Spiking the MERS-coronavirus receptor

A novel coronavirus, the Middle East respiratory syndrome coronavirus, recently emerged through zoonotic transmission, causing a severe lower respiratory tract infection in humans. In two recent papers, one published in Cell Research, the crystal structure of the viral receptor-binding domain in complex with the host CD26/dipeptidyl peptidase 4 receptor has now been characterized.In mid 2012, a novel coronavirus (CoV) was isolated form the sputum of a patient with acute pneumonia and renal failure¹. As of July 10^th 2013, this virus, named Middle East respiratory syndrome (MERS)-CoV, has caused 80 laboratory-confirmed infections of which 44 were fatal². The limited data available suggest that the virus is introduced into the human population through multiple independent, zoonotic transmission events from a — so far unknown — animal source with subsequent limited human-to-human spread. However, scenarios in which a single zoonotic transmission event has led to sustained, largely asymptomatic and non-detected human-to-human transmission cannot be excluded yet. Genetically, MERS-CoV is related to SARS-CoV, which killed nearly 10% of approximately 8 000 persons that were infected in the 2003 outbreak. It is therefore of utmost importance to better understand the biology and pathogenesis of this virus.Coronaviruses infect mammals and birds, and occasionally cross the species barrier. The primary determinant of coronavirus host and cell tropism is the viral spike (S) entry protein that functions by binding to a cell surface receptor. The MERS-CoV S protein is a type I membrane glycoprotein, assembled as trimers that constitute the typical crown-like peplomers on the surface of the enveloped coronavirus. Functionally, two regions, S1 and S2, can be defined in the S protein, which are involved in binding and fusion with host cells, respectively. Recent studies have mapped the receptor-binding domain (RBD) to a ∼231-amino acid long region within the S1 region of MERS-CoV³.MERS-CoV uses a cell surface amino peptidase, dipeptidyl peptidase 4 (DPP4), also known as CD26, as a functional receptor⁴. The multifunctional DPP4 — highly conserved among mammals — plays a major role in glucose metabolism by its degradation of incretins. It has been further implicated in T-cell activation, chemotaxis modulation, cell adhesion, and apoptosis⁵. In humans, it is primarily expressed on the epithelial cells in the lungs, kidney, small intestine, liver and prostate, and on activated leukocytes, while it also occurs in a soluble form in the circulation^4,5.The spike-receptor binding interface can be seen as a lock-and-key interaction where minor mutations within the interacting domain of the S protein or the receptor can abrogate infection, placing a barrier for cross-species transmission. Zoonotic potential of coronaviruses has been attributed to the adaptability of the S protein to human receptor orthologs. Intriguingly, the MERS-CoV S protein seems promiscuous in binding to orthologous receptors. Whereas coronaviruses generally tend to have a narrow host tropism, MERS-CoV can infect cells of a wide variety of species, at least in vitro^4,6. The broad cell species tropism suggests that MERS-CoV has acquired facile cross-species transmissibility by binding to an evolutionarily conserved receptor.Just four months after the discovery of the receptor, two Chinese research teams have now independently described the MERS-CoV spike-receptor interface. The study by Wang et al.⁷ recently published in Cell Research, and a recent study by Lu et al.⁸ published in Nature, both reveal the crystal structure of the RBD of the MERS-CoV S protein bound to its receptor, human DPP4. DPP4, of which the structure was published before⁹, consists of an N-terminal eight-bladed β-propeller domain and a C-terminal α/β-hydrolase domain. The RBD of the MERS-CoV S protein contains two subdomains: a conserved core subdomain and a receptor-binding subdomain, with the latter contacting blades 4 and 5 of the DPP4 β-propeller domain. Structural comparison with the RBD of the related betacoronavirus SARS-CoV (using the ACE2 peptidase as a receptor) reveals a conserved core domain and highly variable — both in length and in residues — receptor-binding region, explaining the differential receptor usage.Both teams have scrutinized the RBD-receptor interface and identified critical residues within the interacting domain of the S protein or receptor, which allow MERS-CoV to bind to its receptor. Structural analysis and mutational analysis have identified several key residues in the RBD of the S protein shown to be critical for DPP4 binding and viral entry. This information is crucial to understand the adaptation of MERS-CoV to humans. Studies with SARS-CoV isolated from humans and civet cats (which function as the intermediate host) revealed 2 amino acids in the RBD that caused an > 1 000-fold difference in binding affinity to human receptor ACE2¹⁰. Analysis of the MERS-CoV RBD sequences of the isolates characterized thus far shows no sequence variation except that 2 virus samples isolated from patients in the UK (GenBank: {"type":"entrez-nucleotide","attrs":{"text":"KC667074","term_id":"453061240","term_text":"KC667074"}}KC667074 and {"type":"entrez-nucleotide","attrs":{"text":"KC164505","term_id":"471258596","term_text":"KC164505"}}KC164505) had a leucine-to-phenylalanine substitution at position 506 of the S protein (L506F). As shown by Wang et al.⁷, residue L506 contacts DPP4 and its substitution to alanine reduced MERS-CoV S-mediated infectivity by over 50%.With the structure available, the promiscuous binding of MERS-CoV to DPP4 orthologs can now be analyzed at the molecular level. Relevant to functional usage of orthologous receptors by MERS-CoV is the degree of conservation of the amino acid residues in DPP4 that were identified to contact the viral RBD^7,8. DPP4 sequence comparison reveals that mammalian DPP4 orthologs (e.g., of macaque, horse, rabbit and pig) have no or little variation for residues contacting MERS-CoV RBD in human DPP4 (

Metagenomic Survey for Viruses in Western Arctic Caribou,Alaska, through Iterative Assembly of Taxonomic Units

Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae.     

DNA Barcode Authentication of Wood Samples of Threatened and Commercial Timber Trees within the Tropical Dry Evergreen Forest of India

Background

India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF) barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group.

Methodology/Principal Findings

We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF) species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1^st tier rbcL; 2^nd tier matK) correctly identified 136 out of 143 species (95%). This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method.

Conclusions

We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value.     

Involvement of Enterobacter cloacae in the mortality of the fish, Mugil cephalus

Aims:  To identify the causative agent of the mortality in the fish, Mugil cephalus , in Muttukadu lagoon.
Methods and Results:  An enteric bacterium from the kidneys of moribund fish M. cephalus , was isolated and identified as Enterobacter cloacae (MK). Mugil cephalus was experimentally infected by this isolate and was re-isolated from the kidneys of the moribund fish. Enterobacter cloacae isolates from the lagoon water (MW1, MW2 and reference strain ATCC 13047) and the reference strain were not able to induce similar pathogenesis. The putative factor imparting pathogenicity to the MK isolate was identified as a cationic molecule, which migrated towards the cathode on agarose gel electrophoresis.
Conclusions:  The Ent. cloacae (MK) isolate harbouring a cationic factor was the causative agent for the mortality of M. cephalus , found in Muttukadu lagoon.
Significance and Impact of the Study:  This study reveals that human enteric bacteria MK which is considered as nonpathogenic to fish, may become pathogenic to fish when it harbours this cationic factor. This cationic factor is found to be pathogenic to the fish M. cephalus leading to mortality. It was also found to be pathogenic to mice. Therefore, the shuttling of Ent. cloacae , harbouring cationic factor, between human and fish may be of human health importance.     

Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer

A thorough understanding of virus diversity in wildlife provides epidemiological baseline information about pathogens. In this study, eye swab samples were obtained from semi-domesticated reindeer ( Rangifer tarandus tarandus) in Norway during an outbreak of infectious eye disease, possibly a very early stage of infectious keratoconjunctivitis (IKC). Large scale molecular virus screening, based on host nucleic acid depletion, sequence-independent amplification and next-generation sequencing of partially purified viral nucleic acid, revealed the presence of a new papillomavirus in 2 out of 8 eye swab samples and a new betaherpesvirus in 3 out of 8 eye swab samples collected from animals with clinical signs and not in similar samples in 9 animals without clinical signs. Whether either virus was responsible for causing the clinical signs or in any respect was associated to the disease condition remains to be determined.     

The Receptor Binding Domain of the New Middle East Respiratory Syndrome Coronavirus Maps to a 231-Residue Region in the Spike Protein That Efficiently Elicits Neutralizing Antibodies

The spike (S) protein of the recently emerged human Middle East respiratory syndrome coronavirus (MERS-CoV) mediates infection by binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). Here we mapped the receptor binding domain in the S protein to a 231-amino-acid fragment (residues 358 to 588) by evaluating the interaction of spike truncation variants with receptor-expressing cells and soluble DPP4. Antibodies to this domain—much less so those to the preceding N-terminal region—efficiently neutralize MERS-CoV infection.     

Scrub Typhus Meningitis in South India — A Retrospective Study

Background

Scrub typhus is prevalent in India although definite statistics are not available. There has been only one study on scrub typhus meningitis 20 years ago. Most reports of meningitis/meningoencephalitis in scrub typhus are case reports

Methods

A retrospective study done in Pondicherry to extract cases of scrub typhus admitted to hospital between February 2011 and January 2012. Diagnosis was by a combination of any one of the following in a patient with an acute febrile illness- a positive scrub IgM ELISA, Weil-Felix test, and an eschar. Lumbar puncture was performed in patients with headache, nuchal rigidity, altered sensorium or cranial nerve deficits.

Results

Sixty five cases of scrub typhus were found, and 17 (17/65) had meningitis. There were 33 males and 32 females. Thirteen had an eschar. Median cerebrospinal fluid (CSF) cell count, lymphocyte percentage, CSF protein, CSF glucose/blood glucose, CSF ADA were 54 cells/µL, 98%, 88 mg/dL, 0.622 and 3.5 U/mL respectively. Computed tomography was normal in patients with altered sensorium and cranial nerve deficits. Patients with meningitis had lesser respiratory symptoms and signs and higher urea levels. All patients had received doxycycline except one who additionally received chloramphenicol.

Conclusion

Meningitis in scrub typhus is mild with quick and complete recovery. Clinical features and CSF findings can mimic tuberculous meningitis, except for ADA levels. In the Indian context where both scrub typhus and tuberculosis are endemic, ADA and scrub IgM may be helpful in identifying patients with scrub meningitis and in avoiding prolonged empirical antituberculous therapy in cases of lymphocytic meningitis.     

Computer-Assisted Radiographic Calculation of Spinal Curvature in Brachycephalic “Screw-Tailed” Dog Breeds with Congenital Thoracic Vertebral Malformations: Reliability and Clinical Evaluation

The objectives of this study were: To investigate computer-assisted digital radiographic measurement of Cobb angles in dogs with congenital thoracic vertebral malformations, to determine its intra- and inter-observer reliability and its association with the presence of neurological deficits. Medical records were reviewed (2009–2013) to identify brachycephalic screw-tailed dog breeds with radiographic studies of the thoracic vertebral column and with at least one vertebral malformation present. Twenty-eight dogs were included in the study. The end vertebrae were defined as the cranial end plate of the vertebra cranial to the malformed vertebra and the caudal end plate of the vertebra caudal to the malformed vertebra. Three observers performed the measurements twice. Intraclass correlation coefficients were used to calculate the intra- and inter-observer reliabilities. The intraclass correlation coefficient was excellent for all intra- and inter-observer measurements using this method. There was a significant difference in the kyphotic Cobb angle between dogs with and without associated neurological deficits. The majority of dogs with neurological deficits had a kyphotic Cobb angle higher than 35°. No significant difference in the scoliotic Cobb angle was observed. We concluded that the computer assisted digital radiographic measurement of the Cobb angle for kyphosis and scoliosis is a valid, reproducible and reliable method to quantify the degree of spinal curvature in brachycephalic screw-tailed dog breeds with congenital thoracic vertebral malformations.