Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia

Background. Recently, we described the discovery of a novel group 2 coronavirus, coronavirus HKU1 (CoV-HKU1), from a patient with pneumonia. However, the clinical and molecular epidemiological features of CoV-HKU1-associated pneumonia are unknown. Methods. Prospectively collected (during a 12-month period) nasopharyngeal aspirates (NPAs) from patients with community-acquired pneumonia from 4 hospitals were subjected to reverse-transcription polymerase chain reaction, for detection of CoV-HKU1. The epidemiological, clinical, and laboratory characteristics of patients with CoV-HKU1-associated pneumonia were analyzed. The pol, spike (S), and nucleocapsid (N) genes were also sequenced. Results. NPAs from 10 (2.4%) of 418 patients with community-acquired pneumonia were found to be positive for CoV-HKU1. All 10 cases occurred in spring and winter. Nine of these patients were adults, and 4 had underlying diseases of the respiratory tract. In the 6 patients from whom serum samples were available, all had a 4-fold change in immunoglobulin (Ig) G titer and/or presence of IgM against CoV-HKU1. The 2 patients who died had significantly lower hemoglobin levels, monocyte counts, albumin levels, and oxygen saturation levels on admission and had more-extensive involvement visible on chest radiographs. Sequence analysis of the pol, S, and N genes revealed 2 genotypes of CoV-HKU1. Conclusions. CoV-HKU1 accounts for 2.4% of community-acquired pneumonia, with 2 genotypes in the study population. Without performance of diagnostic tests, the illness was clinically indistinguishable from other community-acquired pneumonia illnesses. © 2005 by the Infectious Diseases Society of America. All rights reserved.published_or_final_versio

Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses

Using the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G + C content in CoV-HKU1 warrants further studies. © 2007 Elsevier Inc. All rights reserved.link_to_subscribed_fulltex

Actinomyces hongkongensis sp. nov. A Novel Actinomyces species Isolated from a Patient with Pelvic Actinomycosis

A bacterium was isolated from the pus of a patient with pelvic actinomycosis. The cells were strictly anaerobic, straight, non-sporulating, Gram-positive rods. It grows on sheep blood agar as non-haemolytic, pinpoint colonies after 24 hours of incubation at 37 °C in anaerobic environment. It is non-motile and does not produce catalase. 16S ribosomal RNA (rRNA) gene sequencing showed that there were 6.6% difference between the 16S rRNA gene sequence of the bacterium that of Actinomyces marimammalium (GenBank Accession no. AJ276405), a new species described in 2001, isolated from two seals and a porpoise. For these reasons a new species, Actinomyces hongkongensis sp. nov., is proposed, for which HKU8T is the type strain. Further studies should be performed to ascertain the potential of this bacterium to become an important cause of actinomycosis.link_to_subscribed_fulltex

Streptococcus sinensis may react with Lancefield group F antiserum

Lancefield group F streptococci have been found almost exclusively as members of the 'Streptococcus miller' group, although they have been reported very occasionally in some other streptococcal species. Among 302 patients with bacteraemia caused by viridans streptococci over a 6-year period, three cases were caused by Streptococcus sinensis (type strain HKU4T, HKU5 and HKU6). All three patients had infective endocarditis complicating their underlying chronic rheumatic heart diseases. Gene sequencing showed no base differences between the 16S rRNA gene sequences of HKU5 and HKU6 and that of HKU4T. All three strains were Gram-positive, non-spore-forming cocci arranged in chains. All grew on sheep blood agar as α-haemolytic, grey colonies of 0·5-1 mm in diameter after 24 h incubation at 37 °C in ambient air. Lancefield grouping revealed that HKU5 and HKU6 were Lancefield group F, but HKU4T was non-groupable with Lancefield groups A, B, C, D, F or G antisera. HKU4T was identified by the Vitek system (GPI), API system (20 STREP) and ATB system (ID32 STREP) as 99% Streptococcus intermedius, 51·3% S. intermedius and 99·9% Streptococcus anginosus, respectively. Using the same tests, HKU5 was identified as 87% Streptococcus sanguinis/Streptococcus gordonii, 59% Streptococcus salivarius and 99·6% S. anginosus, respectively, and HKU6 as 87% S. sanguinis/S. gordonii, 77% Streptococcus pneumoniae and 98-3% S. anginosus, respectively. The present data revealed that a proportion of Lancefield group F streptococci could be S. sinensis. Lancefield group F streptococci should not be automatically reported as 'S. miller'.link_to_subscribed_fulltex

Characterization of porcine parainfluenza virus 1, a virus with possible association with respiratory disease, from deceased pigs.

Paper Poster Session IV: Viral infection and disease - Poster presentation no. P0887Objectives: Pigs, being farm animals and an important food source of humans, would also be a source of zoonotic disease pathogens, e.g. Influenenza virus A (HIN1) and Nipah virus, in humans. Therefore, understanding more about porcine pathogens is important in preparing for emerging diseases in humans. Recently, our research group has found a porcine paramyxovirus, named porcine parainfluenza 1 (PPIV-1) and detailed analysis was performed based on its genomic data in this study. Methods: The virus studied, PPIV-1, was found by RT-PCR of RNA extracted from samples of deceased pigs from a slaughter house with conserved primers. Complete genomes of three viruses were then sequenced with primer walking strategy. Potential of mRNA editing of phosphoprotein gene was checked by cloning. Characterisation of genomic features, phylogentic analysis and estimation of divergence time were performed using different bioinformatics software tools. Results: RT-PCR for paramyxovirus gene fragment was positive in nasopharyngeal (3.1%) and rectal (0.7%) swab samples, but negative in other samples, namely, liver, lung and blood samples. Annotation of complete genome sequences showed PPIV-1 contain six major genes similar to other paramyxoviruses. Amino acid identities of PPIV-1 were highest with respiroviruses, especially human parainfluenza virus 1 (HPIV-1) and Sendai virus (SeV). Characteristics of intergenic regions and proteins and phylogenetic analysis also suggested PPIV-1 as a member of the genus Respirovirus, with a closer relationship with SeV and HPIV-1 than other respiroviruses. Estimation of divergence dates suggested the divergence time of all respiroviruses were earlier than the group of viruses comprising HPIV-1, SeV and PPIV-1. The Ka/Ks ratios of most coding regions in PPIV-1 were low, suggesting these genes were under purifying selection. Conclusion: The presence of PPIV-1 in mainly respiratory samples suggested a possible association with respiratory disease. A number of common genome characteristics, the phylogenetic analysis and divergence time estimation showed that PPIV-1 is a respirovirus more closely related to HPIV-1 and SeV than other respiroviruses. This suggested that there should be a subtype of 'group 1' viruses in the respiroviruses. The purifying selection in most genes supported swine as the primary host of PPIV-1. To summarise, PPIV-1 should be classified as a 'group 1' respirovirus with a possible association with respiratory disease in swine, its possibly primary host

Detection of Specific Antibodies to Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein for Serodiagnosis of SARS Coronavirus Pneumonia

We report the evaluation of recombinant severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) nucleocapsid protein enzyme-linked immunosorbent assay (ELISA)-based antibody tests for serodiagnosis of SARS-CoV pneumonia and compare the sensitivities and specificities of this ELISA for detection of immunoglobulin G (IgG), IgM, IgA, and their combinations with serum samples from 149 healthy blood donors who donated blood 3 years ago as controls and 106 SARS-CoV pneumonia patients in Hong Kong. The specificities of the ELISA for IgG, IgM, and IgA detection were 95.3, 96.6, and 96.6%, respectively, with corresponding sensitivities of 94.3, 59.4, and 60.4%, respectively. The present ELISA appears to be a sensitive test for serodiagnosis of SARS-CoV pneumonia, is much more economical and less labor-intensive than the indirect immunofluorescence assay, and does not require cultivation of SARS-CoV.published_or_final_versio

SARS coronavirus spike polypeptide DNA vaccine priming with recombinant spike polypeptide from Escherichia coli as booster induces high titer of neutralizing antibody against SARS coronavirus

Different forms of SARS coronavirus (SARS-CoV) spike protein-based vaccines for generation of neutralizing antibody response against SARS-CoV were compared using a mouse model. High IgG levels were detected in mice immunized with intraperitoneal (i.p.) recombinant spike polypeptide generated by Escherichia coli (S-peptide), mice primed with intramuscular (i.m.) tPA-optimize800 DNA vaccine (tPA-S-DNA) and boosted with i.p. S-peptide, mice primed with i.m. CTLA4HingeSARS800 DNA vaccine (CTLA4-S-DNA) and boosted with i.p. S-peptide, mice primed with oral live-attenuated Salmonella typhimurium (Salmonella-S-DNA-control) and boosted with i.p. S-peptide, mice primed with oral live-attenuated S. typhimurium that contained tPA-optimize800 DNA vaccine (Salmonella-tPA-S-DNA) and boosted with i.p. S-peptide, and mice primed with oral live-attenuated S. typhimurium that contained CTLA4HingeSARS800 DNA vaccine (Salmonella-tPA-S-DNA) and boosted with i.p. S-peptide. No statistical significant difference was observed among the Th1/Th2 index among these six groups of mice with high IgG levels. Sera of all six mice immunized with i.p. S-peptide, i.m. DNA vaccine control and oral Salmonella-S-DNA-control showed no neutralizing antibody against SARS-CoV. Sera of the mice immunized with i.m. tPA-S-DNA, i.m. CTLA4-S-DNA, oral Salmonella-S-DNA-control boosted with i.p. S-peptide, oral Salmonella-tPA-S-DNA, oral Salmonella-tPA-S-DNA boosted with i.p S-peptide, oral Salmonella-CTLA4-S-DNA and oral Salmonella-CTLA4-S-DNA boosted with i.p. S-peptide showed neutralizing antibody titers of <1:20-1:160. Sera of all the mice immunized with i.m. tPA-S-DNA boosted with i.p. S-peptide and i.m. CTLA4-S-DNA boosted with i.p. S-peptide showed neutralizing antibody titers of ≥1:1280. The present observation may have major practical value, such as immunization of civet cats, since production of recombinant proteins from E. coli is far less expensive than production of recombinant proteins using eukaryotic systems. © 2005 Elsevier Ltd. All rights reserved.link_to_subscribed_fulltex

Molecular diversity of coronaviruses in bats

The existence of coronaviruses in bats is unknown until the recent discovery of bat-SARS-CoV in Chinese horseshoe bats and a novel group 1 coronavirus in other bat species. Among 309 bats of 13 species captured from 20 different locations in rural areas of Hong Kong over a 16-month period, coronaviruses were amplified from anal swabs of 37 (12%) bats by RT-PCR. Phylogenetic analysis of RNA-dependent-RNA-polymerase (pol) and helicase genes revealed six novel coronaviruses from six different bat species, in addition to the two previously described coronaviruses. Among the six novel coronaviruses, four were group 1 coronaviruses (bat-CoV HKU2 from Chinese horseshoe bat, bat-CoV HKU6 from rickett\u27s big-footed bat, bat-CoV HKU7 from greater bent-winged bat and bat-CoV HKU8 from lesser bent-winged bat) and two were group 2 coronaviruses (bat-CoV HKU4 from lesser bamboo bats and bat-CoV HKU5 from Japanese pipistrelles). An astonishing diversity of coronaviruses was observed in bats