Introduction of SARS-CoV-2 C.37 (WHO VOI lambda) in the Sao Paulo State, Southeast Brazil.

The Lambda variants of interest (VOI) (C37/GR/452Q.V1/21G) was initially reported in Lima, Peru but has gained rapid dissemination through other Latin American countries. Nevertheless, the dissemination and molecular epidemiology of the Lambda VOI in Brazil is unknown apart from a single case report. In this respect, we characterized the circulation of the SARS-CoV-2 Lambda VOI (C37/GR/452Q.V1/21G) in Sao Paulo State, Brazil. From March to June 2021, we identified seven Lambda isolates in a set of approximately 8000 newly sequenced genomes of the Network for Pandemic Alert of Emerging SARS-CoV-2 variants from Sao Paulo State. Interestingly, in three of the positive patients, the Lambda VOI infection was probably related to a contact transmission. These individuals were fully vaccinated to COVID-19 and presented mild symptoms. The remaining positive for Lambda VOI individuals showed different levels of COVID-19 symptoms and one of them needed hospitalization (score 5, WHO). In our study, we present a low level of Lambda VOI circulation in the Sao Paulo State. This reinforces the essential role of molecular surveillance for the effective SARS-CoV-2 pandemic response, especially in regard to circulating variants.

Dengue RNA detection and seroprevalence in blood donors during an outbreak in the São Paulo State, Brazil, 2016.

Most dengue virus (DENV) infections remain asymptomatic. This increases the risk of DENV transfusion transmission (TT-DENV) during outbreaks. We evaluated DENV viremia in 8475 blood donations assembled in minipools for the presence of DENV RNA. The tested samples were obtained between February and May, 2016, during a large DENV outbreak in Ribeirão Preto city, northeast region of the São Paulo State, Brazil. The DENV RNA + samples were serotyped and screened for DENV NS1. We also tested a significant number of plasma samples (n = 372) to estimate the DENV seroprevalence among blood donors in the region. We detected three DENV RNA + samples in the tested blood donations (n = 3/8475, 0.04%). From these, two samples were further serotyped as DENV-1 and one sample as DENV-2. All DENV RNA positive samples were negative for anti-DENV IgG, indicating the presence of primary acute infection. Moreover, two of the DENV RNA + samples were also NS1 antigen positive (antigenemia). The anti-DENV IgG seroprevalence among blood donor population was 50.8% (n = 189/372). Our results are in accordance with the presence of DENV primary infection in blood donors which can lead to transfusion transmission of the infection to recipients. Measures to exclude such donors should be adopted to prevent TT-DENV.

Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil.

Sao Paulo State, currently experiences a second COVID-19 wave overwhelming the healthcare system. Due to the paucity of SARS-CoV-2 complete genome sequencing, we established a Network for Pandemic Alert of Emerging SARS-CoV-2 Variants to rapidly understand and monitor the spread of SARS-CoV-2 variants into the state. Through analysis of 210 SARS-CoV-2 complete genomes obtained from the largest regional health departments we identified cocirculation of multiple SARS-CoV-2 lineages such as B.1.1 (0.5%), B.1.1.28 (23.2%), B.1.1.7 (alpha variant, 6.2%), B.1.566 (1.4%), B.1.544 (0.5%), C.37 (0.5%) P.1 (gamma variant, 66.2%), and P.2 (zeta variant, 1.0%). Our analysis allowed also the detection, for the first time in Brazil, the South African B.1.351 (beta) variant of concern, B.1.351 (501Y.V2) (0.5%), characterized by the following mutations: ORF1ab: T265I, R724K, S1612L, K1655N, K3353R, SGF 3675_F3677del, P4715L, E5585D; spike: D80A, D215G, L242_L244del, A262D, K417N, E484K, N501Y, D614G, A701V, C1247F; ORF3a: Q57H, S171L, E: P71L; ORF7b: Y10F, N: T205I; ORF14: L52F. The most recent common ancestor of the identified strain was inferred to be mid-October to late December 2020. Our analysis demonstrated the P.1 lineage predominance and allowed the early detection of the South African strain for the first time in Brazil. We highlight the importance of SARS-CoV-2 active monitoring to ensure the rapid detection of potential variants for pandemic control and vaccination strategies. Highlights Identification of B.1.351 (beta) variant of concern in the Sao Paulo State. Dissemination of SARS-CoV-2 variants of concern and interest in the Sao Paulo State. Mutational Profile of the circulating variants of concern and interest.

The novel coronavirus SARS-CoV-2: From a zoonotic infection to coronavirus disease 2019.

The novel coronavirus (CoV), severe acute respiratory syndrome (SARS)-CoV-2 is an international public health emergency. Until now, the intermediate host and mechanisms of the interspecies jump of this virus are unknown. Phylogenetic analysis of all available bat CoV complete genomes was performed to analyze the relationships between bat CoV and SARS-CoV-2. To suggest a possible intermediate host, another phylogenetic reconstruction of CoV genomes obtained from animals that were hypothetically commercialized in the Chinese markets was also carried out. Moreover, mutation analysis was executed to suggest genomic regions that may have permitted the adaptation of SARS-CoV-2 to the human host. The phylogenetic analysis demonstrated that SARS-CoV-2 formed a cluster with the bat CoV isolate RaTG13. Possible CoV interspecies jumps among bat isolates were also observed. The phylogenetic tree reconstructed from CoV strains belonging to different animals demonstrated that SARS-CoV-2, bat RaTG13, and pangolin CoV genomes formed a monophyletic cluster, demonstrating that pangolins may be suggested as SARS-CoV-2 intermediate hosts. Three AA substitutions localized in the S1 portion of the S gene were observed, some of which have been correlated to structural modifications of the S protein which may facilitate SARS-CoV-2 tropism to human cells. Our analysis shows the tight relationship between SARS-CoV-2 and bat SARS-like strains. It also hypothesizes that pangolins might have been possible intermediate hosts of the infection. Some of the observed AA substitutions in the S-binding protein may serve as possible adaptation mutations in humans but more studies are needed to elucidate their function.

Vaso-occlusive crisis in a sickle cell patient after transfusion-transmitted dengue infection.

CASE REPORT: A 26-year-old woman with sickle cell disease (SCD) on chronic transfusion therapy complained of severe arthralgia, myalgia, abdominal pain, headache, and fever 24 hours after transfusion of a red blood cells (RBCs). Dengue virus (DENV) infection was suspected and the patient was hospitalized for clinical support and RBC transfusion, to lower the hemoglobin S to less than 30%. The patient's clinical condition improved approximately 8 days after the onset of symptoms. RESULTS: DENV type 2 (DENV-2) TaqMan real-time polymerase chain reaction was negative in the patient's pretransfusion sample while the posttransfusion sample was positive (Ct, 27.8), suggesting a high viral load and an acute infection. To investigate DENV transfusion transmission (TT-DENV) the stored donor serum was tested and was also positive (Ct, 25.8). Molecular typing confirmed the presence of DENV-2. The phylogenetic analysis of the DENV-2 strains obtained from both donor and patient samples were classified as the Southeast Asia-American genotype (Genotype III) and demonstrated 100% genomic identity, indicating TT-DENV. CONCLUSION: This is the first description of TT-DENV in a SCD patient. A presumed high viral load in the transfused RBC unit probably determined the early clinical manifestation. In endemic regions dengue fever should be considered as differential diagnosis in SCD patients with fever and acute pain crisis, mainly during DENV outbreaks.

Parvovirus B19 seroprevalence, viral load, and genotype characterization in volunteer blood donors from southern Brazil.

Usually transmitted via respiratory droplets, parvovirus B19 (B19V) can also be acquired by blood transfusion especially because of viral persistence, resistance to blood treatment procedures, and high viral load during the early infection phase. This is particularly problematic in immunocompromised or anemic patients where the infection can have a severe outcome. As B19V DNA was detected in blood donations from South Brazil during a viral metagenomic survey performed by Next-Generation Sequencing, the objective of this retrospective study was to evaluate the seroprevalence, B19V DNA presence and circulating genotypes in a Hospital Blood Transfusion Service in Santa Maria city in South Brazil (Rio Grande do Sul state). Among 480 volunteer blood donors, 53.9% (n = 258 of 479) were anti-B19V IgG-positive, and 9 (1.9%) plasma samples presented B19V DNA. In almost all cases (n = 7 of 9, 77.8%), B19V DNA load was accompanied by the presence of anti-B19V IgG suggesting a persistent infection. The sequencing of the strains demonstrated that all belong to genotype 1 which is the most prevalent worldwide. The analysis of the recipient information of the positive for B19V DNA units revealed no related posttransfusion adverse effects. Our results demonstrate for the first time, B19V seroprevalence, viral load, and genotypes among blood donors from South Brazil and give a light for the circulation and impact of this B19V in this part of the country.

Prevalence of hepatitis E virus infection in multiple transfused Brazilian patients with thalassemia and sickle cell disease.

Hepatitis E virus (HEV) is a leading cause of acute hepatitis worldwide. The virus is acquired by fecal-oral route; however, it can also be transmitted by blood transfusion. The objective of the study was to examine anti-HEV immunoglobulin G and HEV RNA prevalence in multiple transfused patients with thalassemia and sickle cell disease (SCD), and in blood donors. The HEV seroprevalence in the patients was 13% (20% in thalassemics; 7.7% in SCD), and 11% in blood donors. No positive result for HEV RNA was obtained. This is a pioneer study examining HEV circulation in Brazilian patients with hemoglobinopathies.

Zika virus RNA detection in asymptomatic blood donors during an outbreak in the northeast region of São Paulo State, Brazil, 2016.

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 METHODS: Plasma samples obtained between October 2015 and May 2016 from 1393 volunteer blood donors were tested for ZIKV RNA. The viral load was quantified using an in-house standard curve. Additionally, positive ZIKV RNA samples were tested for anti-ZIKV immunoglobulin (Ig)M and anti-ZIKV IgG. RESULTS: Of the 1393 blood samples, ZIKV RNA was detected in 37 (n = 37/1393; 2.7%). The median infection viral load detected was 7714 copies/mL (ranging from 135-124,220 copies/mL). The majority of the positive samples (70.3%) exhibited a viral load of approximately 103 copies/mL. Six samples that were positive for ZIKV RNA were also positive for anti-ZIKV IgM and IgG (n = 6/37; 13.5%). CONCLUSION: This is the first study evaluating the prevalence of ZIKV RNA among Brazilian blood donors, which was relatively high and might lead to TT-ZIKV infection. It is unclear whether the simultaneous presence of anti-ZIKV IgM and IgG in RNA-positive donations or the viral load influences transfusion transmission of the infection. This study also adds to the global understanding of ZIKV prevalence in blood donors during outbreaks and the transfusion impact of the infection.

Epidemiological and Genomic Analysis of Asymptomatic SARS-CoV-2 Infections during the Delta and Omicron Epidemic Waves in São Paulo City, Brazil.

We examined the asymptomatic rates of SARS-CoV-2 infection during the Delta and Omicron waves in the city of São Paulo. Nasopharyngeal swabs were collected at strategic points of the city (open-air markets, bus terminals, airports) for SARS-CoV-2 RNA testing. Applying the questionnaire, the symptomatic individuals were excluded, and only asymptomatic cases were analyzed. During the Delta wave, a total of 4315 samples were collected, whereas 2372 samples were collected during the first Omicron wave. The incidence of the asymptomatic SARS-CoV-2 infection was 0.6% during the Delta wave and 0.8% during the Omicron wave. No statistical differences were found in the threshold amplification cycle. However, there was a statistical difference observed in the sublineage distribution between asymptomatic and symptomatic individuals. Our study determined the incidence of asymptomatic infection by monitoring individuals who remained symptom-free, thereby providing a reliable evaluation of asymptomatic SARS-CoV-2 carriage. Our findings reveal a relatively low proportion of asymptomatic cases, which could be attributed to our rigorous monitoring protocol for the presence of clinical symptoms. Investigating asymptomatic infection rates is crucial to develop and implement effective disease control strategies.

A Multiplex Nanopore Sequencing Approach for the Detection of Multiple Arboviral Species.

The emergence and continued geographic expansion of arboviruses and the growing number of infected people have highlighted the need to develop and improve multiplex methods for rapid and specific detection of pathogens. Sequencing technologies are promising tools that can help in the laboratory diagnosis of conditions that share common symptoms, such as pathologies caused by emerging arboviruses. In this study, we integrated nanopore sequencing and the advantages of reverse transcription polymerase chain reaction (RT-PCR) to develop a multiplex RT-PCR protocol for the detection of Chikungunya virus (CHIKV) and several orthoflaviviruses (such as dengue (Orthoflavivirus dengue), Zika (Orthoflavivirus zikaense), yellow fever (Orthoflavivirus flavi), and West Nile (Orthoflavivirus nilense) viruses) in a single reaction, which provides data for sequence-based differentiation of arbovirus lineages.

Viral metagenomics in blood donations with post-donation illness reports from Brazil.

BACKGROUND: Post-donation illness can be described as appearance of clinical symptoms in blood donors after donation. The consequent call back of the donor to report these symptoms to the blood collection institution is considered a post-donation illness report (PDIR). The most suitable way to examine whether PDIR is related to infection is to apply next-generation sequencing (NGS) and viral metagenomics. Investigation into a PDIR can reveal its importance for transfusion safety and help elaborate strategies for donor education in order to prevent the transfusion transmission of infections which are not routinely tested by the blood collection services. MATERIALS AND METHODS: We applied NGS and viral metagenomics on blood donations which were deferred due to a PDIR. Thirty-three PDIR donations obtained in the Blood Center of Ribeirão Preto, Southeast Brazil, were evaluated. Sequencing was performed using Illumina NextSeq 550 (Illumina Inc, San Diego, CA, USA) equipment and the reads obtained for each sample were analysed by specific bioinformatic pipeline for the classification and discovery of emerging viruses. The identified viral agents by metagenomics were directly confirmed by molecular methods. RESULTS: In all PDIR donations, we found abundant reads of commensal viruses belonging to the Anelloviridae family as well as human pegivirus-1. However, we were also able to identify blood donations positive for clinically important viruses like dengue serotype-2 (DENV-2) of the Asian-American genotype and parvovirus B19 (B19V). Both viruses were also confirmed by real-time polymerase chain reaction, detecting DENV-2 RNA in a significant number of cases (7 samples, 21.2%), compared to B19V which was confirmed in 1 case (3.0%). DISCUSSION: Our study applies for the first time viral metagenomics to evaluate the significance of PDIRs. We confirm the crucial importance of the donor providing a timely PDIR for the prevention of transfusion transmission of viral infections which are not routinely tested in the blood banks worldwide.

Metagenomic identification of human Gemykibivirus-2 (HuGkV-2) in parenterally infected blood donors from the Brazilian Amazon.

OBJECTIVES: To metagenomically analyse blood units originating from the Brazilian Amazon and positive for parenterally transmitted infections (human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-lymphotropic virus (HTLV), Chagas disease or syphilis). METHODS: Twenty plasma samples (35% HBV-positive, 10% HIV-positive, 10% HCV-positive, 20% positive for syphilis, 20% for Chagas disease, and 5% for HTLV) assembled in pools were analysed by metagenomic next-generation sequencing. The obtained raw sequencing data were submitted to a bioinformatic pipeline set up for identification of emerging viruses. The viral reads of interest were phylogenetically analysed and confirmed by PCR in the individual samples. RESULTS: The metagenomic analysis identified contigs belonging to the emerging human Gemykibivirus-2 (HuGkV-2) in two pools. The HuGkV-1 phylogeny demonstrated that the Amazonian isolate formed a separate cluster with other HuGkV-2 strains obtained from human hosts. The PCR confirmation detected HuGkV-1 DNA in three individual samples (15%). CONCLUSIONS: HuGkV-2 is an emerging virus with unknown clinical impact. The detection of HuGkV-2 DNA in blood donations positive for parenterally transmitted infections showed that HuGkV-2 can be considered as an opportunistic viral agent with a hypothetic parenteral transmission route.

Genetic diversity and chemical variability of Lippia spp. (Verbenaceae).

BACKGROUND: The genus Lippia comprises 150 species, most of which have interesting medicinal properties. Lippia sidoides (syn. L. origanoides) exhibits strong antimicrobial activity and is included in the phytotherapy program implemented by the Brazilian Ministry of Health. Since species of Lippia are morphologically very similar, conventional taxonomic methods are sometimes insufficient for the unambiguous identification of plant material that is required for the production of certified phytomedicines. Therefore, genetic and chemical analysis with chemotype identification will contribute to a better characterization of Lippia species. METHODS: Amplified Length Polymorphism and Internal Transcribed Spacer molecular markers were applied to determine the plants' genetic variability, and the chemical variability of Lippia spp. was determined by essential oil composition. RESULTS: Amplified Length Polymorphism markers were efficient in demonstrating the intra and inter-specific genetic variability of the genus and in separating the species L. alba, L. lupulina and L. origanoides into distinct groups. Phylogenetic analysis using Amplified Length Polymorphism and markers produced similar results and confirmed that L. alba and L. lupulina shared a common ancestor that differ from L. origanoides. Carvacrol, endo-fenchol and thymol were the most relevant chemical descriptors. CONCLUSION: Based on the phylogenetic analysis it is proposed that L. grata should be grouped within L. origanoides due to its significant genetic similarity. Although Amplified Length Polymorphism and Internal Transcribed Spacer markers enabled the differentiation of individuals, the genotype selection for the production of certified phytomedicines must also consider the chemotype classification that reflects their real medicinal properties.

Glycoprotein B genotyping of human cytomegalovirus strains isolated from Brazilian patients with sickle cell disease and beta-thalassemia major.

The role of the human cytomegalovirus (HCMV) infection in individuals with hemoglobinopathies is unclear. Our objective was to examine the molecular and genotypic characteristics of HCMV in patients with sickle cell disease, beta-thalassemia major, and volunteer blood donors by viral load quantitation, glycoprotein B (gB) genotyping, and phylogenetic analysis. The patients with sickle cell disease demonstrated the highest HCMV DNA prevalence (13.8%), followed by the patients with beta-thalassemia major (7.6%), and the blood donors (3%). The infection was characterized by a low mean viral load (3.8×10(3) copies/mL), but infections with higher copy numbers were also observed. Genotype gB2 was detected in the majority of cases (90.9%), followed by genotype gB1 (9.1%). No gB3/gB4 genotype was detected. No statistical significance was observed between HCMV DNAemia/gB genotype and hematological alterations or severity of the disease. The high number of sickle cell disease patients with HCMV DNAemia could be due to their partial immune dysfunction (multiple transfusions, spleen dysfunction, hydroxyurea treatment). The extensive HCMV gB2 prevalence in patients with hemoglobinopathies is probably due to HCMV epidemiologic characteristics in the examined region, and can be important during the clinical management of these patients.

Serological and molecular evaluation of parvovirus B19 (B19V) in blood donors from the Blood Center of Brasília, Brazil: focus on women of childbearing age / Avaliação sorológica e molecular do parvovírus B19 (B19V) em doadores de sangue da Fundação Hemocentro de Brasília, Brasil: foco em mulheres em idade fértil

ABSTRACT Parvovirus B19 (B19V) can be transmitted by the respiratory route, vertically - from the mother to the fetus - and via blood transfusion or organ transplantation. Infection by transfusion of blood or blood products occurs due to the resistance of B19V to viral inactivation methods. Our study evaluated the presence of B19V deoxyribonucleic acid (DNA) and the prevalence of anti-B19V class G immunoglobulin (IgG) in women of childbearing age blood donors of the Federal District, Brazil. Our results demonstrated the absence of B19V DNA in these blood donors. However, the seroprevalence for anti-B19V IgG was observed in 60.7% of this population. This study provides important data of B19V circulation in the Center-West of Brazil.

RESUMO O parvovírus B19 (B19V) pode ser transmitido por via respiratória, verticalmente - da mãe para o feto - e via transfusão de sangue e transplante de órgãos. A infecção por transfusão de sangue ou hemoderivados ocorre devido à resistência do B19V aos métodos de inativação viral. Nosso estudo avaliou a presença do ácido desoxirribonucleico (DNA) B19V e a prevalência de imunoglobulina da classe G (IgG) anti-B19V em mulheres em idade fértil, doadoras de sangue do Distrito Federal, Brasil. Nossos resultados demonstraram a ausência de DNA de B19V nesses doadores. No entanto, foi observada a soroprevalência de IgG anti-B19V em 60,7% dessa população. Este estudo fornece dados importantes da circulação do B19V no Centro-Oeste do Brasil.

Human parvovirus B19: general considerations and impact on patients with sickle-cell disease and thalassemia and on blood transfusions.

Human parvovirus B19 (B19V) is a small (22-24 nm) nonenveloped DNA virus belonging to the genus Erythrovirus (family Parvoviridae). Although it generally causes self-limiting conditions in healthy people, B19V infection may have a different outcome in patients with inherited hemolytic anemias. In such high-risk individuals, the high-titer replication may result in bone marrow suppression, triggering a life-threatening drop of hemoglobin values (profound anemia, aplastic crisis). To date there is no consensus concerning a B19V screening program either for the blood donations used in the hemotherapy or for high-risk patients. Moreover, questions such as the molecular mechanisms by which B19V produces latency and persistent replication, the primary site (sites) of B19V infection and B19V immunopathology are far from being known. This review summarizes general aspects of B19V molecular characteristics, pathogenesis and diagnostic approaches with a focus on the role of this pathogen in blood transfusions and in patients with some hemoglobinopathies (sickle-cell disease, thalassemia).