Alfaro Vasquez, Rosa Maria

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Alfaro Vasquez, Rosa Maria
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rav@upeu.edu.pe
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  • Publicacion
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    Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones
    (2022-03-22)
    Jack A. Collora  
    ;
    Runxia Liu
    ;
    Delia Pinto-Santini
    ;
    Neal G. Ravindra
    ;
    Carmela Ganoza
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    Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species
    (2025-07-02)
    Alan Marín  
    ;
    R. Alfaro
    ;
    Lorenzo E. Reyes‐Flores
    ;
    Claudia Ingar
    ;
    Luis E. Santos‐Rojas
    Molecular identification assays provide crucial support in the research and regulation of aquatic resources. Among them, species-specific primers provide significant discriminatory power for fast and simultaneous differentiation of closely related species. In this study, we developed species-specific primers for environmental DNA (eDNA) monitoring and identification of 10 fish and shellfish species commonly found in the Peruvian seafood sector. To ensure versatility and high specificity, our primers were subjected to various testing methods including PCR, qPCR, and DNA sequencing, supported by robust validation assays. This validation process included a) an in-silico stage using self-generated and public DNA sequences; b) an in-vitro stage using target species sourced from vouchered specimens, as well as fresh and cooked commercial samples, early life stages, and a wide range of non-target species; and c) an in-situ stage using eDNA samples collected from different Peruvian marine ecosystems. Our novel species-specific primers successfully passed the validation process, demonstrating high efficiency and specificity by unequivocally identifying all target species with 100% accuracy and without cross-species reactions. These primers are thus valuable tools for eDNA monitoring, seafood authentication, and combating illegal, unreported, and unregulated fishing. The assays presented in this study can support effective fishery management and conservation efforts not only in the Peruvian fishery sector but also in other countries where our target species are present or imported.
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    Two Randomized Trials of Neutralizing Antibodies to Prevent HIV-1 Acquisition
    (2021-03-17)
    Lawrence Corey  
    ;
    Peter B. Gilbert
    ;
    Michal Juraska
    ;
    David C. Montefiori
    ;
    Lynn Morris
    BACKGROUND: Whether a broadly neutralizing antibody (bnAb) can be used to prevent human immunodeficiency virus type 1 (HIV-1) acquisition is unclear. METHODS: ) of acquired isolates was measured with the TZM-bl assay. RESULTS: <1 μg per milliliter) per 100 person-years was 0.20 among VRC01 recipients and 0.86 among placebo recipients (estimated prevention efficacy, 75.4%; 95% CI, 45.5 to 88.9). The prevention efficacy against sensitive isolates was similar for each VRC01 dose and trial; VRC01 did not prevent acquisition of other HIV-1 isolates. CONCLUSIONS: VRC01 did not prevent overall HIV-1 acquisition more effectively than placebo, but analyses of VRC01-sensitive HIV-1 isolates provided proof-of-concept that bnAb prophylaxis can be effective. (Supported by the National Institute of Allergy and Infectious Diseases; HVTN 704/HPTN 085 and HVTN 703/HPTN 081 ClinicalTrials.gov numbers, NCT02716675 and NCT02568215.).
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    Long-term effects of early antiretroviral initiation on HIV reservoir markers: a longitudinal analysis of the MERLIN clinical study
    (2021-03-23)
    Marta Massanella  
    ;
    Rachel Bender Ignacio
    ;
    Javier R. Lama
    ;
    Amélie Pagliuzza
    ;
    Sayan Dasgupta
    BACKGROUND: Early antiretroviral therapy (ART) initiation (ie, within 3 months of infection) limits establishment of the HIV reservoir. However, the effect of early ART initiation on the long-term dynamics of the pool of infected cells remains unclear. METHODS: In this longitudinal analysis, we included cisgender men who have sex with men (MSM) and transgender women (aged 18-54 years) at high risk for HIV infection, enrolled in the ongoing longitudinal MERLIN study in Peru between Oct 28, 2014, and Nov 8, 2018. Participants were eligible if they had been infected with HIV less than 90 days before enrolment, and if they had cryopreserved peripheral blood mononuclear cell (PBMC) samples. Participants were stratified into three groups on the basis of whether they initiated ART at 30 days or less (acute group), at 31-90 days (early group), or more than 24 weeks (deferred group) after the estimated date of detectable infection. PBMC samples were collected before ART initiation and longitudinally for up to 4 years on ART. The main outcomes were to establish the size of the HIV reservoir before ART initiation and to assess the effect of the timing of ART initiation on the decay of the HIV reservoir over 4 years follow-up. We quantified viral load, and isolated CD4 cells to quantify total HIV DNA, integrated HIV DNA and 2-long terminal repeat circles. Longitudinal analysis of active and inducible HIV reservoirs were measured by quantifying the frequency of CD4 cells producing multiply-spliced HIV RNA ex vivo and after in-vitro stimulation with a tat/rev induced limiting dilution assay (TILDA). A mixed-effects model from the time of ART initiation was used to measure longitudinal decays in viral loads and each HIV reservoir measure in each of the three groups. FINDINGS: We included 56 participants in this analysis, all of whom were MSM: 15 were in the acute group, 19 were in the early group, and 22 were in the deferred group. Participants in all three groups had similar levels of all HIV reservoir markers before ART initiation. All participants, including those in the acute group, had a pool of transcriptionally silent HIV-infected cells before ART initiation, as indicated by a substantial increase in TILDA measures upon stimulation. Longitudinal analysis over 4 years of ART revealed a biphasic decay of all HIV persistence markers, with a rapid initial decline followed by a slower decay in all participants. During the first-phase decay, the half-lives of both total and integrated HIV DNA and TILDA measures were significantly shorter in the acute group than in the early and deferred groups. During the second-phase decay, HIV reservoir markers continued to decline only in participants in the acute group. INTERPRETATION: Participants who initiated ART within 30 days or less of HIV infection showed a steeper and more sustained decay in HIV reservoir measures, suggesting long-term benefit of acute ART initiation on reservoir clearance. FUNDING: The US National Institutes of Health and the Canadian Institutes for Health Research.
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    Clinical and Immunologic Outcomes After Immediate or Deferred Antiretroviral Therapy Initiation During Primary Human Immunodeficiency Virus Infection: The <i>Sabes</i> Randomized Clinical Study
    (2020-02-26)
    Javier R. Lama  
    ;
    Rachel Bender Ignacio
    ;
    Ricardo Alfaro
    ;
    Jessica Ríos
    ;
    Jorge A. Gallardo-Cartagena
    BACKGROUND: In addition to demonstrated public health benefits on reducing transmission, it remains unclear how early antiretroviral therapy (ART) must be started after acquisition of human immunodeficiency virus (HIV) to maximize individual benefits. METHODS: We conducted an open-label randomized clinical study in Lima, Peru among adult men who have sex with men and transgender women with acute (HIV-antibody negative/HIV-1 RNA positive) or recent (confirmed negative HIV-antibody or RNA test within 3 months) HIV infection, who were randomized to start ART immediately versus defer by 24 weeks. We evaluated outcomes by treatment arm and immunologic markers by days since estimated date of detectible infection (EDDI). RESULTS: Of 216 participants, 105 were assigned to immediate arm and 111 to deferred arm (median age 26.8 years, 37% with acute HIV). The incidence of non-ART-related adverse events was lower in immediate versus deferred arm (83 vs 123/100 person-years, IRR 0.67 (95% confidence interval [CI] .47, .95; P = .02), the difference dominated by fewer infections in those treated immediately. After 24 weeks of ART, between-group differences in CD4/CD8 cell ratio lessened (P = .09 overall), but differences between those initiating ART ≤ 30 days from EDDI (median 1.03, interquartile range [IQR] 0.84, 1.37), and those initiating > 90 days (0.88, IQR 0.61, 1.11) remained, P = .02. Principal components analysis of 20 immune biomarkers demonstrated distinct patterns between those starting ART > 90 days from EDDI versus those starting within 30 or 90 days (both P < .001). CONCLUSIONS: To our knowledge, this is the only evaluation of randomized ART initiation during primary HIV and provides evidence to explicitly consider acute HIV in World Health Organization recommendations for universal ART. CLINICAL TRIALS REGISTRATION: NCT01815580.
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    Viral Load Dynamics in Plasma and Semen When Antiretroviral Therapy Is Initiated During Early HIV-1 Infection
    (2023-11-24)
    Trupti Gilada  
    ;
    Angela K. Ulrich
    ;
    Yixin Wang
    ;
    Javier R. Lama
    ;
    Ricardo Alfaro
    We assessed human immunodeficiency virus (HIV) load in plasma and semen during primary HIV infection using serial samples of semen and plasma during the first 24 weeks after diagnosis in untreated participants and those who started antiretroviral therapy (ART) immediately at diagnosis. In the absence of treatment, semen viral load was >1000 copies/mL in almost all specimens (83%) collected 2-10 weeks after the estimated date of HIV acquisition and remained >1000 copies/mL in 35% of untreated participants at the last observed time point. Thus, in the absence of ART, semen viral load remained at a level consistent with transmissibility throughout primary infection.
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    Sexual Behavior and Sexually Transmitted Infection Outcomes Among Men Who Have Sex With Men and Transgender Women Participating in a Study of the Timing of Antiretroviral Therapy in Lima, Peru
    (2020-11-11)
    Michalina A. Montaño  
    ;
    Ricardo Alfaro
    ;
    Tara Ness
    ;
    Carmela Ganoza
    ;
    Pedro Gonzáles
    BACKGROUND: We assessed sexual behavior and incidence of sexually transmitted infections (STIs) among men who have sex with men and transgender women participating in Sabes, a study of an expanded treatment as prevention strategy focused on early diagnosis and treatment of HIV infection in Lima, Peru (2013-2017). METHODS: Sabes participants were tested monthly for HIV to identify acute or early infections, and HIV-positive participants were randomized to receive antiretroviral therapy immediately (immediate arm) or after 24 weeks (deferred arm) during a 48-week follow-up period. Sexual behavior was assessed at randomization (baseline) and every 12 weeks thereafter. Participants were tested for urethral and rectal chlamydia and gonorrhea and for syphilis at baseline, 12, 24, and 48 weeks. We describe patterns of sexual behavior during the 48-week follow-up period and compare sexual behavior and STI incidence between study arms. RESULTS: After randomization, 207 HIV-positive participants completed questionnaires and STI testing at 2 or more visits. After HIV diagnosis, participants in both arms reported increases in condom use with main and casual partners and decreased drug and alcohol use before or during anal sex. We observed no between-arm differences in sexual behavior. Deferred arm participants had higher incidence of chlamydia (incidence rate ratio, 2.33; 95% confidence interval, 1.14-4.77) but not gonorrhea or syphilis. CONCLUSIONS: Despite reported increases in condom use, the overall high incidence of STIs reflects some ongoing condomless sex among HIV-positive men who have sex with men and transgender women, highlighting the importance of regular STI screening and counseling to support consistent condom use among HIV-positive individuals at risk for STIs.
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    Mitochondrial genome of the Peruvian scallop<i>Argopecten purpuratus</i>(Bivalvia: Pectinidae)
    (2014-01-07)
    Alan Marín  
    ;
    R. Alfaro
    ;
    Takafumi Fujimoto
    ;
    Katsutoshi Arai
    The mitochondrial genome of the Peruvian scallop Argopecten purpuratus was determined. The length of the mitochondrial coding region is 15,608 bp. A typical bivalve mitochondrial composition was detected with 12 protein-coding genes, 2 ribosomal RNA genes and 21 transfer RNA genes, with the absence of the atp8 gene. Fifty percent of the protein-coding genes use typical ATG start codon, whereas five genes utilize ATA as their start codon. Only one gene was found to utilize TTG as its start codon. The A. purpuratus mitogenome shows a significant similarity to that of A. irradians irradians, in length as well as in gene composition.
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    A glimpse into the genetic diversity of the Peruvian seafood sector: Unveiling species substitution, mislabeling and trade of threatened species
    (2018-11-16)
    Alan Marín  
    ;
    José Serna
    ;
    Christian Robles
    ;
    Beder Ramírez
    ;
    Lorenzo E. Reyes‐Flores
    Peru is one of the world's leading fishing nations and its seafood industry relies on the trade of a vast variety of aquatic resources, playing a key role in the country's socio-economic development. DNA barcoding has become of paramount importance for systematics, conservation, and seafood traceability, complementing or even surpassing conventional identification methods when target organisms show similar morphology during the early life stages, have recently diverged, or have undergone processing. Aiming to increase our knowledge of the species diversity available across the Peruvian supply chain (from fish landing sites to markets and restaurants), we applied full and mini-barcoding approaches targeting three mitochondrial genes (COI, 16S, and 12S) and the control region to identify samples purchased at retailers from six departments along the north-central Peruvian coast. DNA barcodes from 131 samples were assigned to 55 species (plus five genus-level taxa) comprising 47 families, 24 orders, and six classes including Actinopterygii (45.03%), Chondrichthyes (36.64%), Bivalvia (6.87%), Cephalopoda (6.11%), Malacostraca (3.82%), and Gastropoda (1.53%). The identified samples included commercially important pelagic (anchovy, bonito, dolphinfish) and demersal (hake, smooth-hound, Peruvian rock seabass, croaker) fish species. Our results unveiled the marketing of protected and threatened species such as whale shark, Atlantic white marlin, smooth hammerhead (some specimens collected during closed season), shortfin mako, and pelagic thresher sharks. A total of 35 samples (26.72%) were mislabeled, including tilapia labeled as wild marine fish, dolphinfish and hake labeled as grouper, and different shark species sold as "smooth-hounds". The present study highlights the necessity of implementing traceability and monitoring programs along the entire seafood supply chain using molecular tools to enhance sustainability efforts and ensure consumer choice.
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