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1.
Medicine (Baltimore) ; 100(4): e24524, 2021 Jan 29.
Artículo en Inglés | MEDLINE | ID: mdl-33530280

RESUMEN

ABSTRACT: This study aimed to evaluate the incidence of co-infection with different types of pathogens in patients with hypoxemic pneumonia due to coronavirus disease 2019 (COVID-19) in Reunion Island.This observational study using a prospectively collected database of hypoxemic pneumonia due to COVID-19 cases was conducted at Félix Guyon University Hospital in Reunion Island, France.Between 18 March 2020 and 15 April 2020, 156 patients were admitted to our hospital for COVID-19. A total of 36 patients had hypoxemic pneumonia (23.1%) due to COVID-19. Thirty of these cases (83.3%) were imported by travelers returning mainly from metropolitan France and Spain. Patients were screened for co-infection with other pathogens at admission: 31 (86.1%) by multiplex polymerase chain reaction (PCR) and 16 (44.4%) by cytobacteriological examination of sputum culture. Five patients (13.9%) were found to have co-infection: 1 with influenza virus A H1N1 (pdm09) associated with Branhamella catarrhalis, 1 with Streptococcus pneumoniae associated with Haemophilus influenzae, 1 with Human Coronavirus 229E, 1 with Rhinovirus, and 1 with methicillin-susceptible Staphylococcus aureus. Patients with co-infection had higher D-dimer levels than those without co-infection (1.36 [1.34-2.36] µg/mL vs 0.63 [0.51-1.12] µg/mL, P = .05).The incidence of co-infection in our cohort was higher than expected (13.9%). Three co-infections (with influenza virus A(H1N1) pdm09, Streptococcus pneumoniae, and Staphylococcus aureus) required specific treatment. Patients with hypoxemic pneumonia due to COVID-19 should be screened for co-infection using respiratory cultures or multiplex PCR. Whilst our study has a number of limitations, the results from our study suggest that in the absence of screening, patients should be commenced on treatment for co-infection in the presence of an elevated D-dimer.


Asunto(s)
/epidemiología , Coinfección/epidemiología , Neumonía/epidemiología , Neumonía/microbiología , Adulto , Femenino , Francia/epidemiología , Humanos , Hipoxia , Masculino , Persona de Mediana Edad , Estudios Retrospectivos
2.
Zhonghua Jie He He Hu Xi Za Zhi ; 44(2): 88-95, 2021 Feb 12.
Artículo en Chino | MEDLINE | ID: mdl-33535322

RESUMEN

Objective: To study the clinical and etiological characteristics of viral pneumonia in patients with chronic obstructive pulmonary disease(VP-COPD), and to identify the risk factors associated with poor prognosis. Methods: From August 1, 2017 to August 1, 2019, totally 235 patients in a general hospital in Beijing were prospectively enrolled in this research, and all patients were diagnosed with viral pneumonia by imaging and etiology. The patients were divided into VP-COPD group(n=60) and VP-nCOPD(viral pneumonia in non-COPD patients) group(n=175). Pathogen detection and clinical characteristics were compared between the two groups.Finally, the binomial logistic regression was used to explore the risk factors associated with severe VP-COPD. Results: Compared with the VP-nCOPD group, the VP-COPD group was older(76.5 vs 66.0 years, P=0.001), and the CURB-65 score(2 vs 1, P= 0.001) and the PSI score(111 vs 85, P<0.001) were higher at admission. Pseudomonas aeruginosa(χ²= 10.308, P= 0.001) and Staphylococcus aureus(χ²= 5.953, P=0.028) were the most common co-infection bacteria. In the VP-COPD group type Ⅱ respiratory failure was more common(23.3% vs 6.8%, P<0.001), the number of severely ill patients was larger(48.3% vs 30.3%, P=0.011), the length of hospital stay was longer(13 vs 8, P<0.001), and the mortality rate during hospitalization was higher(18.3% vs 7.4%, P=0.016) in the VP-nCOPD group. Multivariate analysis showed that the level of blood glucose(OR: 1.73, 95%CI: 1.22-2.44, P= 0.002) and pleural effusion(OR: 133.12, 95%CI: 7.57-2 340.36, P=0.001) were risk factors for severe VP-COPD patients. Conclusion: Viral pneumonia in patients with COPD tended to develop into severe cases and had a poor prognosis.


Asunto(s)
Neumonía Viral/etiología , Enfermedad Pulmonar Obstructiva Crónica/complicaciones , Anciano , China/epidemiología , Coinfección , Femenino , Humanos , Tiempo de Internación/estadística & datos numéricos , Masculino , Persona de Mediana Edad , Neumonía Viral/diagnóstico , Neumonía Viral/epidemiología , Neumonía Viral/terapia , Pronóstico , Infecciones por Pseudomonas/epidemiología , Pseudomonas aeruginosa/aislamiento & purificación , Enfermedad Pulmonar Obstructiva Crónica/epidemiología , Enfermedad Pulmonar Obstructiva Crónica/terapia , Respiración Artificial/estadística & datos numéricos , Insuficiencia Respiratoria , Estudios Retrospectivos , Factores de Riesgo , Infecciones Estafilocócicas/epidemiología , Staphylococcus aureus/aislamiento & purificación
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.
Curr Med Sci ; 41(1): 51-57, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33582905

RESUMEN

Coronavirus disease 2019 (COVID-19) occurs in the influenza season and has become a global pandemic. The present study aimed to examine severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infection with influenza A virus (IAV) in an attempt to provide clues for the antiviral interventions of co-infected patients. We described two patients who were co-infected with SARS-CoV-2 and IAV treated at Wuhan Union Hospital, China. In addition, we performed a review in PubMed, Web of Science and CNKI (from January 1 up to November 1, 2020) with combinations of the following key words: "COVID-19, SARS-COV-2, influenza A and co-infection". A total of 28 co-infected patients were enrolled in the analysis. Of the 28 patients, the median age was 54.5 years (IQR, 34.25-67.5) and 14 cases (50.0%) were classified as severe types. The most common symptoms were fever (85.71%), cough (82.14%) and dyspnea (60.71%). Sixteen patients had lymphocytopenia on admission and 23 patients exhibited abnormal radiological changes. The median time from symptom onset to hospital admission was 4 days (IQR, 3-6), and the median time of hospital stay was 14 days (IQR, 8.5-16.75). In conclusion, patients with SARS-COV-2 and IAV co-infection were similar to those infected with SARS-COV-2 alone in symptoms and radiological images. SARS-COV-2 co-infection with IAV could lead to more severe clinical condition but did not experience longer hospital stay compared with patients infected with SARS-COV-2 alone.


Asunto(s)
/epidemiología , Coinfección/epidemiología , Virus de la Influenza A/aislamiento & purificación , Gripe Humana/epidemiología , /aislamiento & purificación , Adulto , Anciano , Femenino , Humanos , Tiempo de Internación , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , Índice de Severidad de la Enfermedad
5.
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
6.
Medicina (B Aires) ; 81(1): 1-5, 2021.
Artículo en Español | MEDLINE | ID: mdl-33611237

RESUMEN

Hepatitis C virus (HCV) infection is currently the main blood-borne viral infection. One of the main obstacles to achieving its control in Argentina is related to difficulties in accessing the diagnosis and timely treatment of infected people. We carried out this study with the aim of characterizing the HCV-infected patients who started treatment with direct-acting antivirals (DAAs) and to describe the experience related to treatment. The medical records of 82 patients, 44 (53.7%) male, 37 (45.1%) female, and one (1.2%) transgender, were selected. The mean age was 49 years. We report a frequency of cirrhosis, 39%, in 32 patients, coinfection with HIV in 48 (58.5%) and with HBV in 27 (32.9%). In 52 patients (63.4%), no risk factor clearly associated with infection was observed. All completed the therapy, of them 72 (87.8%) carried out the control to confirm sustained viral response (SVR), that attained 98.6%. We conclude that universal testing should be implemented over testing based on a risk approach, and that a simplified and decentralized care criterion should be promoted, reserving specialized care for patients with decompensated cirrhosis and liver cancer.


Asunto(s)
Antivirales , Coinfección , Infecciones por VIH , Hepatitis C Crónica , Hepatitis C , Antivirales/uso terapéutico , Argentina/epidemiología , Coinfección/tratamiento farmacológico , Femenino , Infecciones por VIH/tratamiento farmacológico , Hepacivirus , Hepatitis C/diagnóstico , Hepatitis C/tratamiento farmacológico , Hepatitis C/epidemiología , Hepatitis C Crónica/tratamiento farmacológico , Humanos , Cirrosis Hepática , Masculino , Persona de Mediana Edad
7.
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
9.
Med Sci Monit ; 27: e929783, 2021 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-33388738

RESUMEN

BACKGROUND This retrospective study aimed to investigate co-infections with common respiratory pathogens and SARS-CoV-2 and laboratory biochemistry findings in patients with COVID-19 in the Zhuzhou area of China, in order to provide a reference for the disease assessment and clinical treatment of COVID-19. MATERIAL AND METHODS The clinical data of COVID-19 patients admitted to the hospital of Zhuzhou City from January 28 to March 15, 2020, as well as laboratory test results for respiratory pathogens and biochemical indicators, were collected to conduct correlation analyses. All patients were diagnosed based on fluorescence-based PCR assay for SARS-CoV-2. RESULTS Eleven of the 78 patients (14.1%) were co-infected with other respiratory pathogens, among which Mycoplasma pneumoniae (n=5, 45.5%) and respiratory syncytial virus (n=4, 36.4%) were the most frequent. There were 8 patients co-infected with 1 other pathogen and 3 patients co-infected with 2 other pathogens. Compared with mono-infected COVID-19 patients, patients with co-infections had significantly higher levels of procalcitonin (P=0.002). CONCLUSIONS The findings showed that Mycoplasma pneumonia and respiratory syncytial virus were the most common co-infections in patients with COVID-19 pneumonia. Increased levels of PCT in patients with COVID-19 pneumonia were associated with co-infection.


Asunto(s)
/epidemiología , Coinfección/epidemiología , Pandemias , Infecciones del Sistema Respiratorio/epidemiología , /aislamiento & purificación , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Antiinfecciosos/uso terapéutico , Biomarcadores , Proteína C-Reactiva/análisis , /diagnóstico , Niño , Preescolar , China/epidemiología , Creatina Quinasa/sangre , Estudios Transversales , Femenino , Humanos , L-Lactato Deshidrogenasa/sangre , Masculino , Persona de Mediana Edad , Neumonía por Mycoplasma/sangre , Neumonía por Mycoplasma/epidemiología , Polipéptido alfa Relacionado con Calcitonina/sangre , Infecciones por Virus Sincitial Respiratorio/sangre , Infecciones por Virus Sincitial Respiratorio/tratamiento farmacológico , Infecciones por Virus Sincitial Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/sangre , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Estudios Retrospectivos , Índice de Severidad de la Enfermedad , Adulto Joven
10.
Rev Med Suisse ; 17(720-1): 95-101, 2021 Jan 13.
Artículo en Francés | MEDLINE | ID: mdl-33443839

RESUMEN

The current COVID-19 pandemic is the main topic of news worldwide by its magnitude and consequences across the entire planet. From a medical point of view, several risk factors for developing severe illness have been reported in the literature, notably an immunosuppressed status. For people living with HIV, several questions have been raised concerning not only their vulnerability, but also in relation to an eventual protection conferred by antiretroviral therapy. This article will address these two pandemics by looking at the potential impact of SARS-CoV-2 on people living with HIV and, in parallel, exploring similarities and differences in terms of treatment, potential for recovery, prevention and their impact on clinical research. We review also future novel therapies for the treatment of HIV.


Asunto(s)
Infecciones por VIH , Coinfección , Infecciones por VIH/tratamiento farmacológico , Infecciones por VIH/epidemiología , Humanos , Pandemias , Factores de Riesgo
11.
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
12.
PLoS One ; 16(1): e0244937, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33406122

RESUMEN

BACKGROUND: The impact of SARS-CoV-2 in regions endemic for both Dengue and Chikungunya is still not fully understood. Considering that symptoms/clinical features displayed during Dengue, Chikungunya and SARS-CoV-2 acute infections are similar, undiagnosed cases of SARS-CoV-2 in co-endemic areas may be more prevalent than expected. This study was conducted to assess the prevalence of covert cases of SARS-CoV-2 among samples from patients with clinical symptoms compatible with either Dengue or Chikungunya viral infection in the state of Espírito Santo, Brazil. METHODS: Presence of immunoglobulin G (IgG) antibody specific to SARS-CoV-2 nucleoprotein was detected using a chemiluminescent microparticle immunoassay in samples from 7,370 patients, without previous history of COVID-19 diagnosis, suspected of having either Dengue (n = 1,700) or Chikungunya (n = 7,349) from December 1st, 2019 to June 30th, 2020. FINDINGS: Covert cases of SARS-CoV-2 were detected in 210 (2.85%) out of the 7,370 serum samples tested. The earliest undiagnosed missed case of COVID-19 dated back to a sample collected on December 18, 2019, also positive for Dengue Virus. Cross-reactivity with either Dengue virus or other common coronaviruses were not observed. INTERPRETATION: Our findings demonstrate that concomitant Dengue or Chikungunya outbreaks may difficult the diagnosis of SARS-CoV-2 infections. To our knowledge, this is the first study to demonstrate, with a robust sample size (n = 7,370) and using highly specific and sensitive chemiluminescent microparticle immunoassay method, that covert SARS-CoV-2 infections are more frequent than previously expected in Dengue and Chikungunya hyperendemic regions. Moreover, our results suggest that SAR-CoV-2 cases were occurring prior to February, 2020, and that these undiagnosed missed cases may have contributed to the fast expansion of SARS-CoV-2 outbreak in Brazil. Data presented here demonstrate that in arboviral endemic regions, SARS-CoV-2 infection must be always considered, regardless of the existence of a previous positive diagnosis for Dengue or Chikungunya.


Asunto(s)
/epidemiología , Fiebre Chikungunya/epidemiología , Dengue/epidemiología , Adulto , Anticuerpos Antivirales/sangre , Brasil/epidemiología , Virus Chikungunya/patogenicidad , Coinfección/epidemiología , Virus del Dengue/patogenicidad , Errores Diagnósticos/tendencias , Brotes de Enfermedades , Femenino , Humanos , Inmunoglobulina G/sangre , Masculino , Persona de Mediana Edad , Prevalencia , /patogenicidad
13.
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
14.
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
15.
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
16.
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
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
19.
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
20.
Emerg Microbes Infect ; 10(1): 161-166, 2021 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33410371

RESUMEN

SARS-CoV-2 has spread rapidly, causing deaths worldwide. In this study, we evaluated the performance of the BD MAX Open System module for identifying viral pathogens, including SARS-CoV-2, in nasopharyngeal specimens from individuals with symptoms of upper respiratory tract infection. We developed and validated a rapid total nucleic acid extraction method based on real-time reverse transcription-polymerase chain reaction (RT-PCR) for the reliable, high-throughput simultaneous detection of common cold viral pathogens using the BD MAX Platform. The system was evaluated using 205 nasopharyngeal swab clinical samples. For assessment of the limit of detection (LoD), we used SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV) RNA standards. The BD MAX dual multiplex real-time RT-PCR panel demonstrated a sensitivity comparable to that of the World Health Organization-recommended SARS-CoV-2 assay with an LoD of 50 copies/PCR. The LoD of influenza A/B and RSV was 100-200 copies/PCR. The overall percent agreement between the BD MAX panel and laboratory-developed RT-PCR test on 55 SARS-CoV-2-positive clinical samples was 100%. Among the 55 positive cases of COVID-19 analysed, no coinfection was detected. The BD MAX rapid multiplex PCR provides a highly sensitive, robust, and accurate assay for the rapid detection of SARS-CoV-2, influenza A/B, and RSV.


Asunto(s)
/diagnóstico , Gripe Humana/diagnóstico , Reacción en Cadena de la Polimerasa/métodos , Infecciones por Virus Sincitial Respiratorio/diagnóstico , /genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Coinfección/epidemiología , Femenino , Humanos , Masculino , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa Multiplex/métodos , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , Adulto Joven
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