Sep 2020) were reported from the recent evolver SARS-CoV-2 infection. Studies on epidemiology and pathogenicity have shown that the viral spread was potentially caused by the contact route especially through the droplets, aerosols, and contaminated fomites. Genomic studies have confirmed the role of the viral spike protein in virulence and pathogenicity. They target the respiratory tract of the human causing severe progressive pneumonia affecting other organs like central nervous system in case of SARS-CoV, severe renal failure in MERS-CoV, and multi-organ failure in SARS-CoV-2. Herein, with respect to current awareness and role of coronaviruses in global public health, we review the various factors involving the origin, evolution, and transmission including the genetic variations observed, epidemiology, and pathogenicity of the three potential coronaviruses variants SARS-CoV, MERS-CoV, and 2019-nCoV.

Towards a more effective strategy for COVID-19 prevention (Review)

At the end of 2019, a new disease, similar to severe acute respiratory syndrome (SARS) associated with SARS-CoV was reported in Wuhan, China. It was quickly discovered that the etiological factor of the new disease (COVID-19) was a previously unknown SARS coronavirus 2 (SARS-CoV-2). The global spread of of COVID-19 has lead to the declaration of a pandemic status in 2019-2020 as declared by the World Health Organization and Public Health Emergency of International Concern. SARS-CoV-2 characterizes with high epidemic potential and is effectively disseminated between humans. SARS-CoV and SARS-CoV-2 are closely related pathogens. Their prime route of distribution is air-droplet transmission. Combating infectious diseases disseminated by inhalation is very difficult, and mainly relies on the use of vaccines. However, despite the lack of an effective anti-SARS-CoV vaccine and specific antiviral drugs, the strict sanitary procedures proved to be sufficient to stop the SARS epidemic in June 2003. However, epidemic research has indicated that SARS-CoV-2 is transmitted in humans significantly more effectively than SARS-CoV; therefore, the COVID-19 pandemic continues to expand. This indicates that the so far anti-epidemic activities to control COVID-19 are insufficient. In the current review, the possibility of using interferon α (IFN-α) as a preventive agent of COVID-19 is discussed. The current data concerning anti-COVID-19 vaccines and specific drugs against SARS-CoV-2 are also discussed. The aim of the current review is to contribute to the introduction of a more efficient strategy in the protection of the human population against COVID-19.

Autopsy Services and Emergency Preparedness of a Tertiary Academic Hospital Mortuary for the COVID-19 Public Health Emergency: The Yale Plan

Pathology Autopsy and Mortuary Services have been front and center in the severe acute respiratory syndrome coronavirus 2 (SARS-Co-V-2) pandemic. The sheer number of fatalities from the pandemic have been unlike any other in recent memory and needed the rapid creation of new protocols and paradigms to manage the situation. This required rapidly escalating mortuary capacity to manage the increased fatalities from the pandemic with the establishment of lines of communication and networking with governmental entities, institution of new policies for patient flow, and implementation of worker infection control and well-being plans. Autopsies also assumed a crucial role, both to provide insight into the pathomechanisms of a novel disease and to allow tissue retrieval necessary to power research directed towards finding a vaccine. We here outline the plan adopted by the Yale Autopsy and Mortuary Services, in alignment with the institutional mission of high-quality patient care, education, research and health care worker safety and well-being, as the Corona Virus Disease of 2019 (COVID-19) pandemic surged in Connecticut. In the early response phase, ensuring sufficient mortuary capacity necessarily took center stage. As we enter the recovery and plateau phase of the pandemic, setting up a process for a rapid and safe autopsy, that will meet educational and research needs while ensuring the safety of our workforce is being implemented.

Host Receptors of Influenza Viruses and Coronaviruses-Molecular Mechanisms of Recognition

Among the four genera of influenza viruses (IVs) and the four genera of coronaviruses (CoVs), zoonotic αIV and βCoV have occasionally caused airborne epidemic outbreaks in humans, who are immunologically naïve, and the outbreaks have resulted in high fatality rates as well as social and economic disruption and losses. The most devasting influenza A virus (IAV) in αIV, pandemic H1N1 in 1918, which caused at least 40 million deaths from about 500 million cases of infection, was the first recorded emergence of IAVs in humans. Usually, a novel human-adapted virus replaces the preexisting human-adapted virus. Interestingly, two IAV subtypes, A/H3N2/1968 and A/H1N1/2009 variants, and two lineages of influenza B viruses (IBV) in βIV, B/Yamagata and B/Victoria lineage-like viruses, remain seasonally detectable in humans. Both influenza C viruses (ICVs) in γIV and four human CoVs, HCoV-229E and HCoV-NL63 in αCoV and HCoV-OC43 and HCoV-HKU1 in βCoV, usually cause mild respiratory infections. Much attention has been given to CoVs since the global epidemic outbreaks of βSARS-CoV in 2002–2004 and βMERS-CoV from 2012 to present. βSARS-CoV-2, which is causing the ongoing COVID-19 pandemic that has resulted in 890,392 deaths from about 27 million cases of infection as of 8 September 2020, has provoked worldwide investigations of CoVs. With the aim of developing efficient strategies for controlling virus outbreaks and recurrences of seasonal virus variants, here we overview the structures, diversities, host ranges and host receptors of all IVs and CoVs and critically review current knowledge of receptor binding specificity of spike glycoproteins, which mediates infection, of IVs and of zoonotic, pandemic and seasonal CoVs.

Angiotensin-converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection

Coronavirus (CoV) disease 2019 (COVID-19) is an ongoing pandemic caused by severe acute respiratory syndrome CoV 2 (SARS-CoV-2). The highly contagious SARS-CoV-2 belongs to the genus Betacoronavirus, and it is phylogenetically closely related to SARS-CoV, a human CoV that caused an outbreak back in 2002 to 2003. Both SARS-CoV-2 and SARS-CoV enter human cells via the interactions between viral crown-like spike protein and human angiotensin-converting enzyme 2 (ACE2) receptor. Here, we aim to review the involvement of ACE2 in human CoV infections by discussing the roles of ACE2 in CoV evolution, cross-species transmissibility, and COVID-19 susceptibility. We also provide our perspectives on COVID-19 treatment and prevention.

The Novel Coronavirus Disease (COVID-19): A PRISMA Systematic Review and Meta-Analysis of Clinical and Paraclinical Characteristics

An outbreak of pneumonia, caused by a novel coronavirus (SARS-CoV-2), was identified in China in December 2019. This virus expanded worldwide, causing global concern. Although clinical, laboratory, and imaging features of COVID-19 are characterized in some observational studies, we undertook a systematic review and meta-analysis to assess the frequency of these features. We did a systematic review and meta-analysis using three databases to identify clinical, laboratory, and computerized tomography (CT) scanning features of rRT-PCR confirmed cases of COVID-19. Data for 3420 patients from 30 observational studies were included. Overall, the results showed that fever (84.2%, 95% CI 82.6-85.7), cough (62%, 95% CI 60-64), and fatigue (39.4%, 95% CI 37.2-41.6%) are the most prevalent symptoms in COVID-19 patients. Increased CRP level, decreased lymphocyte count, and increased D-dimer level were the most common laboratory findings. Among COVID-19 patients, 92% had a positive CT finding, most prevalently ground-glass opacification (GGO) (60%, 95% CI 58-62) and peripheral distribution opacification (64%, 95% CI 60-69). These results demonstrate the clinical, paraclinical, and imaging features of COVID-19.

Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus

Severe acute respiratory syndrome coronavirus (SARS-CoV) was discovered as a novel pathogen in the 2002-2003 SARS epidemic. The emergence and disappearance of this pathogen have brought questions regarding its source and evolution. Within the genome sequences of 281 SARS-CoVs, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and SARS-related CoVs (SARSr-CoVs), a ~430 bp genomic region (from 27 701 bp to 28 131 bp in AY390556.1) with regular variations was investigated. This ~430 bp region overlaps with the ORF8 gene and is prone to deletions and nucleotide substitutions. Its complexity suggested the need for a new genotyping method for coronaviruses related to SARS-similar coronaviruses (SARS-CoV, SARSr-CoV, and SARS-CoV-2). Bat SARSr-CoV presented 3 genotypes, of which type 0 is only seen in bat SARSr-CoV, type I is present in SARS in the early phase, and type II is found in all SARS-CoV-2. This genotyping also shows potential usage in distinguishing the SARS-similar coronaviruses from different hosts and geographic areas. This genomic region has important implications for predicting the epidemic trend and studying the evolution of coronavirus.

Aromatic Herbs, Medicinal Plant-Derived Essential Oils, and Phytochemical Extracts as Potential Therapies for Coronaviruses: Future Perspectives

After its recent discovery in patients with serious pneumonia in Wuhan (China), the 2019 novel coronavirus (2019-nCoV), named also Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spread quickly. Unfortunately, no drug or vaccine for treating human this coronavirus infection is available yet. Numerous options for controlling or preventing emerging 2019-nCoV infections may be predicted, including vaccines, interferon therapies, and small-molecule drugs. However, new interventions are likely to require months to years to develop. In addition, most of the existing antiviral treatments frequently lead to the development of viral resistance combined with the problem of side effects, viral re-emergence, and viral dormancy. The pharmaceutical industry is progressively targeting phytochemical extracts, medicinal plants, and aromatic herbs with the aim of identifying lead compounds, focusing principally on appropriate alternative antiviral drugs. Spices, herbal medicines, essential oils (EOs), and distilled natural products provide a rich source of compounds for the discovery and production of novel antiviral drugs. The determination of the antiviral mechanisms of these natural products has revealed how they interfere with the viral life cycle, i.e., during viral entry, replication, assembly, or discharge, as well as virus-specific host targets. Presently, there are no appropriate or approved drugs against CoVs, but some potential natural treatments and cures have been proposed. Given the perseverance of the 2019-nCoV outbreak, this review paper will illustrate several of the potent antiviral chemical constituents extracted from medicinal and aromatic plants, natural products, and herbal medicines with recognized in vitro and in vivo effects, along with their structure-effect relationships. As this review shows, numerous potentially valuable aromatic herbs and phytochemicals are awaiting assessment and exploitation for therapeutic use against genetically and functionally different virus families, including coronaviruses.

Development of indigenous IgG ELISA for the detection of anti-SARS-CoV-2 IgG

BACKGROUND & OBJECTIVES

Since the beginning of the year 2020, the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacted humankind adversely in almost all spheres of life. The virus belongs to the genus Betacoronavirus of the family Coronaviridae. SARS-CoV-2 causes the disease known as coronavirus disease 2019 (COVID-19) with mild-to-severe respiratory illness. The currently available diagnostic tools for the diagnosis of COVID-19 are mainly based on molecular assays. Real-time reverse transcription-polymerase chain reaction is the only diagnostic method currently recommended by the World Health Organization for COVID-19. With the rapid spread of SARS-CoV-2, it is necessary to utilize other tests, which would determine the burden of the disease as well as the spread of the outbreak. Considering the need for the development of such a screening test, an attempt was made to develop and evaluate an IgG-based ELISA for COVID-19.

METHODS

A total of 513 blood samples (131 positive, 382 negative for SARS-CoV-2) were collected and tested by microneutralization test (MNT). Antigen stock of SARS-CoV-2 was prepared by propagating the virus in Vero CCL-81 cells. An IgG capture ELISA was developed for serological detection of anti-SARS-CoV-2 IgG in serum samples. The end point cut-off values were determined by using receiver operating characteristic (ROC) curve. Inter-assay variability was determined.

RESULTS

The developed ELISA was found to be 92.37 per cent sensitive, 97.9 per cent specific, robust and reproducible. The positive and negative predictive values were 94.44 and 98.14 per cent, respectively.

INTERPRETATION & CONCLUSIONS

This indigenously developed IgG ELISA was found to be sensitive and specific for the detection of anti-SARS-CoV-2 IgG in human serum samples. This assay may be used for determining seroprevalence of SARS-CoV-2 in a population exposed to the virus.

Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus

Recently, a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by severe acute respiratory syndrome coronavirus (SARS-CoV). Since the SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between the SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here, we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV and may help epidemic surveillance and preventive measures against 2019-nCoV.IMPORTANCE The recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002 to 2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational, and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV.

Origin and evolution of pathogenic coronaviruses

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two highly transmissible and pathogenic viruses that emerged in humans at the beginning of the 21st century. Both viruses likely originated in bats, and genetically diverse coronaviruses that are related to SARS-CoV and MERS-CoV were discovered in bats worldwide. In this Review, we summarize the current knowledge on the origin and evolution of these two pathogenic coronaviruses and discuss their receptor usage; we also highlight the diversity and potential of spillover of bat-borne coronaviruses, as evidenced by the recent spillover of swine acute diarrhoea syndrome coronavirus (SADS-CoV) to pigs.

Viral Respiratory Infections

Acute respiratory illnesses are the most frequently occurring illness in all age groups globally. Disease is mostly limited to the upper airways and is self-limiting, but a small percentage can progress to lower respiratory tract infections as bronchiolitis and pneumonia. Children and elderly people are at increased risk, especially in developing countries.

The most important etiologic agents of severe lower respiratory illness are bacteria such as Streptococcus pneumoniae and Haemophilus influenzae and viruses such as respiratory syncytial virus (RSV) and influenza virus. Efficacious vaccines are available against the two bacteria and the influenza virus. Viruses are much more important in mild upper and middle respiratory tract infections and in bronchiolitis in children, whereas bacteria are the main cause of pneumonia, especially in adults. Clinical syndromes overlap considerably, and there is increasing evidence of bacterial-viral co-infections and of bacterial pneumonia being secondary to viral respiratory tract infection.

DOVE: An Infectious Disease Outbreak Statistics Visualization System

Humans are susceptible to various infectious diseases. However, humanity still has limited responses to emergent and recurrent infectious diseases. Recent developments in medical technology have led to various vaccines being developed, but these vaccines typically require a considerable amount of time to counter infectious diseases. Therefore, one of the best methods to prevent infectious diseases is to continuously update our knowledge with useful information from infectious disease information systems and taking active steps to safeguard ourselves against infectious diseases. Some existing infectious disease information systems simply present infectious disease information in the form of text or transmit it via e-mail. Other systems provide data in the form of files or maps. Most existing systems display text-centric information regarding infectious disease outbreaks. Therefore, understanding infectious disease outbreak information at a glance is difficult for users. In this paper, we propose the infectious disease outbreak statistics visualization system, called to DOVE, which collects infectious disease outbreak statistics from the Korea Centers for Disease Control & Prevention and provides statistical charts with district, time, infectious disease, gender, and age data. Users can easily identify infectious disease outbreak statistics at a glance by simply entering the district, time, and name of an infectious disease into our system. Additionally, each statistical chart allows users to recognize the characteristics of an infectious disease and predict outbreaks by investigating the outbreak trends of that disease. We believe that our system provides effective information to help prevent infectious disease outbreaks. Our system is currently available on the web at http://www.epidemic.co.kr/statistics.

Development of animal models against emerging coronaviruses: From SARS to MERS coronavirus

Two novel coronaviruses have emerged to cause severe disease in humans. While bats may be the primary reservoir for both viruses, SARS coronavirus (SARS-CoV) likely crossed into humans from civets in China, and MERS coronavirus (MERS-CoV) has been transmitted from camels in the Middle East. Unlike SARS-CoV that resolved within a year, continued introductions of MERS-CoV present an on-going public health threat. Animal models are needed to evaluate countermeasures against emerging viruses. With SARS-CoV, several animal species were permissive to infection. In contrast, most laboratory animals are refractory or only semi-permissive to infection with MERS-CoV. This host-range restriction is largely determined by sequence heterogeneity in the MERS-CoV receptor. We describe animal models developed to study coronaviruses, with a focus on host-range restriction at the level of the viral receptor and discuss approaches to consider in developing a model to evaluate countermeasures against MERS-CoV.

Effects of human anti-spike protein receptor binding domain antibodies on severe acute respiratory syndrome coronavirus neutralization escape and fitness

The receptor binding domain (RBD) of the spike (S) glycoprotein of severe acute respiratory syndrome coronavirus (SARS-CoV) is a major target of protective immunity in vivo. Although a large number of neutralizing antibodies (nAbs) have been developed, it remains unclear if a single RBD-targeting nAb or two in combination can prevent neutralization escape and, if not, attenuate viral virulence in vivo. In this study, we used a large panel of human nAbs against an epitope that overlaps the interface between the RBD and its receptor, angiotensin-converting enzyme 2 (ACE2), to assess their cross-neutralization activities against a panel of human and zoonotic SARS-CoVs and neutralization escape mutants. We also investigated the neutralization escape profiles of these nAbs and evaluated their effects on receptor binding and virus fitness in vitro and in mice. We found that some nAbs had great potency and breadth in neutralizing multiple viral strains, including neutralization escape viruses derived from other nAbs; however, no single nAb or combination of two blocked neutralization escape. Interestingly, in mice the neutralization escape mutant viruses showed either attenuation (Urbani background) or increased virulence (GD03 background) consistent with the different binding affinities between their RBDs and the mouse ACE2. We conclude that using either single nAbs or dual nAb combinations to target a SARS-CoV RBD epitope that shows plasticity may have limitations for preventing neutralization escape during in vivo immunotherapy. However, RBD-directed nAbs may be useful for providing broad neutralization and prevention of escape variants when combined with other nAbs that target a second conserved epitope with less plasticity and more structural constraint.

IMPORTANCE

The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 has resulted in severe human respiratory disease with high death rates. Their zoonotic origins highlight the likelihood of reemergence or further evolution into novel human coronavirus pathogens. Broadly neutralizing antibodies (nAbs) that prevent infection of related viruses represent an important immunostrategy for combating coronavirus infections; however, for this strategy to succeed, it is essential to uncover nAb-mediated escape pathways and to pioneer strategies that prevent escape. Here, we used SARS-CoV as a research model and examined the escape pathways of broad nAbs that target the receptor binding domain (RBD) of the virus. We found that neither single nAbs nor two nAbs in combination blocked escape. Our results suggest that targeting conserved regions with less plasticity and more structural constraint rather than the SARS-CoV RBD-like region(s) should have broader utility for antibody-based immunotherapy.

The effects of Nigella sativa (Ns), Anthemis hyalina (Ah) and Citrus sinensis (Cs) extracts on the replication of coronavirus and the expression of TRP genes family

Extracts of Anthemis hyalina (Ah), Nigella sativa (Ns) and peels of Citrus sinensis (Cs) have been used as folk medicine to fight antimicrobial diseases. To evaluate the effect of extracts of Ah, Ns and Cs on the replication of coronavirus (CoV) and on the expression of TRP genes during coronavirus infection, HeLa-CEACAM1a (HeLa-epithelial carcinoembryonic antigen-related cell adhesion molecule 1a) cells were inoculated with MHV-A59 (mouse hepatitis virus–A59) at moi of 30. 1/50 dilution of the extracts was found to be the safe active dose. ELISA kits were used to detect the human IL-8 levels. Total RNA was isolated from the infected cells and cDNA was synthesized. Fluidigm Dynamic Array nanofluidic chip 96.96 was used to analyze the mRNA expression of 21 TRP genes and two control genes. Data was analyzed using the BioMark digital array software. Determinations of relative gene expression values were carried out by using the 2^−∆∆Ct method (normalized threshold cycle (Ct) value of sample minus normalized Ct value of control). TCID₅₀/ml (tissue culture infectious dose that will produce cytopathic effect in 50 % of the inoculated tissue culture cells) was found for treatments to determine the viral loads. The inflammatory cytokine IL-8 level was found to increase for both 24 and 48 h time points following Ns extract treatment. TRPA1, TRPC4, TRPM6, TRPM7, TRPM8 and TRPV4 were the genes which expression levels changed significantly after Ah, Ns or Cs extract treatments. The virus load decreased when any of the Ah, Ns or Cs extracts was added to the CoV infected cells with Ah extract treatment leading to undetectable virus load for both 6 and 8hpi. Although all the extract treatments had an effect on IL-8 secretion, TRP gene expression and virus load after CoV infection, it was the Ah extract treatment that showed the biggest difference in virus load. Therefore Ah extract is the best candidate in our hands that contains potential treatment molecule(s).

Coronavirus

Name of Virus: Coronavirus

Clinical management and infection control of SARS: lessons learned

The outbreak of severe acute respiratory syndrome (SARS) in 2003 was the first emergence of an important human pathogen in the 21st century. Responding to the epidemic provided clinicians with extensive experience in diagnosing and treating a novel respiratory viral disease. In this article, we review the experience of the SARS epidemic, focusing on measures taken to identify and isolate patients, prevent the transmission of infection to healthcare workers and develop effective therapies. Lessons learned from the SARS epidemic will be especially important in responding to the current emergence of another highly pathogenic human coronavirus, the agent of Middle East respiratory syndrome (MERS), and to the recently emerging H7N9 influenza A virus in China. This paper forms part of a symposium in Antiviral Research on "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses."

From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses

•

We review the outbreak of severe acute respiratory syndrome (SARS) in 2002–2003 and antiviral treatment of patients.

•

We review efforts towards the rational design of anti-SARS therapeutics.

•

We present a comprehensive list of all available 3-dimensional structures of coronavirus proteins.

•

We discuss the emerging MERS coronavirus and review the few antivirals available for treatment.

•

We critically discuss which lessons have been learned from SARS and which are yet to be learned.

This article introduces a series of invited papers in Antiviral Research marking the 10th anniversary of the outbreak of severe acute respiratory syndrome (SARS), caused by a novel coronavirus that emerged in southern China in late 2002. Until that time, coronaviruses had not been recognized as agents causing severe disease in humans, hence, the emergence of the SARS-CoV came as a complete surprise. Research during the past ten years has revealed the existence of a diverse pool of coronaviruses circulating among various bat species and other animals, suggesting that further introductions of highly pathogenic coronaviruses into the human population are not merely probable, but inevitable. The recent emergence of another coronavirus causing severe disease, Middle East respiratory syndrome (MERS), in humans, has made it clear that coronaviruses pose a major threat to human health, and that more research is urgently needed to elucidate their replication mechanisms, identify potential drug targets, and develop effective countermeasures. In this series, experts in many different aspects of coronavirus replication and disease will provide authoritative, up-to-date reviews of the following topics:

– clinical management and infection control of SARS;

– reservoir hosts of coronaviruses;

– receptor recognition and cross-species transmission of SARS-CoV;

– SARS-CoV evasion of innate immune responses;

– structures and functions of individual coronaviral proteins;

– anti-coronavirus drug discovery and development; and

– the public health legacy of the SARS outbreak.

Each article will be identified in the last line of its abstract as belonging to the series “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.”

Receptor recognition and cross-species infections of SARS coronavirus

Receptor recognition is a major determinant of the host range, cross-species infections, and pathogenesis of the severe acute respiratory syndrome coronavirus (SARS-CoV). A defined receptor-binding domain (RBD) in the SARS-CoV spike protein specifically recognizes its host receptor, angiotensin-converting enzyme 2 (ACE2). This article reviews the latest knowledge about how RBDs from different SARS-CoV strains interact with ACE2 from several animal species. Detailed research on these RBD/ACE2 interactions has established important principles on host receptor adaptations, cross-species infections, and future evolution of SARS-CoV. These principles may apply to other emerging animal viruses, including the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV). This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses".

Receptor-binding domain as a target for developing SARS vaccines

A decade ago, severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) caused a global pandemic with a mortality rate of 10%. Reports of recent outbreaks of a SARS-like disease caused by Middle East respiratory syndrome coronavirus (MERS-CoV) have raised serious concerns of a possible reemergence of SARS-CoV, either by laboratory escape or the presence of a natural reservoir. Therefore, the development of effective and safe SARS vaccines is still needed. Based on our previous studies, we believe that the receptor-binding domain (RBD) in the S1 subunit of the SARS-CoV spike (S) protein is the most important target for developing a SARS vaccine. In particular, RBD of S protein contains the critical neutralizing domain (CND), which is able to induce highly potent neutralizing antibody response and cross-protection against divergent SARS-CoV strains. Furthermore, a RBD-based subunit vaccine is expected to be safer than other vaccines that may induce Th2-type immunopathology. This review will discuss key advances in the development of RBD-based SARS vaccines and the possibility of using a similar strategy to develop vaccines against MERS-CoV.

Animal models in virus research: their utility and limitations

Viral diseases are important threats to public health worldwide. With the number of emerging viral diseases increasing the last decades, there is a growing need for appropriate animal models for virus studies. The relevance of animal models can be limited in terms of mimicking human pathophysiology. In this review, we discuss the utility of animal models for studies of influenza A viruses, HIV and SARS-CoV in light of viral emergence, assessment of infection and transmission risks, and regulatory decision making. We address their relevance and limitations. The susceptibility, immune responses, pathogenesis, and pharmacokinetics may differ between the various animal models. These complexities may thwart translating results from animal experiments to the humans. Within these constraints, animal models are very informative for studying virus immunopathology and transmission modes and for translation of virus research into clinical benefit. Insight in the limitations of the various models may facilitate further improvements of the models.

Increased antibody affinity confers broad in vitro protection against escape mutants of severe acute respiratory syndrome coronavirus

Even though the effect of antibody affinity on neutralization potency is well documented, surprisingly, its impact on neutralization breadth and escape has not been systematically determined. Here, random mutagenesis and DNA shuffling of the single-chain variable fragment of the neutralizing antibody 80R followed by bacterial display screening using anchored periplasmic expression (APEx) were used to generate a number of higher-affinity variants of the severe acute respiratory syndrome coronavirus (SARS-CoV)-neutralizing antibody 80R with equilibrium dissociation constants (K(D)) as low as 37 pM, a >270-fold improvement relative to that of the parental 80R single-chain variable fragment (scFv). As expected, antigen affinity was shown to correlate directly with neutralization potency toward the icUrbani strain of SARS-CoV. Additionally, the highest-affinity antibody fragment displayed 10-fold-increased broad neutralization in vitro and completely protected against several SARS-CoV strains containing substitutions associated with antibody escape. Importantly, higher affinity also led to the suppression of viral escape mutants in vitro. Escape from the highest-affinity variant required reduced selective pressure and multiple substitutions in the binding epitope. Collectively, these results support the hypothesis that engineered antibodies with picomolar dissociation constants for a neutralizing epitope can confer escape-resistant protection.

Mechanisms of host receptor adaptation by severe acute respiratory syndrome coronavirus

The severe acute respiratory syndrome coronavirus (SARS-CoV) from palm civets has twice evolved the capacity to infect humans by gaining binding affinity for human receptor angiotensin-converting enzyme 2 (ACE2). Numerous mutations have been identified in the receptor-binding domain (RBD) of different SARS-CoV strains isolated from humans or civets. Why these mutations were naturally selected or how SARS-CoV evolved to adapt to different host receptors has been poorly understood, presenting evolutionary and epidemic conundrums. In this study, we investigated the impact of these mutations on receptor recognition, an important determinant of SARS-CoV infection and pathogenesis. Using a combination of biochemical, functional, and crystallographic approaches, we elucidated the molecular and structural mechanisms of each of these naturally selected RBD mutations. These mutations either strengthen favorable interactions or reduce unfavorable interactions with two virus-binding hot spots on ACE2, and by doing so, they enhance viral interactions with either human (hACE2) or civet (cACE2) ACE2. Therefore, these mutations were viral adaptations to either hACE2 or cACE2. To corroborate the above analysis, we designed and characterized two optimized RBDs. The human-optimized RBD contains all of the hACE2-adapted residues (Phe-442, Phe-472, Asn-479, Asp-480, and Thr-487) and possesses exceptionally high affinity for hACE2 but relative low affinity for cACE2. The civet-optimized RBD contains all of the cACE2-adapted residues (Tyr-442, Pro-472, Arg-479, Gly-480, and Thr-487) and possesses exceptionally high affinity for cACE2 and also substantial affinity for hACE2. These results not only illustrate the detailed mechanisms of host receptor adaptation by SARS-CoV but also provide a molecular and structural basis for tracking future SARS-CoV evolution in animals.

Epidemic viral pneumonia and other emerging pathogens

Viruses cause a high percentage of community-acquired pneumonias. The advent of polymerase chain reaction and other molecular techniques has been associated with the detection of a higher prevalence of common respiratory viruses than previously suspected. Better diagnostics have shown new viral pathogens regularly in epidemics, immunocompromised patients, and occasionally children. Despite better diagnostics, treatment for all but influenza is still very limited.

Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences

Bats may host emerging viruses, including coronaviruses (CoV). We conducted an evaluation of CoV in rhinolophid and vespertilionid bat species common in Europe. Rhinolophids carried severe acute respiratory syndrome (SARS)-related CoV at high frequencies and concentrations (26% of animals are positive; up to 2.4×10(8) copies per gram of feces), as well as two Alphacoronavirus clades, one novel and one related to the HKU2 clade. All three clades present in Miniopterus bats in China (HKU7, HKU8, and 1A related) were also present in European Miniopterus bats. An additional novel Alphacoronavirus clade (bat CoV [BtCoV]/BNM98-30) was detected in Nyctalus leisleri. A CoV grouping criterion was developed by comparing amino acid identities across an 816-bp fragment of the RNA-dependent RNA polymerases (RdRp) of all accepted mammalian CoV species (RdRp-based grouping units [RGU]). Criteria for defining separate RGU in mammalian CoV were a >4.8% amino acid distance for alphacoronaviruses and a >6.3% distance for betacoronaviruses. All the above-mentioned novel clades represented independent RGU. Strict associations between CoV RGU and host bat genera were confirmed for six independent RGU represented simultaneously in China and Europe. A SARS-related virus (BtCoV/BM48-31/Bulgaria/2008) from a Rhinolophus blasii (Rhi bla) bat was fully sequenced. It is predicted that proteins 3b and 6 were highly divergent from those proteins in all known SARS-related CoV. Open reading frame 8 (ORF8) was surprisingly absent. Surface expression of spike and staining with sera of SARS survivors suggested low antigenic overlap with SARS CoV. However, the receptor binding domain of SARS CoV showed higher similarity with that of BtCoV/BM48-31/Bulgaria/2008 than with that of any Chinese bat-borne CoV. Critical spike domains 472 and 487 were identical and similar, respectively. This study underlines the importance of assessments of the zoonotic potential of widely distributed bat-borne CoV.

Lessons from the past: perspectives on severe acute respiratory syndrome

On March 12, 2003, the World Health Organization issued a global health alert stating that a new, unrecognizable, flulike disease may spread to health care workers (HCWs). We now know this illness as severe acute respiratory syndrome (SARS). By August 2003, there were 8422 SARS cases and 916 deaths reported from 29 countries. SARS galvanized the world to the threat of emerging infectious diseases and provided a dress rehearsal for subsequent challenges such as H5N1 and H1N1 influenza. Among the insights gained were the following: SARS reminded us that health care work can be hazardous; the effects of SARS extended beyond the infection; general principles for prevention and control were effective against SARS; and SARS posed both a public health and an occupational health threat. Given these perspectives gained, we should be better prepared when faced with similar scenarios in the future.

A 219-mer CHO-expressing receptor-binding domain of SARS-CoV S protein induces potent immune responses and protective immunity

Development of vaccines is essential for the prevention of future recurrences of severe acute respiratory syndrome (SARS), caused by the SARS coronavirus (SARS-CoV). The spike (S) protein, especially receptor-binding domain (RBD) of SARS-CoV, plays important roles in the prevention of SARS infection, and is thus an important component in SARS vaccine development. In this study, we expressed a 219-mer (residues 318-536) RBD protein in Chinese hamster ovary (CHO)-K1 cells (RBD219-CHO), and tested its immune responses and protective immunity in a mouse model. The results showed that this recombinant protein was correctly folded, being able to maintain intact conformation and authentic antigenicity. It could induce strong humoral and cellular immune responses and high titers of neutralizing antibodies in the vaccinated mice. RBD219-CHO protein elicited potent protective immunity that protected all vaccinated mice from SARS-CoV challenge. These results suggest that the recombinant RBD219-CHO protein has great potential for the development of an effective and safe SARS subunit vaccine.

Update on SARS research and other possibly zoonotic coronaviruses

The global outbreak of severe acute respiratory syndrome (SARS) in 2003 led to an intense and effective global response that stopped the spread of the disease by July 2003. There was also an intensive and very productive research effort to identify the aetiological agent, characterise the clinical and epidemiological features of the disease, understand the pathogenesis of the disease and the molecular biology of the virus, and design antiviral drugs and vaccines to treat and prevent the disease. In parallel with the SARS research effort there have been continuous improvements in our ability to detect and characterise other novel viruses. The SARS outbreak illustrates the importance of such detection tools in the response to public health threats. Studies since the SARS outbreak suggest that many novel viruses exist in animals and some, but probably not many, will present a risk to humans.

Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences

Bats may host emerging viruses, including coronaviruses (CoV). We conducted an evaluation of CoV in rhinolophid and vespertilionid bat species common in Europe. Rhinolophids carried severe acute respiratory syndrome (SARS)-related CoV at high frequencies and concentrations (26% of animals are positive; up to 2.4×10(8) copies per gram of feces), as well as two Alphacoronavirus clades, one novel and one related to the HKU2 clade. All three clades present in Miniopterus bats in China (HKU7, HKU8, and 1A related) were also present in European Miniopterus bats. An additional novel Alphacoronavirus clade (bat CoV [BtCoV]/BNM98-30) was detected in Nyctalus leisleri. A CoV grouping criterion was developed by comparing amino acid identities across an 816-bp fragment of the RNA-dependent RNA polymerases (RdRp) of all accepted mammalian CoV species (RdRp-based grouping units [RGU]). Criteria for defining separate RGU in mammalian CoV were a >4.8% amino acid distance for alphacoronaviruses and a >6.3% distance for betacoronaviruses. All the above-mentioned novel clades represented independent RGU. Strict associations between CoV RGU and host bat genera were confirmed for six independent RGU represented simultaneously in China and Europe. A SARS-related virus (BtCoV/BM48-31/Bulgaria/2008) from a Rhinolophus blasii (Rhi bla) bat was fully sequenced. It is predicted that proteins 3b and 6 were highly divergent from those proteins in all known SARS-related CoV. Open reading frame 8 (ORF8) was surprisingly absent. Surface expression of spike and staining with sera of SARS survivors suggested low antigenic overlap with SARS CoV. However, the receptor binding domain of SARS CoV showed higher similarity with that of BtCoV/BM48-31/Bulgaria/2008 than with that of any Chinese bat-borne CoV. Critical spike domains 472 and 487 were identical and similar, respectively. This study underlines the importance of assessments of the zoonotic potential of widely distributed bat-borne CoV.