Francesco R. Simonetti

Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo

Significance Reservoirs of HIV-infected cells persist during antiretroviral therapy, and understanding persistence is essential to develop HIV curative strategies. During replication, HIV integrates into the host genome; most proviruses are not infectious, but some with replication-competent HIV persist. Cells with integrated HIV can proliferate, potentially expanding the reservoir, but whether cells with replication-competent HIV actually undergo expansion is unknown. HIV reactivation is often lethal to infected cells, and others have reported finding no replication-competent HIV in expanded populations. We describe a highly expanded clone containing infectious HIV that was the source of viremia for years in a patient. Clonally expanded populations can represent a long-lived reservoir of HIV. Curative strategies will require targeting this persistence mechanism. Reservoirs of infectious HIV-1 persist despite years of combination antiretroviral therapy and make curing HIV-1 infections a major challenge. Most of the proviral DNA resides in CD4+T cells. Some of these CD4+T cells are clonally expanded; most of the proviruses are defective. It is not known if any of the clonally expanded cells carry replication-competent proviruses. We report that a highly expanded CD4+ T-cell clone contains an intact provirus. The highly expanded clone produced infectious virus that was detected as persistent plasma viremia during cART in an HIV-1–infected patient who had squamous cell cancer. Cells containing the intact provirus were widely distributed and significantly enriched in cancer metastases. These results show that clonally expanded CD4+T cells can be a reservoir of infectious HIV-1.

Origin, evolution, and phylogeography of recent epidemic CHIKV strains

Chikungunya virus (CHIKV) is an arthropod-borne virus of the Alphavirus genus, which is transmitted to humans by Aedes spp. mosquitoes and was firstly identified in Tanzania in the mid 1950s. In this article, the findings of a phylogenetic and phylogeographic analysis of the recent CHIKV pandemic are reported. We estimated time of origin of the ancestral virus, time and place of occurrence of A226V mutation, and the flow of viral strains from an area to the other. The Bayesian phylogenetic and phylogeographic analysis was performed on the whole dataset, which consisted of 195 E1 (envelope 1) CHIKV sequences, and on a subset (D2), including 146 of the 195 previous sequences. Using the relaxed clock model, we estimated a CHIKV E1 mean evolutionary rate (in the whole dataset) of 1.4 × 10(-3)substitution/site/year (95% highest posterior density interval HPD 6.4 × 10(-4)-2.5 × 10(-3)), and of 2.2 × 10(-3) (95% HPD 9.6 × 10(-4)-3.8 × 10(-3)) in the D2 subset, including only the strains involved in the recent Indian Ocean epidemic. The phylogeographical analysis suggested an African origin of CHIKV with a tMRCA of 146 years corresponding to 1863 (95% HPD 1741-1941). Moreover D2 subset most probably originated in Kenya, with a tMRCA corresponding to the year 2002 (95% HPD 2000-2004), then spread following two distinct routes: one throughout the Indian Ocean (Reunion, Comoros) and the other moving from India then scattered in the South East Asia and reached Italy. In conclusion, we reconstructed the geographic spread of CHIKV during the last epidemic wave, which showed an eastward path from Africa to Indian Ocean island to India, and from there to other South East Asian countries. Whether A226V variants followed the same migration path remains undefined, since local independent mutations, followed by fixation due to selective advantage conferred by better adaptation to local vectors of infection, cannot be excluded.

HIV-1 subtype F1 epidemiological networks among Italian heterosexual males are associated with introduction events from South America.

About 40% of the Italian HIV-1 epidemic due to non-B variants is sustained by F1 clade, which circulates at high prevalence in South America and Eastern Europe. Aim of this study was to define clade F1 origin, population dynamics and epidemiological networks through phylogenetic approaches. We analyzed pol sequences of 343 patients carrying F1 subtype stored in the ARCA database from 1998 to 2009. Citizenship of patients was as follows: 72.6% Italians, 9.3% South Americans and 7.3% Rumanians. Heterosexuals, Homo-bisexuals, Intravenous Drug Users accounted for 58.1%, 24.0% and 8.8% of patients, respectively. Phylogenetic analysis indicated that 70% of sequences clustered in 27 transmission networks. Two distinct groups were identified; the first clade, encompassing 56 sequences, included all Rumanian patients. The second group involved the remaining clusters and included 10 South American Homo-bisexuals in 9 distinct clusters. Heterosexual modality of infection was significantly associated with the probability to be detected in transmission networks. Heterosexuals were prevalent either among Italians (67.2%) or Rumanians (50%); by contrast, Homo-bisexuals accounted for 71.4% of South Americans. Among patients with resistant strains the proportion of clustering sequences was 57.1%, involving 14 clusters (51.8%). Resistance in clusters tended to be higher in South Americans (28.6%) compared to Italian (17.7%) and Rumanian patients (14.3%). A striking proportion of epidemiological networks could be identified in heterosexuals carrying F1 subtype residing in Italy. Italian Heterosexual males predominated within epidemiological clusters while foreign patients were mainly Heterosexual Rumanians, both males and females, and South American Homo-bisexuals. Tree topology suggested that F1 variant from South America gave rise to the Italian F1 epidemic through multiple introduction events. The contact tracing also revealed an unexpected burden of resistance in epidemiological clusters underlying the need of public interventions to limit the spread of non-B subtypes and transmitted drug resistance.

High burden of transmitted HIV-1 drug resistance in Italian patients carrying F1 subtype

BACKGROUND Transmitted drug resistance (TDR) is mainly restricted to individuals carrying B subtype, with low prevalence among non-B subtypes when grouped together. Subtype F1 is the most frequent non-B variant found in subjects living in Italy, allowing a specific assessment of TDR associated with this clade. METHODS We analysed pol sequences of HIV-1-positive individuals carrying the F1 variant included in the Antiretroviral Resistance Cohort Analysis database in the 1998-2009 period. Mutations were analysed with the Surveillance Drug Resistance Mutation and the International AIDS Society lists for naive and treated patients, respectively. RESULTS Among 343 HIV-1-infected patients carrying an F1 subtype, resistance was evaluated in a subset of 221 patients whose treatment status was known (169 drug naive and 52 drug experienced). The prevalence of TDR was 15.4% (11.8% for nucleoside/nucleotide reverse transcriptase inhibitors, 6.5% for non-nucleoside reverse transcriptase inhibitors and 7.1% for protease inhibitors). Among the 169 naive patients, 75.1%, 10.1% and 7.1% were Italians, South Americans and Romanians, respectively. Heterosexuals were prevalent among Italians and Romanians, while men who have sex with men were predominant among South Americans. The overall frequency of TDR declined from 21.4% to 7.1% in the 1998-2009 period. Although no statistical difference was detected, the frequency of TDR was higher in South Americans (23.5%) compared with Italian and Romanian naive patients (15% and 8.3%, respectively). DISCUSSION Our study shows a remarkable frequency of TDR in the F1 subtype-infected population. The high prevalence of TDR detected in South American subjects is linked to the homosexual route of infection. However, TDR was considerably high also in Italian subjects harbouring the F1 subtype, deserving careful monitoring.

An outbreak of HIV-1 BC recombinants in Southern Italy

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.

Prolonged inductive effect of rifampicin on linezolid exposure

Sir, Some studies have recently shown that concomitant rifampicin administration significantly reduces linezolid concentrations [1–3]. However, it is currently unknown for how long such effect may persist and, most importantly, when linezolid could be safely administered to guarantee optimal drug exposure in patients previously treated with rifampicin. Here, we describe a patient treated for chronic osteomyelitis initially underexposed to linezolid 2 weeks after rifampicin discontinuation. On September 2014, a young Caucasian man was referred to the Department of Infectious Diseases of our hospital for chronic osteomyelitis involving the tibial plateau secondary to a car accident. In the past 3 years, the patient had been treated with several antibiotic regimens based on positive swab cultures from leg cutaneous fistulas (methicillin-susceptible and then resistant Staphylococcus aureus, Acinetobacter baumannii/haemolyticus) without complete resolution of the infection. Since October 2012, the patient was onmaintenance therapy with rifampicin 600 mg once daily and doxycycline 100 mg twice daily. On the 7th of October 2014, given the poor response to therapy and in vitro susceptibility of the pathogens to linezolid (MIC <2 mg/L), this regimen was replaced by linezolid 600 mg twice daily. Therapeutic drug monitoring (TDM) of linezolid trough concentration on a blood sample drawn 9 days after stopping rifampicin (collected 12 h after the evening drug dose and just before the morning drug intake) retrieved a linezolid concentration of 0.6 mg/L. The patient was not concomitantly taking agents inducing (e.g., St John’s wort) linezolid. We decided to maintain linezolid at the same dose, and a blood sample repeated on October 24th revealed a linezolid trough concentration of 1.1 mg/L. Concomitantly, the patient showed a progressive response to linezolid therapy (mild reduction of C-reactive protein). In order to better investigate the adequacy of exposure of the patient to linezolid, we performed an intensive pharmacokinetic evaluation a week later, showing linezolid trough concentration and AUC0–24 of 1.4 mg/L and 142.8 mg*h/ mL, respectively. This last linezolid trough concentration was similar to previous values (June 6th, 2012—1.4 mg/L; June 24th, 2012—1.5 mg/L) measured when the patient was treated with linezolid 600 mg twice daily for swab samples from the fistula cultured positive for MRSA. At the last visit (November 27th, 2014), linezolid trough concentration was 1.5 mg/L. Due to a new increase of inflammatory markers and the worsening of the follow-up CT scan, surgical debridement has been scheduled for January 2015. In vitro studies documented that rifampicin-inducible drugmetabolizing enzymes have a very minor contribution to C. Gervasoni (*) Department of Infectious Diseases, L. Sacco University Hospital, Via GB Grassi 74, 20157 Milan, Italy e-mail: cristina.gervasoni@unimi.it

HIV-1 A1 Subtype Epidemic in Italy Originated from Africa and Eastern Europe and Shows a High Frequency of Transmission Chains Involving Intravenous Drug Users

Background Subtype A accounts for only 12% of HIV-1 infections worldwide but predominates in Russia and Former Soviet Union countries of Eastern Europe. After an early propagation via heterosexual contacts, this variant spread explosively among intravenous drug users. A distinct A1 variant predominates in Greece and Albania, which penetrated directly from Africa. Clade A1 accounts for 12.5% of non-B subtypes in Italy, being the most frequent after F1 subtype. Aim Aim of this study was to investigate the circulation of A1 subtype in Italy and trace its origin and diffusion through phylogenetic and phylodynamic approaches. Results The phylogenetic analysis of 113 A1 pol sequences included in the Italian ARCA database, indicated that 71 patients (62.8%) clustered within 5 clades. A higher probability to be detected in clusters was found for patients from Eastern Europe and Italy (88.9% and 60.4%, respectively) compared to those from Africa (20%) (p < .001). Higher proportions of clustering sequences were found in intravenous drug users with respect to heterosexuals (85.7% vs. 59.3%, p = .056) and in women with respect to men (81.4% vs. 53.2%, p < .006). Subtype A1 dated phylogeny indicated an East African origin around 1961. Phylogeographical reconstruction highlighted 3 significant groups. One involved East European and some Italian variants, the second encompassed some Italian and African strains, the latter included the majority of viruses carried by African and Italian subjects and all viral sequences from Albania and Greece. Conclusions Subtype A1 originated in Central Africa and spread among East European countries in 1982. It entered Italy through three introduction events: directly from East Africa, from Albania and Greece, and from the area encompassing Moldavia and Ukraine. As in previously documented A1 epidemics of East European countries, HIV-1 A1 subtype spread in Italy in part through intravenous drug users. However, Eastern European women contributed to the penetration of such variant, probably through sex work.

Local and global spatio-temporal dynamics of HIV-1 subtype F1.

Previous studies have attempted to explore the origin of the F1 subtype, but the precise origin of the Romanian and South American F1 variants remains controversial. As the F1 subtype is the most frequent non‐B variant among Europeans residing in Italy, the aim of this study was to estimate its phylogeography in order to reconstruct its origin and route of dispersion. The phylogeographical analyses, which were made using the Bayesian Markov Chain Monte Carlo approach and BEAST software, revealed two significant clades: the first included all of the Romanian strains together with a few Italian and four African isolates; the second encompassed all of the South American sequences and the large majority of Italian variants. By putting the African reference sequences into two discrete groups based on specific countries, phylogeographic analysis indicated that the F1 epidemic originated in Cameroon/Democratic Republic of Congo in the early 1940s, and was exported to South America 10 years later. Subsequently, the F1 virus spread to Angola and, from there, was exported to Romania in the early 1960s. It reached Italy in the 1970s from South America and Romania. The South American and Romanian variants of F1 have different African countries of origin and different temporal spreads. The South American variant seems to be characterized by multiple introduction events, whereas the Romanian strain probably spread as a result of a single entry. Two different pathways from South America and Romania led the F1 variant to Italy in the 1970s. J. Med. Virol. 86:186–192, 2014.

Relapse of Kaposi's Sarcoma and HHV-8 viremia in an HIV-infected patient switching from protease inhibitor to integrase inhibitor-based antiretroviral therapy

Combination antiretroviral therapy (cART) reduced the incidence of Kaposis Sarcoma (KS), mainly mediated by the suppression of HIV replication and the recovery of the immune system. The effect of specific classes of antiretrovirals on KS remains unclear. However, both in vitro and clinical studies provided evidences that protease inhibitors (PI) can inhibit Human Herpesvirus 8 (HHV-8) replication and reduce KS risk and progression. Moreover, relapses of KS in HIV-infected patients switching from a PI to a non-nucleoside reverse transcriptase inhibitor-based cART have been reported. We describe here the case of a patient who experienced a relapse of KS and a rebound of HHV-8 viremia two months after switching from a PI to an integrase inhibitor-based cART.

Pregnancy-related changes of antiretroviral pharmacokinetics: an argument for TDM.

Here we describe a case of an HIV-infected young woman with extensive drug-resistant virus, who was successfully switched from a raltegravir-based regimen to a dolutegravir-based intensified antiretroviral regimen a few days before scheduled caesarean section because of the still detectable viral load. The trough concentrations of all antiretroviral drugs before and after delivery are also described. Our case underlines both the difficult management of young women, HIV-infected at young age with very limited treatment options and the great variability in the pregnancy-related physiological changes affecting the pharmacokinetics of antiretrovirals.