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According to both definitions of US Centers for Disease Control and Prevention and World Health Organization, Neglected Tropical Diseases (NTDs) are a group of preventable and treatable parasitic, viral, and bacterial diseases that affect more than one billion people globally. They generally afflict the more indigent patients of the world and historically have not received as much attention as other diseases. NTDs tend to thrive in low-income regions, where water quality, sanitation and access to health care are substandard. They are common in several countries of Africa, Asia, and Latin America. In this literature review, we want to focus on Human African Trypanosomiasis (HAT), also known as “sleeping sickness”, one of the most common neglected diseases in Africa. It is caused by infection with the subspecies of the parasitic protozoan Trypanosoma brucei, and it is transmitted by the bite of the tsetse fly. It puts 70 million people at risk throughout sub-Saharan Africa and it is usually fatal if untreated or inadequately treated. This review covers several aspects of the disease. We focused our interests on most recent epidemiological data, novel diagnostic methods with their advantages and limitations, new improved treatment and orphan drugs and eradication programs, including vector control, according to a “One Health” approach, to achieve the new goals recently set by WHO.

Human Onchocerciasis, caused by infection by the filarial nematode Onchocerca volvulus, is a neglected public health disease that affects millions of people in the endemic regions of sub-Saharan Africa and Latin America. It is also called river blindness because the Blackflies that transmit infection breeds in rapidly flowing fresh water streams and rivers. This review features state-of-the-art data on the parasite, its endobacteria Wolbachia, the prevalence of the infection and its geographical distribution, its diagnostics, the interaction between the parasite and its host, and the pathology of Onchocerciasis. By development and optimization of the control measures, transmission by the vector has been interrupted in foci of countries in the Americas (Colombia, Ecuador, Mexico, and Guatemala)and inSudan, followed by Onchocerciasis eliminations. The current state and future perspectives for vector control and elimination strategy are described.

Background This is a “proof-of-concept” study aiming to evaluate the impact of a multistep bundles intervention in the management and outcomes of patients with gram-negative bloodstream infections (GN-BSIs). Methods This was a single-center, quasi-experimental design study. In the pre-phase (January 2019 to May 2020), patients were retrospectively enrolled. During the post-phase (June 2020 to September 2021), all patients were prospectively enrolled in a nonmandatory 3-step bundles intervention arm including (i) step 1: imaging to detect deep foci of infection, follow-up blood cultures and procalcitonin monitoring; (ii) step 2: early targeted antibiotic treatment and surgical source control; (iii) step 3: discontinuation of antibiotics within 7–10 days in case of uncomplicated BSI. Patients were followed up to 28 days from BSI onset. The primary outcome was 28-day mortality. Results A total of 271 patients were enrolled: 127 and 144 in the pre- vs post-phase, respectively. Full application of step 1 (67% vs 42%; P < .001), step 2 (83% vs 72%; P = .031), and step 3 (54% vs 2%; P < .001) increased in the post-phase. Overall, the intervention reduced 28-day mortality (22% vs 35%, respectively; P = .016) and the median duration of total (11 vs 15 days; P < .001) and targeted (8 vs 12 days; P = .001) antibiotic therapy. Finally, the multivariate Cox regression confirmed the independent protective effect of adherence to step 1 (adjusted hazard ratio [aHR], 0.36; 95% CI, 0.20–0.63) and step 2 (aHR, 0.48; 95% CI, 0.29–0.81) on risk of 28-day mortality. Conclusions Clinical management and outcomes of patients with GN-BSIs may be improved by providing a pre-established multistep bundles intervention.

Background. The mortality rate for coronavirus disease-19 (COVID-19) increases with age. Some anti-inflammatory drugs such as tocilizumab or steroids have been proposed for the treatment of severe disease; however, few data are available in the elderly. Methods. A retrospective case-series of patients hospitalized between March 1st and June 15th, 2020 with confirmed COVID-19 by RT-PCR testing on throat/nasopharyngeal swabs and age ≥ 65 years was analysed. Patients were retrospectively divided into three groups according to the chosen treatment [standard of care (SOC), tocilizumab or corticosteroids] and patient characteristics and occurrence of adverse events were compared among groups. Results. Overall, 206 patients were included, 148 treated with standard of care, 42 with steroids and 16 with tocilizumab. Patients treated with steroids or Tocilizumab presented more frequently with fever (p = .003), dyspnea (p < .001), bilateral opacities/infiltrates at chest X-ray (p =.026) or CT-scan (p = .020), and more frequently required non-invasive/invasive ventilation (p < .001). Crude mortality was 27%, without differences among groups (p = .074). No specific adverse events were observed during/after the administration of steroids or tocilizumab; however, a trend towards an increased risk of secondary infections was described compared to SOC (p = .097). At multivariate logistic regression, only tocilizumab administration was an independent predictor of secondary infections (aOR = 6.72, 95% CI = 1.43-31.39, p = .015). Conclusions. Tocilizumab and corticosteroid could have a possible role for severe form of pneumonia in course of COVID-19 also in elderly patients, even if great attention to the monitoring of infectious complications should be paid in this special population.

Background: Italy was declared malaria free by the World Health Organization in 1970. Despite this, nonimport malaria cases are on the increase in Italy and throughout the Mediterranean area. In It...

The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including

The aim of this study was the reconstruction of SARS-CoV-2 evolutionary dynamics in time and space in Italy and Europe between February and June 2020. The cluster analysis showed that pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 entered Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, the reconstructed ancestral scenario suggests a central role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.

Background The spectrum of clinical manifestations of CoronaVirus Disease-19 (COVID-19) is not yet completely known. In elderly, mortality and extra-pulmonary involvement appear to be more frequent than expected. Methods A multicentric-retrospective-case-series of patients hospitalized between March 1st and June 15th, 2020 with confirmed COVID-19 by RT-PCR testing on throat/nasopharyngeal swabs and age ≥65 years was analysed. Based on the “Clinical Frailty Scale” (CFS), patients were classified into three groups according to the resulting score: 1-3 (group A), 4-6 (group B), 7-9 (group C). Results Overall, 206 patients were included. Crude mortality was 27%. According to CFS, on admission, 60 patients (29%) were assigned to group A, 60 (29%) to group B, and 86 (42%) to group C. The following features were significantly more frequent among group C patients in comparison with groups B and A: mental confusion (65% vs 33% vs 7%, respectively, p

Data regarding the immunological memory and long‐time kinetics of immunoglobulin (IgG) against viral nucleoprotein (NP) and spike protein S1 receptor‐binding domain (S1RBD) of Severe Acute Respiratory Syndrome‐associated Coronavirus 2 (SARS‐CoV‐2) are lacking. All consecutive COVID‐19 patients admitted to our Clinic between March 1, 2020, and May 1, 2020, who were tested at hospital admission for anti‐S1RBD and anti‐NP IgG were enrolled. Serum samples were tested for anti‐SARS‐CoV‐2 antibodies with the use of two commercially available enzyme‐linked immunosorbent assays. Results are expressed as optical density measurements at 450 nm (OD450). Overall, 111 patients were included; the median (q1–q3) age was 57 (49–73) years, 59 (53%) males. According to disease severity, 31 (28%), 47 (42%), and 33 (30%) patients were considered affected by mild/moderate, severe, and critical SARS‐CoV‐2 infection, respectively. During hospitalization, patients with the critical disease showed a higher peak value of both anti‐NP (median OD450: 3.66 vs. 3.06 vs. 3.00 respectively, p = .043) and anti‐S1RBD IgG (median OD450: 2.33 vs. 1.6 vs. 0.91, respectively, p, Highlights ‐Antibodies against SARS‐CoV‐2 persisted several months after the disease.‐ Infection severity apparently did not affect IgG seroconversion.‐ SARS‐CoV‐2 vaccination could be a valid strategy to fight the pandemic.

Background Cardiac involvement significantly contributes to coronavirus disease 2019 (COVID-19)mortality.12-lead electrocardiogram (ECG) represents a fast, cheap, and easy to perform exam with the adjunctive advantage of the remote reporting possibility. In this study, we sought to investigate if electrocardiographic parameters are able to identify patients, deemed at low-risk at admission,who will face in-hospital unfavourable course. Methods From March 1, 2020 through March 30, 2021, 384 consecutive patients with confirmed low-risk COVID-19 were hospitalized at the AziendaOspedalieroUniversitariaPoliclinico di Bari (Italy). Criteria for low-risk were: admission to the division of Pneumology or Infectious Diseases, no need for immediate (within 24 hours from admission) transfer to Intensive Care Unit or for respiratory support with invasive mechanical ventilation (IMV) or for circulation support (either mechanical or pharmacological). Admission ECGs were reviewed and interpreted by two expert cardiologists. The primary outcomes were in-hospital death and the composite outcome of in-hospitaldeath and IMV. Results In low-risk COVID-19 patients, atrial fibrillation (AF), poor R wave progression (PRWP), tachycardia, and right bundle branch block (RBBB) resulted as statistically significant and independent predictors of in-hospital all-cause mortality; AF, PRWP, Tachycardia, RBBB, and corrected QT interval showed to be statistically significant and independent risk factors for the occurrence of the composite endpoint of death and IMV. Conclusions Our study demonstrated for the first time that RBBB and PRWP, assessed upon admission with ECG, are associated with unfavourable clinical course in a baseline low-risk population hospitalized for COVID-19.

Background A growing body of observational evidence supports the value of ceftazidime-avibactam (CAZ-AVI) in managing infections caused by carbapenem-resistant Enterobacteriaceae. Methods We retrospectively analyzed observational data on use and outcomes of CAZ-AVI therapy for infections caused by Klebsiella pneumoniae carbapenemase–producing K. pneumoniae (KPC-Kp) strains. Multivariate regression analysis was used to identify variables independently associated with 30-day mortality. Results were adjusted for propensity score for receipt of CAZ-AVI combination regimens versus CAZ-AVI monotherapy. Results The cohort comprised 577 adults with bloodstream infections (n = 391) or nonbacteremic infections involving mainly the urinary tract, lower respiratory tract, and intra-abdominal structures. All received treatment with CAZ-AVI alone (n = 165) or with ≥1 other active antimicrobials (n = 412). The all-cause mortality rate 30 days after infection onset was 25% (146/577). There was no significant difference in mortality between patients managed with CAZ-AVI alone and those treated with combination regimens (26.1% vs 25.0%, P = .79). In multivariate analysis, mortality was positively associated with presence at infection onset of septic shock (P = .002), neutropenia (P < .001), or an INCREMENT score ≥8 (P = .01); with lower respiratory tract infection (LRTI) (P = .04); and with CAZ-AVI dose adjustment for renal function (P = .01). Mortality was negatively associated with CAZ-AVI administration by prolonged infusion (P = .006). All associations remained significant after propensity score adjustment. Conclusions CAZ-AVI is an important option for treating serious KPC-Kp infections, even when used alone. Further study is needed to explore the drug’s seemingly more limited efficacy in LRTIs and potential survival benefits of prolonging CAZ-AVI infusions to ≥3 hours.

There is limited information on the presenting characteristics, prognosis, and therapeutic approaches of young patients hospitalized for coronavirus disease 2019 (COVID-19). We sought to investigate the baseline characteristics, in-hospital treatment, and outcomes of a wide cohort

An autochthonous case of lymphocutaneous sporotrichosis caused by Sporothrix schenckii is reported. The patient developed skin lesions localized along the lymphatics that appeared after he suffered an injury while collecting wicker canes in marshy water. The fungus was identified as Sporothrix schenckii by MALDI-TOF and sequencing. Phylogenetic analysis was also performed. Low MIC values were detected for all tested echinocandins and azoles except for fluconazole. The patient was treated with itraconazole without significant improvement. A regression of lesions was observed after 3 months of therapy with voriconazole. Few cases of sporotrichosis have been reported in Europe. However, several cases of sporotrichosis have been described in Italy. The incidence of sporotrichosis in Italy may be underestimated and microbiologists, and clinicians must be aware of this fungal infection.

Pertussis vaccination coverage in the Marche region is one of the lowest in Italy, with the province of Pesaro-Urbino remaining stable below 95% coverage since at least 2013. In this paper, we retrospectively analyzed all whooping cough notification cards arriving at the prevention department of the Area Vasta 1 Health Office in the Marche region and relating to the Pesaro-Urbino province (Italy). Between 2012 and 2017, there were 28 reported cases of pertussis with a peak in 2016 (11 cases, of which seven were in Urbino). The 28 patients were mostly male (65%), and had a mean age of 9 years. Three of these were not Italian. Between 2012 and 2017, the district of Pesaro reported the highest number of cases (almost 46.5% of the total), followed by Urbino (28.5%) and Fano (25%). The average incidence in the province in the period in question, still under 2 cases/100,000 inhabitants, arrived in 2016 at 4 cases/100,000 inhabitants. In particular, in Urbino there was an unforeseen incidence8 cases/100,000 inhabitants. There were no deaths, although two children (both under 12 months of age) were hospitalized. Our data confirm that in 2016 there was a pertussis epidemic in Urbino (Italy).

OBJECTIVES We assessed whether changes in community viral load (CVL) over time were associated with the rate of new HIV diagnoses (NDs). METHODS HIV-1-positive individuals referred to our institute and permanently residing in our province were considered for inclusion in the study. A total of 861 HIV-infected adults with at least one HIV RNA measurement (12 530 measurements in total) between 2008 and 2014 were included. Viraemia copy-years were calculated from all HIV RNA values for each patient using the trapezoidal rule; multiple CVL indicators were considered. Total NDs and recent infections (< 1 year) were analysed separately. The association between NDs and CVL was tested by means of mixed Poisson models, with CVL as a fixed effect and year as a random effect. RESULTS The incidence of NDs was 2.28 per 100 000 residents in 2008 and 2.52 per 100 000 residents in 2014. Total numbers of NDs and recent infections did not vary significantly over time (P for trend 0.879 and 0.39, respectively). Mean HIV RNA decreased from 31 095.8 HIV-1 RNA copies/mL in 2008 to 21 231.5 copies/mL in 2014 (P < 0.001); a downward trend was always observed regardless of the CVL indicator considered. Depending on the indicator, there were some differences in CVL by patient characteristics. The most substantial contributors to CVL appeared to be male individuals, men who have sex with men (MSM), non-Italians, and untreated subjects (all P < 0.05). The relative risk of ND increased among Italians and MSM with an increasing proportion of subjects having an undetectable HIV RNA, and decreased in the same population with increasing levels of CVL. CONCLUSIONS In our setting, CVL represented a good marker of access to care and treatment; however, reduced CVL did not coincide with a reduction in the rate of NDs.

Schistosomiasis is the most prevalent tropical disease in the world after malaria. According to the World Health Organization, the disease afflicts more than 240 million people in about 80 countries. Recently, an epidemiological surveillance study performed between 1997 and 2010 by the European Network for Tropical Medicine and Health Travel regarding schistosomiasis between immigrants and travelers has been published. No data are available in the literature regarding the situation in South Italy. Herein, we report the prevalence of urinary schistosomiasis in a population of migrants in Apulia referring to our outpatient clinic for immigrant diseases in the period 2006–2016. Since all cases of schistosomiasis were related to the last three years of observation, the demographic and clinical characteristics of the study population were compared before and after 2014. Nearly 51% of all patients visited (1762) were from high/moderate endemic countries for schistosomiasis, and nine cases of urinary schistosomiasis were diagnosed. Prevalence was 1% among migrants from endemic areas and 10% in those from Mali and Senegal. Our findings confirm that schistosomiasis is a widespread infection among immigrants, even if it is often underdiagnosed because of the multifaceted clinical presentation. Changes in migratory dynamics can affect clinical observations very quickly.

Human dirofilariosis is a zoonosis caused by different Dirofilaria species: D. repens, D. immitis, D. tenuis and D. ursi, thin nematodes belonging to the Onchocercidae family, whose larval stages are generally found in the natural (felines and canids) or accidental (human) definitive host. In Europe, human infection is rare, even in areas considered endemic such as Spain or Italy. In this paper we describe the case of an 82-year-old woman living in Modugno (Bari municipality), who came to our observation for a subcutaneous nodule on her right thigh that had appeared in the previous two weeks and gradually became necrotic. The woman lived in an apartment with a dog. An adult worm, white, thin, about 140 mm long, came out of the necrotic area spontaneously. After microscopic examination, the worm was identified as D. repens. In Apulia, a South-Italy region, human dirofilariosis is a rare disease and since 1885 only 11 cases have been reported. In recent years we have witnessed an increase in the number of diseases transmitted by vectors at all latitudes, and in our region an increase in the Aedes albopticus population has been reported, so it is reasonable to expect an increase in dirofilariosis cases in humans.

Pertussis is a contagious, infectious disease that affects mainly children and is caused by Bordetella pertussis. The pertussis vaccine has changed the epidemiology of the disease up to the point when it almost vanished, with a minimum number of cases recorded in Italy (2008) when vaccination coverage was 97%. For the same reason the natural history of the disease was also modified. Indeed, in high-income countries the lack of immunity acquired with the vaccine causes adolescents and adults to become an important source of infection for unvaccinated subjects, the newborn and children who have not completed their primary education. The reduction in the vaccinated pediatric population and the loss of acquired immunity could be the cause of the re-emergence of a disease which, in developing countries, has a 4% mortality rate among children under one year of age. In this work we describe three cases of pertussis that are apparently unrelated. They occurred in the area of Urbino in a period of slightly under a month. Italy is going through a historical moment of great suspicion regarding pediatric vaccination, despite scientific evidence that should allay such suspicion. To increase people's awareness of vaccinations with a view to comments made regarding older children and adults it is our view that more effective intervention methods are needed.

This paper, part of a larger epidemiological study carried out between 2004 and 2010, analyzed immigrants frequenting the largest Apulian regional hospital (Bari Policlinico). Our aim was to evaluate the perception on the part of undocumented immigrants of their rights of access to the National Health Care services and whether this privilege is actually utilized. An anonymous multi-language questionnaire was distributed to all patients with STP (code number for temporary presence of foreigners) at the immigrant outpatient Infectious Diseases Clinic of Bari from June 2009 to June 2010. Questions were related to nationality, date of arrival in Italy, use of health facilities in the 2 years prior to the compilation of the questionnaire, and their understanding of STP. The patients were also screened for infectious diseases (HIV-Ab, HBsAg, HCV-Ab, VDRL, TPHA and Mantoux). A total of 256/272 patients completed the questionnaire; the meaning of STP was unknown to 156/256 (60.9 %) patients, only 54/256 (21 %) knew the exact meaning of STP and only 42/54 (76.6 %) of the latter knew how long STP was valid. Moreover, 128/256 (50.7 %) were aware that doctors from the emergency unit were not allowed to notify police regarding presence of illegal immigrants. Regarding clinical data 3 % were HIV+ (8/256), 5 % (13 patients) positive for TPHA, 5 % for HBsAg, 2 % were HCV (five patients). A >10 mm diameter infiltrate of Mantoux test was noted for 44 % of patients. A lower prevalence than expected for infections such as HIV, HBV or HCV was noted for immigrants compared to data from their countries of origin. At present, large-scale political solutions to the challenges of facilitating access to health facilities for undocumented immigrants are lacking in Italy. The development of communication systems is fundamental to improving access to health services and to creating links between immigrants and the healthcare system.

HIV-1 recombination, reverse transcriptase (RT) low fidelity and high replication rate are the drivers of variability and evolution on the global scale. Only few of these HIV-1 chimeric forms have been characterized in Europe, despite 20% of infections are due to unique or circulating recombinant forms worldwide. An outbreak of BC recombinants has been recently described in a southern region of Italy, Apulia, in men having sex with men (MSM) seeking sexual partners on-line. We analyzed the full length genome of HIV-1 BC recombinants harbored by three recently infected subjects, two MSM and a heterosexual woman, with no evidence of epidemiological link. The recombination analysis showed a unique recombination pattern of a subtype C genome with 3 subtype B fragments corresponding to HXB2 positions: [1-463] in the 5'LTR , [2804-3037] in RT and [8662-9548] corresponding to the C-terminal segment of gp41, nef and most of 3'LTR. Phylogenetic analysis revealed the South American origin of the C subtype parental strain. A research conducted in an Italian nationwide database provided six additional similar sequences from other Italian regions with identical recombination pattern in pol gene; a further BLAST search retrieved one full length genome isolated in France with the same mosaic pattern, except an additional B subtype short fragment in the integrase region. These recombinant isolates, designated CRF60_BC, led to the identification of the first Italian circulating recombinant form, which gave rise to an epidemic burst mainly involving MSM.

To compare clinical characteristics and therapeutic management of newly HIV-diagnosed immigrants to natives. Patients with a first HIV diagnosis from 1996 to 2010 were included. Of 716 new diagnoses, 85 (12 %) were immigrants. Migrants were younger, more frequently females and sexually infected, less likely to voluntarily request testing, and less HCV-coinfected. Late presenters (CD4

Tuberculosis remains one of the major worldwide problems regarding public health. This study evaluates the burden of this disease in the BAT Province of the Apulia region (Italy); 12,295 patients were studied, including 310 immigrants. Tubercular disease and mycobacteriosis were found in 129 patients. The number of new TB cases/year ranged from three in 2005 to 12 in 2009. TB was more frequently localized in the lung (70.5%). 14.4% of cases were institutionalized patients for severe neurological and/or psychiatric disease. The database evidenced certain aspects of our study population: the large number of TB patients institutionalized between natives, but no larger presence of TB among HIV-positive patients in immigrants compared to Italians. Our findings should help to redefine the alarm regarding the spread of an epidemical form of TB but also to present certain criticisms regarding patient management (especially immigrants) regarding costs, hospitalization, and difficulty of reinstating the patient in the community. Further our data underscore the importance of prevalence of TB in bedridden, institutionalized patients.

Viral isolation and V3 sequencing were performed for 52 patients with non-subtype B viruses. The HIV-1 isolation rate was 93%, and 98% of isolates were characterized as NSI. V3 sequences corresponding to NSI isolates were compared to non-subtype B sequences with corresponding SI isolates from the Los Alamos database. The two sequence groups significantly differed in number of sequences with 35 amino acids, net charge, Brigg's coefficient, loss of NGS at positions 6–8, and 11/25 genotype (p

SUMMARYThis study assessed changes in prevalence and distribution of HIV-1 non-subtype B viruses in Italian and immigrant patients over two decades in a province in Italy. All HIV-positive patients who underwent genotypic resistance testing were selected. Prevalence of non-subtype B viruses in 3-year periods was calculated. All sequences of non-subtype B and those provided by REGA as unassigned were analysed for phylogenetic relationships. In total, 250/1563 (16%) individuals were infected with a non-subtype B virus. Prevalence increased over time, reaching a peak (31·5%) in 2004–2006. In Italian patients, the most frequent subtypes were B (92·5%) and F1 (4%). F1 subtype was also prevalent in patients from South America (13·6%); in patients of African origin, CRF02_AG (54·9%) and G (12·3%) were the most frequent. HIV-1 non-subtype B infections in Italians were mostly found in patients who acquired HIV sexually. A phylogenetic relationship between F subtypes in Italian and representative HIV-1 sequences from Brazil was found. C subtypes in Italians were phylogenetically related to subtypes circulating in Brazil. Inter-subtype recombinants were also found in the latest years. The HIV-1 epidemic in Brescia province evolved to the point where about 1/3 patients recently diagnosed harboured non-B HIV subtypes. The distribution of HIV-1 non-B subtypes in Italian patients resembled that in South American patients and phylogenetic relatedness between some Italian and South American HIV-1 strains was found. The possible epidemiological link between these two populations would have been missed by looking only at risk factors for HIV acquisition declared by patients. The evidence of inter-subtype recombinants points to significant genetic assortment. Overall our results support phylogenetic analysis as a tool for epidemiological investigation in order to guide targeted prevention strategies.

The distribution of different HIV subtypes follows a geographical trend. HIV-1 (the most widespread type of HIV worldwide) is classified into three genetic groups: major (M), outlier (O) and novel (N). HIV-1 group M viruses have been classified into nine subtypes. Analysis of full-length genome sequencing has revealed intersubtype recombinants, which are thought to originate from individuals simultaneously infected with viruses of two or more subtypes. The extensive genetic variability of HIV-1 and international travel are important factors in its spread worldwide. The aim of this review is to describe the changing patterns of nonsubtype B prevalence in resource-rich countries and verify how these subtypes influence transmission, disease progression, mutational patterns of resistance, as well as response to therapy.

One hundred and ninety-two pol sequences of drug-naïve and drug-experienced subjects infected with non-B HIV-1 subtypes were analyzed to identify treatment-related amino acid changes which might be relevant for drug-resistance and possibly not included in the accepted mutation list for the B subtype. The correspondence analysis identified non-B-specific and subtype-specific polymorphisms which should not be mistaken for mutations. Multiple chi(2) were performed to detect the differences between naïve vs treated subjects and between different subtypes. To verify the contribution of each single mutation to the resistance levels as predicted by the Virtual Phenotype-LM, simple univariate linear regression was used with fold resistance as a dependent variable and individual mutations as predictors. Commonly accepted protease (PR) and reverse transcriptase (RT) positions along with mutants at RT positions 118 and 90 were significantly associated with treatment. Two unusual PR (K14R and I66F) and five RT positions (E28K, S68G, H221Y, L228R/H and P294A) were also associated with treatment (p0.01). Only minimal variations were observed with respect to commonly accepted amino acid changes. All amino acid changes correlated with treatment influenced the resistance levels to each single drug. Our findings demonstrate that there are no substantial differences regarding known resistance-associated mutations and the newly emergent substitutions between non-B and B subtype strains.

Thirty pol gene plasma-derived sequences clustering with the circulating recombinant form (CRF) 02_AG (IbNG) (bootstrap 100%) were evaluated to analyze the genomic composition. Subtype assignment was also phylogenetically confirmed by C2-V3 region analysis for 18/21 sequences evaluated. Thereafter, we compared the genomic recombination of the CRF02_AG/IbNG prototype as predicted by bootscanning and Jumping HMMER software (jpHMM) to that of our strains. With these methods, 27% and 50%, respectively, of our clinical sequences demonstrated the same pol structure as the prototype CRF02_A/G-IbNG. However, in subtrees built for each segment predicted by jpHMM (with a bootstrap value of more than 75%), all fragments clustered with IbNG and were distinct from A and G clades. Overall, our sequences resulted in true members of CRF02_AG-IbNG, which, however, appeared to be a subtype phylogenetically separate from A or G, at least with regard to the pol gene.

A total of 347 pol gene sequences from 88 Tuscan and 259 Apulian subjects (including 52 non-Italians and 9 children) were analyzed phylogenetically. Forty-four (12.6%) non-B subtypes were found, including 3.4% C, 1.4% F1, 0.8% G, and 0.3% each for J and A pure subtypes, and 3.7% CRF02_AG, 1.4% CRF01_AE, 0.6% BF, and 0.3% CRF06-cpx recombinant forms. An additional sample close-matched the pol gene of an unique recombinant form (URF AGK 99GR303). The non-B subtypes were from 40 adults and 4 children; 12 of these 44 patients were epidemiologically linked. Thirty-three of the 44 non-B viruses pertained to non-Italian immigrants and 11 to Italians, signifying that 63.4% immigrants and 3.7% Italians harbored non-B subtypes. The overall frequency of non-B subtypes was higher in Tuscany than in Apulia (18.1% vs. 10.8%). Moreover, 6.1% and 3.0% non-B subtypes were found among Italians from Florence and Apulia, respectively, while 52.1% and 72.4% of immigrants living in Tuscany and Apulia harbored non-B subtypes. Women infected by means of sexual contact prevailed among non-Italian adults; the majority of Italians were males and admitted high-risk sexual behavior. Four Italians had a history of extensive travel in countries of high endemicity. Social and epidemiological changes are responsible for an increasing circulation of non-B subtypes in Italy. Although non-B subtypes principally infect non-Italian patients, in Italy they can no longer be considered exclusively restricted to subjects from endemic areas.

Blood and concurrent rectal biopsy samples of human immunodeficiency virus type 1 (HIV-1)-positive highly active antiretroviral therapy (HAART)-treated patients were tested for genotypic resistance by direct sequencing of reverse transcriptase (RT) and protease (PR) regions to compare the patterns of resistance in these compartments. Fourteen subjects (five with undetectable plasma viral load (pVL) and nine persistently viremic) were studied. Four of five patients with undetectable pVL also had undetectable mucosal HIV RNA; sequence analyses from proviral DNA (PBMCs and rectal biopsy) were obtained with none or few resistance-associated mutations and no alteration of susceptibility profile. All viremic patients, and one with negative pVL, had detectable levels of mucosal HIV RNA (1.93–4.21 log10 copies/mg); sequences of HIV RNA (plasma and/or rectal biopsy) were also obtained, and multiple mutations generally compatible with current/past medications were detected. Overall, 40 HIV-1 PR and 42 RT sequences were analyzed, yielding a total of 42 PR and 47 RT sequence pairs (plasma/tissue-RNA; plasma-RNA/tissue-DNA; PBMC/tissue-DNA; tissue-DNA/RNA; tissue-RNA/PBMC-DNA; PBMC-DNA/plasma-RNA), which almost always differed at the total amino acid level (median percentage discordance 8.08% in the PR, 4.8% in RT). The median percentage of resistance position discordance equaled 88.8% (IQR = 20–100) in the PR and 74.55% (IQR = 31.75–100%) in the RT pairs, respectively. Different resistance levels were detected by means of a computer-assisted interpretation of mutational profiles. The results support the multiform evolution of HIV genotype in various body compartments and emphasize the participation of intestinal mucosa in HIV genotype selection. Samples from diverse tissues should be used for resistance evaluation to obtain a complete picture of drug resistance for antiretroviral-treated patients. J. Med. Virol. 70: 1–9, 2003. © 2003 Wiley-Liss, Inc.

Background Triple therapy including Telaprevir or Boceprevir still represents in many European countries the standard of care for patients with Hepatitis C Virus genotype 1 infection. The number of patients who received this treatment resulted generally lower than expected. We investigated, among naive patients, number and characteristics of treatment candidates who were started on triple or dual therapy in comparison to those who were deferred. Patients and Methods 621 naive treatment candidates were prospectively evaluated at each center. Factors associated with decision to defer or treat with dual or triple therapy were investigated by univariate and multivariate analyses. Rates of Sustained Virological Response and safety profile were analysed. Results Of candidates to treatment, 33% did not received it. It was mostly due to high risk of Interferon-induced decompensation. Of 397 patients who were started on treatment, 266 (67%) received triple, 131 dual. Among patient receiving treatment, unfavorable IL28B, severe liver damage and higher albumin were independently associated with the physician decision to administer triple therapy. Sustained Virological Response after dual therapy was 66.4%, after triple 73.7% (p = 0.14). 142 patients received Telaprevir. The choice of Telaprevir-based therapy was associated with higher Body Mass Index and advanced liver disease. Sustained Virological Response rates were 71.1% after Telaprevir and 76.6% after Boceprevir. Conclusions Individualizing treatment with available regimens allows to maximize Sustained Virological Response and to reduce the number of patients who remain untreated. High proportion of patients with severe liver damage urgently need Interferon free treatment.

We report a case (IC) of multidrug-resistant (MDR) HIV-1 infection in which the identification of the source patient (S) was supported by phylogenetic analysis of the pol gene and by the similarity of env sequences. HIV isolates from IC and S were characterized as non-syncytium viruses: a X4 variant (R(11) E(26)) was identified in both cases according to the V3 loop sequence. The pol mutational profile of IC included multiple protease and reverse-transcriptase inhibitor mutations similar to those in S. The lamivudine/tenofovir/tipranavir/ritonavir/enfuvirtide association was effective for IC but not for S.

Background In Western Europe, a previously subtype B HIV-1 restricted area, BC recombinants have been rarely reported. Objective To describe an outbreak of HIV-1 BC recombinants in southern Italy. Study design We analyzed pol (protease/reverse transcriptase) sequences from 135 newly diagnosed HIV-1-infected patients during the years 2009–2011. For phylogenetic relationships, sequences were aligned to the most recent reference data set from the Los Alamos database using BioEdit (version 7.1.3). The resulting alignment was analyzed with the Phylip package (version 3.67) building a neighbor-joining tree based on the Kimura two-parameter substitution model. The reliability of the tree topology was assessed through bootstrapping using 1000 replicates. The recombination pattern was characterized using SimPlot 3.5.1 and SplitsTree 4. Results At phylogenetic analysis, 22 (16.2%) isolates whose sequences were not unequivocally assigned to a pure subtype or known CRF, formed a distinct monophyletic clade (100% of bootstrap value). For these isolates, the recombination analysis identified a BC mosaic pattern with two breakpoints at positions 2778 ± 5 and 3162 ± 8 (HXB2 numbering) which differed from those of known BC CRFs. All patients from whom these sequences were derived were highly educated youth Italians, 91% males and 82% MSM. Sequences of pol integrase, gp120 and gp41 from these same patients were classified as C subtype. Conclusions This outbreak which further reflects the increasing heterogeneity of HIV epidemic in our country is the first report of an Italian outbreak of a BC recombinant, possibly a novel candidate CRF.

HIV coreceptor tropism (CTR) testing is a prerequisite for prescribing a coreceptor antagonist. CTR is increasingly deduced by analyzing the V3 loop sequence of gp120. We investigated the impact of mutations outside V3 on CTR as determined by the enhanced-sensitivity Trofile assay (ESTA). Paired ESTA and gp120 sequencing (population sequencing; from codon 32 of the conserved C1 to the variable V5 domains) were obtained from 60 antiretroviral treatment (ART)-naïve patients (15 with AIDS) infected with subtype B HIV-1. For gp120 sequence analysis, nucleotide mixtures were considered when the second highest electropherogram peak was >25%; sequences were translated into all possible permutations and classified as X4, dual/mixed (DM), and R5 based on coincident ESTA results. ESTA identified R5 and DM viruses in 72 and 28% of patients, respectively; no pure X4 was labeled. Forty percent of AIDS patients had R5 strains. Thirty-two positions, mostly outside V3, were significantly ( P < 0.05) different between R5 and DM sequences. According to multivariate analysis, amino acid changes at 9 and 7 positions within the C1 to C4 and V1 to V5 regions, respectively, maintained a statistical significance, as did the net charge of V3 and C4. When analyzing only R5 sequences, 6 positions in the variable regions were found which, along with the V4 net charge, were significantly different for sequences from early- and end-stage disease patients. This study identifies specific amino acid changes outside V3 which contribute to CTR. Extending the analysis to include pure X4 and increasing the sample size would be desirable to define gp120 variables/changes which should be included in predictive algorithms.