Rio Negro Virus Infection, Bolivia, 2021.

In May 2021, an agricultural worker originally from Trementinal, Argentina, sought treatment for febrile illness in Tarija, Bolivia, where he resided at the time of illness onset. The patient tested negative for hantavirus RNA, but next-generation sequencing of a serum sample yielded a complete genome for Rio Negro virus.

CRISPR Libraries and Whole-Genome Screening to Identify Essential Factors for Viral Infections.

The CRISPR-Cas9 system has revolutionized genetics and offers a simple and inexpensive way of generating perturbation that results in gene repression, activation, or editing. The advances in this technique make possible the development of CRISPR libraries which consist of a set of sgRNAs to cause perturbations in several genes in the same cell population. The use of libraries raised the CRISPR-Cas9 technique to a genomic scale and provides a powerful approach for identifying previously unknown molecular mechanisms and pathways involved in a specific phenotype or biological process. More specifically, the CRISPRko libraries (set of sgRNAs for gene knockout) and their high-throughput screenings are widely used in research with viral agents, and it was enlarged even more with the COVID-19 pandemic. With this chapter, we aim to point out how this tool helps in understanding virus-host relationships, such as the mechanisms of virus entry into the cell, the essential factors for its replication, and the cellular pathways involved in the response against the pathogen. The chapter also provided some practical considerations for each step of an experimentation using these tools that include choosing the library and screening type, the target cell, the viral strain, the library amplification and guaranteeing its coverage, the strategies for the gene screening pipeline by bioinformatics, and finally, target validation. To conclude, it was presented a table reviewing the last updates in the research for antiviral therapies using CRISPR libraries.

Lactantes febriles menores de tres meses sin foco aparente: ¿es necesario cambiar la estrategia de evaluación?: probamos el step by step / Febrile infants of under three months of age without apparent focus: is it necessary to change the assessment strategy?: we tested the step-by-step approach / Lactentes febris com menos de três meses de idade e sem foco aparente: é necessário alterar a estratégia de avaliação?: tentamos o "passo a passo"

Introducción: la fiebre es un motivo muy frecuente de consulta y hasta en un 20% de los pacientes no se encuentra la causa. En el ámbito de la emergentología pediátrica clásicamente ha existido interés en homogeneizar la forma de evaluar los lactantes febriles menores de tres meses. Contar con un protocolo que permita detectar precozmente el niño que cursa una infección bacteriana invasiva (IBI) sin realizar conductas desproporcionadas es todo un desafío. Objetivo: evaluar y comparar la capacidad para identificar IBI en la pauta actual de fiebre sin foco (FSF) como en la estrategia step by step, en lactantes con FSF valorados en el DEP-CHPR. Material y métodos: estudio observacional, descriptivo, retrospectivo y de pruebas diagnósticas. Criterios de inclusión: lactantes menores de 90 días de vida que consultaron en 2017 y 2018 en DEP-CHPR con diagnóstico de FSF. Resultados: se incluyeron 261 lactantes evaluados con la pauta de FSF actual, en ellos se aplicó la estrategia step by step. El rango de edad fue de 84 días (4-88 días) con una media de 41 días. Sexo masculino 148 niños (56,7%). Se registraron 37 infecciones bacterianas (14,2%) de las cuales 3 fueron IBI (1,1%) y 34 fueron no-IBI (13,1%). La sensibilidad para step by step fue de 0,94% y de 0,89 para la pauta actual, con un VPN de 0,98 para ambas estrategias. Discusión: los lactantes menores de 3 meses son más susceptibles por características fisiológicas a infecciones bacterianas invasivas y cuanto más pequeño aumenta aún más la frecuencia. El step by step discrimina a menores de 1 mes en menores de 21 días y otro grupo de más de 21 días. Nuestra pauta no hace esta discriminación y realiza por igual laboratorio en sangre, orina y líquido cefalorraquídeo; realizando en ocasiones estudios cruentos no necesarios. Conclusiones: ambas estrategias aplicadas en esta población resultaron altamente sensibles para identificar infección bacteriana con un VPN elevado. La aplicación de step by step presenta como beneficio adicional evitar con seguridad la punción lumbar en recién nacidos entre los 21 y 28 días.

Introduction: fever is a very frequent reason for consultation and in up to 20% of patients the cause has not been found. In the field of pediatric emergentology, there has been a traditional interest in homogenizing the way of assessing febrile infants under three months of age. Having a protocol that enables early detection of children with IBIs without engaging in disproportionate procedures is a challenge. Objective: to evaluate and compare the ability to identify IBIs in the present FSF regimen as in the Step-by-Step strategy, in infants with FSF assessed at the Pereira Rossell Pediatric Hospital Center. Material and methods: observational, descriptive, retrospective study and diagnostic tests. Inclusion criteria: Infants under 90 days of age who consulted in 2017 and 2018 at the DEP-CHPR with a diagnosis of FSF. Results: 261 infants diagnosed with FSF regimen were included and they all received a Step-by-Step approach. The age range was 84 days (4 - 88) days with a mean of 41 days. Males 148 children (56.7%). There were 37 bacterial infections (14.2%), of which 3 were IBI (1.1%) and 34 were Non-IBI (13.1%). The sensitivity for the Step-by-Step approach was 0.94% and 0.89 for the current regimen, with a NPV of 0.98 for both strategies. Discussion: infants younger than 3 months-old are more susceptible due to physiological characteristics to invasive bacterial infections, and the younger they are, the higher the frequency. The Step-by-Step Approach splits children of under 1 month of age into those under or over 21 days of age. Our guideline does not make this discrimination and performs the same blood, urine and cerebrospinal fluid laboratory tests sometimes carrying out blood tests is not necessary. Conclusions: both approaches used in this population were highly sensitive to the identification of bacterial infections with a high NPV. The application of the "Step-by-Step" approach has the additional benefit of avoiding lumbar puncture to newborns of between 21 and 28 days of age.

Introdução: a febre é um motivo muito comum de consulta e em até 20% dos pacientes a causa não é encontrada. No campo da emergência pediátrica, tradicionalmente tem havido interesse em homogeneizar a forma de avaliação de lactentes febris menores de três meses de idade. Ter um protocolo que permita a detecção precoce de uma criança com IBI sem realizar procedimentos desproporcionais é um desafio. Objetivo: avaliar e comparar a capacidade de identificação de IBI na atual Diretriz da FSF e na estratégia Passo a Passo, em lactentes com FSF avaliados no DEP-CHPR. Material e métodos: estudo observacional, descritivo, retrospectivo e de testes diagnósticos. Critérios de inclusão: Lactentes com menos de 90 dias de idade que consultaram em 2017 e 2018 no Hospital Pediátrico Pereira Rossell do Uruguai com diagnóstico de FSF. Resultados: Foram incluídos 261 lactentes avaliados com a atual diretriz da FSF, nos quais foi aplicada a estratégia Passo a Passo. A faixa etária foi de 84 dias (4 - 88) dias com média de 41 dias. Sexo masculino 148 crianças (56,7%). Foram registradas 37 infecções bacterianas (14,2%), sendo 3 IBI (1,1%) e 34 Não IBI (13,1%). A sensibilidade para Passo a Passo foi de 0,94% e 0,89 para o esquema atual, com VPN de 0,98 para ambas estratégias. Discussão: crianças menores de 3 meses de idade são mais suscetíveis a infecções bacterianas invasivas devido às características fisiológicas e quanto menores, mais frequentes. O Passo a Passo separa crianças menores de 1 mês em dois grupos: menores de 21 dias e acima de 21 dias. Nossa diretriz não faz essa discriminação e realiza exames laboratoriais de sangue, urina e líquido cefalorraquidiano da mesma forma; às vezes realizando estudos de sangue que não são necessários. Conclusões: ambas as estratégias aplicadas nesta população foram altamente sensíveis para identificar infecção bacteriana com alto VPN. A aplicação do "Passo a Passo" apresenta como benefício adicional evitar a punção lombar em recém-nascidos entre 21 e 28 dias.

Viral Metagenomics for Identification of Emerging Viruses in Transfusion Medicine.

Viral metagenomics has revolutionized our understanding for identification of unknown or poorly characterized viruses. For that reason, metagenomic studies gave been largely applied for virus discovery in a wide variety of clinical samples, including blood specimens. The emerging blood-transmitted virus infections represent important problem for public health, and the emergence of HIV in the 1980s is an example for the vulnerability of Blood Donation systems to such infections. When viral metagenomics is applied to blood samples, it can give a complete overview of the viral nucleic acid abundance, also named "blood virome". Detailed characterization of the blood virome of healthy donors could identify unknown (emerging) viral genomes that might be assumed as hypothetic transfusion threats. However, it is impossible only by application of viral metagenomics to assign that one viral agent could impact blood transfusion. That said, this is a complex issue and will depend on the ability of the infectious agent to cause clinically important infection in blood recipients, the viral stability in blood derivatives and the presence of infectious viruses in blood, making possible its transmission by transfusion. This brief review summarizes information regarding the blood donor virome and some important challenges for use of viral metagenomics in hemotherapy for identification of transfusion-transmitted viruses.

Respiratory virus infections in hospitalized and non-hospitalized children: determinants of severe course of the disease.

INTRODUCTION: Viral respiratory disease constitutes a great burden worldwide mainly among children. OBJECTIVE: One pursued to compare disease characteristics of children who required hospitalization from those who did not require hospitalization due to a viral respiratory disease. METHODOLOGY: Medical and demographic data were collected through questionnaires and nasopharyngeal aspirates were tested for detection of respiratory disease viruses of in and outpatients up to five years old, presenting acute respiratory infection. RESULTS: Respiratory syncytial virus predominated among hospitalized children while other viruses (Human rhinovirus, Influenza virus, Parainfluenza virus, Adenovirus, and Human metapneumovirus) together predominated among non-hospitalized patients. Although children with underlying risk condition required longer hospitalization, previously healthy children presented severe disease and required hospitalization as well. Also, clinical characteristics were not found that may distinguish RSV infected children who had comorbidities from those previously healthy. CONCLUSIONS: Children who were hospitalized due to respiratory distress had well defined characteristics: early age, respiratory syncytial virus infection, bronchiolitis and presence of comorbidity. Nevertheless, rapid respiratory syncytial virus identification among early age children may be of great value in order to avoid medical misconduct, such as unnecessary antibiotic prescription and preventive health care before an eventual clinical worsening encompassing previous health status.

Assessing the Impact of Acute Respiratory Illnesses on the Risk of Subsequent Respiratory Illness.

BACKGROUND: Whether acute respiratory illnesses (ARIs), often associated with virus detection, are associated with lower risk for subsequent ARI remains unclear. We assessed the association between symptomatic ARI and subsequent ARI in young children. METHODS: In a prospective cohort of Peruvian children <3 years, we examined the impact of index ARI on subsequent ARI risk. Index ARI were matched with ≤3 asymptomatic observations and followed over 28 days. We compared risk of subsequent ARI between groups using conditional logistic regression adjusting for several covariates, accounting for repeat observations from individual children. RESULTS: Among 983 index ARI, 339 (34%) had an ARI event during follow-up, compared with 876/2826 (31%) matched asymptomatic observations. We found no significant association of index ARI and subsequent ARI risk during follow-up overall (adjusted odds ratio [aOR], 1.10; 95% confidence interval [CI], .98-1.23) or when limited to index ARI with respiratory viruses detected (aOR, 1.03; 95% CI, .86-1.24). Similarly, when the outcome was limited to ARI in which viruses were detected, no significant association was seen (aOR, 1.05; 95% CI, .87-1.27). CONCLUSIONS: ARIs were not associated with short-term protection against subsequent ARI in these children. Additional longitudinal studies are needed to understand drivers of recurrent ARI in young children.

Relevance of codetection of respiratory viruses in the severity of acute respiratory infection in hospitalized children. / Relevancia de la co-detección de virus respiratorios en la severidad de la infección respiratoria aguda en niños hospitalizados.

INTRODUCTION: Multiplex polymerase chain reaction (PCR) allows simultaneous detection of respiratory viruses, raising questions about their relevance in the clinical feature. OBJECTIVE: To evaluate the contribution of clinical, epidemiological, and virological factors in the clinical course of children hospitalized due to ARI with viral co-detection. PATIENTS AND METHOD: Pediatric patients ≤ 15 years old, hospitalized due to ARI at the UC-CHRISTUS Health Network Clinical Hospital between June and October 2014, and who presented a positive respiratory molecular panel test, were included. Respiratory samples (nasopharyngeal swab, tracheal aspiration, or bronchoalveolar lavage) with positive panel tests by Seeplex® RV15 OneStep ACE Detection Seegene® technique, were analyzed with a second technique (xTAG-RVP-FASTv2 Luminex®, USA), which allows simultaneous and semi-quantitative detection of 17 respiratory viruses. Clinical and epidemiological records were collected. RESULTS: One virus was identified in 42/57 children (74%) and two or more in 15/57 (26%). Intensive care unit (ICU) hospi talization was significantly more frequent in patients with viral co-detection (OR = 5,5; IC 95%: 1,5 19,6). The most frequently detected viruses were rhinovirus/enterovirus (HRV/EV) (29%) and res piratory syncytial virus (RSV) (25%), and the most common co-detection was HRV/EV-RSV (33%). In x-rays, patients with HRV/EV infection presented interstitial images more frequently, while RSV was associated with condensations (p = 0.002). For HRV/EV, median fluorescence intensity (MFI, semi-quantification) were 1788 and 2456 in co-detection and single agent, respectively (p = 0.022). Children with HRV/EV co-detection had a longer hospital stay compared to isolated identification (5 versus 3 days, p = 0,028). CONCLUSION: In children hospitalized due to ARI, viral co-detection is frequent and associated with more ICU hospitalizations. Our study highlights the presence of HRV/ EV in viral co-detection and longer length of stay. More studies are needed to define the relevance of viral co-detection in hospitalized pediatric patients.

Infecções virais na prática odontológica: riscos e prevenção / Viral infections in dental practice: risks and prevention

Objetivo: revisar a literatura sobre as principais patologias virais associadas à área odontológica, tais como varicela, herpes zoster, sarampo, mononucleose infecciosa, síndrome da imunodeficiência adquirida (Aids), hepatites virais e infecções associadas ao herpes-vírus simples (HSV) e ao papilomavírus humano (HPV), com o intuito de descrever as manifestações orais relacionadas a essas patologias e informar e esclarecer aos profissionais da área odontológica os riscos e os cuidados durante a prática clínica. Métodos: foi realizada uma busca nas bases de dados Google Acadêmico, SciELO, LILACS e PubMed sobre o tema infecções virais na prática odontológica. Foram incluídos nesta revisão 31 artigos, publicados no período de 2000 a 2020. Também foram utilizados como fonte bibliográfica 4 livros que abordavam o assunto em questão. Revisão de literatura: o consultório odontológico é um local propício à propagação de agentes biológicos patógenos causadores de infecção, nos quais se incluem os vírus. O profissional da área deve adotar medidas de biossegurança para evitar possíveis infecções. As precauções universais eficazes na redução do risco ocupacional baseiam-se no uso de equipamentos de proteção individual (EPIs), na prevenção da exposição a sangue e fluidos corpóreos, na prevenção de acidentes com instrumentos perfurocortantes e no descarte adequado dos resíduos contaminados. Considerações finais: as infecções virais representam um assunto relevante para o odontólogo, pois, além de serem transmissíveis por vários meios, também apresentam manifestações orais. Dessa forma, o cirurgião-dentista deve ter conhecimento suficiente sobre o tema para nortear a sua conduta clínica.(AU)

Objective: the present study aims to review the literature regarding the main viral pathologies associated with the dental field, such as chickenpox, herpes zoster, measles, infectious mononucleosis, acquired immunodeficiency syndrome (AIDS), viral hepatitis, and infections associated with herpes simplex virus (HSV) and human papillomavirus (HPV), in order to describe the oral manifestations related to these pathologies, and inform and clarify to the dental professionals the risks and care during clinical practice. Methods: a search was performed using Google Scholar, SciELO, LILACS and PubMed databases on the topic of viral infections in dental practice. This review included 31 articles, published from 2000 to 2020. Four books on the subject were also used as a bibliographic source. Literature review: the dental office is a place susceptible to the spread of pathogenic biological agents that cause infection, including viruses. The professional must adopt biosafety measures to avoid possible infections. Universal precautions that are effective in reducing occupational risk are based on the use of personal protective equipment (PPE), the prevention of exposure to blood and bodily fluids, the prevention of accidents with sharps, and the proper disposal of contaminated waste. Final considerations: viral infections represent a relevant issue for the dentist, because in addition to being transmissible through various means, they also present oral manifestations. Thus, the dentist must have sufficient knowledge on the subject to guide his clinical conduct.(AU)

Impact of the use of multiplex PCR on etiological diagnosis and treatment of acute respiratory infections in a private hospital of the north of the country.

BACKGROUND AND OBJECTIVE: Diseases of the respiratory system represent one of the leading causes of medical care and antibiotic prescriptions. Currently, new technologies are used for the diagnosis of respiratory diseases of viral origin, such as the FilmArray Respiratory Panel®, approved in 2012 by the FDA. The purpose of this study was to identify the correlation between the diagnosis and treatment of respiratory tract infections and the result of the polymerase chain reaction test for respiratory viruses. MATERIAL AND METHODS: The study is of a retrospective, cross-sectional, descriptive type. One-hundred and thirty-four patients who underwent a viral panel for respiratory viruses, which was positive for one or more viruses, were included. For all cases, the positive results of said test and the treatment received by patients were analyzed. RESULTS: Of the patients who underwent nasopharyngeal aspirate during hospitalization, 58 % received antibiotic treatment at admission, 13 % received combined treatment (antibiotic + antiviral), 27 % of the patients received symptomatic treatment since admission and 2 % did it with antivirals. After receiving a positive result for respiratory viruses, 38 % continued with antibiotics, 30 % with antibiotics and antivirals, 13.8 % were managed only with antivirals and 18.2 % with symptomatic treatment. CONCLUSION: Despite the global alert regarding antimicrobial resistance, patients continue to be treated with antibiotics, due to a situation that we ignore, but that is believed to be influenced by several factors.

ANTECEDENTES Y OBJETIVO: Las enfermedades del sistema respiratorio son causa frecuente de prescripción de antibióticos. Actualmente se emplean nuevas tecnologías para su diagnóstico como el FilmArray Respiratory Panel. El objetivo de este estudio es identificar la correlación entre el diagnóstico y tratamiento de infecciones de vías respiratorias con el resultado de PCR para virus respiratorios. MATERIAL Y MÉTODOS: Estudio descriptivo, transversal, retrospectivo, se incluyeron 134 pacientes atendidos en el Hospital Christus Muguerza en Saltillo, Coahuila. Para todos los casos se analizaron los resultados del panel y el tratamiento que recibieron los pacientes. RESULTADOS: El 58 % recibió tratamiento antibiótico a su ingreso, el 13 % tratamiento combinado (antibiótico + antiviral), 27 % recibió tratamiento sintomático y el 2 % fue tratado con antiviral de primera instancia. Posterior al resultado el 38 % continuó con antibiótico, el 30 % con antibiótico y antiviral, 13.8 % se manejó con antiviral y el 18.2 % con tratamiento sintomático. CONCLUSIÓN: A pesar de la alerta mundial por la resistencia a los antimicrobianos se sigue tratando a los pacientes con antibióticos, por una situación que se cree está influenciada por varios factores.

The impact of viral infections on childhood central nervous system infections.

BACKGROUND: Viruses are a common cause of central nervous system (CNS) infections. However, studies of CNS viral pathogens in pediatric patients are poorly explored because viral infections are often erroneously diagnosed as bacterial infections. METHODS: 299 CNS samples were collected from pediatric patients aged from one month to 14 years old. A total of 140 viral meningitis cases that met the inclusion criteria were included in this study. In 38 of the 140 cerebral spinal fluid (CSF) samples (27.1%), conventional and real-time PCR were used to identify viruses commonly associated with CNS infections. RESULTS: Among them, 23 patients (16.5%) tested positive for flaviviruses such as dengue, Zika, and yellow fever virus, eight patients (5.7%) were positive for enterovirus (ENTV), and six patients (4.3%) were positive for human herpesvirus 1/2. We also identified one case of dengue virus and ENTV co-infection. CONCLUSIONS: A correlation between clinical symptoms and laboratory findings for the viruses was identified. Our study also reinforces the importance of including viruses in the laboratory diagnosis of CNS infections especially flaviviruses, which assists public health authorities in implementing early interventions.

Rapid multiplex PCR assays in patients with respiratory viral infections: is semi-quantitative data useful? A pilot study.

Viral respiratory rapid multiplex PCR assays FilmArray® (FA) and ePlex® (eP) provide qualitative results which may not reflect clinical relevance. In a pilot study, we report retrospectively whether the semi-quantitative PCR assay R-GENE® would have facilitated clinical interpretation. Forty-four patients were hospitalized for various respiratory manifestations; all of them have benefited from a respiratory sample during acute symptoms. Among the 44 patients, FA detected 23 positive samples including 31 viruses, 26 of them gave high or moderate R-GENE® scores (cycle threshold < 35), and all but one were consistent with clinical history. Semi-quantitative scores would have allowed for critical interpretation of the results; those are a key additional element for an optimal exploitation of the rapid multiplex PCR assays power.

Impacto del uso de PCR múltiple en diagnóstico etiológico y tratamiento de infecciones respiratorias agudas en un hospital privado del norte del país / Impact of the use of multiplex PCR on etiological diagnosis and treatment of acute respiratory infections in a private hospital of the north of the country

Resumen Antecedentes y objetivo: Las enfermedades del sistema respiratorio son causa frecuente de prescripción de antibióticos. Actualmente se emplean nuevas tecnologías para su diagnóstico como el FilmArray Respiratory Panel. El objetivo de este estudio es identificar la correlación entre el diagnóstico y tratamiento de infecciones de vías respiratorias con el resultado de PCR para virus respiratorios. Material y métodos: Estudio descriptivo, transversal, retrospectivo, se incluyeron 134 pacientes atendidos en el Hospital Christus Muguerza en Saltillo, Coahuila. Para todos los casos se analizaron los resultados del panel y el tratamiento que recibieron los pacientes. Resultados: El 58 % recibió tratamiento antibiótico a su ingreso, el 13 % tratamiento combinado (antibiótico + antiviral), 27 % recibió tratamiento sintomático y el 2 % fue tratado con antiviral de primera instancia. Posterior al resultado el 38 % continuó con antibiótico, el 30 % con antibiótico y antiviral, 13.8 % se manejó con antiviral y el 18.2 % con tratamiento sintomático. Conclusión: A pesar de la alerta mundial por la resistencia a los antimicrobianos se sigue tratando a los pacientes con antibióticos, por una situación que se cree está influenciada por varios factores.

Abstract Background and objective: Respiratory system diseases represent one of the leading cause of prescription of antibiotics. At present, new technologies for the diagnosis are being used, including the FilmArray Respiratory Panel. The objective was to identify the correlation between the diagnosis and treatment of respiratory tract infections with the result of PCR for respiratory viruses. Material and methods: Descriptive, cross-sectional, restrospective study. 134 patients were included treated at the Christus Muguerza Hospital in Saltillo, Coahuila. For all cases, the positive results of this test and the treatment patients received were analyzed. Results: 58 % received antibiotic treatment at admission, 13 % received combined treatment (antibiotic + antiviral), 27 % received symptomatic treatment since their admission and 2 % whit antiviral. After receiving a positive result for respiratory viruses, 38 % continued with antibiotics, 30 % with antibiotics and antivirals, 13.8 % only managed with antivirals and 18.2% with symptomatic treatment. Conclusion: Although we are currently on global alert for resistance to antibiotics, there is a lack of awareness about the prescription of antibiotics, due to a situation which is believed to be influenced by several factors.

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.

Infecciones respiratorias virales en episodios de fiebre en niños con trasplante de precursores hematopoyéticos / Respiratory viral infections during episodes of fever in children undergoing hematopoietic stem cell transplantation

Resumen Introducción: Los niños que reciben trasplante de precursores hematopoyéticos (TPH) pueden presentar infecciones respiratorias virales (IRV) durante episodios febriles. Los datos sobre su evolución clínica son escasos, así como la comparación de ellos con infecciones bacterianas (IB). Objetivo: Caracterizar la evolución clínica de pacientes con IRV, en comparación con IB en niños con TPH, cursando un episodio febril. Método: Estudio prospectivo en pacientes ≤ 18 años con cáncer y TPH ingresados por fiebre en el Hospital Luis Calvo Mackenna (2016-2019). Se realizó evaluación clínica y de laboratorio: hemocultivos, RPC para patógenos respiratorios (Filmarray®), cuantificación viral y medición de citoquinas en muestra nasal (Luminex®, 38 citoquinas). Se compararon los grupos IRV, IB y los de etiología no precisada (ENP) en relación con: infección respiratoria aguda (IRA), citoquinas nasales, ingreso a UCI, necesidad de ventilación mecánica, mortalidad y suspensión de antimicrobianos. Resultados: De 56 episodios febriles, 35 fueron IRV, 12 IB y 9 de ENP. Mediana de edad fue 8,5 años, 62% masculino. Un 94% de los casos IRV presentó IRA sintomática, versus 33% en los grupos IB y ENP (p < 0,001), con IRA baja en 69% de las IRV (p < 0,001). Rinovirus (54%) y coronavirus (15%) fueron las etiologías más frecuentemente detectadas. No hubo diferencias en citoquinas nasales entre los grupos IRV e IB. Ingreso a UCI: 11% del grupo IRV, 17% de IB y 11% de ENP (p = 0,88). Requirieron ventilación mecánica sólo 2 pacientes (p = 0,37) sin fallecimiento. Tras la detección viral respiratoria por RPC, se suspendió antimicrobianos en 26% de los casos con IRV (p = 0,04). Conclusión: Las IRV son frecuentes en niños con TPH y episodios febriles. La detección viral podría optimizar y racionalizar el uso de antimicrobianos en esta población.

Abstract Background: Children undergoing hematopoietic stem cell transplant (HSCT) can develop respiratory viral infections (RVI) during fever episodes. There are few data about clinical outcomes in RVI and compared to bacterial infections (BI) in this population. Aim: To determine clinical outcome of RVI, compared to BI in children with HSCT. Methods: Prospective study, patients ≤ 18 years with cancer and HSCT admitted with fever at a National Bone Marrow Transplant Center (Hospital Calvo Mackenna), Chile, (April-2016 to May-2019). Clinical assessment, laboratory tests, blood cultures, nasopharyngeal sample for multiplex-PCR (Filmarray®), viral loads by PCR and cytokine panel (Luminex®, 38 cytokines) were performed. The following outcomes were evaluated: upper/lower respiratory tract disease (RTD), admission to ICU, mechanical ventilation, mortality and antimicrobial withdrawal. Results: Of 56 febrile episodes, 35 (63%) were RVI, 12 (21%) BI and 9 (16%) with unknown etiology (UE). Median of age was 8.5 years, 62% male gender. Rhinovirus (54%) and coronavirus (15%) were the more frequent detected viruses. No significant differences in cytokine levels were observed between RVI and BI. 94% of RVI patients had symptomatic RTD, versus 33% in BI and 33% in UE group (p < 0.001), with lower-RTD in 69% of RVI group (p < 0,001). Admission to ICU was 11% in RVI, 17% in BI and 11% in UE group (p = 0.88); only 2 patients required mechanical ventilation (p = 0.37) and no mortality was reported. After an RVI was detected by PCR, antimicrobials were withdrawal in 26% of patients with RVI (p: 0.04). Conclusion: RVI are frequent etiologic agents in febrile episodes of patients with HSCT. Viral detection might help to rationalize the use of antimicrobials in this population.

[Respiratory viral infections during episodes of fever in children undergoing hematopoietic stem cell transplantation]. / Infecciones respiratorias virales en episodios de fiebre en niños con trasplante de precursores hematopoyéticos.

BACKGROUND: Children undergoing hematopoietic stem cell transplant (HSCT) can develop respiratory viral infections (RVI) during fever episodes. There are few data about clinical outcomes in RVI and compared to bacterial infections (BI) in this population. AIM: To determine clinical outcome of RVI, compared to BI in children with HSCT. METHODS: Prospective study, patients ≤ 18 years with cancer and HSCT admitted with fever at a National Bone Marrow Transplant Center (Hospital Calvo Mackenna), Chile, (April-2016 to May-2019). Clinical assessment, laboratory tests, blood cultures, nasopharyngeal sample for multiplex-PCR (Filmarray®), viral loads by PCR and cytokine panel (Luminex®, 38 cytokines) were performed. The following outcomes were evaluated: upper/lower respiratory tract disease (RTD), admission to ICU, mechanical ventilation, mortality and antimicrobial withdrawal. RESULTS: Of 56 febrile episodes, 35 (63%) were RVI, 12 (21%) BI and 9 (16%) with unknown etiology (UE). Median of age was 8.5 years, 62% male gender. Rhinovirus (54%) and coronavirus (15%) were the more frequent detected viruses. No significant differences in cytokine levels were observed between RVI and BI. 94% of RVI patients had symptomatic RTD, versus 33% in BI and 33% in UE group (p < 0.001), with lower-RTD in 69% of RVI group (p < 0,001). Admission to ICU was 11% in RVI, 17% in BI and 11% in UE group (p = 0.88); only 2 patients required mechanical ventilation (p = 0.37) and no mortality was reported. After an RVI was detected by PCR, antimicrobials were withdrawal in 26% of patients with RVI (p: 0.04). CONCLUSION: RVI are frequent etiologic agents in febrile episodes of patients with HSCT. Viral detection might help to rationalize the use of antimicrobials in this population.

Causes of equine abortion, stillbirth, and perinatal mortality in Brazil / Causas de abortamento, natimortalidade e mortalidade em equinos no Brasil

Abortion and complications in reproduction are important causes of economic loss in horse breeding. Studies of its causal agents can help to identify the primary pathogens or other factors involved and define appropriate measures to reduce its occurrence. This research aimed to investigate the primary causes of equine abortion, stillbirth, and perinatal mortality in regions of Brazil. Tissue from aborted fetuses, stillbirths, neonates and foals submitted to the Biological Institute of São Paulo, Brazil, from January 2010 to July 2013 were processed for viral and bacterial isolation, polymerase chain reaction (PCR), histology, and immunohistochemistry. Bacterial infection was the primary detected cause of abortion, found in 16 of the 53 animals submitted for bacterial analysis followed by viruses analysis in 2 of 105 animals, and noninfectious causes (neonatal isoerythrolysis) in 2 of 105 animals. Fungi were found in a single sample of 53 tested. The most frequent bacteria recovered were Escherichia coli, Enterobacter aerogenes, combined E. coli and Streptococcus spp., Staphylococcus spp., and Bacillus spp. The following agents were each observed in a single sample: Arcanobacterium pyogenes, Streptococcus spp., Corynebacterium spp., Actinobacillus spp., and Rhodococcus equi. The predominant identification of fecal and other opportunistic bacteria as opposed to pathogens commonly associated with equine abortion, such as Leptospira spp. and equine herpesvirus type 1 (EHV-1), suggests the need of improving hygiene management of breeding mares to prevent bacterial infection that may cause fetal loss, stillbirth, and perinatal mortality.(AU)

Abortamento e complicações na reprodução são importantes causas de perda econômica na equideocultura. Estudos dos agentes causais podem ajudar a identificar patógenos ou outros fatores envolvidos e definir medidas apropriadas para reduzir sua ocorrência. Esta pesquisa investigou as causas primárias de aborto, natimortalidade e mortalidade perinatal em equinos de diversas regiões do Brasil. Tecidos de fetos abortados, natimortos e potros submetidos ao Instituto Biológico de São Paulo, Brasil, no período de janeiro de 2010 a julho de 2013, foram processados por meio de técnicas de isolamento viral e bacteriano, PCR, histologia e imuno-histoquímica. Infecção bacteriana foi a causa mais detectada, encontrada em 16 de 53 amostras submetidas à análise bacteriana, seguida de causa viral em 2 de 105 amostras, e causas não infecciosas (isoeritrólise neonatal) em 2 de 105 amostras. Fungo foi encontrado em uma única amostra de 53 testadas. As bactérias isoladas mais frequentemente foram Escherichia coli, Enterobacter aerogenes, E. coli associada a Streptococcus spp., Staphylococcus spp. associado a Bacillus spp. Os seguintes agentes foram observados em uma única amostra cada: Arcanobacterium pyogenes, Streptococcus spp., Corynebacterium spp., Actinobacillus spp. e Rhodococcus equi. A identificação predominante de bactérias fecais e outras bactérias oportunistas, ao invés de outros patógenos comumente associados a quadros de abortamento equino, tais como Leptospira spp. e Herpesvírus equino tipo 1, sugere a necessidade de maior atenção no manejo higiênico das éguas em reprodução, a fim de prevenir infecções bacterianas que possam causar perda fetal, natimortalidade e mortalidade perinatal.(AU)

Existence of a Conserved Quantity and Stability of In Vitro Virus Infection Dynamics Models with Absorption Effect.

The estimation of parameters in biomathematical models is useful to characterize quantitatively the dynamics of biological processes. In this paper, we consider some systems of ordinary differential equations (ODEs) modelling the viral dynamics in a cell culture. These models incorporate the loss of viral particles due to the absorption into target cells. We estimated the parameters of models by least-squares minimization between numerical solution of the system and experimental data of cell cultures. We derived a first integral or conserved quantity, and we proved the use of experimental data in order to test the conservation law. The systems have nonhyperbolic equilibrium points, and the conditions for their stability are obtained by using a Lyapunov function. We complemented these theoretical results with some numerical simulations.

Alternative PCR primers for genotyping of Brazilian WSSV isolates.

White spot syndrome virus (WSSV) is one of the major challenges faced by global shrimp farming in recent decades. The characterization of WSSV genetic variability has been used to determine viral dispersion and is a promising method to determine the association between genotype and virulence. The major variable regions that have been used as markers to differentiate the WSSV genomes include the VNTR loci inside ORF94, ORF75, ORF125, and insertions/deletions interspersing ORF14/15 and ORF23/24. The primers used to amplify these regions were described at least 10 years ago, but some of them do not work efficiently to identify new WSSV variants. The objective of this work was to develop improved PCR primers for WSSV genotyping based on sequence alignments that include new sequences described in recent years. We validated these new primers in a pilot study to verify the genetic variability of the WSSV in Rio Grande do Norte state (northeast Brazil), and efficiency was compared to that of other previously described primers. We confirmed that the primers we developed were more efficient for genotype Brazilian WSSV isolates, enabling us to genotype a larger number of samples. In addition, our results also introduce new data about the genetic characterization of the WSSV isolates that occur in the northeastern region of Brazil.

"Differential risk of hospitalization among single virus infections causing influenza-like illnesses".

BACKGROUND: Acute respiratory infections are a major cause of morbidity in children and are often caused by viruses. However, the relative severity of illness associated with different viruses is unclear. The objective of this study was to evaluate the risk of hospitalization from different viruses in children presenting with an influenza-like illness (ILI). METHODS: Data from children 5 years old or younger participating in an ILI natural history study from April 2010 to March 2014 was analyzed. The adjusted odds ratio for hospitalization was estimated in children with infections caused by respiratory syncytial virus (RSV), metapneumovirus, bocavirus, parainfluenza viruses, rhinovirus/enterovirus, coronavirus, adenovirus, and influenza. RESULTS: A total of 1486 children (408 outpatients and 1078 inpatients) were included in this analysis. At least one virus was detected in 1227 (82.6%) patients. The most frequent viruses detected as single pathogens were RSV (n = 286), rhinovirus/enterovirus (n = 251), parainfluenza viruses (n = 104), and influenza A or B (n = 99). After controlling for potential confounders (age, sex, recruitment site, days from symptom onset to enrollment, and underlying illnesses), children with RSV and metapneumovirus infections showed a greater likelihood of hospitalization than those infected by parainfluenza viruses (OR 2.7 and 1.9, respectively), rhinovirus/enterovirus (OR 3.1 and 2.1, respectively), coronaviruses (OR 4.9 and 3.4, respectively), adenovirus (OR 4.6 and 3.2, respectively), and influenza (OR 6.3 and 4.4, respectively). CONCLUSIONS: Children presenting with ILI caused by RSV and metapneumovirus were at greatest risk for hospitalization, while children with rhinovirus/enterovirus, parainfluenza, coronavirus, adenovirus, and influenza were at lower risk of hospitalization.

Implications of bovine viral diseases for udder health / As implicações das doenças virais para a saúde da glândula mamária bovina

Several factors can affect bovine mammary gland health and although bacterial mastitis is the most studied and reported cause, viral infections may also have negative effects on bovine udder health. Viral infections can indirectly damage the papillary duct of the teat, and induce or exacerbate signs of bovine mastitis due to viral-induced immunosuppressive effects that may lead to a greater susceptibility to bacterial mastitis and even intensify the severity of established bacterial infections. Some viruses (Bovine alphaherpesvirus2, cowpox, pseudocowpox, foot-and-mouth disease, vesicular stomatitis and papillomavirus) affect the integrity of the udder skin, leading to teat lesions, favoring the entry of mastitis-causing pathogens. It is therefore possible that the association between mastitis and viruses is underestimated and may, for example, be associated with negative bacterial culture results. Few milk samples are tested for the presence of viruses, mainly because of the more laborious and expensive procedures required. Furthermore, samples for virus testing would require specific procedures in terms of collection, handling and storage. Thus, there is a knowledge gap in regard to the actual impact of viruses on bovine udder health. Despite the fact that serum anti-virus antibodies can be detected, there is not enough evidence to confirm or exclude the effect of viruses on udder health. However, any expectation of milk production from healthy animals should consider the possible impact of viral infections in mastitis development and not underestimate the importance of actions to diagnose and control the disease. Therefore, the purpose of this review is to describe the association of diagnosis and control of viral diseases and their effect on bovine udder health.(AU)

Diversos fatores podem afetar a saúde da glândula mamária bovina e embora a mastite bacteriana seja a causa mais estudada e relatada, as infecções virais também podem ter efeitos negativos sobre a saúde da glândula mamária bovina. De forma indireta as infecções virais podem danificar o ducto papilar do teto ou ainda, induzir ou agravar a mastite bovina, devido aos seus efeitos imunossupressores que podem levar a uma maior susceptibilidade para casos de mastite bacteriana e até mesmo intensificar a severidade das infecções bacterianas já estabelecidas. Alguns vírus (Alphaherpesvirus bovino 2, cowpox, pseudocowpox, febre aftosa, estomatite vesicular e papilomavírus) afetam a integridade da pele do úbere, levando a lesões no teto, favorecendo a entrada de patógenos causadores de mastite. Portanto é possível que a associação entre mastites e viroses seja subestimada e podem, por exemplo, estar associada às amostras de diagnóstico de mastite bacteriana com resultados de cultura bacteriana negativa. Além disso, as amostras de leite de vacas com mastite não são coletadas, tratadas e armazenadas adequadamente para pesquisa de vírus que requer cuidados específicos, além de um diagnóstico mais trabalhoso e caro. Desse modo, há lacunas a serem preenchidas quanto ao real impacto das viroses sobre a saúde da glândula mamária bovina. Apesar da possibilidade de detecção de anticorpos séricos contra os vírus, não existem evidências suficientes para incluir ou excluir os efeitos das viroses a saúde da glândula mamária bovina. Porém, a expectativa de produção de leite por meio de animais saudáveis deve considerar os possíveis impactos das infecções virais no desenvolvimento de mastites, não se pode, portanto, subestimar a importância de ações para o diagnóstico e controle das mesmas. Sendo assim, o propósito desta revisão é descrever as relações entre o diagnóstico de controle das doenças virais e seus potenciais impactos sobre a saúde da glândula mamária bovina.(AU)