Toxoplasmosis outbreak in São Paulo, Brazil: Epidemiology and visual outcome.

PURPOSE: To describe a 2019 acute toxoplasmosis outbreak in the city of São Paulo, Brazil, and to evaluate the laboratory serological profile for toxoplasmosis for three consecutive years. The ophthalmological manifestations of the patients involved in the outbreak were also studied. METHODS: A cross-sectional descriptive study of a toxoplasmosis outbreak in São Paulo, Brazil, between February and May 2019. Epidemiological data were described, as were the observed ocular manifestations. As part of this study the number of patients with positive IgM toxoplasmosis serology was obtained from a large laboratory network (DASA) for three consecutive years, including the year of the outbreak (2018, 2019, 2020). RESULTS: Eighty-three individuals were identified in the outbreak and two clusters were studied. The clinical picture of at least 77% of the patients, the epidemiological analysis, and the short incubation period (5-8 days) suggested contamination by oocysts. Serological laboratory data analysis revealed an increase of positive toxoplasmosis IgM in 2019 of 73% compared to the previous year. Ophthalmological examination revealed that at least 4.8% of the patients developed toxoplasmic retinochoroiditis, none of whom had been treated during the acute systemic disease. CONCLUSION: Our findings indicate vegetable contamination as the possible source of this outbreak, a high prevalence of toxoplasmosis in São Paulo during the outbreak period, and a drop in the number of tests during the COVID-19 pandemic. Retinochoroiditis was observed in at least 4.8% of the cases. We confirm the need to implement effective means for the prevention, diagnosis, and treatment of the disease. This may involve raising awareness among the population of the importance of vegetable hygiene, and improved quality control of food and water.

COVID-19 in hematopoietic stem cell transplant recipients during three years of the pandemic: a multicenter study in Brazil.

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, from January 2020 to June 2022. The primary outcome was all-cause mortality. Of 49 cases, 63.2% were male with a median age of 47 years. Allogeneic-HSCT (51.2%) and autologous-HSCT (48.9%) patients were included. The median time from HSCT to COVID-19 diagnosis was 398 days (IQR: 1211-134), with 22 (44.8%) cases occurring within 12 months of transplantation. Most cases occurred during the first year of the pandemic, in non-vaccinated patients (n=35; 71.4%). Most patients developed severe (24.4%) or critical (40.8%) disease; 67.3% received some medication for COVID-19, primarily corticosteroids (53.0%). The probable invasive aspergillosis prevalence was 10.2%. All-cause mortality was 40.8%, 51.4% in non-vaccinated patients and 14.2% in patients who received at least one dose of the vaccine. In the multiple regression analyses, the variables mechanical ventilation (OR: 101.01; 95% CI: 8.205 - 1,242.93; p = 0.003) and chest CT involvement at diagnosis ≥50% (OR: 26.61; 95% CI: 1.06 - 664.26; p = 0.04) remained associated with all-cause mortality. Thus, HSCT recipients with COVID-19 experienced high mortality, highlighting the need for full vaccination and infection prevention measures.

Comparison of four different human papillomavirus genotyping methods in cervical samples: Addressing method-specific advantages and limitations.

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 for HPV detection and genotyping: real-time PCR (Cobas® HPV test), nested PCR followed by conventional Sanger sequencing, reverse hybridization (High + Low PapillomaStrip® kit) and next-generation sequencing (NGS) at an Illumina HiSeq2500 platform. Cervical samples from patients followed at the Family Health Strategy from Juiz de Fora, Minas Gerais, Brazil, were collected and subjected to the real-time PCR. Of those, 114 were included in this study according to the results obtained with the real-time PCR, considered herein as the gold standard method. For the 110 samples tested by at least one methodology in addition to real-time PCR, NGS showed the lowest concordance rates of HPV and high-risk HPV identification compared to the other three methods (67-75 %). Real-time PCR and Sanger sequencing showed the highest rates of concordance (97-100 %). All methods differed in their sensitivity and specificity. HPV genotyping contributes to individual risk stratification, therapeutic decisions, epidemiological studies and vaccine development, supporting approaches in prevention, healthcare and management of HPV infection.

COVID-19 in hematopoietic stem cell transplant recipients during three years of the pandemic: a multicenter study in Brazil

ABSTRACT 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, from January 2020 to June 2022. The primary outcome was all-cause mortality. Of 49 cases, 63.2% were male with a median age of 47 years. Allogeneic-HSCT (51.2%) and autologous-HSCT (48.9%) patients were included. The median time from HSCT to COVID-19 diagnosis was 398 days (IQR: 1211-134), with 22 (44.8%) cases occurring within 12 months of transplantation. Most cases occurred during the first year of the pandemic, in non-vaccinated patients (n=35; 71.4%). Most patients developed severe (24.4%) or critical (40.8%) disease; 67.3% received some medication for COVID-19, primarily corticosteroids (53.0%). The probable invasive aspergillosis prevalence was 10.2%. All-cause mortality was 40.8%, 51.4% in non-vaccinated patients and 14.2% in patients who received at least one dose of the vaccine. In the multiple regression analyses, the variables mechanical ventilation (OR: 101.01; 95% CI: 8.205 - 1,242.93; p = 0.003) and chest CT involvement at diagnosis ≥50% (OR: 26.61; 95% CI: 1.06 - 664.26; p = 0.04) remained associated with all-cause mortality. Thus, HSCT recipients with COVID-19 experienced high mortality, highlighting the need for full vaccination and infection prevention measures.

Toxoplasmosis outbreak in São Paulo, Brazil: Epidemiology and visual outcome

ABSTRACT Purpose: To describe a 2019 acute toxoplasmosis outbreak in the city of São Paulo, Brazil, and to evaluate the laboratory serological profile for toxoplasmosis for three consecutive years. The ophthalmological manifestations of the patients involved in the outbreak were also studied. Methods: A cross-sectional descriptive study of a toxoplasmosis outbreak in São Paulo, Brazil, between February and May 2019. Epidemiological data were described, as were the observed ocular manifestations. As part of this study the number of patients with positive IgM toxoplasmosis serology was obtained from a large laboratory network (DASA) for three consecutive years, including the year of the outbreak (2018, 2019, 2020). Results: Eighty-three individuals were identified in the outbreak and two clusters were studied. The clinical picture of at least 77% of the patients, the epidemiological analysis, and the short incubation period (5-8 days) suggested contamination by oocysts. Serological laboratory data analysis revealed an increase of positive toxoplasmosis IgM in 2019 of 73% compared to the previous year. Ophthalmological examination revealed that at least 4.8% of the patients developed toxoplasmic retinochoroiditis, none of whom had been treated during the acute systemic disease. Conclusion: Our findings indicate vegetable contamination as the possible source of this outbreak, a high prevalence of toxoplasmosis in São Paulo during the outbreak period, and a drop in the number of tests during the COVID-19 pandemic. Retinochoroiditis was observed in at least 4.8% of the cases. We confirm the need to implement effective means for the prevention, diagnosis, and treatment of the disease. This may involve raising awareness among the population of the importance of vegetable hygiene, and improved quality control of food and water.

Prevention of multiple whole blood donations by an individual at the same month through the creation of a national Deferred Donor Registry (DDR).

INTRODUCTION: The Colombian National Institute of Health administers the National Information System of Haemovigilance (SIHEVI-INS). Today, SIHEVI-INS constitutes a national blood donor and recipient database, which contains a national deferred donor registry (DDR), allowing blood banks to take acceptance or rejection decisions of a potential donor in real time. The study aimed to determine the rate of people who have made more than one whole blood donation monthly in Colombia, violating the national guideline of intervals between donations (three months for men and four for women), since DDR implementation. METHODS: We detected the unique personal identification number of people who, in 30 calendar days, made more than one whole blood donation at any of the 83 blood banks set up in Colombia. There were three comparison periods: 01/01/2018-08/31/2019 (launch of SIHEVI-INS and first national feedback); 09/01/2019-12/31/2020 (second feedback) and 01/01/2021-09/30/2022 (massive incorporation of web services). RESULTS: For the first period, blood banks accepted 18.0 donations per 1000 people. There was a rate of 28.8 people/10,000 donations who had donated whole blood twice within 30 days. In the second period, there were 17.0 donations/1000 people and a rate of 2.1 people/10,000 donations (OR:14.0 CI95 %:12.2-16.0). For the last period, there were 18.2 donations/1000 people and a rate of 0.9 individuals/10,000 donations (OR:31.3 CI95 %:26.6-36.9, p < 0.001). CONCLUSION: DDR reduced by 31 times the acceptance of blood donors who made more than one whole blood donation in the same month. It was necessary to provide periodic feedback and promote web service implementation to reduce this risky behavior.

Genital Human Papillomavirus Infection in women from Florianópolis - Santa Catarina, Brazil / Infecção genital pelo Papilomavírus Humano em mulheres de Florianópolis - Santa Catarina, Brasil

Introduction: Human Papillomavirus (HPV) infection is the most common sexually transmitted infection in women. About 80% of sexually active women will have contact with this virus at some age in their lives. Most infections will be transient, but when the infection becomes persistent, associated with high oncogenic risk HPV, there may be progression to cancer, especially cervical cancer. The best way to prevent HPV infection is through the use of vaccines. Objective: To assess which are the most prevalent types of HPV in the city of Florianópolis, Brazil and if the majority of the diagnosed types are contained in the HPV vaccines currently available on the market and in the public health sector. Methods: More than 14,727 HPV tests were evaluated for the diagnosis of genital HPV infection in women from Florianópolis. The prevalence of infection was evaluated according to age of the women. HPV detection was performed using molecular biology tests, such as hybrid capture (for diagnosis of the HPV group, high or low oncogenic risk) and PCR (viral genotyping) techniques. Results: The diagnosis of HPV infection was made for women between one and 102 years of age. The highest positivity of the exams was observed in women aged 20­25 years (51% of the exams). The most prevalent age group was 31­35 years old (23.5%), and the lowest was for women aged 70 and above (0.6%). High oncogenic risk HPV was detected in 94.1% of positive samples and was the most frequent in all age groups. Mixed infection (high- and low-risk HPV) was more prevalent in the 66­70 age group (25.6%). The most frequent genotypes were non-16/18 high oncogenic risk HPV (77% of positive cases). HPV 16 was found in 17.1% of positive cases, and HPV 18 in 6.5%. Conclusion: The most prevalent types of HPV in Florianópolis in the last 6 years are non-16/18 high oncogenic risk HPV types, viral types not covered by the current HPV vaccine available in the public health sector in Brazil.

Introdução: A infecção pelo Papilomavírus Humano (HPV)é a infecção sexualmente transmissível mais frequente na mulher. Cerca de 80% das mulheres sexualmente ativas irão entrar em contato com este vírus em algum momento da sua vida. A maioria das infecções será transitória, mas quando a infecção se torna persistente, associada aos HPV de alto risco oncogênico, poderá haver a progressão para o câncer, principalmente o câncer de colo de útero. A melhor forma de prevenção da contaminação pelo HPV é através da utilização das vacinas. Objetivo: Avaliar quais são os tipos de HPV mais prevalentes na cidade de Florianópolis, Brasil, e se a maioria dos tipos diagnosticados estão contidos nas vacinas contra o HPV atualmente disponíveis no mercado e no setor público de saúde. Métodos: Foram avaliados 14.727 exames para diagnóstico da infecção genital pelo HPV em mulheres de Florianópolis, de acordo com a idade das mulheres. A detecção do HPV foi realizada através dos exames de biologia molecular pelas técnicas de captura híbrida (para diagnóstico do grupo de HPV, alto ou baixo risco oncogênico) e PCR (genotipagem viral). Resultados: Foram avaliados exames para diagnóstico da infecção de mulheres entre um e 102 anos de idade. A maior positividade dos exames foi observada em mulheres dos 20­25 anos (51% dos exames). A faixa etária de maior prevalência foi dos 31­35 anos (23,5%), e a menor, após os 70 anos (0,6%). O HPV de alto risco oncogênico foi detectado em 94,1% dos casos positivos e foi o mais frequente em todas as faixas etárias. A infecção mista (HPV de alto e baixo risco) foi mais prevalente na faixa etária dos 66­70 anos (25,6%). Os genótipos mais frequentes foram os HPV de alto risco oncogênico não 16/18 (77% dos casos positivos). O HPV 16 foi encontrado em 17,1% dos casos positivos, e o HPV 18 em 6,5%. Conclusão: Os tipos de HPV mais prevalentes em Florianópolis nos últimos 6 anos são os HPV de alto risco oncogênico não 16/18, tipos virais não cobertos pela atual vacina contra o HPV disponível no setor público de saúde do Brasil.Palavras-chave: HPV. Tipos de HPV. Câncer de colo de útero. Cobertura vacinal.

Zika virus RNA detection in blood donors in São Paulo, Brazil

ABSTRACT 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 proposed to ensure the blood safety. This study implemented an "in-house" method to detect ZIKV RNA in blood sample donations. Methods: Primary plasma tubes are submitted to nucleic acid extraction on an automated platform. After extraction, the NAT set-up is performed in the robotic pipettor, in which an amplification mixture containing primers and probes for ZIKV and Polio vaccine virus (PV) are added in duplex as an internal control. The real-time polymerase chain reaction is then performed in a thermocycler, using the protocol established by the supplier. Results: From May 2016 to May 2018, 3,369 samples were collected from 3,221 blood donors (confidence coefficient 95%), of which 31 were considered false positive (0.92%), as they did not confirm initial reactivity when repeated in duplicates and 14 (0.42%) had their results invalid due to repeat failure in the internal control, 4 (0.12%), due to insufficient sample volume and 2 (0.05%), due to automatic pipettor failures. No Zika RNA reactive sample was identified. Conclusion: The test showed feasible to be incorporated into the blood screening routine. Our data do not indicate the need to screen for ZIKV RNA in São Paulo during the evaluated period. However, a generic NAT system covering a group of flaviviruses which are circulating in the region, such as DENV and YFV, among others, could be a useful tool.

Reduced gut microbiota diversity in patients with congenital generalized lipodystrophy.

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 diabetes since the first years of life, could provide insights into these relationships. METHODS: A cross-sectional study was conducted with patients with CGL (n = 17) and healthy individuals (n = 17). The gut microbiome study was performed by sequencing the 16S rRNA gene through High-Throughput Sequencing (BiomeHub Biotechnologies, Brazil). RESULTS: The median age was 20.0 years old, and 64.7% were female. There was no difference between groups in pubertal stage, BMI, ethnicity, origin (rural or urban), delivery, breastfeeding, caloric intake, macronutrient, or fiber consumption. Lipodystrophic patients presented a lower alpha diversity (Richness index: 54.0 versus 67.5; p = 0.008). No differences were observed in the diversity parameters when analyzing the presence of diabetes, its complications, or the CGL subtype. CONCLUSION: In this study, we demonstrate for the first time a reduced gut microbiota diversity in individuals with CGL. Dysbiosis was present despite dietary treatment and was also observed in young patients. Our findings allow us to speculate that the loss of intestinal microbiota diversity may be due to metabolic abnormalities present since the first years of life in CGL. Longitudinal studies are needed to confirm these findings, clarifying the possible causal link between dysbiosis and insulin resistance in humans.

SARS-CoV-2 BA.1 and BA.2 coinfection detected by genomic surveillance in Brazil, January 2022.

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.

Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil.

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 AY.101 and AY.99.2. In this study we performed a detailed analysis of the COVID-19 scenario in Brazil from April to December 2021 by using data collected by the largest private medical diagnostic company in Latin America (Dasa), and SARS-CoV-2 genomic sequences generated by its SARS-CoV-2 genomic surveillance project (GENOV). For phylogenetic and Bayesian analysis, SARS-CoV-2 genomes available at GISAID public database were also retrieved. We confirmed that the Brazilian AY.99.2 and AY.101 were the most prevalent lineages during this period, overpassing the Gamma variant in July/August. We also estimated that AY.99.2 likely emerged a few weeks after the entry of the B.1.617.2 in the country, at some point between late April and May and rapidly spread to other countries. Despite no increased fitness described for the AY.99.2 lineage, a rapid shift in the composition of Delta SARS-CoV-2 lineages prevalence in Brazil took place. Understanding the reasons leading the AY.99.2 to become the dominant lineage in the country is important to understand the process of lineage competitions that may inform future control measures.

Genital infection by Human Papillomavirus (HPV) in women from Santa Catarina/Brazil / Infecção genital pelo Papilomavírus Humano (HPV) em mulheres de Santa Catarina/Brasil

Human Papillomavirus (HPV) infection is the most common sexually transmitted infection in women. About 80% of sexually active women will have contact with this virus at some point in their lives. Most infections will be transient, but when the infection becomes persistent and associated with a high oncogenic risk of Human Papillomavirus, there may be progression to cancer, especially cervical cancer. The best way to prevent Human Papillomavirus infection is through the use of vaccines, which have been available to the public in Brazil since 2014. Objective: This study aimed to assess the most prevalent types of Human Papillomavirus in the state of Santa Catarina, Brazil, and its mesoregions and if the majority of diagnosed types are contained in the Human Papillomavirus vaccines currently available on the market. Methods: A total of 20,000 Human Papillomavirus tests were evaluated for the diagnosis of genital Human Papillomavirus infection in women from the state of Santa Catarina, Brazil. The prevalence of infection was evaluated according to age and the city of origin of the exams. Human Papillomavirus detection was performed using molecular biology tests, such as hybrid capture (for diagnosis of the Human Papillomavirus group, high or low oncogenic risk) and polymerase chain reaction (viral genotyping) techniques. Results: The diagnosis of Human Papillomavirus infection was performed on women between 1 and 102 years of age. The age with the highest Human Papillomavirus positivity, as expected, was 20­25 years (45.6%) and the lowest after 70 years (7.1%). The highest Human Papillomavirus positivity of the exams was observed in the Serrana region of Santa Catarina state (58.9% of the exams). A high-oncogenic-risk Human Papillomavirus was detected in 93% of positive samples and was the most frequent in all age groups. Mixed infection (high- and low-risk Human Papillomavirus) was more prevalent in the 66­70 age group (29.3%) and in the Southern Region of Santa Catarina (26.4%). The most frequent genotypes in the state of Santa Catarina were non-16/18 high oncogenic risk Human Papillomavirus (76.9% of positive cases). Human Papillomavirus 16 was found in 17.1% of positive cases and Human Papillomavirus 18 in 6.6%. Conclusion: The most prevalent types of Human Papillomavirus in the state of Santa Catarina in the past 6 years are the non-16/18 high oncogenic risk Human Papillomavirus types, which are viral types not covered by the current Human Papillomavirus vaccines available in Brazil.

A infecção por Papilomavírus Humano é a infecção sexualmente transmissível mais frequente na mulher. Cerca de 80% das mulheres sexualmente ativas entrarão em contato com esse vírus em algum momento. A maioria das infecções será transitória, mas quando ela é persistente, associada aos Papilomavírus Humano de alto risco oncogênico, poderá progredir para câncer, principalmente de colo de útero. A melhor forma de se prevenir da contaminação pelo vírus é por meio de vacina, disponível no sistema público do Brasil desde 2014. Objetivo: Avaliar os tipos de Papilomavírus Humano mais prevalentes no estado de Santa Catarina e suas mesorregiões, e se a maioria dos tipos diagnosticados estão contidos nas vacinas contra o Papilomavírus Humano atualmente disponíveis no mercado. Métodos: Foram avaliados 20 mil exames para diagnóstico da infecção genital pelo Papilomavírus Humano em mulheres de todo o estado. A prevalência da infecção foi comparada de acordo com a idade e a procedência dos exames. A detecção do Papilomavírus Humano deu-se pelos exames de biologia molecular pelas técnicas de captura híbrida (para diagnóstico do grupo de Papilomavírus Humano, alto ou baixo riscos oncogênicos) e de PCR (genotipagem viral). Resultados: Foram avaliados exames para diagnóstico da infecção de mulheres entre um e 102 anos de idade. A faixa etária de maior positividade, como era de ser esperado, foi dos 20 aos 25 anos (45.6%) e a menor depois dos 70 anos (7.1%). A maior positividade dos exames foi observada na região Serrana do estado (58.9% dos exames). O Papilomavírus Humano de alto risco oncogênico foi detectado em 93% dos casos positivos e foi o mais frequente em todas as faixas etárias. A infecção mista (Papilomavírus Humano de alto e baixo riscos) foi mais prevalente na faixa etária dos 66 aos 70 anos (29.3%) e na região Sul Catarinense (26.4%). Os genótipos mais frequentes no estado foram os Papilomavírus Humano de alto risco oncogênico não 16/18 (76.9% dos casos positivos). O Papilomavírus Humano 16 foi encontrado em 17.1% dos casos positivos e o Papilomavírus Humano 18 em 6.6%. Conclusão:Os tipos de Papilomavírus Humano mais prevalentes no estado de Santa Catarina, nos últimos seis anos, são os Papilomavírus Humano de alto risco oncogênico não 16/18, tipos virais não cobertos pelas atuais vacinas contra o Papilomavírus Humano disponíveis no Brasil.

Human Papillomavirus (HPV) seroprevalence, cervical HPV prevalence, genotype distribution and cytological lesions in solid organ transplant recipients and immunocompetent women in Sao Paulo, Brazil.

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: Cross-sectional study including SOT and immunocompetent women aged 18 to 45 years who denied previous HPV-related lesions. Cervical samples were screened for HPV-DNA by a polymerase chain reaction (PCR)-based DNA microarray system (PapilloCheck®) and squamous intraepithelial lesions (SIL) by liquid-based cytology. A multiplexed pseudovirion-based serology assay (PsV-Luminex) was used to measure HPV serum antibodies. RESULTS: 125 SOT and 132 immunocompetent women were enrolled. Cervical samples were collected from 113 SOT and 127 immunocompetent women who had initiated sexual activity. HPV-DNA prevalence was higher in SOT than in immunocompetent women (29.6% vs. 20.2%, p = 0.112), but this difference was not statistically significant. High-risk (HR)-HPV was significantly more frequent in SOT than in immunocompetent women (19.4% vs. 7.9%, p = 0.014). Simultaneous infection with ≥2 HR-HPV types was found in 3.1% of SOT and 0.9% of immunocompetent women. HPV seropositivity for at least one HPV type was high in both groups: 63.8% of 105 SOT and 69.7% of 119 immunocompetent women (p = 0.524). Low-grade (LSIL) and high-grade SIL (HSIL) were significantly more frequent in SOT (9.7% and 5.3%, respectively) than in immunocompetent women (1.6% and 0.8%, respectively) (p = 0.001). CONCLUSIONS: These results may reflect the increased risk of HPV persistent infection and disease progression in SOT women due to chronic immunosuppression.

Zika virus RNA detection in blood donors in São Paulo, Brazil.

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 proposed to ensure the blood safety. This study implemented an "in-house" method to detect ZIKV RNA in blood sample donations. METHODS: Primary plasma tubes are submitted to nucleic acid extraction on an automated platform. After extraction, the NAT set-up is performed in the robotic pipettor, in which an amplification mixture containing primers and probes for ZIKV and Polio vaccine virus (PV) are added in duplex as an internal control. The real-time polymerase chain reaction is then performed in a thermocycler, using the protocol established by the supplier. RESULTS: From May 2016 to May 2018, 3,369 samples were collected from 3,221 blood donors (confidence coefficient 95%), of which 31 were considered false positive (0.92%), as they did not confirm initial reactivity when repeated in duplicates and 14 (0.42%) had their results invalid due to repeat failure in the internal control, 4 (0.12%), due to insufficient sample volume and 2 (0.05%), due to automatic pipettor failures. No Zika RNA reactive sample was identified. CONCLUSION: The test showed feasible to be incorporated into the blood screening routine. Our data do not indicate the need to screen for ZIKV RNA in São Paulo during the evaluated period. However, a generic NAT system covering a group of flaviviruses which are circulating in the region, such as DENV and YFV, among others, could be a useful tool.

Hydroxychloroquine plus azithromycin early treatment of mild COVID-19 in an outpatient setting: a randomized, double-blinded, placebo-controlled clinical trial evaluating viral clearance.

BACKGROUND: Hydroxychloroquine has shown potential to block viral replication of SARS-CoV-2 in some in vitro studies. This randomised, double-blinded, placebo controlled clinical trial evaluated the efficacy of hydroxychloroquine plus azithromycin (HCQ/AZT) in reducing viral loads in patients with early and mild SARS-CoV-2 infection. METHODS: A single-centre randomised placebo-controlled clinical trial was conducted with outpatients with early and mild SARS-CoV-2 infection. Inclusion criteria were: patients aged 18-65 years with symptoms suggestive of COVID-19 for < 5 days, no significant comorbidities, and positive nasopharyngeal/oropharyngeal swab screening tests (POCT-PCR). Randomised patients received either hydroxychloroquine for 7 days plus azithromycin for 5 days or placebo. The primary endpoint was viral clearance within a 9-day period. Secondary endpoints included viral load reduction, clinical evolution, hospitalization rates, chest computed tomography evolution, and adverse effects. RESULTS: From 107 potential trial participants, 84 were enrolled following predetermined criteria. Statistical analyses were performed on an intention-to-treat (N = 84) and per-protocol (PP) basis (N = 70). On the PP analysis, the treatment (N = 36) and placebo (N = 34) groups displayed similar demographic characteristics. At 95% CI, no statistically significant between-group differences were found in viral clearance rates within 9 days following enrolment (P = 0.26). CONCLUSIONS: This randomised, double-blinded, placebo-controlled clinical trial evaluating outpatients with early and mild COVID-19 showed that viral clearance rates within a 9-day period from enrolment did not change with HCQ/AZT treatment compared with placebo, although no major cardiovascular events were observed in participants without comorbidities. Secondary outcomes were also not significantly improved with HCQ/AZT treatment compared with placebo. These findings do not support use of HCQ/AZT in this setting.

SARS-CoV-2 saliva testing is a useful tool for Covid-19 diagnosis.

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 nosocomial infections. In this study, we describe two SARS-CoV-2 RNA extraction-free single RT-PCR protocols on saliva samples and compared the results with the paired oro/nasopharyngeal swab specimens from 400 patients. The two saliva protocols demonstrated a substantial agreement when compared to the oro/nasopharyngeal swab protocol. Moreover, the positivity rate of saliva protocols increased according to the disease period. The 95 % limit of detection of one of the therefore implemented saliva protocol was determined as 9441 copies/mL. Our results support the conclusion that RNA extraction-free RT-PCR using self-collected saliva specimens is an alternative to nasopharyngeal swabs, especially in the early phase of symptom onset.

Performance evaluation of the fully automated molecular system Alinity m in a high-throughput central laboratory.

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 laboratory. STUDY DESIGN: Alinity m HIV-1, HCV, and HBV assay precision, reproducibility, and sensitivity were assessed using commercial customized dilution panels. Clinical performance of the Alinity m and m2000 assay systems was compared using standard lab protocols and residual, de-identified patient specimens. A workflow analysis of 1,068 samples compared turnaround times (TATs) on five m2000 systems and one Alinity m system running Alinity m HIV-1, HCV, HBV, HR HPV, and STI assays. RESULTS: The Alinity m assay system demonstrated high detectability and precision at clinical decision points and excellent correlation with Abbott RealTime assay results. Processing TAT for 100 % of results was 117 min on Alinity m. Sample onboard TAT, from sample loading to 95 % of results, was 5:15 h for Alinity m and 7:30 h for m2000. 100 % of STAT samples were processed within 4 h on Alinity m. Total TAT for 100 % of results from all five assays was 80 h for m2000 versus 9 h for Alinity m. CONCLUSIONS: The Alinity m system produces assay results comparable to those of the Abbott RealTime m2000 system, but with significantly faster turnaround times due to continuous loading and the ability to run multiple assays simultaneously on the same sample.

High prevalence of anal high-risk HPV infection among transwomen: estimates from a Brazilian RDS study.

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 a respondent-driven sampling (RDS)-based survey conducted between August 2015 and January 2016 self-collected anal samples, which were promptly stored at minus 80°C. After DNA extraction, HPV detection and genotyping were performed using the PapilloCheck test. We estimated HPV prevalences and evaluated the correlates of anal hr-HPV infection using a regression logistic model. RESULTS: Out of 345 transwomen, 272 (78.8%) were included in this analysis (122 [44.9%] HIV-positive). No participant had ever received HPV vaccination. Among participants enrolled, 212 (77.9%) were positive for any anal HPV type and 165 (60.7%) for hr-HPV. Most common hr-HPV were as follows: HPV16 (17.6%), HPV68 (14.7%), HPV39 (14.3%), HPV56 (12.5%), HPV51 (11.4%) and HPV52 (11.0%). HIV-positive transwomen had three times the odds of having an hr-HPV compared to HIV-negative transwomen. Participants who had a current rectal Neisseria gonorrhoeae infection had 3.7 times the odds of being coinfected with hr-HPV. Among HIV-positive transwomen, neither antiretroviral therapy use, undetectable viral load, current and nadir CD4 counts were associated with anal hr-HPV infection. CONCLUSIONS: Brazilian transwomen in our study exhibit some of the highest population-specific rates of HPV and hr-HPV. There is an urgent need to elucidate the burden of HPV infection, prevalence of HPV-related diseases and access to and uptake of HPV vaccination among transwomen, especially from low- and middle-income settings.

COL1A1, COL4A3, TIMP2 and TGFB1 polymorphisms in cervical insufficiency.

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 collagen type I alpha 1 chain (COL1A1), rs1882435 in collagen type IV alpha 3 chain (COL4A3), rs2277698 in metallopeptidase inhibitor 2 (TIMP2), and rs1800468 in transforming growth factor beta 1 (TGFB1). RESULTS: We found a higher frequency of the normal allele in the control group (65.5%) and the homozygous mutated genotype in the case group (64.3%) for rs2586490 in COL1A1 (p=0.023). An unplanned finding in the cervical insufficiency group was a higher gestational age of delivery (median≥38 weeks) in the mutated allele than in the wild-type genotype (median of 28.2 weeks) for rs2857396, which is also in the COL1A1 gene (p=0.011). CONCLUSIONS: The findings of the present study corroborate the hypothesis that cervical insufficiency has a genetic component and probably involves genes encoding proteins in the extracellular matrix, in addition to inflammatory processes.

Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020.

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 reported.