Dataset Information

Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus.

ABSTRACT: Plasma from patients with dengue-like symptoms was collected in 2013 to 2016 from the Brazilian states of Tocantins and Amapa. 781 samples testing negative for IgM against Dengue, Zika, and Chikungunya viruses and for flaviviruses, alphaviruses and enteroviruses RNA using RT-PCRs were analyzed using viral metagenomics. Viral particles-associated nucleic acids were enriched, randomly amplified, and deep sequenced in 102 mini-pools generating over 2 billion reads. Sequence data was analyzed for the presence of known and novel eukaryotic viral reads. Anelloviruses were detected in 80%, human pegivirus 1 in 19%, and parvovirus B19 in 17% of plasma pools. HIV and enteroviruses were detected in two pools each. Previously uncharacterized viral genomes were also identified, and their presence in single plasma samples confirmed by PCR. Chapparvovirus and ambidensovirus genomes, both in the Parvoviridae family, were partially characterized showing 33% and 34% identity in their NS1 sequences to their closest relative. Molecular surveillance using pre-existing plasma from febrile patients provides a readily scalable approach for the detection of novel, potentially emerging, viruses.

SUBMITTER: Fahsbender E

PROVIDER: S-EPMC7058308 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus.

Fahsbender Elizabeth E Charlys da-Costa Antonio A Elise Gill Danielle D Augusto de Padua Milagres Flavio F Brustulin Rafael R Julio Costa Monteiro Fred F Octavio da Silva Rego Marlisson M Soares D'Athaide Ribeiro Edcelha E Cerdeira Sabino Ester E Delwart Eric E

PloS one 20200305 3

Plasma from patients with dengue-like symptoms was collected in 2013 to 2016 from the Brazilian states of Tocantins and Amapa. 781 samples testing negative for IgM against Dengue, Zika, and Chikungunya viruses and for flaviviruses, alphaviruses and enteroviruses RNA using RT-PCRs were analyzed using viral metagenomics. Viral particles-associated nucleic acids were enriched, randomly amplified, and deep sequenced in 102 mini-pools generating over 2 billion reads. Sequence data was analyzed for th ...[more]

PMID: 32134963

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Project description:To conduct a pilot trial of a primary care Symptoms Clinic for patients with medically unexplained symptoms and evaluate recruitment and retention, and acceptability of the intervention and to estimate potential treatment effects for a full trial.Randomised parallel group pilot trial.Primary care in one locality.Primary care database and postal questionnaire were used to identify patients with multiple specialist referrals and multiple physical symptoms unlikely to be explained by disease.General practitioner (GP) with special interest 'Symptoms Clinic' + usual care versus usual care alone. The Symptoms Clinic comprised one long (1 h) and three short (20 min) appointments.Number of patients identified and recruited; acceptability of the intervention (items from Client Satisfaction Questionnaire and interview); Medical Outcomes Survey Short Form 12 (SF-12) physical component summary.Automated blocked randomisation accessed by telephone.None. NUMBERS RANDOMIZED: 16 to intervention and 16 to usual care alone.72 patients, from seven GP practices, had repeated specialist referrals and a Patient Health Questionnaire (PHQ)-15 score of ?10 indicating a high probability of medically unexplained symptoms. 15 were ineligible and 25 declined to participate. NUMBERS ANALYSED: 26 patients; two patients randomised to the intervention group were incorrectly included, three patients in the intervention group and one control did not complete outcome measures.Most patients randomised to the Symptoms Clinic found the intervention acceptable: eight out of 11 reported the intervention helped them to deal with their problems. The mean difference between groups in SF-12 physical component summary, adjusted for baseline, was 3.8 points (SD 6).No observed harms.Patients with multiple medically unexplained symptoms can be systematically identified in primary care; a randomised trial comparing the Symptoms Clinic with usual care is feasible and has the potential to show clinically meaningful benefit.ISRCTN63083469.

Project description:BackgroundHuman parvovirus B19 (B19V) is a common contaminant found in plasma pools and plasma derivatives. Previous studies were mainly focused on limited aspects, further assessment of prevalence of B19V DNA and antibodies in plasma donors, the contamination of B19V in pooled plasma and plasma derivatives should be performed in China.Study design and methodsIndividual plasma donors' samples from four provinces and pooled plasma from four Chinese blood product manufacturers were collected and screened using B19V DNA diagnostic kits between October 2018 and May 2020. The positive samples were investigated for the seroprevalence of B19V antibodies and subjected to sequence analysis and alignment for phylogenetic studies. Moreover, 11 plasma donors who were B19V DNA-positive at their first testing were also followed during the later donation period. Additionally, 400 plasma pools and 20 batches of plasma derivatives produced by pooled plasma with a viral load of B19V DNA exceeding 104IU/mL were also collected and tested for B19V DNA and antibodies.ObjectivesTo comprehensively and systematically determine the frequency and viral load of B19V DNA in plasma donors, pooled plasma, and plasma derivatives from four Chinese blood product manufacturers.ResultsA total of 17,187 plasma donors were analyzed and 44 (0.26%) specimens were found positive for B19V DNA. The quantitative DNA levels ranged from 1.01 × 101 to 5.09 × 1012 IU/mL. Forty-four DNA-positive specimens were also investigated for the seroprevalence of B19V antibodies, 75.0% and 2.3% of which were seropositive for B19V IgG and IgM antibodies, respectively. The phylogenic analyses showed that the prevalent genotypes in the four provinces' plasma donors belonged to B19V Genotype 1. Eleven individual plasma donors who were B19V DNA-positive at the first donation were then followed for a period, and in general, the DNA levels of B19V gradually decreased. Moreover, 64.8% (259/400) of the pooled plasma was contaminated by B19V, with concentrations of 1.05 × 100-3.36 × 109IU/mL. Approximately 72.6% of the DNA-positive plasma pools were only moderately contaminated (<104 IU/mL), while 27.4% contained >104 IU/mL. Twenty batches of plasma derivatives produced by pooled plasma with a viral load of B19V DNA exceeding 104IU/mL were also tested. B19V was detected in 5/5 PCC samples and 5/5 factor VIII samples but was not found in the intravenous immune globulin and albumin samples.ConclusionThe contamination of B19V in pooled plasma and plasma-derived clotting factor concentrates is serious. Whether B19V nucleic acid testing (NAT) screening of plasma and plasma derivatives is launched in China, blood product manufacturers should spontaneously perform B19V NAT screening in plasma donors and mini-pool plasma. These measures can ensure that samples with high titer B19V DNA are discarded in order to prevent and control this transfusion transmitted virus.

Dataset Information

Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus.

Publications

Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus.

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