Showing papers by "Patrick C. Y. Woo published in 2013"

Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group.

Abstract: During the summer of 2012, in Jeddah, Saudi Arabia, a hitherto unknown coronavirus (CoV) was isolated from the sputum of a patient with acute pneumonia and renal failure ([1][1], [2][2]). The isolate was provisionally called human coronavirus Erasmus Medical Center (EMC) ([3][3]). Shortly thereafter

Delayed induction of proinflammatory cytokines and suppression of innate antiviral response by the novel Middle East respiratory syndrome coronavirus: implications for pathogenesis and treatment

Abstract: The high mortality associated with the novel Middle East respiratory syndrome coronavirus (MERS-CoV) has raised questions about the possible role of a cytokine storm in its pathogenesis. Although recent studies showed that MERS-CoV infection is associated with an attenuated IFN response, no induction of inflammatory cytokines was demonstrated during the early phase of infection. To study both early and late cytokine responses associated with MERS-CoV infection, we measured the mRNA levels of eight cytokine genes [TNF-α, IL-1β, IL-6, IL-8, IFN-β, monocyte chemotactic protein-1, transforming growth factor-β and IFN-γ-induced protein (IP)-10] in cell lysates of polarized airway epithelial Calu-3 cells infected with MERS-CoV or severe acute respiratory syndrome (SARS)-CoV up to 30 h post-infection. Among the eight cytokine genes, IL-1β, IL-6 and IL-8 induced by MERS-CoV were markedly higher than those induced by SARS-CoV at 30 h, whilst TNF-α, IFN-β and IP-10 induced by SARS-CoV were markedly higher than those induced by MERS-CoV at 24 and 30 h in infected Calu-3 cells. The activation of IL-8 and attenuated IFN-β response by MERS-CoV were also confirmed by protein measurements in the culture supernatant when compared with SARS-CoV and Sendai virus. To further confirm the attenuated antiviral response, cytokine response was compared with human HCoV-229E in embryonal lung fibroblast HFL cells, which also revealed higher IFN-β and IP-10 levels induced by HCoV-229E than MERS-CoV at 24 and 30 h. Whilst our data supported recent findings that MERS-CoV elicits attenuated innate immunity, this represents the first report to demonstrate delayed proinflammatory cytokine induction by MERS-CoV. Our results provide insights into the pathogenesis and treatment of MERS-CoV infections.

Genetic Characterization of Betacoronavirus Lineage C Viruses in Bats Reveals Marked Sequence Divergence in the Spike Protein of Pipistrellus Bat Coronavirus HKU5 in Japanese Pipistrelle: Implications for the Origin of the Novel Middle East Respiratory Syndrome Coronavirus

Abstract: While the novel Middle East respiratory syndrome coronavirus (MERS-CoV) is closely related to Tylonycteris bat CoV HKU4 (Ty-BatCoV HKU4) and Pipistrellus bat CoV HKU5 (Pi-BatCoV HKU5) in bats from Hong Kong, and other potential lineage C betacoronaviruses in bats from Africa, Europe, and America, its animal origin remains obscure. To better understand the role of bats in its origin, we examined the molecular epidemiology and evolution of lineage C betacoronaviruses among bats. Ty-BatCoV HKU4 and Pi-BatCoV HKU5 were detected in 29% and 25% of alimentary samples from lesser bamboo bat (Tylonycteris pachypus) and Japanese pipistrelle (Pipistrellus abramus), respectively. Sequencing of their RNA polymerase (RdRp), spike (S), and nucleocapsid (N) genes revealed that MERS-CoV is more closely related to Pi-BatCoV HKU5 in RdRp (92.1% to 92.3% amino acid [aa] identity) but is more closely related to Ty-BatCoV HKU4 in S (66.8% to 67.4% aa identity) and N (71.9% to 72.3% aa identity). Although both viruses were under purifying selection, the S of Pi-BatCoV HKU5 displayed marked sequence polymorphisms and more positively selected sites than that of Ty-BatCoV HKU4, suggesting that Pi-BatCoV HKU5 may generate variants to occupy new ecological niches along with its host in diverse habitats. Molecular clock analysis showed that they diverged from a common ancestor with MERS-CoV at least several centuries ago. Although MERS-CoV may have diverged from potential lineage C betacoronaviruses in European bats more recently, these bat viruses were unlikely to be the direct ancestor of MERS-CoV. Intensive surveillance for lineage C betaCoVs in Pipistrellus and related bats with diverse habitats and other animals in the Middle East may fill the evolutionary gap.

Differential cell line susceptibility to the emerging novel human betacoronavirus 2c EMC/2012: implications for disease pathogenesis and clinical manifestation.

Abstract: The emerging novel human betacoronavirus 2c EMC/2012 (HCoV-EMC) was recently isolated from patients with severe pneumonia and renal failure and was associated with an unexplained high crude fatality rate of 56%. We performed a cell line susceptibility study with 28 cell lines. HCoV-EMC was found to infect the human respiratory tract (polarized airway epithelium cell line Calu-3, embryonic fibroblast cell line HFL, and lung adenocarcinoma cell line A549), kidney (embryonic kidney cell line HEK), intestinal tract (colorectal adenocarcinoma cell line Caco-2), liver cells (hepatocellular carcinoma cell line Huh-7), and histiocytes (malignant histiocytoma cell line His-1), as evident by detection of high or increasing viral load in culture supernatants, detection of viral nucleoprotein expression by immunostaining, and/or detection of cytopathic effects. Although an infected human neuronal cell line (NT2) and infected monocyte and T lymphocyte cell lines (THP-1, U937, and H9) had increased viral loads, their relatively lower viral production corroborated with absent nucleoprotein expression and cytopathic effects. This range of human tissue tropism is broader than that for all other HCoVs, including SARS coronavirus, HCoV-OC43, HCoV-HKU1, HCoV-229E, and HCoV-NL63, which may explain the high mortality associated with this disease. A recent cell line susceptibility study showed that HCoV-EMC can infect primate, porcine, and bat cells and therefore may jump interspecies barriers. We found that HCoV-EMC can also infect civet lung fibroblast and rabbit kidney cell lines. These findings have important implications for the diagnosis, pathogenesis, and transmission of HCoV-EMC.

Human enterovirus 71 epidemics: what's next?

Abstract: Human enterovirus 71 (EV71) epidemics have affected various countries in the past 40 years. EV71 commonly causes hand, foot and mouth disease (HFMD) in children, but can result in neurological and cardiorespiratory complications in severe cases. Genotypic changes of EV71 have been observed in different places over time, with the emergence of novel genotypes or subgenotypes giving rise to serious outbreaks. Since the late 1990s, intra- and inter-typic recombination events in EV71 have been increasingly reported in the Asia-Pacific region. In particular, 'double-recombinant' EV71 strains belonging to a novel genotype D have been predominant in mainland China and Hong Kong over the last decade, though co-circulating with a minority of other EV71 subgenotypes and coxsackie A viruses. Continuous surveillance and genome studies are important to detect potential novel mutants or recombinants in the near future. Rapid and sensitive molecular detection of EV71 is of paramount importance in anticipating and combating EV71 outbreaks.

Identification of microRNA-like RNAs in mycelial and yeast phases of the thermal dimorphic fungus Penicillium marneffei.

Abstract: Background Penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in China and Southeast Asia. While miRNAs are increasingly recognized for their roles in post-transcriptional regulation of gene expression in animals and plants, miRNAs in fungi were less well studied and their potential roles in fungal dimorphism were largely unknown. Based on P. marneffei genome sequence, we hypothesize that miRNA-like RNAs (milRNAs) may be expressed in the dimorphic fungus. Methodology/Principal Findings We attempted to identify milRNAs in P. marneffei in both mycelial and yeast phase using high-throughput sequencing technology. Small RNAs were more abundantly expressed in mycelial than yeast phase. Sequence analysis revealed 24 potential milRNA candidates, including 17 candidates in mycelial and seven in yeast phase. Two genes, dcl-1 and dcl-2, encoding putative Dicer-like proteins and the gene, qde-2, encoding Argonaute-like protein, were identified in P. marneffei. Phylogenetic analysis showed that dcl-2 of P. marneffei was more closely related to the homologues in other thermal dimorphic pathogenic fungi than to Penicillium chrysogenum and Aspergillus spp., suggesting the co-evolution of dcl-2 among the thermal dimorphic fungi. Moreover, dcl-2 demonstrated higher mRNA expression levels in mycelial than yeast phase by 7 folds (P<0.001). Northern blot analysis confirmed the expression of two milRNAs, PM-milR-M1 and PM-milR-M2, only in mycelial phase. Using dcl-1KO, dcl-2KO, dclDKO and qde-2KO deletion mutants, we showed that the biogenesis of both milRNAs were dependent on dcl-2 but not dcl-1 or qde-2. The mRNA expression levels of three predicted targets of PM-milR-M1 were upregulated in knockdown strain PM-milR-M1KD, supporting regulatory function of milRNAs. Conclusions/Significance Our findings provided the first evidence for differential expression of milRNAs in different growth phases of thermal dimorphic fungi and shed light on the evolution of fungal proteins involved in milRNA biogenesis and possible role of post-transcriptional control in governing thermal dimorphism.

Clinical Spectrum of Exophiala Infections and a Novel Exophiala Species, Exophiala hongkongensis

Abstract: We characterized 12 Exophiala strains isolated from patients over a 15-year period to the species level using phenotypic tests and internal transcribed spacer (ITS) and Rpb1 sequencing and described the clinical spectrum of the 12 patients. Eight patients had nail or skin infections, two had invasive infections, and two had colonization of the gastrointestinal tract. ITS and Rpb1 sequencing showed that 11 of the 12 strains were known Exophiala species (E. oligosperma [n = 3], E. jeanselmei [n = 2], E. lecanii-corni [n = 2], E. bergeri [n = 1], E. cancerae [n = 1], E. dermatitidis [n = 1], and E. xenobiotica [n = 1]), which included the first reported cases of onychomycosis caused by E. bergeri and E. oligosperma. The 12th strain (HKU32T), isolated from the nail clipping of the right big toe of a 68-year-old female patient with onychomycosis, possessed unique morphological characteristics distinct from other Exophiala species. It grew very slowly and had a velvety colony texture after 28 days, short conidiophores of the same olivaceous color as the supporting hyphae, numerous spores, and no chlamydospore-like cells. ITS, Rpb1, β-tubulin, and β-actin gene sequencing unambiguously showed that HKU32T was clustered with but formed branches distinct from other Exophiala species in phylogenetic trees. We propose the new species Exophiala hongkongensis to describe this novel fungus.

Structural diversity of class 1 integrons and their associated gene cassettes in Klebsiella pneumoniae isolates from a hospital in China

Abstract: Background Klebsiella pneumoniae strains carrying class 1 integrons are becoming more common worldwide, and their role in the dissemination of drug resistance is significant. The aim of this study was to characterize the structural diversity of class 1 integrons and their associated gene cassettes in K. pneumoniae isolates from hospital settings. Methodology/Principal Findings We analyzed a total of 176 K. pneumoniae isolates in a tertiary-care hospital in Beijing, China for the period of November 1, 2010-October 31, 2011. The presence of class 1 integrons and gene cassettes was analyzed by PCR and sequencing. The prevalence of class 1 integrons was 51.1% (90/176). Fourteen different gene cassettes and 10 different gene cassette arrays were detected. dfrA and aadA cassettes were predominant and cassette combination dfrA1-orfC was most frequently found (13.6%, 24/176). Strong association between resistance to a variety of drugs (both phenotypes and the associated genes) and the presence of class 1 integrons was observed. In addition, we also identified an association between some previously identified prevalent sequence types (such as ST11, ST15, ST147, ST562, and ST716) and the presence of class 1 integrons. Conclusions/Significance Data from this study demonstrated that class 1 integrons are highly diverse and are associated with a variety of drug resistance phenotypes, drug resistance genes, as well as genotypes among K. pneumoniae isolates. Continuous monitoring of gene cassettes in class 1 integrons is warranted to improve the understanding and control of drug resistance among hospital settings.

Genetic characterization of EV71 isolates from 2004 to 2010 reveals predominance and persistent circulation of the newly proposed genotype D and recent emergence of a distinct lineage of subgenotype C2 in Hong Kong

Abstract: Enterovirus 71 (EV71) is a common etiological agent of hand, foot and mouth disease (HFMD) in children. EV71 epidemics have been reported in Hong Kong in recent years, and yet the genetic information of EV71 strains circulating in our locality is limited. The objective of this study was to investigate the genetic evolution of these EV71 isolates in Hong Kong over a 7-year period. Twenty-two EV71 isolates from Hong Kong during 2004–2010 were included for phylogenetic analysis using partial VP2-VP3, 2C and 3D regions. Eight EV71 strains were selected for complete genome sequencing and recombination analysis. Among the 22 EV71 isolates, 20 belonged to subgenotype C4 and 2 belonged to subgenotype C2 based on the phylogenetic analysis of partial VP2-VP3, 2C and 3D gene regions. Phylogenetic, similarity plot and bootscan analyses using complete genome sequences of seven EV71 isolates of subgenotype C4 supported that the “double-recombinant” strains of subgenotype C4 persistently circulating in Hong Kong should belong to a newly proposed genotype D. Further analysis revealed two clusters, subgenotypes C4b and C4a (proposed genotypes D1a and D1b respectively), with “genotype D1b” strains being predominant in recent years in Hong Kong. A distinct lineage of EV71 subgenotype C2 has emerged in Hong Kong in 2008. The evolutionary rate of EV71 was 3.1 × 10-3 nucleotide substitutions per site per year similar to that of other enterovirus, such as EV68, but was relatively lower than those of echovirus 30 and poliovirus. Molecular clock analysis using VP1 gene dated the time to the most recent common ancestor of all EV71 genotypes to 1900s, while the EV71 “double-recombinant” strains of “genotype D” were detected as early as 1998. This study provides the molecular basis for proposing a new “genotype D” of EV71 and assigning a discrete lineage of subgenotype C2. EV71 strains of “genotype D” have been circulating in Hong Kong for over 7 years, with “genotype D1b” being predominant.

Genotypic Analysis of Klebsiella pneumoniae Isolates in a Beijing Hospital Reveals High Genetic Diversity and Clonal Population Structure of Drug-Resistant Isolates

Abstract: Background The genetic diversity and the clinical relevance of the drug-resistant Klebsiella pneumoniae isolates from hospital settings are largely unknown. We thus conducted this prospective study to analyze the molecular epidemiology of K. pneumoniae isolates from patients being treated in the 306 Hospital in Beijing, China for the period of November 1, 2010–October 31, 2011.

Identification and characterization of a novel paramyxovirus, porcine parainfluenza virus 1, from deceased pigs.

Abstract: We describe the discovery and characterization of a novel paramyxovirus, porcine parainfluenza virus 1 (PPIV-1), from swine. The virus was detected in 12 (3.1 %) of 386 nasopharyngeal and two (0.7 %) of 303 rectal swab samples from 386 deceased pigs by reverse transcription-PCR, with viral loads of up to 106 copies ml−1. Complete genome sequencing and phylogenetic analysis showed that PPIV-1 represented a novel paramyxovirus within the genus Respirovirus, being most closely related to human parainfluenza virus 1 (HPIV-1) and Sendai virus (SeV). In contrast to HPIV-1, PPIV-1 possessed a mRNA editing function in the phosphoprotein gene. Moreover, PPIV-1 was unique among respiroviruses in having two G residues instead of three to five G residues following the A6 run at the editing site. Nevertheless, PPIV-1, HPIV-1 and SeV share common genomic features and may belong to a separate group within the genus Respirovirus. The presence of PPIV-1 in mainly respiratory samples suggests a possible association with respiratory disease, similar to HPIV-1 and SeV.

Proteome profiling of the dimorphic fungus Penicillium marneffei extracellular proteins and identification of glyceraldehyde-3-phosphate dehydrogenase as an important adhesion factor for conidial attachment

Abstract: Despite being the most important thermal dimorphic fungus causing systemic mycosis in Southeast Asia, the pathogenic mechanisms of Penicillium marneffei remain largely unknown. By comparing the extracellular proteomes of P. marneffei in mycelial and yeast phases, we identified 12 differentially expressed proteins among which glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and heat shock protein 60 (HSP60) were found to be upregulated in mycelial and yeast phases respectively. Based on previous findings in other pathogens, we hypothesized that these two extracellular proteins may be involved in adherence during P. marneffei–host interaction. Using inhibition assays with recombinant GAPDH (rGAPDH) proteins and anti-rGAPDH sera, we demonstrated that adhesion of P. marneffei conidia to fibronectin and laminin was inhibited by rGAPDH or rabbit anti-rGAPDH serum in a dose-dependent manner. Similarly, a dose-dependent inhibition of conidial adherence to A549 pneumocytes by rGAPDH or rabbit anti-rGAPDH serum was observed, suggesting that P. marneffei GAPDH can mediate binding of conidia to human extracellular matrix proteins and pneumocytes. However, HSP60 did not exhibit similar inhibition on conidia adherence, and neither GAPDH norHSP60 exhibited inhibition on adherence to J774 or THP-1 macrophage cell lines. This report demonstrates GAPDH as an adherence factor in P. marneffei by mediating conidia adherence to host bronchoalveolar epithelium during the early establishment phase of infection.

Recombinant coxsackievirus A2 and deaths of children, Hong Kong, 2012.

Abstract: A natural recombinant of coxsackievirus A2 was found in 4 children with respiratory symptoms in Hong Kong, China, during the summer of 2012. Two of these children died. Vigilant monitoring of this emerging recombinant enterovirus is needed to prevent its transmission to other regions.

Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei

Abstract: Penicillium marneffei is an opportunistic fungal pathogen endemic in Southeast Asia, causing lethal systemic infections in immunocompromised patients. P. marneffei grows in a mycelial form at the ambient temperature of 25°C and transitions to a yeast form at 37°C. The ability to alternate between the mycelial and yeast forms at different temperatures, namely, thermal dimorphism, has long been considered critical for the pathogenicity of P. marneffei, yet the underlying genetic mechanisms remain elusive. Here we employed high-throughput sequencing to unravel global transcriptional profiles of P. marneffei PM1 grown at 25 and 37°C. Among ∼11,000 protein-coding genes, 1,447 were overexpressed and 1,414 were underexpressed at 37°C. Counterintuitively, heat-responsive genes, predicted in P. marneffei through sequence comparison, did not tend to be overexpressed at 37°C. These results suggest that P. marneffei may take a distinct strategy of genetic regulation at the elevated temperature; the current knowledge concerning fungal heat response, based on studies of model fungal organisms, may not be applicable to P. marneffei. Our results further showed that the tandem repeat sequences (TRSs) are overrepresented in coding regions of P. marneffei genes, and TRS-containing genes tend to be overexpressed at 37°C. Furthermore, genomic sequences and expression data were integrated to characterize gene clusters, multigene families, and species-specific genes of P. marneffei. In sum, we present an integrated analysis and a comprehensive resource toward a better understanding of temperature-dependent genetic regulation in P. marneffei.

Complete genome sequence of a novel feline astrovirus from a domestic cat in Hong Kong.

Abstract: We report the first complete genome sequence of a feline astrovirus (FAstV), FAstV2 strain 1637F, identified from a domestic cat. The genome is 6,779 nucleotides (nt) in length and consists of three overlapping open reading frames (ORF1a-ORF1b-ORF2). Sequence analysis suggests that FAstV2 represents a new FAstV genotype that is closely related to human astroviruses.

Characterization of a Tsukamurella Pseudo-Outbreak by Phenotypic Tests, 16S rRNA Sequencing, Pulsed-Field Gel Electrophoresis, and Metabolic Footprinting

Abstract: We report a pseudo-outbreak of Tsukamurella due to improperly wrapped scissors used for processing of tissue specimens. A polyphasic approach, involving biochemical, genetic, and metabolomic techniques, was used in the laboratory investigation. This report highlights that early recognition of pseudo-outbreaks is important in preventing unnecessary and incorrect treatment of patients.

Streptococcus hongkongensis sp. nov., isolated from a patient with an infected puncture wound and from a marine flatfish.

Abstract: A bacterium, HKU30(T), was isolated from the infected tissue of a patient with wound infection after puncture by a fish fin. Cells are facultative anaerobic, non-spore-forming, non-motile, Gram-positive cocci arranged in chains. Colonies were non-haemolytic. The strain was catalase, oxidase, urease and Voges-Proskauer test negative. It reacted with Lancefield's group G antisera and was resistant to optochin. It grew on bile aesculin agar and in 5 % NaCl. It was unidentified by three commercial identification systems. 16S rRNA gene sequence analysis indicated that the bacterium shared 98.2, 97.7, 97.4 and 97.1 % nucleotide identities with Streptococcus iniae, Streptococcus pseudoporcinus, Streptococcus parauberis and Streptococcus uberis, respectively. The DNA G+C content was 35.6 ± 0.9 mol% (mean ± sd). In view of the occupational exposure of the patient, an epidemiological study was performed to isolate the bacterium from marine fish. Two strains, with similar phenotypic and genotypic characteristics to those of HKU30(T), were isolated from a three-lined tongue sole (Cynoglossus abbreviatus) and an olive flounder (Paralichthys olivaceus) respectively. Phylogenetic analysis of four additional housekeeping genes, groEL, gyrB, sodA and rpoB, showed that the three isolates formed a distinct branch among known species of the genus Streptococcus, being most closely related to S. parauberis (CCUG 39954(T)). DNA-DNA hybridization demonstrated ≤ 53.8 % DNA relatedness between the three isolates and related species of the genus Streptococcus. A novel species, Streptococcus hongkongensis sp. nov., is proposed. The type strain is HKU30(T) ( = DSM 26014(T) = CECT 8154(T)).

Functional Status of Older Nursing Home Residents Can Affect the Efficacy of Influenza Vaccination

Abstract: BACKGROUND The efficacy of influenza vaccination in older nursing home residents is frequently overestimated due to frailty selection bias. Limited data exist to examine this issue. METHODS We conducted a prospective cohort study from December 2009 to November 2010 to evaluate the efficacy of influenza vaccination in old nursing home residents with respect to their functional status. Participants were stratified according to the Barthel Index (BI) into good functioning (GF; BI > 60), intermediate functioning (IF; BI = 5-60), and poor functioning (PF; BI = 0). Participants were vaccinated by monovalent H1N1 2009 and trivalent seasonal influenza vaccinations (H1N1-TIV), TIV alone, or remained unvaccinated by choice. The associations between all-cause mortality, vaccination efficacy, and functional status were examined. RESULTS A total of 711 older nursing home residents were enrolled (GF group: N = 230; IF group: N = 246; PF group: N = 235). At 12 months, H1N1-TIV recipients had the lowest all-cause mortality, whereas unvaccinated residents had the highest all-cause mortality in all three functional status groups. In the comparison between H1N1-TIV recipients and TIV alone recipients, the hazard ratios (HRs) of all-cause mortality were lower in the GF group and higher in the PF group (GF group: HR 0.30 [0.07-0.95], p < .05; IF group: HR 0.40 [0.18-0.86], p < .05; PF group: HR 0.53 [0.28-0.99], p < .05). The same observation was found in comparison between other vaccination statuses (H1N1-TIV vs unvaccinated and TIV alone vs unvaccinated). CONCLUSIONS Influenza vaccination was associated with reduced all-cause mortality in older nursing home residents with different functional statuses. Vaccine efficacy in reducing mortality declined with increasingly impaired functional status.

Re-Annotation of Protein-Coding Genes in 10 Complete Genomes of Neisseriaceae Family by Combining Similarity-Based and Composition-Based Methods

Abstract: In this paper, we performed a comprehensive re-annotation of protein-coding genes by a systematic method combining composition- and similarity-based approaches in 10 complete bacterial genomes of the family Neisseriaceae First, 418 hypothetical genes were predicted as non-coding using the composition-based method and 413 were eliminated from the gene list Both the scatter plot and cluster of orthologous groups (COG) fraction analyses supported the result Second, from 20 to 400 hypothetical proteins were assigned with functions in each of the 10 strains based on the homology search Among newly assigned functions, 397 are so detailed to have definite gene names Third, 106 genes missed by the original annotations were picked up by an ab initio gene finder combined with similarity alignment Transcriptional experiments validated the effectiveness of this method in Laribacter hongkongensis and Chromobacterium violaceum Among the 106 newly found genes, some deserve particular interests For example, 27 transposases were newly found in Neiserria meningitidis alpha14 In Neiserria gonorrhoeae NCCP11945, four new genes with putative functions and definite names (nusG, rpsN, rpmD and infA) were found and homologues of them usually are essential for survival in bacteria The updated annotations for the 10 Neisseriaceae genomes provide a more accurate prediction of protein-coding genes and a more detailed functional information of hypothetical proteins It will benefit research into the lifestyle, metabolism, environmental adaption and pathogenicity of the Neisseriaceae species The re-annotation procedure could be used directly, or after the adaption of detailed methods, for checking annotations of any other bacterial or archaeal genomes

Matrix-assisted laser desorption ionisation–time of flight mass spectrometry for rapid identification of Laribacter hongkongensis

Abstract: Laribacter hongkongensis is a Gram-negative, facultative anaerobic, motile, S-shaped, urease-positive bacillus associated with invasive infections in liver cirrhosis patients and community-acquired gastroenteritis. Most cases of L hongkongensis infections occur in eastern countries. Information is lacking on the usefulness of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of bacteria important in eastern countries. Using the Bruker database extended with 21 L hongkongensis reference strains, all 240 L hongkongensis isolates recovered from patients, fish, frogs and water were correctly identified, with 224 (93.3%) strains having top match scores ≥2.0. Notably, the strain of Chromobacterium violaceum was not reliably identified although it is included in the database. MALDI-TOF MS is useful for the accurate routine identification of L hongkongensis after adding reference L hongkongensis main spectra to the database. The number of strains for each species in MALDI-TOF MS databases should be expanded to cover intraspecies variability.

Genetic characterization of Betacoronavirus lineage C viruses in bats

Abstract: ABSTRACT While the novel Middle East respiratory syndrome coronavirus (MERS-CoV) is closely related to Tylonycteris bat CoV HKU4 (Ty-BatCoV HKU4) and Pipistrellus bat CoV HKU5 (Pi-BatCoV HKU5) in bats from Hong Kong, and other potential lineage C betacoronaviruses in bats from Africa, Europe, and America, its animal origin remains obscure. To better understand the role of bats in its origin, we examined the molecular epidemiology and evolution of lineage C betacoronaviruses among bats. Ty-BatCoV HKU4 and Pi-BatCoV HKU5 were detected in 29% and 25% of alimentary samples from lesser bamboo bat (Tylonycteris pachypus) and Japanese pipistrelle (Pipistrellus abramus), respectively. Sequencing of their RNA polymerase (RdRp), spike (S), and nucleocapsid (N) genes revealed that MERS-CoV is more closely related to Pi-BatCoV HKU5 in RdRp (92.1% to 92.3% amino acid [aa] identity) but is more closely related to Ty-BatCoV HKU4 in S (66.8% to 67.4% aa identity) and N (71.9% to 72.3% aa identity). Although both viruses were under purifying selection, the S of Pi-BatCoV HKU5 displayed marked sequence polymorphisms and more positively selected sites than that of Ty-BatCoV HKU4, suggesting that Pi-BatCoV HKU5 may generate variants to occupy new ecological niches along with its host in diverse habitats. Molecular clock analysis showed that they diverged from a common ancestor with MERS-CoV at least several centuries ago. Although MERS-CoV may have diverged from potential lineage C betacoronaviruses in European bats more recently, these bat viruses were unlikely to be the direct ancestor of MERS-CoV. Intensive surveillance for lineage C betaCoVs in Pipistrellus and related bats with diverse habitats and other animals in the Middle East may fill the evolutionary gap.

Romance of the three domains: how cladistics transformed the classification of cellular organisms.

Abstract: Cladistics is a biological philosophy that uses genealogical relationship among species and an inferred sequence of divergence as the basis of classification. This review critically surveys the chronological development of biological classification from Aristotle through our postgenomic era with a central focus on cladistics. In 1957, Julian Huxley coined cladogenesis to denote splitting from subspeciation. In 1960, the English translation of Willi Hennig’s 1950 work, Systematic Phylogenetics, was published, which received strong opposition from pheneticists, such as numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomist, Ernst Mayr, and sparked acrimonious debates in 1960–1980. In 1977–1990, Carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellular life and established major prokaryotic phyla. Cladistics has since dominated taxonomy. Despite being compatible with modern microbiological observations, i.e. organisms with unusual phenotypes, restricted expression of characteristics and occasionally being uncultivable, increasing recognition of pervasiveness and abundance of horizontal gene transfer has challenged relevance and validity of cladistics. The mosaic nature of eukaryotic and prokaryotic genomes was also gradually discovered. In the mid-2000s, high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of life. While genomics only indirectly leads to understanding of functional adaptations to ecological niches, computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be bridged. Controversies are not expected to settle as taxonomic classifications shall remain subjective to serve the human scientist, not the classified.

Is nursing home residence an independent risk factor of mortality in Chinese older adults

Abstract: infection, “didn’t know” whether receiving PPV is important for older adults in nursing homes, and perceived that “receiving PPV not important for older adults in nursing homes” (Table 1). This study suggests that 40.2% of NHHCWs had encouraged older adults in nursing homes to receive the PPV. This was the first study to examine this question but this prevalence was unsatisfactory. The low prevalence rate may be associated with the low PPV vaccination rate in older adults in nursing homes in HKWC. Although 99.1% of NHHCWs had heard of PPV, nearly half of them did not know its efficacy, the severity of pneumococcal infection, or whether PPV was important for older adults in nursing homes. A high percentage of “don’t know” answers to these questions suggests inadequate knowledge regarding PPV in NHHCWs. The health authority should provide more information regarding the efficacy, safety, and importance of PPV. Prevaccination talks should be arranged in nursing homes or locations convenient for NHHCWs. The importance of their encouraging older adults in nursing homes to receive PPV must be emphasized. Information leaflets should be distributed to all nursing home staff. This is particularly important for NHHCWs who cannot attend prevaccination talks. The health authority should also advertise more in the mass media, with an emphasis on the efficacy, safety, and importance of PPV. There were several limitations of this study. First, it was performed in HKWC only instead of a random sampling from all nursing homes in Hong Kong, although because there are standard requirements for NHHCWs in Hong Kong, characteristics of NHHCWs should be similar in different districts of Hong Kong. Second, this study was based on self-reported data, which might lead to recall bias. In conclusion, 40.2% of NHHCWs had encouraged older adults in nursing homes to receive PPV. Inadequate knowledge regarding the efficacy and importance of PPV of NHHCWs were the main barriers to this action.

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

Abstract: 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. J. Med. Virol. 85:874–879, 2013. © 2013 Wiley Periodicals, Inc.

A novel paramyxovirus and uses thereof

Abstract: An isolated paramyxovirus, a morbillivirus (FmoPV), isolated nucleic acids encoding the genome of FmoPV, isolated amino acid sequences of FmoPV protein, antibodies to FmoPV and its proteins, and uses thereof are provided. In certain embodiments, the modified FmoPV is a feline morbillivirus. A recombinant FmoPV comprising a modified FmoPV gene or gene segments and the use of such virus are provided. The recombinant FmoPV may be used in the prevention and/or treatment of diseases related to FmoPV or as a delivery vector. A diagnostic assay for the FmoPV is provided. In certain embodiments, the FmoPV causes kidney disease. In certain embodiments, the kidney disease is in felines. In certain embodiments, the kidney disease is tubulo interstitial nephritis ("TIN"). A quantitative assay for the detection of the FmoPV, natural or artificial variants, analogs, or derivatives thereof is provided. In certain embodiments, the quantitative assay is reverse transcription and polymerase chain reaction (RT-PCR). A vaccine and a kit containing the vaccine for the prevention and treatment of FmoPV infection are provided. A diagnosis kit that comprises nucleic acid molecules for the detection of the FmoPV is also provided.