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Order Amarillovirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
The Amarillovirales order currently involves one family, namely Flaviviridae, 4 genera, and 89 species. The genera are Flavivirus, Hepacivirus, Pegivirus, and Pestivirus. Most infect mammals and birds. Many of them are host-specific and highly pathogenic, such as hepatitis C virus (HCV) of the genus Hepacivirus. After HCV, a major human pathogen-causing progressive liver disease (Yu ML and Chuang 2021), the Hepacivirus genus involves several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows, and primates (Scheel et al. 2015).
Role of structural disorder in the multi-functionality of flavivirus proteins
Published in Expert Review of Proteomics, 2022
Shivani Krishna Kapuganti, Aparna Bhardwaj, Prateek Kumar, Taniya Bhardwaj, Namyashree Nayak, Vladimir N. Uversky, Rajanish Giri
The viruses under the family Flaviviridae are enveloped with positive-sense single-stranded, non-segmented RNA genome ranging from 9 to 13kb. Mostly, the viruses are pathogenic to humans and their pathogenicity ranges from asymptomatic/mild symptoms to lethal hemorrhagic and neurological damages. This family is further classified into four genera: Flavivirus, Hepacivirus, Pegivirus, and Pestivirus, having 53, 14, 11, and 11 species, respectively. Some of the well-known examples of flaviviruses are Dengue virus (DENV), Japanese encephalitis virus (JEV), Tick-borne encephalitis virus (TBEV), West Nile virus (WNV), Yellow fever virus (YFV), and Zika virus (ZIKV) from Flaviviruses.
Next-generation sequencing-based clinical metagenomics identifies Prevotella pleuritidis in a diabetic adolescent with large parapneumonic effusion and negative growth of pleural fluid culture: a case report
Published in British Journal of Biomedical Science, 2021
T Galliguez, PY Tsou, A Cabrera, J Fergie
Next-generation sequencing-based clinical metagenomics is able to provide culture-independent unbiased detection, quantification and genetic profiling of pathogens through a shotgun approach, and the timely and accurate identification of pathogens [14]. Our clinical experience with the results of next-generation sequencing-based clinical metagenomics leading to change of patient care resonated with prior literature. Zhou et al. identified Prevotella spp. in a diabetic adult presented with thoracic empyema who was initially received prolonged treatment for tuberculosis [4]. Another strength of next-generation sequencing is its ability to identify pathogens that are species unrecognized before or are genetically divergent strains not detectable using PCR. With next-generation sequencing-based metagenomics, there are a few limitations that must be considered. First of all, upon identifying a pathogen in a sample, it can be difficult to determine the clinical significance in identifying whether the pathogen is causing an active infection, contaminant or host normal flora. For instance, in this case, in addition to Prevotella pleuritidis, next-generation sequencing-based clinical metagenomics reported the identification of Human Pegivirus, a virus of unclear pathogenicity [15]. The interpretation of the presence of this virus raises the question of its relevance in its pathogenicity of the parapneumonic effusion. Secondly, as compared to multiplex respiratory PCR, next-generation sequencing-based metagenomics has a relatively long turnaround time from library preparation and sequencing. Moreover, the cost of next-generation sequencing-based metagenomics and the need for computational power may be a prohibitory factor preventing its generalization. However, metagenomic testing may potentially shorten the length of hospitalization and unnecessary antibiotics exposure, reducing the total medical expenditure. There are also exciting applications in development which are able to mine antimicrobial resistance data as well as host response (transcriptome) information from clinical metagenomic data. Given the strengths and limitations of next-generation sequencing-based metagenomics, we considered it a reasonable alternative for immunocompromised patients and when routine therapeutic approaches and traditional diagnostic methods (e.g. culture-based method) fail. Table 2 compared the pros and cons between next-generation sequencing-based metagenomics and culture for diagnosing infectious diseases.