Quasispecies tropism and compartmentalization in gut and peripheral blood during early and chronic phases of HIV-1 infection: possible correlation with immune activation markers.

HIV quasispecies was analysed in plasma and proviral genomes hosted by duodenal mucosa and peripheral blood cells (PBMC) from patients with early or chronic infection, with respect to viral heterogeneity, tropism compartmentalization and extent of immune activation. Seventeen HIV-1-infected combined antiretroviral therapy naive patients were enrolled (11 early infection and six chronic infection). V3 and nef genomic regions were analysed by ultra-deep pyrosequencing. Sequences were used to infer co-receptor usage and to construct phylogenetic trees. As markers of immune activation, plasma sCD14 and soluble tumour necrosis factor receptor II (sTNFRII) levels were measured. Median diversity of HIV RNA was lower in patients with early infection versus chronic infection patients. Overall, direct correlation was observed between V3 diversity and X4 frequency; V3 diversity of HIV RNA was inversely correlated with CD4 T-cell count; median sCD14 and sTNFRII values were similar in early and chronic patients, but X4 frequency of HIV RNA was directly correlated with plasma sCD14. The proportion of patients harbouring X4 variants and median intra-patient X4 frequency of proviral genomes tended to be higher in chronic infection than early infection patients. More pronounced compartmentalization of proviral quasispecies in gut compared with PBMC samples was observed in patients with early infection compared with chronic patients. The loss of gut/PBMC compartmentalization in more advanced stages of HIV infection was confirmed by longitudinal observation. More studies are needed to understand the pathogenetic significance of early HIV quasispecies compartmentalization and progressive intermixing of viral variants in subsequent phases of the infection, as well as the role of immune activation in tropism switch.

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.

A case of dengue type 3 virus infection imported from Africa to Italy, October 2009.

In October 2009, a traveller returning from Africa to Italy was hospitalised with symptoms suggestive of a haemorrhagic fever of unknown origin. The patient was immediately placed in a special biocontainment unit until laboratory investigations confirmed the infection to be caused by a dengue serotype 3 virus. This case reasserts the importance of returning travellers as sentinels of unknown outbreaks occurring in other countries, and highlights how the initial symptoms of dengue fever resemble those of other haemorrhagic fevers, hence the importance of prompt isolation of patients until a final diagnosis is reached.

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.

Frequency of detection of respiratory viruses in the lower respiratory tract of hospitalized adults.

BACKGROUND: Respiratory infections are the most common infections in humans. The prevalence of respiratory viruses in adults is largely underestimated, and relevant data mostly concern infants and children. OBJECTIVES: To evaluate the prevalence of respiratory viruses in adults hospitalized in Italy. STUDY DESIGN: During April 2004--May 2005, 510 consecutive lower respiratory tract samples were prospectively collected. These were evaluated with a molecular panel that detected 12 respiratory viruses. RESULTS: Two hundred and fifteen samples were positive for at least one viral pathogen, with an overall sample prevalence of 42.2%. Human rhinoviruses (HRVs) were the most commonly detected viruses (32.9%), followed by influenza virus (FLU)-A (9.0%); the other viruses were 2% or less. Multiple agents were detected in 30 samples from 29 patients, resulting in a co-infection rate of 6.7%. CONCLUSIONS: This study shows a high prevalence of viruses in the lower respiratory tract samples of hospitalized adults, mostly HRV and FLU-A. It is not possible to establish the role of viruses detected at low frequency, but our findings suggest the necessity to consider them as potential causes or precursors of lower respiratory tract infections (LRTIs).

Markers of human papillomavirus infection and their correlation with cervical dysplasia in human immunodeficiency virus-positive women.

Human papillomavirus (HPV) genotypes and HPV DNA load were analysed in cervical smears from 76 human immunodeficiency virus (HIV)-positive and 54 HIV-negative women. The prevalence of genotypes was similar for all women, with the exception of HPV62, which was over-represented in HIV-positive samples. HIV-positive women showed a higher prevalence of multiple genotypes that correlated neither with CD4(+) T-cell counts nor with cervical dysplasia. No significant differences were observed in terms of total or single-type HPV DNA load. The HPV DNA load in both HIV-positive and HIV-negative women was significantly higher in squamous intra-epithelial lesions than in negative Pap smears.

[HPV infections in the lower genital tract in the female. Results of beta-interferon treatment]. / Lesioni da HPV del tratto genitale inferiore femminile. Risultati del trattamento con beta-interferone.

The Authors have analyzed the results obtained by treating 60 patients affected by HPV lesions of the lower female genital tract (flat vulvar, vaginal and cervical condylomatosis) with beta-interferon. At vulvovaginal level, the action of the drug is independent from the colposcopic aspect of the lesion but is closely correlated to its extension. The drug proved to be more efficacious at cervical level in case of condylomatous cervicitis rather than ANTZ with a reduction in the size of the lesion and disappearance, if present, of the dysplasia. The positive action of the beta-interferon has never occurred before 2-6 months from the end of the farmacologic treatment. The best results have been obtained in case of condylomatous cervicitis with complete remission in 58% of the cases, and in vaginal condylomatosis (CR at 6 months: 45%). On the basis of these results we may conclude that in these HPV lesions priority should be given to medical treatment whereas in vulvar condylomatosis (especially if extended greater than 1/3) where results are not very satisfactory (not more than 20% of CR) physical therapy is advisable.

The incidence of Chlamydia trachomatis-induced infection in women suffering from cervicovaginitis.

The results of a research on Chlamydia T. (direct survey of both the antigen in the uterine cervix and plasmatic antibodies) in a group of subjects suffering for cervico-vaginitis are provided. The incidence of the Chlamydia infection (proved by either the presence of this bacterium or antibody positivity) is not different from the values reported in literature. Conversely, the presence of neither specific cytological or colposcopic patterns nor of priviledged comites at vaginal level could be demonstrated. Our data, however, confirm a greater incidence of this infection in women reporting early sexual life and a high number of partners. As for the relationship between Chlamydia and contraceptives a slightly higher incidence of positivity in the cervix of patients using oestro-progestinics was registered, whereas no significant difference was noted in the use of other contraceptives IUD included.

PIP: Physicians examined 173 sexually active, non pregnant women suffering from lower genitalia inflammation. They responded to questions pertaining to their past and recent obstetric/gynecological history, to their partner's possible urogenital inflammations, the age of 1st intercourse, number of partners, and contraceptive use. 27.2% of the patients tested positive using immunoenzymatic techniques for Chlamydia trachomatis (CT). No specific symptoms of CT were observed. A correlation exists between early sexual intercourse and a large number of partners and a greater incidence of CT infections. Almost 98% of all CT positive patients reported 1st sexual intercourse between 16 and 21 years. Antibody positivity ranged from 33% (1st intercourse before 15 years) to 24% (1st intercourse between 16-21 years) and decreased to 5.89% when 1st intercourse occurred 21 years. In addition, CT positive patients had many partners. A greater positivity in the cervix occurred in those using oral contraceptives, however. On the other hand, no positivity was noted for those who used IUDs. Those women who used several contraceptives, such as oral contraceptives, IUD, and barrier methods, had a higher incidence of CT positivity (53.2%) than other groups. Perhaps this is due to clinical cervicovaginitis symptoms prompting the women to change techniques. Specific colposcopy patterns and cytological alterations which some physicians believe indicate CT infections did not identify patients with Chlamydia. These data suggest that it is impossible to make a diagnosis based on symptoms, past sexual history, and contraceptive use. Therefore the data indicate that immunoenzymatic tests are needed.