Viral Origin
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2021 ◽  
Vol 2021 ◽  
pp. 1-9
Asmae Lamrani Hanchi ◽  
Morad Guennouni ◽  
Meriem Rachidi ◽  
Toufik Benhoumich ◽  
Hind Bennani ◽  

Sever acute respiratory infections (SARIs) are a public health issue that are common in children and are associated with an important morbidity and mortality rate worldwide. Although SARI are mainly caused by viruses, they are still a cause of antibiotic overuse. The use of molecular methods especially real-time multiplex PCR allowed to detect a wide range of respiratory viruses and their subtype as well as some atypical bacteria. The aim of this study was to investigate the epidemiology of respiratory pathogens detected in children admitted with SARI and to highlight the role of real-time multiplex PCR in the rapid diagnosis of viral and bacterial SARI. This work is a descriptive observational study from January 2018 to December 2019 including nasopharyngeal secretions collected from 534 children hospitalised in paediatric department. The detection of respiratory viruses and bacteria was performed by the FilmArray® Respiratory Panel. A total of 387 (72.5%) children were tested positive for at least one respiratory pathogen, and 23.3% of them were coinfected with more than one pathogen. Viral aetiology was found in 91.2% (n = 340). The most common viruses detected were HRV (n = 201) and RSV (n = 124), followed by PIV (n = 35) influenza A (n = 29) and human metapneumovirus (n = 27). Bacteria was found in 8.8% (n = 47), and Bordetella pertussis was the most detected. Respiratory syncytial virus and Bordetella pertussis were significantly higher in infants less than 6 months old. The detection of RSV and influenza A presented a pic in winter, and HMPV was statistically significant in spring ( p < 0.01 ). This study described the epidemiology of respiratory pathogens involved in severe respiratory infections in children that were affected by several factors such as season and age group. It also highlighted the importance of multiplex PCR in confirming viral origin, thus avoiding irrational prescription of antibiotics in paediatric settings.

Viruses ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 52
Dalila Crucitti ◽  
Marco Chiapello ◽  
Daniele Oliva ◽  
Marco Forgia ◽  
Massimo Turina ◽  

Wine yeasts can be natural hosts for dsRNA, ssRNA viruses and retrotransposon elements. In this study, high-throughput RNA sequencing combined with bioinformatic analyses unveiled the virome associated to 16 Saccharomyces cerevisiae and 8 non-Saccharomyces strains of oenological interest. Results showed the presence of six viruses and two satellite dsRNAs from four different families, two of which—Partitiviridae and Mitoviridae—were not reported before in yeasts, as well as two ORFan contigs of viral origin. According to phylogenetic analysis, four new putative mycoviruses distributed in Totivirus, Cryspovirus, and Mitovirus genera were identified. The majority of commercial S. cerevisiae strains were confirmed to be the host for helper L-A type totiviruses and satellite M dsRNAs associated with the killer phenotype, both in single and mixed infections with L-BC totiviruses, and two viral sequences belonging to a new cryspovirus putative species discovered here for the first time. Moreover, single infection by a narnavirus 20S-related sequence was also found in one S. cerevisiae strain. Considering the non-Saccharomyces yeasts, Starmerella bacillaris hosted four RNAs of viral origin—two clustering in Totivirus and Mitovirus genera, and two ORFans with putative satellite behavior. This study confirmed the infection of wine yeasts by viruses associated with useful technological characteristics and demonstrated the presence of complex mixed infections with unpredictable biological effects.

Plant Disease ◽  
2021 ◽  
Satish Kumar Gupta ◽  
Monika Sharma ◽  
Santanu Mukherjee

Tomato in India is commonly exposed to various diseases of fungal, bacterial, and viral origin, resulting in substantial yield losses (≥50%). Buckeye rot (caused by Phytophthora nicotianae var. parasitica) is among the major constraints in the successful cultivation of tomato crops in various parts of the world including the Solan district of Himachal Pradesh state, India. The fruit rot becomes more devastating under high humidity and wet soils. Symptoms generally appear on green fruit as alternate dark and light brown concentric rings. The genome size of P. nicotianae var. parasitica is 82 Mb with >23,000 predicted genes. High humidity (> 60%) and optimal temperatures (20-25 ºC), along with rainfall (≥ 10 mm), help to disperse the pathogen as the inoculum reaches the fruit through splashing rains. Sporangia germinate indirectly by producing zoospores at 20-25o C, or directly via germ tubes at >25ºC. In the absence of suitable resistant varieties, no single management practice is sufficient to keep the disease below the economic threshold level; therefore, integration of cultural and chemical methods is preferable. This paper aims to focus on the etiology, and management challenges of buckeye rot. We recommend innovative disease management strategies like identification and deployment of resistant cultivars as well as spraying of synthetic chemical fungicides, biocontrol agents, and use of abiotic chemicals that induce resistance, for developing sustainable crop production practices.

2021 ◽  
Vol 9 (11) ◽  
pp. 319-322
Yeswanth Sai Kumar Thota ◽  
Harshitha Uriti ◽  
Sree Lakshmi Mandadapu ◽  
Shaik Mohammed Junaid ◽  

Rice production is constrained by diseases of fungal, bacterial and viral origin. The Internet of Things (IoT) – network of interconnected devices - is an application for disease related uses, collection of data, processing for testing and monitoring. This review article aims about how IoT can track and allows disease resistance studies in in Oryza species. Among them Xanthomonas oryzae, Magnaporthe grisea, RYMV (Rice yellow mottle virus), and brown planthopper causes the high yield losses. Disease resistance genes are identified and they are screened by the SSR (simple sequence repeats), RAPD (Randomly Amplified Polymorphic DNA) and RFLP (restriction fragment length polymorphisms) analysis.

Biomedicines ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1732
Eleonore Fröhlich

Acute respiratory distress syndrome (ARDS) is a serious affection of the lung caused by a variety of pathologies. Great interest is currently focused on ARDS induced by viruses (pandemic influenza and corona viruses). The review describes pulmonary changes in ARDS and specific effects of the pandemic viruses in ARDS, and summarizes treatment options. Because the known pathogenic mechanisms cannot explain all aspects of the syndrome, the contribution of pulmonary lymphatics to the pathology is discussed. Organization and function of lymphatics in a healthy lung and in resorption of pulmonary edema are described. A future clinical trial may provide more insight into the role of hyaluronan in ARDS but the development of promising pharmacological treatments is unlikely because drugs play no important role in lymphedema therapy.

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S279-S279
Lauren Groft ◽  
Iulia Opran ◽  
Yeabsera Tadesse ◽  
Hang Vo ◽  
Emily Heil ◽  

Abstract Background Patients with COVID-19 receive high rates of antibiotic therapy, despite viral origin of infection. Reports of bacterial coinfection range from 3.5 to 8% in the early phase of infection. This study aimed to evaluate the relationship between diagnostic tests and antibiotic utilization in patients admitted with COVID-19 at the University of Maryland Medical Center to better inform future prescribing practices. Methods Retrospective cohort study of adult patients with a positive SARS-CoV-2 PCR on admission from March 2020 through June 2020. Associations between diagnostic tests employed and antibiotic initiation and duration were explored using bivariate analysis (SPSS®). Results Baseline characteristics of 224 included patients are reported in Table 1. Excluding SARS-CoV-2 PCRs, most frequently performed diagnostic tests included blood cultures (65.6%), MRSA nasal surveillance (45.1%), respiratory cultures (36.2%), respiratory viral panel (RVP) (33.0%), and Legionella (28.6%) and pneumococcal (26.3%) urine antigens. Positivity of RVP, Legionella, pneumococcus, blood, and respiratory tests were low (1.3%, 0.4%, 0.9%, 1.8%, and 6.7%, respectively). A total of 62% of patients were initiated on antibacterial therapy with a median cumulative antibiotic duration of 77.9 hours (IQR 41.4, 111.8). History of chronic respiratory disease (76% vs. 58.6%; P=0.025), any degree of oxygen requirement on admission (72% vs. 42.6%; P=0.006), and performance of blood cultures (70.7% vs. 46.8%, P&lt; 0.0001) were associated with antibiotic initiation. Positive bacterial diagnostic respiratory culture (median duration 72.8h [IQR 46.7, 96.6] vs. 97.3h [IQR 79.8, 194.1]; P=0.027) and positive blood culture (median duration 80.1h [IQR 42.1, 111.7] vs. 97.5h [IQR 71.8, 164.8]; P=0.046) were associated with longer antibiotic duration. Patients who did not have respiratory cultures performed had similar antibiotic durations as those with negative respiratory cultures. Table 1. Baseline Characteristics Conclusion Despite low coinfection rates, negative diagnostic tests did not result in shorter empiric antibacterial duration. These findings highlight the ongoing need for both diagnostic and antimicrobial stewardship in COVID-19. Disclosures Emily Heil, PharmD, MS, BCIDP, Nothing to disclose Kimberly C. Claeys, PharmD, GenMark (Speaker’s Bureau)

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S248-S248
Aileen Martinez ◽  
Lyssette Cardona ◽  
Nina Ricci

Abstract Background The 2019 coronavirus SARS-CoV-2 continues to affect global population health. Patients with severe disease that require hospitalization due to COVID-19 pneumonia remain at further risk of bacterial co-infections. There is limited evidence suggesting up to 3.5% bacterial co-infection upon admission and up to 13.5% of secondary infections after hospitalization for pneumonia yet antibacterial therapy usage remain as high, or even higher, than data seen for viral pneumonia, such as influenza. Unnecessary use of antimicrobial therapy may lead to further resistance and requires stewardship attention. Methods A single-center retrospective chart review was conducted in a community health system on all inpatient influenza admissions between October 1st 2019 to March 31st 2020 and all COVID-19 admissions during the same 6-month period one year later. Patients were excluded if age &lt; 18, observation or emergency visit. The study aims to determine the percentage of patients that were prescribed antibacterial therapy during influenza season compared to during the COVID-19 pandemic. Results A total of 175 patients were included in the influenza group while 1411 patients were included in the COVID-19 group (Table 1). The percent of inpatients with positive bacterial respiratory cultures were 12% in both influenza and COVID-19 groups. Positive bacterial respiratory cultures collected within 48 hours of admission were 3.4% in the influenza group compared to 1.2% in the COVID -19 group. Seventy-three percent of patients in the influenza group received antibiotics during admission compared to 78% in the COVID -19 group. Azithromycin and/or ceftriaxone was most commonly prescribed (58% vs. 60%) (Figure 1). The median length of stay was 3 days in the influenza group compared to 5 days in the COVID-19 group. In hospital mortality was higher in the COVID-19 group (1.7% vs. 9%). Conclusion Despite the viral origin of influenza and COVID-19 and low incidence of bacterial infection, antibacterials were frequently prescribed in both indications but it appears to trend more so in the COVID-19 group. There is an opportunity to enhance antimicrobial stewardship for the treatment of COVID-19 in acute care settings. Disclosures All Authors: No reported disclosures

2021 ◽  
Irina Yuri Kawashima ◽  
Maria Claudia Negret Lopez ◽  
Marielton dos Passos Cunha ◽  
Ronaldo Fumio Hashimoto

Abstract The genetic diversity of the Coronaviruses gives them different biological abilities, such as infect different cells and/or organisms, a wide spectrum of clinical manifestations in a single host, their different routes of dispersion, and viral transmission in a specific host. In recent decades, different Coronaviruses have emerged that are highly adapted for humans and causing serious diseases, leaving their host of unknown origin. The viral genome information is particularly important to enable the recognition of patterns linked to their biological characteristics, such as the specificity in the host-parasite relationship. Here, based on a previously computational tool, the seq2host, we developed a novel approach which uses new variables obtained from the frequency of spike-Coronaviruses codons, the Relative Synonymous Codon Usage (RSCU) to shed new light on the molecular mechanisms involved in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) host specificity. By using the RSCU obtained from nucleotide sequences before the SARS-CoV-2 pandemic, we assessed the possibility of know the hosts capable to be infected by these new emerging species, which was first identified infecting humans during 2019 in Wuhan, China. According to the tool trained and validated using sequences available before the pandemic, bats are the most likely susceptible host to the SARS-CoV-2 infection, as previously suggested in other studies that searched for the host viral origin.

2021 ◽  
Vol 12 ◽  
Pierpaolo Trimboli ◽  
Carlo Cappelli ◽  
Laura Croce ◽  
Lorenzo Scappaticcio ◽  
Luca Chiovato ◽  

Subacute thyroiditis (SAT) is a thyroid disease of viral or post-viral origin. Whether SAT represents a complication of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still unclear. Our aim was to systematically review the literature to 1) explore the size of the literature about SAT in COVID-19 and 2) evaluate the clinical characteristics of SAT. PubMed/MEDLINE, Embase, and Scopus were searched until April 20, 2021. Original papers, case reports, and case series reporting SAT in COVID-19 patients were included. Authors and their country, journal, year of publication, COVID-19 and SAT clinical presentation, thyroid function, therapy, and follow-up data were extracted. Nineteen papers (17 case reports and 2 case series) were included, describing 27 patients, 74.1% females, aged 18 to 69 years. COVID-19 was diagnosed by nasopharyngeal swab in 66.7% cases and required hospitalization in 11.1%. In 83.3% cases, SAT occurred after COVID-19. Neck pain was present in 92.6% cases and fever in 74.1%. Median TSH, fT3, and fT4 were 0.01 mU/l, 10.79 pmol/l, and 27.2 pmol/l, respectively. C-reactive-protein and erythrocyte sedimentation rate were elevated in 96% of cases. Typical ultrasonographic characteristics of SAT were observed in 83.3% of cases. Steroids were the most frequent SAT therapy. Complete remission of SAT was recorded in most cases. In conclusion, the size and quality of published data of SAT in COVID-19 patients are poor, with only case reports and case series being available. SAT clinical presentation in COVID-19 patients seems to be similar to what is generally expected.

Cáceres-Toledo Odalys ◽  
Cáceres-Toledo María ◽  
Zhao Runse ◽  
Laurencio Yeimi Carolina ◽  
O-Lozano Yarlín La ◽  

Optic neuritis presents as an acute or subacute inflammatory episode. Objective: Describe the clinical-epidemiological characteristics in 7 cases with unilateral optic neuritis and evaluate the therapeutic results obtained. Material and method: A series of cases with a diagnosis of unilateral optic neuritis who attended the Neurophthalmology consultation at the Hermanos Ameijeiras Hospital in Havana, Cuba, from August 6 to November 16, 2018, from Havana and Matanzas, were studied. An unusual increase in the incidence of NO was recorded in the period analyzed. Results: An unusual increase in the incidence of unilateral optic neuritis was recorded. The average age was 33.5 years. All reported unilateral painless visual loss. Four patients reported general signs and symptoms suggestive of having suffered a respiratory disease of viral origin, between 7 and 15 days before optic neuritis. In the examination carried out, great impairment of visual acuity (≤0.05) and colors (0/21) was found. The centro-caecal scotoma was the most frequent campimetric defect. Optical Coherence Tomography (OCT) in the affected eye showed increased neuroretinal thickness, decreased nerve fiber layer, and ganglion cell damage. Treatment was with intravenous methylprednisolone and B vitamins. Conclusions: An unusual increase in patients with unilateral optic neuritis was observed. The OCT revealed damage to the structures at the level of the retina and the optic nerve. The therapeutic effectiveness was conditioned by the time of evolution of the neuritis.

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