Detection of haemagglutinin D222 polymorphisms in influenza A(H1N1)pdm09-infected patients by ultra-deep pyrosequencing.

This study was aimed at establishing the genetic heterogeneity of influenza virus haemagglutinin (HA) gene quasi-species and the polymorphisms at codon 222, by application of ultra-deep pyrosequencing (UDPS) to respiratory samples from patients hospitalized for influenza A(H1N1)pdm09 infection, presenting with severe or moderate-mild disease. HA diversity was significantly higher in samples collected from patients with severe manifestations than in those from patients with moderate-mild manifestations (p 0.02). D222 polymorphism was detected in 40.7% of patients by UDPS, and in only 7.1% by Sanger sequencing. D222E, D222G, D222N and D222A were observed in 37.0%, 11.1%, 7.4% and 3.7% of patients, respectively; 10.7% of samples harboured more than two variants. The relative frequency of each single variant showed a wide range of intrapatient variation. D222G/N/A were detected, as either minor or predominant variants, only in severe cases, whereas D222E was equally represented in severe and moderate-mild infections. Other amino acid variants were observed at different positions within the analysed HA fragment. Consistent with higher heterogeneity, non-D222 variants were more frequently detected in severe cases than in moderate-mild cases. In addition, seven non-D222 mutations carried by minority variants, not previously described, were observed.

Early co-circulation of different clades of influenza A/H1N1v pandemic virus in northern Italy.

INTRODUCTION: The spatial diffusion over time of pandemic influenza A/HINI virus (A/HIN1v) was surveyed in Northern Italy (nearly 10 million inhabitants)from April to December 2009, and the molecular characteristics of circulating viruses were analyzed to identify the appearance of drift variants. About 45% of analyzed samples were laboratory-confirmed cases of A/HINlv. Sporadic cases occurred until the middle of June 2009, then, case numbers began to increase delineating distinct epidemiological phases of viral circulation. METHODS: RNA was extracted using RNeasy Mini kit (QIAGEN GmbH, Germany). Virological diagnosis of A/HINlv infection was carried out by real-time RT-PCR assay. Sequence analysis of hemagglutinin (HA) gene was performed through a RT-PCR assay specific for a 995 bp fragment (nt. 64-1,058) in the HAl domain. The nucleotide sequences were obtained by automated DNA sequencing. The HAl sequences were aligned with other sequences collected from GenBank database by ClustalX software. The multiple sequence alignment was used to perform a basic phylogenetic analysis and a phylogenetic tree from HA sequences was constructed. RESULTS: The HA gene sequences ofA/HINlv analyzed segregated into three genetically distinct clades and were characterized by the appearance of amino acid variations that were progressively fixed in the field viral population under scrutiny. CONCLUSIONS: These data suggest an early co-circulation of genetically distinct A/HNINv variants and emphasize the importance of a close molecular surveillance to detect rapidly the spread of new viral variants and to define their epidemiological impact.

Severe outcome of influenza A/H1N1/09v infection associated with 222G/N polymorphisms in the haemagglutinin: a multicentre study.

In a multicentre study, influenza A/H1N1/09v 222G/N variants were more frequently detected in patients admitted to the intensive-care unit for invasive mechanical ventilation or extracorporeal membrane oxygenation (10/23; 43.5%) than in patients hospitalized in other units (2/27; 7.4%) and community patients (0/81; 0.0%) (p <0.01). A significantly higher virus load (p 0.02) in the lower vs the upper respiratory tract was observed. Predominance of 222G/N variants in the lower respiratory tract (40% of total virus population) vs the upper respiratory tract (10%) was shown by clonal analysis of haemagglutinin sequences in paired nasal swab and bronchoalveolar lavage samples. The time from illness onset to sampling was significantly longer in patients with severe infection vs community patients (p <0.001). It was concluded that the 222G/N variants showed increased virulence; mutant variants were probably selected in individual patients; and the longer duration of illness might have favoured the emergence of adaptive mutations through multiple replication cycles.

Clinical severity and molecular typing of human rhinovirus C strains during a fall outbreak affecting hospitalized patients.

BACKGROUND: The circulation rate and the clinical severity of infections caused by members of the new human rhinovirus C (HRV-C) species remain to be defined. OBJECTIVES: To investigate the epidemiologic and clinical impact of HRV-C strains in a fall outbreak interesting hospitalized patients. STUDY DESIGN: HRV species (A-C) were determined by phylogenetic analysis following amplification of two genome regions (5'NCR and VP4/VP2) by RT-PCR. HRV species were correlated with age, respiratory tract involvement, clinical symptoms, and HRV load in respiratory secretions. RESULTS: During the first week of the period October-November 2008, single HRV infections were associated with 95% of all respiratory syndromes affecting hospitalized patients. Then, HRV infections (single+coinfections) interested about 90% of positive samples until the end of October, when they declined in frequency until reaching about 30% at the end of November. Overall, 104 HRV strains were detected and, of these, 90 could be classified by phylogenetic analysis, as follows: 45 HRV-A, 12 HRV-B, 28 HRV-C, and 5 human enterovirus D strains. HRV-C identity was confirmed by detection of cis-acting replication elements (cre) in 23/23 strains. As for severity of respiratory syndromes, unlike HRV-A and HRV-B strains, HRV-C strains were responsible for a significantly higher rate (p<0.05) of lower respiratory tract infections in the pediatric as compared to adult patient population. CONCLUSIONS: HRV-C strains have been shown to circulate at a rate intermediate between HRV-A and HRV-B strains, showing a greater degree of clinical severity in the pediatric population.

Phylogenetic analysis of human coronavirus NL63 circulating in Italy.

BACKGROUND: Five known human coronaviruses infect the human respiratory tract: HCoV-OC43, HCoV-229E, SARS-CoV, HCoV-NL63 and HCoV-HKU1. OBJECTIVES: To evaluate the prevalence of HCoV-NL63 in hospitalized adult patients and to perform molecular characterization of Italian strains. STUDY DESIGN: HCoV-NL63 was sought by RT-PCR in 510 consecutive lower respiratory tract (LRT) samples, collected from 433 Central-Southern Italy patients over a 1-year period. Phylogenetic analysis was performed by partial sequencing of S and ORF1a. Additional S sequences from Northern Italy were included in the phylogenetic trees. RESULTS: HCoV-NL63 was detected in 10 patients (2.0%) with symptomatic respiratory diseases, mainly during winter. Phylogenetic analysis indicated a certain degree of heterogeneity in Italian isolates. The ORF1a gene clustering in phylogenetic trees did not match with that of the S gene. CONCLUSIONS: As observed by others, HCoV-NL63 is often associated with another virus. Phylogenetic characterization of HCoV-NL63 circulating in Italy indicates that this virus circulates as a mixture of variant strains, as observed in other countries.

Correlation of viral load as determined by real-time RT-PCR and clinical characteristics of respiratory syncytial virus lower respiratory tract infections in early infancy.

BACKGROUND: In infants hospitalized for a lower respiratory tract infection (RTI) caused by respiratory syncytial virus (RSV), the correlation between viral load (VL) and patient clinical characteristics remains to be defined. OBJECTIVES: To define this correlation. STUDY DESIGN: prospective study of 47 infants admitted to hospital in the period November 2006-May 2007 with a diagnosis of lower RTI. Nasopharyngeal aspirates (NPAs) were taken at admission, discharge, and at post-discharge control visits. VL was quantified by real-time RT-PCR for RSV subgroups A and B. RESULTS: Patients with bronchiolitis were compared with young patients with lower RTI other than bronchiolitis. Patients with bronchiolitis had a significantly lower age than patients with other syndromes, and a significantly longer duration of symptoms. Duration of hospitalization was not different in the two groups of patients, and was not related to RSV subgroup or viral coinfection. A sustained decrease in VL was observed in the general patient population between admission, discharge and post-discharge follow-up visits. CONCLUSIONS: (i) patients with bronchiolitis were significantly younger than patients with other lower RTIs; (ii) symptom duration was significantly longer in patients with bronchiolitis; (iii) RSV VL significantly decreased between admission and discharge.

Human cytomegalovirus UL131A, UL130 and UL128 genes are highly conserved among field isolates.

Coding sequences of the UL131A, UL130, and UL128 genes of human cytomegalovirus (HCMV) were found to be highly conserved among 34 field isolates from pregnant women with primary HCMV infection and their fetuses or newborns, as well as from solid organ transplant recipients and patients with AIDS. No strain clustering was observed. In contrast, sequencing of UL55 (gB coding gene) allowed the 34 isolates to be clustered into 4 genotypes. The conservation of the UL131A-UL128 locus is consistent with the conclusion that the three encoded proteins are all essential for growth of HCMV in endothelial cells and virus transfer to leukocytes.

The immunosuppressive effect of human cytomegalovirus infection in recipients of allogeneic hematopoietic stem cell transplantation.

In immune-competent individuals, human cytomegalovirus (HCMV) infection is associated with impairment of T-cell function. Our goal was to evaluate prospectively whether clinically asymptomatic HCMV infection in allogeneic hematopoietic stem cell transplantation (alloHSCT) recipients, treated pre emptively with ganciclovir, influences T-cell function as well. Mitogen-stimulated T-cell proliferative activity, together with cell surface markers, was tested in 49 patients on days + 30, + 45, + 60, and + 90 after alloHSCT and, additionally, in cases of positive HCMV pp65-antigenemia. HCMV infection was diagnosed in 19 patients. None of them developed HCMV disease. T-cell proliferative activity was significantly decreased on days when HCMV antigenemia was positive as compared to days without antigenemia. The number of pp65-positive cells negatively correlated with proliferative response. Comparison of patients who did experience HCMV infection with those who did not reveals significant decrease of T-cell proliferative activity observed on days + 30 and + 45, a time period when antigenemia was most frequently found to be positive, whereas no difference was detected on days + 60 and + 90. We conclude that, even clinically asymptomatic, HCMV infection has negative impact on T-cell proliferation capacity in alloHSCT recipients. However, pre emptive therapy with ganciclovir makes this immunosuppressive effect transient and restricted to the time of infection duration.

Changing circulation rate of human metapneumovirus strains and types among hospitalized pediatric patients during three consecutive winter-spring seasons. Brief report.

From 2001 through 2004, 808 pediatric patients admitted to hospital because of acute respiratory infections were examined for presence of respiratory viruses by either direct fluorescent staining using monoclonal antibodies or RT-PCR during three consecutive winter-spring seasons. On the whole, 336 (42%) patients were detected as positive for one or more respiratory viruses. The most widely circulating virus was human respiratory syncytial virus (hRSV) infecting 50% of positive patients, followed by human metapneumovirus (hMPV) found in 13% of patients, and then by influenza virus type A, human parainfluenzaviruses and coinfections. Significant variations in the circulation rate of hRSV, hMPV and influenzavirus type A were observed during the individual seasons. In addition, the circulation rates of the different types of hMPV changed yearly. In 2001-2002 and 2002-2003 hMPV circulated at a significant lower proportion than hRSV, while in 2003-2004 the circulation rates of the two viruses were closer. In conclusion, the 4 hMPV subtypes circulated yearly in Northern Italy flanking hRSV as major respiratory pathogens in the infantile patient population.

Comparison of contaminant and residue levels in organic and conventional milk and meat products from northern Italy.

Due to the growing interest in organic products, a comparison between the chemical safety of organic and conventional products was undertaken. Milk and meat were the products chosen for study. The parameters evaluated to assess chemical safety were organochlorine pesticides, polychlorinated biphenyls (PCBs), lead, cadmium and mycotoxin contamination. Pesticides and PCBs residues in both organic and conventional milk and meat were lower than legal limits. Lead and cadmium residues were very low and did not differ between organic and conventional products. However, aflatoxin M1 contamination in some but not all samples of organic milk was significantly higher than those of conventional milk, although factors other than organic production might be implicated.

Analysis of HIV drug-resistant quasispecies in plasma, peripheral blood mononuclear cells and viral isolates from treatment-naive and HAART patients.

The pattern of HIV-1 reverse transcriptase and protease mutations conferring resistance to antiretroviral drugs was studied in five treatment-naive patients and five HIV-infected patients receiving HAART [two reverse transcriptase inhibitors + one protease inhibitor] for > or = 1 year. Direct sequencing was performed on plasma HIV RNA, HIV DNA from peripheral blood mononuclear cells (PBMCs), and RNA from viral isolates. In addition, reverse transcriptase and protease PCR products from PBMCs HIV DNA, plasma HIV RNA, and viral isolate RNA were cloned in a plasmid to study the quasispecies distribution of drug-resistance associated mutations. Direct sequencing of HIV DNA from PBMCs and HIV RNA from plasma and viral isolates did not show the presence of drug resistance associated mutations in both reverse transcriptase and protease of HIV from all five treatment-naive patients. On the contrary, mutation analysis obtained by cloning plasma HIV RNA and PBMCs DNA showed the presence of drug-resistance related mutations at a low frequency in both HIV enzymes of four out of five treatment-naive patients. On the other hand, direct sequencing of plasma HIV RNA showed the presence of several reverse transcriptase and protease mutations in all five treated patients. Mutation analysis performed by cloning PBMCs HIV DNA, and HIV RNA from plasma and viral isolates, revealed additional reverse transcriptase and protease changes compared to direct sequencing of the relevant biological samples. All the additional changes were observed in a minority of clones. In conclusion, the data suggest that less frequent drug-resistant viral variants not detected by direct sequencing of PBMCs, plasma samples, or viral isolates are present in both treatment-naive and treatment-experienced HIV patients. These findings may have important implications in the understanding of the selection process of drug-resistant variants under drug pressure.

Oxidative stability and dietary treatment with vitamin E, oleic acid and copper of fresh and cooked pork chops.

Research has been conducted on the effects of feed supplementation with vitamin E, oleic acid (sunflower oil) and copper on some quality characteristics of pork chops. The study was based on the measurement of pH 45' and 24 hr post mortem, proximate composition, colour both objective and sensory, colour stability after packing in oxygen permeable film and protective atmosphere, copper and iron contents, vitamin E content in fresh and cooked chops, peroxide and TBARS value in raw and cooked meat, total cholesterol, cholesterol oxides and aldehydes in cooked meat, sensory evaluation of the eating quality of cooked chops and iodine number of subcutaneous fat. Vitamin E content was significantly higher with oil and vitamin supplementation. No variation has been observed in copper and iron contents. A higher stability of the colour of meat packed under modified atmosphere has been observed with increasing vitamin E content, but the same did not apply with meat packed in oxygen permeable film. No differences have been observed on fatty acid oxidative stability of fresh m. longissimus dorsi and cooked chops (peroxide and TBARS values), on cholesterol oxidation and aldehydes production of cooked chops with increasing vitamin E content. Iodine number in supplemented animals reached levels normally considered at risk for fat firmness.

Lipid and cholesterol oxidation in frozen stored pork, salame Milano and mortadella.

An investigation has been carried out on oxidative processes of fresh and stored frozen pork and of two pork products (salame Milano and mortadella). Wholesale pork cuts (shoulder, ham trimmings, belly and backfat) were checked fresh and after frozen storage (1, 3 and 6 months). The streaky bacon was studied fresh and after scalding at 80 °C. Salame Milano and mortadella were produced with fresh and frozen raw materials and a few commercial samples were also part of the study. No real differences have been observed between commercial and experimentally produced salame and mortadella. Peroxide and TBARS values were low in all cases. Among the cholesterol oxides determined (7ß-hydroxycholesterol, 5,6α-epoxycholesterol, 7-ketocholesterol and 25-hydroxycholesterol) those dangerous for human health were either absent or their concentration was below toxic levels. The results are discussed on the light of literature reports and Italian pork products technologies.

Comparative evaluation of some antioxidants in salame Milano and mortadella production.

Six formulations of salame Milano and mortadella were produced, one without antioxidants, two with sodium ascorbate (0.05-0.1 and O.2%), one with catechin, one with phytic acid, and one with sesamol. The products were studied for oxidation levels (peroxide value, TBARS, cholesterol oxides) and colour stability. The evaluation of the latter took place in conditions simulating commercial types of packaging (vacuum and modified atmosphere) and display. A significant difference emerged in colour stability. With the exception of salame Milano packed under modified atmosphere, in all cases salame and mortadella produced without Na ascorbate had significantly lower colour stability. Both in salame and mortadella, peroxide values and TBARS determination gave indications of a possible pro-oxidant effect of ascorbate 0.2% compared with an effective antioxidant activity of the other compounds tested. Cholesterol oxidation in salame appeared to be inhibited by sesamol and ascorbate while catechin was much less effective. In mortadella the prooxidant effect of Na ascorbate was confirmed. All lipid oxidation parameters, though, showed low oxidation values so that no quality nor health deficiencies could be envisaged with any of the formulations adopted. Lower colour stability scores, though, would create commercial problems.

A vitamin-free minimal synthetic medium for Cryptococcus neoformans.

The use of a simple synthetic medium is essential for study on the growth and physiology of Cryptococcus neoformans. In the present study, a minimal synthetic liquid medium (MSM) was tested for the growth of 23 C. neoformans strains. This medium contained a low concentration of glucose, ammonium sulphate and inorganic salts with a pH value of 4.5, but no amino acids or vitamins. The strains were starved for 4 days to eliminate nutrients which might have been carried over from their pre-culture medium. Then, they were inoculated in the MSM as an initial OD of 0.020 at 550 nm and incubated at 37 degrees C for 20 days. Cell growth was generally monitored daily by measuring the absorbance at 550 nm. The medium supported the growth of the strains tested and gave an average final OD of 0.500. The results obtained indicate that C. neoformans may be autotrophic with respect to vitamins and in particular to thiamine. The MSM medium is easy to prepare and store. It is highly reproducible and useful for studies on the growth and physiology of C. neoformans.

Glucose influence on germ tube production in Candida albicans.

The influence of different glucose concentrations was tested in minimal synthetic medium on Candida albicans strain. After 18 hours of starvation, germ-tube (GT) production, amount of consumed glucose, oxygen and the pH of the medium were checked every hour from the beginning through the end of the experiment. Optimal GT production was obtained with 1 g/l of glucose. At this concentration the greatest glucose and oxygen consumption were also noted. No pH variations in the medium were observed in all of the glucose concentrations used. At 3 and 5 g/l glucose concentrations a lower GT production were obtained. The Crab-tree effect might interfere with GT production when glucose concentration is higher than 1 g/l. This data may support the hypothesis that GT production is strictly glucose dependent.

Lean colour of green and matured Parma hams: Comparative evaluation and technological relevance of sensory and objective data.

Research has been conducted on the relationship between sensory evaluation and objective measurement of pork colour. The study also investigated the relationship between the colour of fresh meat and the colour of matured hams. Sensory evaluation was carried out at 24 h post mortem on the freshly cut surfaces of green hams trimmed for Parma ham production. Objective measurements were performed at the same time on Semimembranosus and Biceps femoris muscles with a Minolta Chromameter Reflectance II CR200/08. Cold carcass weight, lean content, trimmed ham weight, 45 min and 24 h post mortem pH of Semimembranosus muscle were also recorded. The hams were processed according to Parma ham technology. Weight losses at standard processing times were collected. At the end of processing a sample of about one-third of the hams was evaluated for internal lean colour and lean firmness both by sensory panel and objective measurements. Proximate composition was also determined. The results showed highly significant relationships between colour sensory scores and the coordinates L (∗), b (∗) and hue of the C.I.E. L (∗)a (∗)b (∗) colour system. Among the other parameters measured on fresh meat only 24 h pH was related at a very significant level with sensory and objective colour values. Correlation coefficients were generally higher for Semimembranosus than Biceps femoris. Matured ham colour was linked with fresh meat sensory judgements, L (∗), hue and a (∗) values. The relationship, though, was not sufficiently strong for use in predicting the colour of matured hams from green ham characteristics. Processing appears to have a positive effect on the colour of pale meat. Weight losses were mainly linked with lean meat content; other quality attributes being less important. Lean firmness of matured hams was related to the colour and pH of the fresh meat.