Correction to: Recommendations for the nomenclature of enteroviruses and rhinoviruses.

Unfortunately, one of the affiliations of author "A. E. Gorbalenya" was missed in original version. The affiliation is updated here.

Recommendations for the nomenclature of enteroviruses and rhinoviruses.

Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as "coxsackieviruses", "polioviruses" and "echoviruses", which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series of recommendations for the nomenclature of EV and RV types and their abbreviations. We believe their adoption will promote greater clarity and consistency in the terminology used in the scientific and medical literature. The recommendations will additionally provide a useful reference guide for journals, other publications and public databases seeking to use standardised terms for the growing multitude of enteroviruses and rhinoviruses described worldwide.

Middle East respiratory syndrome: making the case for surveillance of transboundary coronaviruses in the Middle East.

Middle East respiratory syndrome (MERS) is a zoonotic viral disease identified in both animals and human beings. More than 2,200 laboratory-confirmed cases have been reported in humans from 27 countries, with a crude case fatality rate of 35% since the disease's emergence in the Middle East in 2012. In the coming years, MERS will continue to pose a severe threat to economic development as well as to the elimination of poverty and advances in food security. An important gap in the effort to keep MERS at bay is the lack of surveillance of animals in the Middle East. The authors identify the need for international collaboration to conduct MERS coronavirus (CoV) surveillance in animals in the Middle East, since the emergence of new MERS-CoV variants with the ability to sustain efficient person-to-person transmission is a genuine threat. However, effective surveillance will be very difficult, if not impossible, to achieve. There are multiple obstacles in the region to overcome, including a lack of transparency as governments in the Middle East generally do not disclose detailed information on animal diseases. In addition, there is minimal collaboration between local and international agencies in both the human and animal health sectors and a limited number of readily available qualified laboratories to screen animals for MERS- CoV. Last, but not least, there is a lack of adequate active communication between all relevant laboratories, local and abroad. However, with the support of the Food and Agriculture Organization of the United Nations (FAO), the World Organisation for Animal Health (OIE), and other partners, the responsibility of the Mediterranean Zoonosis Control Centre in Athens, Greece, could be widened to include the countries of the Middle East. This would foster a stronger alliance and far more effective collaboration in the spirit of One Health.

Le syndrome respiratoire du Moyen-Orient (MERS) est une maladie virale zoonotique qui affecte à la fois l'homme et les animaux. Plus de 2 200 cas humains confirmés au laboratoire ont été notifiés dans 27 pays depuis l'apparition de la maladie au Moyen-Orient en 2012, avec un taux brut de létalité de 35 %. Dans les années à venir, le MERS continuera à représenter une menace aussi bien pour le développement économique que pour la réussite des objectifs d'élimination de la pauvreté et de sécurisation de l'approvisionnement alimentaire. L'un des principaux obstacles empêchant de tenir le MERS en échec est l'absence de surveillance sanitaire exercée sur les populations animales au Moyen-Orient. Les auteurs soulignent la nécessité d'une collaboration internationale en matière de surveillance du coronavirus responsable du MERS (MERS-Cov) chez les animaux au Moyen-Orient, d'autant que l'émergence de nouveaux variants du MERS-CoV qui entretiennent l'infection en favorisant la transmission de personne à personne constitue un véritable danger. Toutefois, il sera extrêmement difficile, voire impossible de mettre en place une surveillance efficace. En effet les obstacles sont nombreux dans la région, en particulier l'absence de transparence puisque les gouvernements du Moyen-Orient ne publient généralement pas d'informations détaillées sur les maladies animales présentes sur leur territoire. En outre, la collaboration entre les agences locales et internationales des secteurs de la santé publique et animale est réduite au minimum et rares sont à ce jour les laboratoires possédant les compétences requises pour procéder au dépistage de l'infection par le MERS-CoV chez les animaux. Dernière difficulté mais non la moindre, les laboratoires compétents dans les pays et à l'étranger ne communiquent pas entre eux de manière proactive. Dans ce contexte, il est envisagé d'élargir la portée du Centre méditerranéen de lutte contre les zoonoses, situé à Athènes (Grèce) afin d'y intégrer les pays du Moyen-Orient, avec le soutien de l'Organisation des Nations Unies pour l'alimentation et l'agriculture (FAO), de l'Organisation mondiale de la santé animale (OIE) et d'autres partenaires. Cette initiative permettrait de renforcer les alliances et de déployer une collaboration bien plus efficace, dans une perspective Une seule santé.

El síndrome respiratorio de Oriente Medio (MERS, por su acrónimo inglés) es una enfermedad viral zoonótica que se ha descrito tanto en animales como en personas. Desde que en 2012 surgió en el Oriente Medio, se han notificado más de 2 200 casos confirmados en laboratorio que afectan a personas de 27 países, con una tasa bruta de letalidad del 35%. En los próximos años, el MERS seguirá constituyendo una grave amenaza para el desarrollo económico y también para el avance hacia la eliminación de la pobreza y la seguridad alimentaria. A la hora de poner coto a la enfermedad, un importante problema es la deficiente vigilancia zoosanitaria en el Oriente Medio. Los autores señalan la necesidad de colaboración internacional para hacer efectiva en la región la vigilancia del coronavirus (CoV) del MERS en los animales, pues la aparición de nuevas variantes de este virus capaces de transmitirse eficaz y sostenidamente entre las personas constituye un verdadero peligro. Sin embargo, resultará difícil, si no imposible, efectuar una vigilancia eficaz, habida cuenta de la multitud de obstáculos que hay que superar en el Oriente Medio, incluida la falta de transparencia de los gobiernos, que no acostumbran a revelar información detallada sobre las enfermedades animales. Además, la colaboración entre instancias locales y organismos internacionales en los sectores de la salud humana y la sanidad animal es mínima, y hay contados laboratorios cualificados para la detección del MERS­CoV en animales que estén en condiciones de intervenir con presteza. Por último, pero no menos importante, no hay una adecuada comunicación activa entre todos los laboratorios competentes, ya sean de los propios países o del extranjero. No obstante, con apoyo de la Organización de las Naciones Unidas para la Alimentación y la Agricultura (FAO), la Organización Mundial de Sanidad Animal (OIE) y otros colaboradores, sería posible extender a los países del Oriente Medio el ámbito de responsabilidad y actuación del Centro de Control de Zoonosis del Mediterráneo, sito en Atenas (Grecia), cosa que favorecería alianzas más sólidas y mucho más eficaces, conforme al espíritu de Una sola salud.

First genome sequences of buffalo coronavirus from water buffaloes in Bangladesh.

We report the complete genome sequences of a buffalo coronavirus (BufCoV HKU26) detected from the faecal samples of two domestic water buffaloes (Bubalus bubalis) in Bangladesh. They possessed 98-99% nucleotide identities to bovine coronavirus (BCoV) genomes, supporting BufCoV HKU26 as a member of Betacoronavirus 1. Nevertheless, BufCoV HKU26 possessed distinct accessory proteins between spike and envelope compared to BCoV. Sugar-binding residues in the N-terminal domain of S protein in BCoV are conserved in BufCoV HKU26.

Genomics and zoonotic infections: Middle East respiratory syndrome.

The emergence of Middle East respiratory syndrome (MERS) and the discovery of MERS coronavirus (MERS-CoV) in 2012 suggests that another SARS-like epidemic is occurring. Unlike the severe acute respiratory syndrome (SARS) epidemic, which rapidly disappeared in less than one year, MERS has persisted for over three years. More than 1,600 cases of MERS have been reported worldwide, and the disease carries a worryingly high fatality rate of >30%. A total of 182 MERS-CoV genomes have been sequenced, including 94 from humans and 88 from dromedary camels. The 182 genomes all share >99% identity, indicating minimal variation among MERS-CoV genomes. MERS-CoV is a lineage C Betacoronavirus (ßCoV). MERS-CoV genomes can be roughly divided into two clades: clade A, which contains only a few strains, and clade B, to which most strains belong. In contrast to ORF1ab and structural proteins, the putative proteins encoded by ORF3, ORF4a, ORF4b, ORF5 and ORF8b in the MERS-CoV genome do not share homology with any known host or virus protein, other than those of its closely related lineage C ßCoVs. Human and dromedary viral genomes have intermingled, indicating that multiple camel-to-human transmission events have occurred. The multiple origins of MERS-CoV suggest that the virus has been resident in dromedaries for many years. This is consistent with the detection of anti-MERS-CoV antibodies in dromedary camels as early as the 1980s.

L'émergence du syndrome respiratoire du Moyen-Orient (SRMO, ou MERS d'après son sigle anglais) et l'identification en 2012 du coronavirus responsable de cette maladie (MERS-CoV) indiquent que nous sommes en présence d'une épidémie semblable à celle du syndrome respiratoire aigu sévère (SRAS). Toutefois, contrairement à l'épidémie du SRAS qui avait rapidement disparu en moins d'un an, le MERS persiste depuis plus de trois ans. Plus de 1 600 cas de MERS ont été notifiés dans le monde ; la maladie présente un taux de létalité particulièrement préoccupant, s'élevant à plus de 30 %. Au total, 182 génomes du MERS-CoV ont été séquencés jusqu'à présent, dont 94 provenaient de virus isolés chez l'homme et 88 chez des dromadaires. Ces 182 génomes ont en commun un pourcentage d'identité de 99 %, dénotant une très faible variabilité des génomes viraux. Le MERS-CoV appartient à la lignée C du genre Betacoronavirus (ßCoV). Les génomes du MERSCoV se répartissent, dans leurs grandes lignes, en deux clades : le clade A, qui ne contient que quelques souches, et le clade B regroupant l'immense majorité des souches. Contrairement à ce qui se produit avec la protéine ORF1ab et les protéines structurales, les protéines potentiellement codées par les gènes ORF3, ORF4a, ORF4b, ORF5 et ORF8b du génome du MERS-CoV ne présentent aucune homologie avec des protéines virales ou de l'hôte autres que celles d'autres bêtacoronavirus de la lignée C, qui lui sont étroitement apparentés. Les génomes des virus affectant l'homme et le dromadaire se sont entremêlés, ce qui montre que le virus a connu de multiples épisodes de transmission des camélidés à l'homme. Les origines multiples du MERS-CoV témoignent d'une présence prolongée du virus (plusieurs années) chez les dromadaires. Ce constat est corroboré par le fait que des anticorps anti-MERS-CoV ont été détectés chez des dromadaires dès le début des années 80.

La aparición del síndrome respiratorio de Oriente Medio (MERS, por sus siglas en inglés) y el descubrimiento del coronavirus que lo causa (MERS-CoV) en 2012 parecen apuntar al advenimiento de una nueva epidemia análoga a la del síndrome respiratorio agudo severo (SRAS). Pero a diferencia de lo ocurrido con la epidemia de SRAS, que en menos de un año había desaparecido, el MERS lleva más de tres años presente. En el mundo se han notificado más de 1.600 casos de MERS, y la enfermedad presenta una tasa de letalidad muy alta y preocupante, superior al 30%. Hasta ahora se han secuenciado un total de 182 genomas del MERS-CoV, 94 de ellos obtenidos a partir de personas y 88 a partir de dromedarios. Estos 182 genomas comparten identidad en más de un 99%, lo que pone de manifiesto un nivel mínimo de variación entre los genomas coronavíricos. El coronavirus del MERS pertenece al linaje C del género Betacoronavirus (ßCoV). Los genomas de este virus pueden ser divididos, a grandes rasgos, en dos clados: el clado A, que agrupa unas pocas cepas; y el clado B, al que pertenecen la gran mayoría de las cepas. A diferencia de lo que ocurre con la proteína ORF1ab y las proteínas estructurales, las proteínas que supuestamente codifican los genes ORF3, ORF4a, ORF4b, ORF5 y ORF8b del genoma del MERS-CoV no comparten homología con ninguna proteína conocida de otros virus o anfitriones, salvo con proteínas de otros betacoronavirus del linaje C estrechamente emparentados con él. Los genomas de los virus que afectan a personas y dromedarios se han entremezclado, lo que indica que se han producido numerosos episodios de transmisión de camélidos a humanos. De los múltiples orígenes del MERS-CoV se deduce que el virus lleva muchos años siendo residente en dromedarios, lo que concuerda con el hecho de que ya en los años ochenta se detectaran anticuerpos anti-MERS-CoV en dromedarios.

Use of the human colorectal adenocarcinoma (Caco-2) cell line for isolating respiratory viruses from nasopharyngeal aspirates.

The human colorectal adenocarcinoma-derived Caco-2 cell line was evaluated as a means isolating common respiratory viruses from nasopharyngeal aspirates for the diagnosis of respiratory diseases. One hundred eighty-nine direct immunofluorescence positive nasopharyngeal aspirates obtained from patients with various viral respiratory diseases were cultured in the presence of Caco-2 cells or the following conventional cell lines: LLC-MK2, MDCK, HEp-2, and A549. Caco-2 cell cultures effectively propagated the majority (84%) of the viruses present in nasopharyngeal aspirate samples compared with any positive cultures obtained using the panel cells (78%) or individual cell line MDCK (38%), HEp-2 (21%), LLC-MK2 (27%), or A549 (37%) cell lines. The differences against individual cell line were statistically significant (P = < 0.000001). Culture in Caco-2 cells resulted in the isolation of 85% (36/42) of viruses which were not cultivated in conventional cell lines. By contrast, 80% (24/30) of viruses not cultivated in Caco-2 cells were isolated using the conventional panel. The findings indicated that Caco-2 cells were sensitive to a wide range of viruses and can be used to culture a broad range of respiratory viruses.

Development of monoclonal antibody-based galactomannoprotein antigen-capture ELISAs to detect Aspergillus fumigatus infection in the invasive aspergillosis rabbit models.

Aspergillus fumigatus is one of the most prominent opportunistic fungal pathogens in immunocompromised hosts. Early recognition of this infection along with prompt antifungal therapy may increase the survival rate. We expressed two potential bio-markers of A. fumigatus infection-galactomannoprotein Afmp1p and Afmp4p in Pichia pastoris. We generated 33 monoclonal antibodies (MAbs), 20 against recombinant Afmp1p (rAfmp1p) and the other 13 against recombinant Afmp4p (rAfmp4p). Subsequently, we developed two antigen-capture enzyme-linked immunosorbent assays (ELISAs) which employed MAbs as both the capture and the detection antibodies for rAfmp1p and rAfmp4p. The two antigen-capture ELISAs specifically detected Afmp1p/Afmp4p in cultures of A. fumigatus and had no cross-reaction with other tested pathogenic fungi, including Penicillium marneffei and other pathogenic Aspergillus species. The Afmp1p-captured ELISA would be positive even when the culture supernatant of A. fumigatus had been diluted to 128-fold of its original concentration. The two antigen ELISAs could capture circulating or excreted antigens during the acute phase of invasive aspergillosis (IA) in the animal model, and had no cross-reactivity to other Aspergillus-challenged animal models. We developed two antigen-capture ELISAs for the laboratory diagnosis of A. fumigatus infection. These two antigen-capture ELISAs may be useful in the clinical diagnosis of aspergillosis.

First report of chronic implant-related septic arthritis and osteomyelitis due to Kytococcus schroeteri and a review of human K. schroeteri infections.

We report the first case of Kytococcus schroeteri implant-related septic arthritis and osteomyelitis, identified by phenotypic tests and 16S rRNA sequencing, which responded to implant removal and doxycycline. 16S rRNA sequencing was useful for the accurate and rapid identification of the organism as it exhibited three different colonial morphologies in vitro.

Epidemiology of coronavirus-associated respiratory tract infections and the role of rapid diagnostic tests: a prospective study.

1. Coronaviruses accounted for 1.6% (98/6272) of respiratory tract infections based on nasopharyngeal aspirate samples. 2. HCoV-OC43 was the most common coronavirus detected,followed by HCoV-NL63, CoVHKU1,and HCoV-229E. 3. Although CoV-HKU1 infections were most often associated with the upper respiratory tract, more severe illness (pneumonia,acute bronchiolitis, and asthmatic exacerbation) may occur, especially in those with underlying disease. In young children, CoV-HKU1 infection is associated with a high rate of febrile seizures (50%). 4. CoV-HKU1 and HCoV-OC43 infections peaked in winter, in contrast to HCoV-NL63, which mainly occurred in early summer and autumn, but was absent in winter. 5. Reverse transcriptase polymerase chain reaction is useful for the rapid diagnosis of coronavirus infections.

Wild animal surveillance for coronavirus HKU1 and potential variants of other coronaviruses.

1. Although CoV-HKU1 was not identified in any of the studied animals, a coronavirus closely related to SARS-CoV (bat-SARS-CoV) was identified in 23 (19%) of 118 wild Chinese horseshoe bats by reverse transcriptase polymerase chain reaction (RT-PCR). 2. Complete genome sequencing and phylogenetic analysis showed that bat-SARS-CoV formed a distinct cluster with SARS-CoV as group 2b coronaviruses, distantly related to known group 2 coronaviruses. 3. Most differences between the bat-SARS-CoV and SARS-CoV genomes were observed in the spike gene. The presence of a29-bp insertion in ORF 8 of bat-SARS-CoV genome, not in most human SARS-CoV genomes, suggests that it has a common ancestor with civet SARS-CoV. 4. Antibody against recombinant bat-SARS-CoV nucleocapsid protein was detected in 84% of Chinese horseshoe bats using an enzyme immunoassay.Neutralising antibody to human SARS-CoV was also detected in those with lower viral loads.5. This study also revealed a previously unknown diversity of coronaviruses in bats, which are important natural reservoir for coronaviruses including SARS-CoV-like viruses.

Efficacy of dual vaccination of pandemic H1N1 2009 influenza and seasonal influenza on institutionalized elderly: a one-year prospective cohort study.

BACKGROUND: The influenza A (H1N1) 2009 pandemic was declared by the WHO in April 2009. In Hong Kong, the vaccination program began in December 2009 in addition to the annual seasonal trivalent influenza vaccination program. The clinical efficacy of dual vaccination was unknown. METHOD: From December 2009 to November 2010, a prospective 12-month cohort study on institutionalized elderly of nine nursing homes was conducted. Elderly persons who were followed up by the Hong Kong West Community Geriatric Assessment Team and had been vaccinated by the Department of Health were included. Outcome measures included all cause mortality, all cause hospitalization, hospitalization for fever on admission and hospitalization for pneumonia based on ICD-9-CM. RESULTS: 711 elderly persons were included. 274 received both seasonal influenza vaccine and (H1N1) 2009 vaccine (H1N1-TIV), 368 received seasonal influenza vaccine only (TIV alone) and 69 received no vaccination (unvaccinated). Baseline characteristics were well matched between the groups, except there were fewer females in the TIV alone. The 12-month mortality rates of the H1N1-TIV, TIV alone and unvaccinated were 10.6%, 19.8% and 29%, respectively. Multivariate analysis demonstrated that dual vaccination in the institutionalized elderly significantly reduced all cause mortality by 54% (Hazard Ratio [HR] 0.46; 95% confidence interval [CI] 0.29-0.72; p<0.001) and 74% (HR 0.26; CI 0.13-0.49; p<0.001), compared with vaccination of seasonal vaccination alone and no vaccination, respectively. Dual vaccination also reduced all cause hospitalization, hospitalization for fever on admission and hospitalization for pneumonia compared with seasonal vaccination alone and the unvaccinated group. CONCLUSION: Dual vaccination with both H1N1 and seasonal vaccinations provided additional protection to institutionalized elderly in reducing mortality and hospitalization.

Primary infective spondylodiscitis caused by Lactococcus garvieae and a review of human L. garvieae infections.

We report the first case of primary infective spondylodiscitis due to Lactococcus garvieae, confirmed by 16S rRNA gene sequencing, in the absence of concomitant endocarditis in a patient with long-standing gastritis on famotidine. He responded to a 6-week course of ampicillin. The gastrointestinal tract is probably the source of infection.