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1.
Viruses ; 13(2)2021 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-33530573

RESUMEN

Sapovirus is a common cause of acute gastroenteritis in all age groups. Sapovirus infections are seldom investigated in Spain, and its epidemiology in the country is not well known. The use of molecular diagnostic procedures has allowed a more frequent detection of sapoviruses in patients with diarrhea. A total of 2545 stool samples from patients with acute gastroenteritis attended from June 2018 to February 2020 at the Clinic University Hospital in Valencia, Spain, were analyzed by reverse transcription (RT) and real-time multiplex PCR (RT-PCR) to investigate the etiology of enteric infections. Sapovirus was the second enteric virus detected with a positive rate of 8%, behind norovirus (12.2%) and ahead of rotavirus (7.1%), astrovirus (4.9%) and enteric adenoviruses (2.9%). Most sapovirus infections occurred in infants and young children under 3 years of age (74%) with the highest prevalence in autumn and early winter. Coinfections were found in 25% of the patients with sapovirus diarrhea, mainly with other enteric viruses. Genotyping demonstrated the circulation of seven different genotypes during the study period, with a predominance of genotypes GI.1, GI.2, and GII.1. Phylogenetic analysis showed that genogroup GII strains form a cluster separated from genogroup GI and GV, being genotype GV.1 strains related to genotype GI.1 and GI.2 strains.


Asunto(s)
Infecciones por Caliciviridae/epidemiología , Infecciones por Caliciviridae/virología , Gastroenteritis/epidemiología , Gastroenteritis/virología , Sapovirus/genética , Factores de Edad , Infecciones por Caliciviridae/diagnóstico , Coinfección/epidemiología , Coinfección/microbiología , Coinfección/virología , Diarrea/diagnóstico , Diarrea/epidemiología , Diarrea/virología , Femenino , Gastroenteritis/diagnóstico , Variación Genética , Genotipo , Humanos , Masculino , Epidemiología Molecular , Reacción en Cadena de la Polimerasa Multiplex , Filogenia , Prevalencia , ARN Viral/genética , Sapovirus/clasificación , Sapovirus/aislamiento & purificación , Estaciones del Año , España/epidemiología
2.
mBio ; 12(1)2021 02 16.
Artículo en Inglés | MEDLINE | ID: mdl-33593982

RESUMEN

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is leading to public health crises worldwide. An understanding of the pathogenesis and the development of treatment strategies is of high interest. Recently, neutrophil extracellular traps (NETs) have been identified as a potential driver of severe SARS-CoV-2 infections in humans. NETs are extracellular DNA fibers released by neutrophils after contact with various stimuli and accumulate antimicrobial substances or host defense peptides. When massively released, NETs are described to contribute to immunothrombosis in acute respiratory distress syndrome and in vascular occlusions. Based on the increasing evidence that NETs contribute to severe COVID-19 cases, DNase treatment of COVID-19 patients to degrade NETs is widely discussed as a potential therapeutic strategy. Here, we discuss potential detrimental effects of NETs and their nuclease degradation, since NET fragments can boost certain bacterial coinfections and thereby increase the severity of the disease.


Asunto(s)
/metabolismo , Coinfección/metabolismo , Trampas Extracelulares/metabolismo , Neutrófilos/metabolismo , Infecciones Bacterianas/metabolismo , Coinfección/microbiología , Coinfección/virología , Humanos
3.
Sci Rep ; 11(1): 3209, 2021 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-33547380

RESUMEN

Viral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed PACIFIC, a deep-learning algorithm that accurately detects SARS-CoV-2 and other common RNA respiratory viruses from RNA-seq data. Using in silico data, PACIFIC recovers the presence and relative concentrations of viruses with > 99% precision and recall. PACIFIC accurately detects SARS-CoV-2 and other viral infections in 63 independent in vitro cell culture and patient datasets. PACIFIC is an end-to-end tool that enables the systematic monitoring of viral infections in the current global pandemic.


Asunto(s)
/diagnóstico , Coinfección/diagnóstico , Aprendizaje Profundo , Infecciones por Virus ARN/diagnóstico , Virus ARN/aislamiento & purificación , /aislamiento & purificación , Coinfección/virología , Coronaviridae/aislamiento & purificación , Humanos , Metapneumovirus/clasificación , Metapneumovirus/aislamiento & purificación , Redes Neurales de la Computación , Orthomyxoviridae/clasificación , Orthomyxoviridae/aislamiento & purificación , Infecciones por Virus ARN/virología , Virus ARN/clasificación , RNA-Seq , Rhinovirus/clasificación , Rhinovirus/aislamiento & purificación , Sensibilidad y Especificidad
4.
Sci Rep ; 11(1): 3934, 2021 02 16.
Artículo en Inglés | MEDLINE | ID: mdl-33594223

RESUMEN

Accumulating evidence supports the high prevalence of co-infections among Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients, and their potential to worsen the clinical outcome of COVID-19. However, there are few data on Southern Hemisphere populations, and most studies to date have investigated a narrow spectrum of viruses using targeted qRT-PCR. Here we assessed respiratory viral co-infections among SARS-CoV-2 patients in Australia, through respiratory virome characterization. Nasopharyngeal swabs of 92 SARS-CoV-2-positive cases were sequenced using pan-viral hybrid-capture and the Twist Respiratory Virus Panel. In total, 8% of cases were co-infected, with rhinovirus (6%) or influenzavirus (2%). Twist capture also achieved near-complete sequencing (> 90% coverage, > tenfold depth) of the SARS-CoV-2 genome in 95% of specimens with Ct < 30. Our results highlight the importance of assessing all pathogens in symptomatic patients, and the dual-functionality of Twist hybrid-capture, for SARS-CoV-2 whole-genome sequencing without amplicon generation and the simultaneous identification of viral co-infections with ease.


Asunto(s)
/diagnóstico , Coinfección/diagnóstico , Coinfección/virología , Análisis de Secuencia de ADN , /genética , Australia/epidemiología , Coinfección/epidemiología , Biología Computacional , Genoma Viral , Humanos , Sistemas de Lectura Abierta/genética , Reproducibilidad de los Resultados , Secuenciación Completa del Genoma
5.
mSphere ; 6(1)2021 02 10.
Artículo en Inglés | MEDLINE | ID: mdl-33568452

RESUMEN

Compared to other human coronaviruses, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) are relatively understudied. We report a fatal case of COVID-19 pneumonia coinfected with HCoV-229E in Hong Kong. Genome sequencing of SARS-CoV-2 and HCoV-229E from a nasopharyngeal sample of the patient showed that the SARS-CoV-2 strain HK13 was most closely related to SARS-CoV-2 type strain Wuhan-Hu-1 (99.99% nucleotide identity), compatible with his recent history of travel to Wuhan. The HCoV-229E strain HK20-42 was most closely related to HCoV-229E strain SC0865 from the United States (99.86% nucleotide identity). To investigate if it may represent a newly emerged HCoV-229E genotype in Hong Kong, we retrieved 41 archived respiratory samples that tested positive for HCoV-229E from 2004 to 2019. Pneumonia and exacerbations of chronic airway diseases were common among infected patients. Complete RdRp, S, and N gene sequencing of the 41 HCoV-229E strains revealed that our contemporary HCoV-229E strains have undergone significant genetic drift with clustering of strains in chronological order. Two novel genogroups were identified, in addition to previously described genogroups 1 to 4, with recent circulating strains including strain HK20-42 belonging to novel genogroup 6. Positive selection was detected in the spike protein and receptor-binding domain, which may be important for viral evolution at the receptor-binding interphase. Molecular dating analysis showed that HCoV-229E shared the most recent common ancestor with bat and camel/alpaca 229E-related viruses at ∼1884, while camel/alpaca viruses had a relatively recent common ancestor at ∼1999. Further studies are required to ascertain the evolutionary origin and path of HCoV-229E.IMPORTANCE Since its first appearance in the 1960s, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) have been relatively understudied. In this study, we report a fatal case of COVID-19 coinfected with HCoV-229E in Hong Kong. Genome sequencing revealed that our SARS-CoV-2 strain is highly identical to the SARS-CoV-2 strain from Wuhan, compatible with the patient's recent travel history, whereas our HCoV-229E strain in this study is highly identical to a recent strain in the United States. We also retrieved 41 archived HCoV-229E strains from 2004 to 2019 in Hong Kong for sequence analysis. Pneumonia and exacerbations of chronic airway diseases were common diagnoses among the 41 patients. The results showed that HCoV-229E was evolving in chronological order. Two novel genogroups were identified in addition to the four preexisting HCoV-229E genogroups, with recent circulating strains belonging to novel genogroup 6. Molecular clock analysis dated bat-to-human and bat-to-camelid transmission to as early as 1884.


Asunto(s)
/patología , Resfriado Común/patología , Coronavirus Humano 229E/genética , Variación Genética/genética , /genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Secuencia de Bases , Niño , Preescolar , Coinfección/virología , Evolución Molecular , Femenino , Genoma Viral/genética , Hong Kong , Humanos , Lactante , Masculino , Persona de Mediana Edad , Dominios Proteicos/genética , Análisis de Secuencia de ARN , Glicoproteína de la Espiga del Coronavirus/genética , Adulto Joven
6.
Arch Virol ; 166(2): 501-510, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33394169

RESUMEN

With the introduction of direct-acting antiviral treatment (DAA), Tunisia has committed to achieving the international goal of eliminating viral hepatitis. Because the specific DAA prescribed depends on viral genotype, viral genotyping remains of great importance. The aim of the present study was to outline the trends in the distribution of HCV genotypes from 2002 to 2017 in the Tunisian general population in order to guide authorities towards the most appropriate therapeutic strategies for preventing HCV infection. A total of 2532 blood samples were collected over a 16-year period and from all regions of Tunisia. Genotyping showed that genotype 1 (subtype 1b) was the most prevalent genotype in the country (n = 2012; 79.5%), followed by genotype 2 (n = 339; 13.3%). Genotypes 3, 4 and 5 were detected in 4.8%, 2.2% and 0.1% of the country's population, respectively. Mixed infections with different HCV genotypes were detected in 0.1% of the population (one case each of genotypes 1b + 4, 1b + 2 and 2 + 4). Interestingly, a significant increase in genotypes 2, 3 and 4 was observed over time (p = 0.03). Sixteen different subtypes were detected over the study period, most of which were subtypes of genotype 2, and some of these subtypes appeared to be new. Patients infected with genotypes 1a, 3 and 4 were significantly younger than those infected with genotypes 1b and 2 (p < 0.01). Furthermore, genotypes 1b and 2 were detected more often in women than men, while genotypes 1a and 3 were detected mostly in men (P < 0.01). Our study confirms a large predominance of genotype1/subtype1b in Tunisia and shows a significant increase in the prevalence of other genotypes over time. These findings reinforce the need for an additional HCV genotype survey to improve the design of treatment strategies in Tunisia.


Asunto(s)
Hepacivirus/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Preescolar , Coinfección/virología , Femenino , Genotipo , Hepatitis C/virología , Humanos , Masculino , Persona de Mediana Edad , Prevalencia , Estudios Retrospectivos , Túnez , Adulto Joven
7.
BMC Infect Dis ; 21(1): 7, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33407198

RESUMEN

BACKGROUND: Little is known about the etiology of childhood diarrhea in the United Arab Emirates (UAE) especially after the introduction of rotavirus vaccines. This study aimed to identify gastrointestinal pathogens in children with diarrhea (cases) and the carriage rate of these pathogens in asymptomatic children (controls). METHODS: Stool samples were collected from 203 cases and 73 controls who presented to two major hospitals in Al Ain city, UAE. Samples were analyzed with Allplex™ Gastrointestinal Full Panel Assay for common entero-pathogens. The association between diarrhea and the isolated pathogens was calculated in a multivariate logistic regression model. The adjusted attributable fractions (aAFs) were calculated for all pathogens significantly associated with cases. RESULTS: At least one pathogen was identified in 87 samples (42.8%) from cases and 17 (23.3%) from controls (P < 0.001). Rotavirus, norovirus GII and adenovirus were significantly more prevalent in cases. Their aAFs with 95% ci are 0.95 (0.64, 1.00) for rotavirus, 0.86 (0.38, 0.97) for norovirus GII and 0.84 (0.29, 0.96) for adenovirus. None of the 13 bacteria tested for were more commonly found in the cases than in controls. Cryptosporidium spp. were more significantly detected in cases than in controls. Co-infections occurred in 27.9% of the children. Viruses and parasites were significantly more likely to occur together only in the cases. CONCLUSIONS: Multiplex PCR revealed high positivity rates in both cases and controls which demand a cautious interpretation. Rotavirus remains the main childhood diarrhea pathogen in UAE. Effective strategies are needed to better control rotavirus and other causative pathogens.


Asunto(s)
Infecciones por Adenovirus Humanos/epidemiología , Adenovirus Humanos/genética , Infecciones por Caliciviridae/epidemiología , Coinfección/epidemiología , Criptosporidiosis/epidemiología , Cryptosporidium/genética , Diarrea/epidemiología , Norovirus/genética , Infecciones por Rotavirus/epidemiología , Rotavirus/genética , Infecciones por Adenovirus Humanos/virología , Adenovirus Humanos/aislamiento & purificación , Animales , Infecciones por Caliciviridae/virología , Estudios de Casos y Controles , Preescolar , Coinfección/parasitología , Coinfección/virología , Criptosporidiosis/parasitología , Cryptosporidium/aislamiento & purificación , Diarrea/parasitología , Diarrea/virología , Heces/parasitología , Heces/virología , Femenino , Humanos , Lactante , Masculino , Reacción en Cadena de la Polimerasa Multiplex/métodos , Norovirus/aislamiento & purificación , Rotavirus/aislamiento & purificación , Infecciones por Rotavirus/virología , Vacunas contra Rotavirus , Emiratos Árabes Unidos/epidemiología
8.
Artículo en Inglés | MEDLINE | ID: mdl-33436481

RESUMEN

We present a case of haemorrhagic enterocolitis in a patient with SARS-CoV-2 who recovered from respiratory failure after support with venovenous extracorporeal membrane oxygenation. We describe clinicopathological features consistent with the systemic coinfection/reactivation of cytomegalovirus (CMV) concurrent with COVID-19 infection and the protracted clinical course of resolution of gastrointestinal inflammation after the treatment of CMV infection. Stool PCR, abdominal CT perfusion scan and histological examination of ileal and colonic tissues excluded enterocolitis secondary to other causes of infection (common viral, bacterial and protozoal gastrointestinal pathogens), macrovascularand microvascular ischaemia and classic inflammatory bowel disease, respectively. We propose possible synergistic pathophysiologic mechanisms for enterocolitis complicating severe COVID-19 infection: (1) T lymphocyte depletion and immune response dysregulation, (2) use of immunomodulators in the management of severe COVID-19 infection and (3) high concentration of ACE-2 receptors for COVID-19 virus in the gastrointestinal tract.


Asunto(s)
/complicaciones , Coinfección/virología , Infecciones por Citomegalovirus/complicaciones , Enterocolitis/complicaciones , Hemorragia Gastrointestinal/virología , /terapia , Diarrea/virología , Enterocolitis/virología , Oxigenación por Membrana Extracorpórea , Femenino , Humanos , Persona de Mediana Edad
9.
mBio ; 12(1)2021 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-33419872

RESUMEN

In December 2019 a new coronavirus (CoV) emerged as a human pathogen, SARS-CoV-2. There are few data on human coronavirus infections among individuals living with HIV. In this study we probed the role of pneumococcal coinfections with seasonal CoVs among children living with and without HIV hospitalized for pneumonia. We also described the prevalence and clinical manifestations of these infections. A total of 39,836 children who participated in a randomized, double-blind, placebo-controlled clinical trial on the efficacy of a 9-valent pneumococcal conjugate vaccine (PCV9) were followed for lower respiratory tract infection hospitalizations until 2 years of age. Nasopharyngeal aspirates were collected at the time of hospitalization and were screened by PCR for four seasonal CoVs. The frequency of CoV-associated pneumonia was higher in children living with HIV (19.9%) than in those without HIV (7.6%, P < 0.001). Serial CoV infections were detected in children living with HIV. The case fatality risk among children with CoV-associated pneumonia was higher in those living with HIV (30.4%) than without HIV (2.9%, P = 0.001). C-reactive protein and procalcitonin levels were elevated in 36.8% (≥40 mg/liter) and 64.7% (≥0.5 ng/ml), respectively, of the fatal cases living with HIV. Among children without HIV, there was a 64.0% (95% CI: 22.9% to 83.2%) lower incidence of CoV-associated pneumonia hospitalizations among PCV9 recipients compared to placebo recipients. These data suggest that Streptococcus pneumoniae infections might have a role in the development of pneumonia associated with endemic CoVs, that PCV may prevent pediatric CoV-associated hospitalization, and that children living with HIV with CoV infections develop more severe outcomes.IMPORTANCE SARS-CoV-2 may cause severe hospitalization, but little is known about the role of secondary bacterial infection in these severe cases, beyond the observation of high levels of reported inflammatory markers, associated with bacterial infection, such as procalcitonin. We did a secondary analysis of a double-blind randomized trial of PCV to examine its impact on human CoV infections before the pandemic. We found that both children living with and without HIV randomized to receive PCV had evidence of less hospitalization due to seasonal CoV, suggesting that pneumococcal coinfection may play a role in severe hospitalized CoV infections.


Asunto(s)
Infecciones Oportunistas Relacionadas con el SIDA/prevención & control , Infecciones por Coronavirus/prevención & control , Vacunas Neumococicas/administración & dosificación , Neumonía Viral/prevención & control , Streptococcus pneumoniae/inmunología , Infecciones Oportunistas Relacionadas con el SIDA/epidemiología , Infecciones Oportunistas Relacionadas con el SIDA/patología , Coinfección/epidemiología , Coinfección/microbiología , Coinfección/prevención & control , Coinfección/virología , Coronavirus/clasificación , Coronavirus/aislamiento & purificación , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/patología , Estudios de Seguimiento , Hospitalización/estadística & datos numéricos , Humanos , Incidencia , Lactante , Neumonía Neumocócica/epidemiología , Neumonía Neumocócica/prevención & control , Neumonía Viral/epidemiología , Prevalencia , Ensayos Clínicos Controlados Aleatorios como Asunto
10.
PLoS One ; 16(1): e0245547, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33444422

RESUMEN

Endemic human coronaviruses (HCoVs) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are members of the family Coronaviridae. Comparing the findings of the infections caused by these viruses would help reveal the novel characteristics of SARS-CoV-2 and provide insight into the unique pathogenesis of SARS-CoV-2 infection. This study aimed to compare the clinical and radiological characteristics of SARS-CoV-2 and endemic HCoVs infection in adult hospitalized patients with community-acquired pneumonia (CAP). This study was performed at a university-affiliated tertiary hospital in the Republic of Korea, between January 1, 2015, and July 31, 2020. A total of 109 consecutive patients who were over 18 years of age with confirmed SARS-CoV-2 and endemic HCoVs were enrolled. Finally, 19 patients with SARS-CoV-2 CAP were compared to 40 patients with endemic HCoV CAP. Flu-like symptoms such as cough, sore throat, headache, myalgia, and prolonged fever were more common in SARS-CoV-2 CAP, whereas clinical findings suggestive of bacterial pneumonia such as dyspnea, leukocytosis with left shift, and increased C-reactive protein were more common in endemic HCoV CAP. Bilateral peripherally distributed ground-glass opacities (GGOs) were typical radiologic findings in SARS-CoV-2 CAP, whereas mixed patterns of GGOs, consolidations, micronodules, and pleural effusion were observed in endemic HCoV CAP. Coinfection was not observed in patients with SARS-CoV-2 CAP, but was observed in more than half of the patients with endemic HCoV CAP. There were distinctive differences in the clinical and radiologic findings between SARS-CoV-2 and endemic HCoV CAP. Further investigations are required to elucidate the mechanism underlying this difference. Follow-up observations are needed to determine if the presentation of SARS-CoV-2 CAP changes with repeated infection.


Asunto(s)
/diagnóstico por imagen , Neumonía Viral/diagnóstico por imagen , Anciano , /patología , Estudios de Cohortes , Coinfección/diagnóstico por imagen , Coinfección/epidemiología , Coinfección/patología , Coinfección/virología , Infecciones Comunitarias Adquiridas , Coronavirus/aislamiento & purificación , Enfermedades Endémicas , Femenino , Humanos , Pulmón/diagnóstico por imagen , Masculino , Persona de Mediana Edad , Coronavirus del Síndrome Respiratorio de Oriente Medio/aislamiento & purificación , Pandemias , Neumonía Viral/epidemiología , Neumonía Viral/patología , Neumonía Viral/virología , Radiografía Torácica/métodos , República de Corea/epidemiología , Estudios Retrospectivos , Factores de Riesgo , Tórax/diagnóstico por imagen
11.
BMC Infect Dis ; 21(1): 43, 2021 Jan 09.
Artículo en Inglés | MEDLINE | ID: mdl-33422002

RESUMEN

BACKGROUND: Acute respiratory infections (ARIs) are a worldwide public health problem. It is estimated that up to 80% of cases of ARIs are caused by viruses. In Central America, however, we identified few epidemiologic studies on the main ARI-related viruses in hospitalized children. METHODS: This study retrospectively analyzed the clinical charts of patients ages 29 days to 14 years admitted with diagnoses of ARIs in a pediatric reference hospital in central Panama during 2016. The variables analyzed were age, sex, signs, symptoms, and diagnosis at admission. Samples of patients to whom a viral panel was indicated were analyzed via quantitative polymerase chain reaction, qPCR. RESULTS: The most common virus was respiratory syncytial virus (RSV; 25.9%), followed by influenza A virus (10.6%), rhinovirus (10.6%), parainfluenza type 3 (PIV-3; 8.2%) and adenovirus (5.9%). However, virus detection varied with patient age and season. RSV and Influenza virus were respectively identified mainly during July-November and May-July. All cases of viral co-infection occurred in children < 5-years-old. Both influenza A (H1N1) pdm09 and rhinovirus were detected in all pediatric ages analyzed in this study, unlike RSV and PIV-3, which were only present in children < 5-years-old. CONCLUSIONS: This study analyzed the epidemiological patterns of different respiratory viruses in pediatric patients with ARI from central Panama and found that the prevalence of the specific respiratory viruses identified varied with season and age. The most common viruses were RSV, influenza A, and rhinovirus. There were no reports of human metapneumovirus associated with ARI, which may be explained by the time and geographic location of the study. Knowledge of the local epidemiology of respiratory viruses in tropical countries is helpful in forecasting the peaks of hospitalizations due to ARIs and may help improve prevention efforts aiming at respiratory disease control in these settings.


Asunto(s)
Infecciones del Sistema Respiratorio/virología , Virosis/virología , Virus/aislamiento & purificación , Adolescente , Niño , Preescolar , Coinfección/epidemiología , Coinfección/virología , Femenino , Hospitalización , Hospitales/estadística & datos numéricos , Humanos , Lactante , Masculino , Metapneumovirus/genética , Panamá/epidemiología , Pediatría , Reacción en Cadena en Tiempo Real de la Polimerasa , Infecciones del Sistema Respiratorio/epidemiología , Estudios Retrospectivos , Estaciones del Año , Virosis/epidemiología , Virus/clasificación , Virus/genética
12.
BMC Infect Dis ; 21(1): 63, 2021 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-33435896

RESUMEN

BACKGROUND: Chest X-ray (CXR) interpretation remains a central component of the current World Health Organization recommendations as an adjuvant test in diagnosis of smear-negative tuberculosis (TB). With its low specificity, high maintenance and operational costs, utility of CXR in diagnosis of smear-negative TB in high HIV/TB burden settings in the Xpert MTB/RIF era remains unpredictable. We evaluated accuracy and additive value of CXR to Xpert MTB/RIF in the diagnosis of TB among HIV-positive smear-negative presumptive TB patients. METHODS: HIV co-infected presumptive TB patients were recruited from the Infectious Diseases Institute outpatient clinic and in-patient medical wards of Mulago Hospital, Uganda. CXR films were reviewed by two independent radiologists using a standardized evaluation form. CXR interpretation with regard to TB was either positive (consistent with TB) or negative (normal or unlikely TB). Sensitivity, specificity and predictive values of CXR and CXR combined with Xpert MTB/RIF for diagnosis of smear-negative TB in HIV-positive patients were calculated using sputum and/or blood mycobacterial culture as reference standard. RESULTS: Three hundred sixty-six HIV co-infected smear-negative participants (female, 63.4%; hospitalized, 68.3%) had technically interpretable CXR. Median (IQR) age was 32 (28-39) years and CD4 count 112 (23-308) cells/mm3. Overall, 22% (81/366) were positive for Mycobacterium tuberculosis (Mtb) on culture; 187/366 (51.1%) had CXR interpreted as consistent with TB, of which 55 (29.4%) had culture-confirmed TB. Sensitivity and specificity of CXR interpretation in diagnosis of culture-positive TB were 67.9% (95%CI 56.6-77.8) and 53.7% (95%CI 47.7-59.6) respectively, while Xpert MTB/RIF sensitivity and specificity were 65.4% (95%CI 54.0-75.7) and 95.8% (95%CI 92.8-97.8) respectively. Addition of CXR to Xpert MTB/RIF had overall sensitivity and specificity of 87.7% (95%CI 78.5-93.9) and 51.6% (95%CI 45.6-57.5) respectively; 86.2% (95%CI 75.3-93.5) and 48.1% (95%CI 40.7-55.6) among inpatients and 93.8% (95%CI 69.8-99.8) and 58.0% (95%CI 47.7-67.8) among outpatients respectively. CONCLUSION: In this high prevalence TB/HIV setting, CXR interpretation added sensitivity to Xpert MTB/RIF test at the expense of specificity in the diagnosis of culture-positive TB in HIV-positive individuals presenting with TB symptoms and negative smear. CXR interpretation may not add diagnostic value in settings where Xpert MTB/RIF is available as a TB diagnostic tool.


Asunto(s)
Infecciones Oportunistas Relacionadas con el SIDA/complicaciones , Coinfección/diagnóstico , VIH/aislamiento & purificación , Radiografías Pulmonares Masivas/métodos , Mycobacterium tuberculosis/genética , Técnicas de Amplificación de Ácido Nucleico/métodos , Tuberculosis Pulmonar/complicaciones , Tuberculosis Pulmonar/diagnóstico , Infecciones Oportunistas Relacionadas con el SIDA/epidemiología , Infecciones Oportunistas Relacionadas con el SIDA/virología , Adulto , Recuento de Linfocito CD4 , Coinfección/epidemiología , Coinfección/virología , Exactitud de los Datos , Femenino , Recursos en Salud , Humanos , Masculino , Sensibilidad y Especificidad , Esputo/microbiología , Tuberculosis Pulmonar/epidemiología , Tuberculosis Pulmonar/microbiología , Uganda/epidemiología
13.
BMC Infect Dis ; 21(1): 68, 2021 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-33441085

RESUMEN

BACKGROUND: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus that was first discovered in December 2019 in Wuhan, China. With the growing numbers of community spread cases worldwide, the World Health Organization (WHO) declared the COVID-19 outbreak as a pandemic on March 11, 2020. Like influenza viruses, SARS-CoV-2 is thought to be mainly transmitted by droplets and direct contact, and COVID-19 has a similar disease presentation to influenza. Here we present a case of influenza A and COVID-19 co-infection in a 60-year-old man with end-stage renal disease (ESRD) on hemodialysis. CASE PRESENTATION: A 60-year-old man with ESRD on hemodialysis presented for worsening cough, shortness of breath, and diarrhea. The patient first developed a mild fever (37.8 °C) during hemodialysis 3 days prior to presentation and has been experiencing worsening flu-like symptoms, including fever of up to 38.6 °C, non-productive cough, generalized abdominal pain, nausea, vomiting, and liquid green diarrhea. He lives alone at home with no known sick contacts and denies any recent travel or visits to healthcare facilities other than the local dialysis center. Rapid flu test was positive for influenza A. Procalcitonin was elevated at 5.21 ng/mL with a normal white blood cell (WBC) count. Computed tomography (CT) chest demonstrated multifocal areas of consolidation and extensive mediastinal and hilar adenopathy concerning for pneumonia. He was admitted to the biocontainment unit of Nebraska Medicine for concerns of possible COVID-19 and was started on oseltamivir for influenza and vancomycin/cefepime for the probable bacterial cause of his pneumonia and diarrhea. Gastrointestinal (GI) pathogen panel and Clostridioides difficile toxin assay were negative. On the second day of admission, initial nasopharyngeal swab came back positive for SARS-CoV-2 by real-time reverse-transcriptase polymerase chain reaction (RT-PCR). The patient received supportive care and resumed bedside hemodialysis in strict isolation, and eventually fully recovered from COVID-19. CONCLUSIONS: We presented a case of co-infection of influenza and SARS-CoV-2 in a hemodialysis patient. The possibility of SARS-CoV-2 co-infection should not be overlooked even when other viruses including influenza can explain the clinical symptoms, especially in high-risk patients.


Asunto(s)
/diagnóstico , Gripe Humana/diagnóstico , /diagnóstico por imagen , Coinfección/diagnóstico , Coinfección/diagnóstico por imagen , Coinfección/virología , Hospitalización , Humanos , Virus de la Influenza A/genética , Virus de la Influenza A/aislamiento & purificación , Virus de la Influenza A/fisiología , Gripe Humana/diagnóstico por imagen , Gripe Humana/virología , Fallo Renal Crónico/terapia , Masculino , Persona de Mediana Edad , Pandemias , Diálisis Renal , /aislamiento & purificación , Tomografía Computarizada por Rayos X
14.
Viruses ; 13(1)2021 Jan 18.
Artículo en Inglés | MEDLINE | ID: mdl-33477649

RESUMEN

BACKGROUND: Co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with respiratory viruses, bacteria and fungi have been reported to cause a wide range of illness. OBJECTIVES: We assess the prevalence of co-infection of SARS-CoV-2 with seasonal respiratory viruses, document the respiratory viruses detected among individuals tested for SARS-CoV-2, and describe characteristics of individuals with respiratory virus co-infection detected. METHODS: Specimens included in this study were submitted as part of routine clinical testing to Public Health Ontario Laboratory from individuals requiring testing for SARS-CoV-2 and/or seasonal respiratory viruses. RESULTS: Co-infection was detected in a smaller proportion (2.5%) of individuals with laboratory confirmed SARS-CoV-2 than those with seasonal respiratory viruses (4.3%); this difference was not significant. Individuals with any respiratory virus co-infection were more likely to be younger than 65 years of age and male than those with single infection. Those with SARS-CoV-2 co-infection manifested mostly mild respiratory symptoms. CONCLUSIONS: Findings of this study may not support routine testing for seasonal respiratory viruses among all individuals tested for SARS-CoV-2, as they were rare during the study period nor associated with severe disease. However, testing for seasonal respiratory viruses should be performed in severely ill individuals, in which detection of other viruses may assist with patient management.


Asunto(s)
/epidemiología , Coinfección/epidemiología , Infecciones del Sistema Respiratorio/epidemiología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Canadá/epidemiología , Niño , Preescolar , Coinfección/virología , Estudios Transversales , Femenino , Humanos , Masculino , Persona de Mediana Edad , Ontario/epidemiología , Prevalencia , Infecciones del Sistema Respiratorio/complicaciones , Infecciones del Sistema Respiratorio/virología , Adulto Joven
15.
J Proteome Res ; 20(2): 1451-1454, 2021 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-33393790

RESUMEN

In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabitating potential pathogens in COVID-19 patients using mass spectrometry-based analysis. From a sample collected from gargling solutions, we detected Streptococcus pneumoniae (opportunistic and multidrug-resistant pathogen) and Lactobacillus rhamnosus (a probiotic component) along with SARS-Cov-2. We could also detect Pseudomonas sps. Bc-h from COVID-19 positive samples and Acinetobacter ursingii and Pseudomonas monteilii from COVID-19 negative samples collected from oro- and nasopharyngeal samples. We believe that the early detection and characterization of coinfections by using metaproteomics from COVID-19 patients will potentially impact the diagnosis and treatment of patients affected by SARS-CoV-2 infection.


Asunto(s)
Infecciones Bacterianas/diagnóstico , Proteómica/métodos , /metabolismo , Acinetobacter/aislamiento & purificación , Infecciones Bacterianas/complicaciones , Infecciones Bacterianas/microbiología , /virología , Coinfección/microbiología , Coinfección/virología , Humanos , Espectrometría de Masas/métodos , Nasofaringe/microbiología , Nasofaringe/virología , Pseudomonas/aislamiento & purificación , Streptococcus pneumoniae/aislamiento & purificación
16.
Viruses ; 13(2)2021 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-33498165

RESUMEN

Anal squamous cell carcinoma is the most frequent virus-related non-AIDS-defining neoplasia among HIV-infected individuals, especially MSM. The objectives of this study were to analyze the effectiveness of the quadrivalent HPV (qHPV) vaccine to prevent anal ≥ high-grade squamous intraepithelial lesions (≥HSILs), external ano-genital lesions (EAGLs), and infection by qHPV vaccine genotypes in HIV+ MSM, and to study the immunogenicity of the vaccine and risk factors for ≥ HSILs. This study is nested within a randomized, double-blind, placebo-controlled trial of the qHPV vaccine, which enrolled participants between May 2012 and May 2014, with a 48-month follow-up. A vaccine or placebo was administered at 0, 2, and 6 months, and vaccine antibody titers were evaluated at 7, 12, 24, 36, and 48 months. Data were gathered at 12, 24, 36, and 48 months on sexual habits, CD4/CD8 cell/counts, HIV viral load, and the results of cytology (Thin Prep® Pap Test), HPV PCR genotyping (Linear Array HPV Genotyping Test), and high-resolution anoscopy (Zeiss 150 fc© colposcope). The study included 129 patients (mean age of 38.8 years, 40 [31%] with a history of AIDS, 119 [92.2%] receiving ART, and 4 [3.3%] with virological failure), 66 (51.2%) in vaccine arm and 63 (48.4%) in placebo arm. The vaccine and placebo groups did not differ in ≥ HSILs (14.1 vs. 13.1%, respectively, p = 0.98) or EAGL (11.1 vs. 6.8%, p = 0.4) rates during follow-up; however, a protective effect against HPV 6 was observed during the first year of follow-up in the vaccine versus placebo group (7.5% vs. 23.4%; p = 0.047). A between-arm difference (p = 0.0001) in antibodies against qHPV vaccine genotypes was observed at 7 months (76.9% in vaccine arm vs. 30.2% in placebo arm), 12 months (68.1% vs. 26.5%), 24 months (75% vs. 32.5%), 36 months (90% vs. 24.4%), and 48 months (87.2% vs. 30%). Finally, the factor associated with the risk of anal ≥ HSIL onset during the four-year follow-up was the receipt of the last dose of the vaccine less than 6 months earlier in comparison to those vaccinated for a longer period (82.4% vs. 17.6% (OR 0.869 [95% CI, 0.825-0.917]). Vaccine and placebo arms did not significantly differ in ≥ HSIL or EAGL rates or in protection against infection by HPV genotype vaccine except for HPV6 at 12 months after the first dose. A long-lasting immune response was observed in almost all the vaccinated men. The main protective factor against ≥ HSIL was to have completed the vaccination regimen more than 6 months earlier.


Asunto(s)
Anticuerpos Antivirales/sangre , Neoplasias del Ano/prevención & control , Vacuna Tetravalente Recombinante contra el Virus del Papiloma Humano Tipos 6, 11 , 16, 18/administración & dosificación , Vacuna Tetravalente Recombinante contra el Virus del Papiloma Humano Tipos 6, 11 , 16, 18/inmunología , Infecciones por Papillomavirus/prevención & control , Adulto , Canal Anal/virología , Neoplasias del Ano/virología , Recuento de Linfocito CD4 , Coinfección/virología , Infecciones por VIH/virología , Homosexualidad Masculina , Humanos , Masculino , Persona de Mediana Edad , Análisis Multivariante , Infecciones por Papillomavirus/inmunología , Infecciones por Papillomavirus/virología , Análisis de Regresión , Minorías Sexuales y de Género , España , Carga Viral/inmunología
17.
ACS Infect Dis ; 7(2): 203-205, 2021 02 12.
Artículo en Inglés | MEDLINE | ID: mdl-33502840

RESUMEN

Bacterial coinfection in COVID-19 patients has the potential to complicate treatments and accelerate the development of antibiotic resistance in the clinic due to the widespread use of broad-spectrum antibiotics, including in Indonesia. The surge of COVID-19 patients may worsen antibiotic overuse; therefore, information on the actual extent of bacterial coinfection in COVID-19 patients in Indonesia is crucial to inform appropriate treatment. This Viewpoint elaborates on a nascent research project focused on sequencing of swab samples to detect bacterial coinfection in COVID-19 patients in Indonesia. Supported by a L'Oréal-UNESCO For Women in Science National Fellowship, it is designed to inform better clinical management of COVID-19 in Indonesia.


Asunto(s)
Bacterias/aislamiento & purificación , Infecciones Bacterianas/virología , Coinfección/microbiología , Coinfección/virología , Antibacterianos/farmacología , Infecciones Bacterianas/tratamiento farmacológico , Infecciones Bacterianas/microbiología , /terapia , Coinfección/tratamiento farmacológico , Coinfección/epidemiología , Farmacorresistencia Bacteriana , Humanos , Indonesia , /aislamiento & purificación
18.
Arch Virol ; 166(2): 403-411, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33392818

RESUMEN

This study was conducted to investigate the genetic diversity of porcine circovirus type 2 (PCV2) and its coinfecting pathogens in pigs with respiratory disease in Vietnam. Samples from 127 clinical cases were obtained from different southern provinces of Vietnam from January 2018 to January 2020 for PCR and sequence analysis. The infection rate of PCV2 was 78.8%, and the major pathogens found in coinfections with PCV2 were porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, and Haemophilus parasuis. Forty-three PCV2-positive clinical samples were selected for amplification and sequencing of the ORF2 region. Phylogenetic analysis of PCV2 ORF2 showed that five of the sequences belonged to PCV2b (11.6%) and 38 belonged to PCV2d (88.4%), indicating that PCV2d strains were predominant in southern provinces of Vietnam. Alignment of the predicted amino acid sequences of the PCV2 capsid protein revealed polymorphic sites in the antibody recognition regions. This study demonstrates the prevalence of the PCV2d genotype in southern Vietnam and presents a comprehensive overview of the coinfecting pathogens associated with PCV2 in young pigs with respiratory disease.


Asunto(s)
Infecciones por Circoviridae/virología , Circovirus/genética , Coinfección/virología , Enfermedades Respiratorias/virología , Enfermedades de los Porcinos/virología , Secuencia de Aminoácidos , Animales , Proteínas de la Cápside/genética , Genotipo , Prevalencia , Porcinos , Vietnam
20.
Pediatr Infect Dis J ; 40(1): e36-e39, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33044434

RESUMEN

The clinical presentation of human coronavirus (HCoV) infections in children varies strongly. We show that children with an HCoV-associated lower respiratory tract infection more frequently had respiratory syncytial virus codetected and higher abundance of Haemophilus influenzae/haemolyticus than asymptomatic HCoV carriers as well as children with a non-HCoV-associated lower respiratory tract infection. Viral and bacterial cooccurrence may drive symptomatology of HCoV-associated infections including coronavirus disease 2019.


Asunto(s)
Coinfección/microbiología , Coinfección/virología , Infecciones por Coronavirus/patología , Infecciones del Sistema Respiratorio/patología , Bacterias/clasificación , Bacterias/aislamiento & purificación , Preescolar , Coinfección/epidemiología , Coinfección/patología , Coronavirus , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/microbiología , Infecciones por Coronavirus/virología , Femenino , Haemophilus/clasificación , Haemophilus/aislamiento & purificación , Humanos , Lactante , Masculino , Países Bajos/epidemiología , Virus Sincitial Respiratorio Humano/aislamiento & purificación , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Estaciones del Año , Índice de Severidad de la Enfermedad
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