José Eduardo Levi

• Researcher at Hospital Israelita Albert Einstein

An immunocompromised patient was infected by the SARS-CoV-2 variant of interest named Zeta (P.2) in February 2021. More than one year later, he suffered from symptomatic COVID-19 and sequencing revealed the same variant, which accumulated 23 substitutions. This case illustrates intra-host evolution of a particular SARS-CoV-2 variant, highlighting t...

Introduction Immunocompromised persons are at high risk of persistent Human Papilloma Virus (HPV) infection and associated diseases. Few studies evaluated HPV vaccines in immunocompromised persons. This study aimed to evaluate the quadrivalent HPV vaccine (4vHPV) immunogenicity and safety in solid organ transplant (SOT) recipients, in comparison to...

Background: Cervical cancer (CC) is associated with persistent high-risk human papillomavirus (HPV) infection and it causes about 265,000 deaths per year worldwide, thus becoming an important public health problem. Objective: This study aimed to describe the epidemiological profile, clinical history, and cytological findings of 55 women infected wi...

Hematopoietic stem cell transplant (HSCT) recipients are at -increased risk for severe COVID-19. The aim of this study was to evaluate the burden of COVID-19 in a cohort of HSCT recipients. This retrospective study evaluated a cohort of adult hospitalized HSCT recipients diagnosed with COVID-19 in two large hospitals in São Paulo, Brazil post-HSCT,...

Since human papillomavirus (HPV) is recognized as the causative agent of cervical cancer and associated with anogenital non-cervical and oropharyngeal cancers, the characterization of the HPV types circulating in different geographic regions is an important tool in screening and prevention. In this context, this study compared four methodologies fo...

Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism...

Background Previous studies suggest intestinal dysbiosis is associated with metabolic diseases. However, the causal relationship between them is not fully elucidated. Gut microbiota evaluation of patients with congenital generalized lipodystrophy (CGL), a disease characterized by the absence of subcutaneous adipose tissue, insulin resistance, and d...

In January 2022, our genomic surveillance network identified a SARS-CoV-2 BA.1 and BA.2 coinfection in a sample from a patient residing in Brazil. Our results suggest that the true number of SARS-CoV-2 coinfections remains largely underestimated.

The year of 2021 was marked by the emergence and dispersal of a number of SARS-CoV-2 lineages, resulting in the “third wave” of COVID-19 in several countries despite the level of vaccine coverage. Soon after the first confirmed cases of COVID-19 by the Delta variant in Brazil, at least seven Delta sub-lineages emerged, including the globally spread...

Since the emergence of the variant of concern (VOC) B.1.1.529 (Omicron) in November 20211, nearly 100 sublineages have been assigned by Pango. Recently, the co-circulation of Omicron and Delta lineages, as well as its diverse set of sublineages, has brought to attention the identification of several recombinant events. A putative new recombinant an...

In January 2022, the genomic surveillance of DASA laboratories identified a SARS-CoV-2 BA.1 and BA.2 co-infection in a sample from a patient resident in Brazil. The bioinformatics protocols using Dragen TM Covid Lineage App do not allow the detection of recombinants or mixed-infections. Therefore, the number of co-infections is certainly underestim...

Objective To evaluate molecular tools to detect low-level parasitemia and the five species of Plasmodium that infect humans for use in control and elimination programs, and in reference laboratories. Methods We evaluated 145 blood samples from patients who tested positive by nested polymerase chain reaction (nPCR), from asymptomatic individuals an...

Introduction Solid organ transplant (SOT) recipients are at increased risk of Human Papillomavirus (HPV) persistent infection and disease. This study aimed to evaluate HPV seroprevalence, cervical HPV prevalence, genotype distribution, and frequency of HPV-related cervical lesions in SOT recipients in comparison to immunocompetent women. Methods C...

Brazil is the country with the second-largest number of deaths due to the coronavirus disease-2019 (COVID-19). Two variants of concern (VOCs), Alpha (B.1.1.7) and Gamma (P.1), were first detected in December 2020. While Alpha expanded within an expected rate in January and February 2021, its prevalence among new severe acute respiratory syndrome co...

Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism...

Background It is estimated that everyday over 1 million individuals contract a curable sexually transmitted infection (STI) worldwide. For an appropriate STI treatment, it is necessary to have an accurate diagnosis. The Alinity m STI assay is a multiplex RT-PCR assay that identifies four STI pathogens: Chlamydia trachomatis (CT), Neisseria gonorrho...

SARS-CoV-2 is the etiologic agent of coronavirus disease 2019 (COVID-19) and is mainly detected by RT-PCR methods from upper respiratory specimens, as recommended by the World Health Organization. Oro/nasopharyngeal swabbing can be discomfortable to the patients, requires trained healthcare personnel and may generate aerosol, increasing the risk of...

Introduction: The Zika Virus (ZIKV) is a single-stranded RNA genome virus, belonging to the family Flaviviridae, genus Flavivirus. Outbreaks around the world have demonstrated that the presence of asymptomatic viremic blood donors provides an increase in the risk of transfusion transmission (TT) and nucleic acid test (NAT) screening has been propos...

Introduction As the leading sexually transmitted infection worldwide, human papillomavirus (HPV) may disproportionately affect transwomen. We aimed to estimate anal HPV prevalence, especially focusing on high‐risk (hr)‐HPV types and evaluate their associated factors among transwomen living in Rio de Janeiro, Brazil. Methods Transwomen enrolled in...

Background New partially or fully automated molecular diagnostic testing platforms are being developed to address the growing demand for fast, accurate, and cost-effective testing. Objectives To evaluate the analytical and clinical performance of the Alinity m system compared to the Abbott RealTime m2000 assay system in a large central molecular l...

Background The present study determined the HBV antigen, antibody, and DNA status in blood donations deemed to be HBV positive. Individuals with an occult HBV infection (OBI), defined as being positive for HBV DNA but negative for HBV surface antigen (HBsAg), as well as those with active infection (HBsAg‐positive), were identified and characterized...

Objectives To investigate the association between selected single nucleotide polymorphisms (SNPs) with cervical insufficiency and its relationship with obstetric history. Methods Twenty-eight women with cervical insufficiency (case group) and 29 non-pregnant women (control group) were included. The SNPs sequenced included rs2586490 in COL1A1 , rs1...

In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than...

Background The increasing incidence of syphilis worldwide has called attention to the risk of transmission by transfusion. Aims To determine the prevalence of active syphilis in blood donors and characterise the serological profile of syphilis‐positive donors. Methods Samples positive for Treponema pallidum using the chemiluminescent microparticl...

Malaria is an infectious vector-borne disease with other important routes of transmission, such as blood transfusion and organ/tissue transplantation, due to asymptomatic reservoirs of Plasmodium presenting with low parasitemia. Reports of transfusion-transmitted malaria have shown that in immunosuppressed recipients, infections can be fatal if the...

Objective To investigate factors associated with colposcopy attendance in HPV‐positive women in São Paulo, Brazil. Methods We analyzed data from a prospective cohort of women positive for high‐risk HPV (hr‐HPV) undergoing cervical cancer screening in primary care services in São Paulo, Brazil. Non‐pregnant women attending routine screening between...

The spread of SARS-CoV-2 in Brazil Brazil has been hard-hit by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Candido et al. combined genomic and epidemiological analyses to investigate the impact of nonpharmaceutical interventions (NPIs) in the country. By setting up a network of genomic laboratories using harmonized pr...

As HPV is recognized as the causative agent of cervical cancer and associated with anogenital non-cervical, head and neck cancers, the characterization of the HPV types circulating in different geographic regions is an important tool in screening and prevention, as a diagnostic complement and evaluation of the effectiveness of the vaccines availabl...

Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Due to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus transmission and epidemic spread remain challenging. We investigate the impact of NPIs in Brazil using epidemiological, mobility and genomic data. Mobility-dr...

Background In Brazil, penile cancer (PC) is not uncommon. The highest incidence of PC is in the North and Northeast of the country. In addition to phimosis, the Human Papillomavirus (HPV) and Epstein-Baar Virus (EBV) infections are also related as risk factors for PC. The overexpression of p16INK4a is a surrogate sensitive marker of HPV infection i...

Introduction: The challenges related to the diagnosis of sexually transmitted infections present more complex factors in remote and hard-to-reach areas. The use of self-collection devices that facilitate the obtaining of a biological sample with high quality for sensitive molecular tests have been examined. This study aimed to evaluate the perform...

Background: Reactivation of Chagas disease after heart transplantation is characterized by proliferation and dissemination of Trypanosoma cruzi parasites to several organs. Reactivation affecting the allograft can simulate acute cellular rejection, from which it should be distinguished through the analysis of endomyocardial biopsies (EMB). Method...

p>Every year there are approximately 16,000 new cases of cervical cancer (CC) in Brazil. Novel screening technologies may reduce this number by expanding the population coverage but also by improving the detection rate of precursor lesions. We aimed to evaluate HPV-DNA testing in the context of routine CC screening in the public health system of th...

Background: Yellow fever virus infection results in death in around 30% of symptomatic individuals. The aim of this study was to identify predictors of death measured at hospital admission in a cohort of patients admitted to hospital during the 2018 outbreak of yellow fever in the outskirts of São Paulo city, Brazil. Methods: In this observational...

ABSTRACT Zika virus (ZIKV) clinical presentation and frequency/duration of shedding need further clarification. Symptomatic ZIKV-infected individuals identified in two hospitals in Sao Paulo State, Brazil, were investigated regarding clinical characteristics, shedding in body fluids, and serodynamics. Ninety-four of 235 symptomatic patients (Site A...

Objectives This study was performed to determine whether neutralizing antibodies against yellow fever virus (YFV) generated by YFV vaccine could interfere in the specificity of dengue virus (DENV) and Zika virus (ZIKV) IgG ELISA tests. Methods Seventy-nine pairs of serum samples (pre- and post-vaccination), collected during the years 1997–1998 fro...

Purpose To evaluate the parasitic load of the protozoan Trypanosoma cruzi (etiologic agent of Chagas disease) in sequential endomyocardial biopsies (EMB) of heart-transplanted, chagasic patients who presented reactivation of the disease affecting the allograft. Methods Chagas disease reactivation was diagnosed in 13 patients (aged 25 to 66 years,...

Background: There is a significant inter-individual heterogeneity of Vel antigen expression which can lead to inaccuracies on Vel phenotyping of blood donors and, potentially, to hemolytic post-transfusion reactions. Our aim was to evaluate the impact of genetic variants in the SMIM1 intron 2 on the expression of Vel antigen among Brazilian blood...

Chlamydia trachomatis infection is the most common sexually transmitted bacterial infection among women. In Brazil, there is no organized screening program for C. trachomatis, and the actual prevalence of infection is unknown. This study aimed to determine the prevalence of C. trachomatis infection in women living in riverside communities in the Am...

Pandemic arboviruses have emerged as a major global health problem in the past four decades. Predicting where and when the next arbovirus epidemic will occur is a challenge, but history suggests that arboviral black swan events (epidemics that are difficult to predict and that have an extreme effect) will continue to occur as urban growth and globa...

Objective The aim of our work was to establish a semi‐automated high‐throughput DNA amplification method for the universal screening of bacteria in platelet concentrates (PCs). Background Among cases of transfusion transmission of infectious agents, bacterial contamination ranks first in the number of events, morbidity and mortality. Transmission...

Objective To evaluate both the performance and acceptability of a method coupling self-sampling with detection of cervical malignancy via elevated HPV 16 and 18 E6 oncoproteins (OncoE6™ Cervical Test) in remote areas in Brazil. Methods Women living in rural villages in proximity to Coari city, Amazonas, Brazil were invited to participate in a cerv...

Historically, emerging infectious agents have been an important driving force toward the enhancement of blood safety, illustrated by the sharp reduction in the transmission of infectious agents by blood transfusion after human immunodeficiency virus (HIV) epidemics. In general, Latin American (LATAM) countries have introduced screening for microorg...

Objectives: This study aimed to evaluate the influence of prior knowledge of human papillomavirus (HPV) status in cervical cytopathology readings. Methods: Participants comprised 2,376 women who underwent parallel cytology and HPV-DNA testing. Smears were read twice by the same team, first with previous knowledge of HPV-DNA status. Results: Overall...

Objectives: This study aimed to evaluate the influence of prior knowledge of human papillomavirus (HPV) status in cervical cytopathology readings. Methods: Participants comprised 2,376 women who underwent parallel cytology and HPV-DNA testing. Smears were read twice by the same team, first with previous knowledge of HPV-DNA status. Results: Overall...

Objectives: This study aimed to evaluate the influence of prior knowledge of human papillomavirus (HPV) status in cervical cytopathology readings. Methods: Participants comprised 2,376 women who underwent parallel cytology and HPV-DNA testing. Smears were read twice by the same team, first with previous knowledge of HPV-DNA status. Results: Ov...

We investigated how somatic changes in HNSCC interact with environmental and host risk factors and whether they influence the risk of HNSCC occurrence and outcome. 180-paired samples diagnosed as HNSCC in two high incidence regions of Europe and South America underwent targeted sequencing (14 genes) and evaluation of copy number alterations (SCNAs)...

Mutation calling validation. (A) Venn diagram of number of TP53 mutations detected in the Gencapo Series. Example: TP53Asn239Asp mutation previously detected by Sanger sequencing (B) Plots of mutational calling showing an example of independent libraries sequenced from the same case. (PDF)

Diagrams of mutation distribution in genes with frequent SNVs. Mutation colours represent: Green: Missense Mutations; red: Truncating Mutations (Nonsense, Nonstop, Frameshift deletion, Frameshift insertion, Splice site), black: Inframe Mutations (Inframe deletion, Inframe insertion). Circles colored with purple indicate residues that are affected b...

(A) Mutually exclusive alterations between the 14 genes sequenced (Significance p-value of mutual exclusivity derived from the Z-score) (B) Co-occurrence of alterations (Significance p-value of co-occurrence derived from the Z-Score). Z score based on deviation of the observed mutations compared to expected, obtained by permuting events. (PDF)

Mutational Profile and copy number losses in HPV positive cases. (A) Mutational frequencies of the 14 genes sequenced in 15 HPV16E6 positive cases. (B) Comparison of Significant Focal copy number losses between HPV positive and HPV negative cases. (*) Regions significantly associated with overall survival. (PDF)

Survival analysis of main demographic, clinical and genomic variables. (XLSX)

GISTIC list of focal copy number amplifications and deletions. In red regions significantly associated with overall survival and head and neck cancer related genes. (XLSX)

List of filtered and annotated somatic mutations (SNVS). (XLSX)

Dengue virus (DENV) and Zika virus (ZIKV) are members of the Flaviviridae and are predominantly transmitted via mosquito bites. Both viruses are responsible for a growing number of infections in tropical and subtropical regions. DENV infection can cause lethargy with severe morbidity and dengue shock syndrome leading to death in some cases. ZIKV is...

Lymphocytes count in acute and convalescent DENV infection (n = 24, A). Representative flow plots of CD38 and HLA-DR co-expression by MAIT cells in acute and convalescent DENV infection (B). CD127 expression level by MAIT cells in acute and convalescent DENV infection (C). Representative flow plots of PD-1 expression by MAIT cells in acute and conv...

Co-expression of CD38 and HLA-DR by conventional CD8 T cells (excluding MAIT cells) during acute and convalescent DENV infection (n = 10) and healthy controls (n = 23) (A). PD-1 expression by conventional CD8 T cells in acute and convalescent DENV infection (n = 10) and healthy controls (n = 23) (B). CD127 expression by convetional CD8 T cells in a...

Representative flow plots showing IFNγ production by unstimulated MAIT cells in acute and convalescent dengue infection (A). IFNγ production by unstimulated MAIT cells in acute and convalescent dengue infection (n = 12, B). IFNγ production by E. coli stimulated MAIT cells in convalescent dengue infection (n = 15) and control subjects (n = 10) (C)....

MAIT cell frequency in convalescent DENV infection (n = 25) and healthy controls (n = 26), (A). Co-expression of CD38 and HLA-DR by MAIT cells in convalescent DENV infection (n = 15) and healthy controls (n = 26), (B). PD-1 expression by MAIT cells in convalescent DENV infection (n = 15) and healthy controls (n = 26), (C). CD127 expression (MFI) by...

Associations between sCD14 levels and co-expression of CD38 and HLA-DR by MAIT cells (A) and MAIT cell count (B) in acute DENV infection. (TIFF)

Objectives: This study aimed to evaluate the influence of prior knowledge of human papillomavirus (HPV) status in cervical cytopathology readings. Methods: Participants comprised 2,376 women who underwent parallel cytology and HPV-DNA testing. Smears were read twice by the same team, first with previous knowledge of HPV-DNA status. Results: Overall...

Introduction: Cervical cancer remains an important burden for HIV-infected women in the era of combination antiretroviral therapy. Recommendations for cervical screening in these women diverge and may include high-risk HPV (HRHPV) testing. We aimed to evaluate the clinical usefulness of a single HRHPV testing for cervical screening of HIV-infected...

OBJECTIVE Estimate the prevalence of cervical HPV infection among women assisted by the Family Health Strategy and identify the factors related to the infection. METHODS A cross-sectional study involving 2,076 women aged 20–59 years old residing in Juiz de Fora, State of Minas Gerais, who were asked to participate in an organized screening carried...

Background: Chagas' disease (CD) is caused by infection with the protozoan Trypanosoma cruzi. The disease can affect the heart and/or the gastrointestinal (GI) tract, but around 70% of infected individuals remain asymptomatic in the chronic form. Organ transplantation from T. cruzi-infected donors is often avoided because of the risk of disease tr...

Background: In 2015, there was a large Zika virus (ZIKV) outbreak in Brazil. The proportion of asymptomatic infections is very high, and it is possible for transfusion-transmitted ZIKV (TT-ZIKV) infection to occur. The prevalence of asymptomatic ZIKV infection among Brazilian blood donors during this epidemic outbreak is unknown. Study design and...

Background Invasive cervical cancer (ICC) is the third most common malignant neoplasm affecting Brazilian women. Little is known about the impact of specific HPV genotypes in the prognosis of ICC. We hypothesized that HPV genotype would impact ICC clinical presentation and survival. Methods Women diagnosed with ICC at the Instituto do Câncer do Es...

HPV DNA genotype frequency in the population studied. (DOCX)

Cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) molecule is expressed on T-lymphocyte membrane and negatively influences the antigen-presenting process. Reduced expression of CTLA-4 due to gene polymorphisms is associated with increased risk of autoimmune disorders, whose physiopathology is similar to that of post-transfusion red blood cell (R...

OBJECTIVES Quantitative fluorescence polymerase chain reaction (QF-PCR) is a rapid and reliable method for screening aneuploidies, but in Brazil, it is not used in public services. We investigated the accuracy of QF-PCR for the prenatal recognition of common aneuploidies and compared these results with cytogenetic results in our laboratory. METHOD...

The isolation of neutralizing monoclonal antibodies (nmAbs) against the Zika virus (ZIKV) might lead to novel preventative strategies for infections in at-risk individuals, primarily pregnant women. Here we describe the characterization of human mAbs from the plasmablasts of an acutely infected patient. One of the 18 mAbs had the unusual feature of...

Gene usage and SHM levels in the plasmablast-derived mAbs. (PDF)

Plasmablast gating and sort strategy. (EPS)

Plasma samples. (PDF)

Background: Blood donors are, in principle, healthy individuals who may be revealed as infectious for blood-borne agents by the laboratory screening process, depicting the asymptomatic burden of the disease. Therefore, monitoring hepatitis C virus (HCV)-infected donor and human immunodeficiency virus (HIV)-infected donor and associating to their d...

Background High‐throughput molecular assays are essential tools for the search of rare blood donors. Aims and methods To evaluate a fully automated workflow designed for genotyping blood donors’ red blood cell ( RBC ) and platelets ( PTL ) antigens using the OpenArray Real‐time PCR system. Results 5487 blood donors were genotyped using the propos...

Background: Zika virus (ZIKV) has spread rapidly in the Pacific and throughout the Americas and is associated with severe congenital and adult neurologic outcomes. Nucleic acid amplification technology (NAT) assays were developed for diagnostic applications and for blood donor screening on high-throughput NAT systems. We distributed blinded panels...

Human papillomavirus (HPV) causes oropharyngeal squamous cell carcinoma (OPSCC), although strongly divergent results have been reported regarding the prevalence of HPV16 in different countries, whether this represents important differences in etiology remains unclear. Applying rigorous protocols for sample processing, we centrally evaluated 1420 he...

Brazil has experienced successive outbreaks of dengue in the last three decades, with more than one million cases per year since 2014, as vector control has proven unsuccessful. In 2014, Chikungunya and Zika viruses were introduced to Brazil in different sites. Currently, all three agents are spread all over the country, posing a considerable burde...

Objectives To explore whether HPV-related biomarkers predict oropharyngeal squamous cell cancer (OPSCC) survival similarly across different global regions, and to explore their prognostic utility among non-oropharyngeal (non-OP) head and neck cancers. Methods Data from 1362 head and neck SCC (HNSCC) diagnosed 2002–2011 was used from epidemiologic...

Background and objectives To date, it is unclear whether antigen matching is effective in reducing antibody development and whether transfusing blood from non‐Caucasian donors reduces alloimmunization in sickle cell disease patients ( SCP ). This study was designed to evaluate the effectiveness of an antigen‐matching strategy supplied by a mixed do...

Human papillomaviruses (HPVs) are the etiologic agents of cervical cancer, the unique human neoplasia that has one single necessary cause. The diversity of HPVs is well described, with 200 HPV types existing as distinct taxonomic units and each receiving an Arabic number. On a clinical basis, they are usually grouped by their site of occurrence and...

Objective To evaluate the reproducibility and accuracy of the HPV16/18-E6 test. Methods The study population was comprised of 448 women with a previously abnormal Pap who were referred to the Barretos Cancer Hospital (Brazil) for diagnosis and treatment. Two cervical samples were collected immediately before colposcopy, one for the hr-HPV-DNA test...

Objective: To examine the accuracy of fetal RHD genotype and RHD pseudogene determination in a multiethnical population. Methods: Prospective study involving D-negative pregnant women. Cell-free DNA was extracted from 1 ml of maternal plasma by an automated system (MagNA Pure Compact, Roche) and real-time PCR was performed in triplicate targetin...

Hospital-Acquired Vector-Transmitted Dengue Fever: An Overlooked Problem? - Volume 37 Issue 11 - Juliana Almeida-Nunes, Izabel Marcilio, Maura S. Oliveira, Elenice M.N. Gonçalves, Marjorie V. Batista, Alfredo Mendrone, José E. Levi, Silvia F. Costa, Anna S. Levin

Anal cancer is a rare type of digestive tract disease, which has had a crescent incidence in a number of regions. Carcinomas are most frequently found, with squamous cell carcinoma (SCC) comprising ~95% of all anal tumors. The major risk factor for development of this type of tumor is human papillomavirus (HPV) infection. However, previous studies...

Background Human Papillomavirus (HPV) genotype distribution varies according to the method of assessment and population groups. This study analyzed type-specific HPV infections among women ranging from 14–95 years old, displaying normal and abnormal cytology, from São Paulo and Barretos cities, Brazil. Methods Women found positive for High Risk-HPV...

Introduction:: This study aimed to investigate Flavivirus infection in birds captured in green areas of São Paulo. Methods:: Oropharyngeal swabs, cloacal swabs, and blood samples from 170 birds captured in two green areas in São Paulo, Brazil were subjected to real time-polymerase chain reaction (RT-qPCR) analysis of Flavivirus specific NS5 gene...