High-throughput sequencing (HTS) for the analysis of viral populations

Pérez‐Losada, Marcos; Arenas, Miguel; Galán, Juan Carlos; Bracho, María Alma; Hillung, Julia; García-González, Neris; Gónzález-Candelas, Fernando

doi:10.1016/j.meegid.2020.104208

Cited by 51 publications

(34 citation statements)

References 306 publications

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“… Plasmid and virus isolation and amplification (PCR, MDA, TRACA) methods are biased towards small plasmids. ( Jones and Marchesi, 2007 ; Thurber et al., 2009 ; Sentchilo et al., 2013 ; Smalla et al., 2015 ) Viral metagenomics ( Edwards and Rohwer, 2005 ; Thurber et al., 2009 ; Parsley et al., 2010a , Parsley et al., 2010b ; Pérez-Losada et al., 2020 ) Single-cell analysis MGEs and host cells can be linked. The assembly of MGEs becomes easier by decreasing the complexity of the sample.…”

Section: Methods For Mobile Genetic Elements Analysis In Environmentamentioning

confidence: 99%

“…The study of viral communities in WWTPs has been limited due to the low percentage of host bacteria that can be cultured in the laboratory. However, recent advances in high-throughput sequencing technologies have enabled researchers to sequence the whole viral metagenome in several samples ( Edwards and Rohwer, 2005 ; Pérez-Losada et al., 2020 ). Genes identified in the phage metagenomes of several WWTPs and other environments such as the mouse gut include ARGs and 16S rRNA genes from Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria ( Parsley et al., 2010a , Parsley et al., 2010b ; Del Casale et al., 2011 ; Modi et al., 2013 ).…”

Section: Catabolic Mobile Genetic Elements In Wastewater Treatment Plmentioning

confidence: 99%

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The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

2020

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Wastewater treatment plants (WWTPs) are crucial for producing clean effluents from polluting sources such as hospitals, industries, and municipalities. In recent decades, many new organic compounds have ended up in surface waters in concentrations that, while very low, cause (chronic) toxicity to countless organisms. These organic micropollutants (OMPs) are usually quite recalcitrant and not sufficiently removed during wastewater treatment. Microbial degradation plays a pivotal role in OMP conversion. Microorganisms can adapt their metabolism to the use of novel molecules via mutations and rearrangements of existing genes in new clusters. Many catabolic genes have been found adjacent to mobile genetic elements (MGEs), which provide a stable scaffold to host new catabolic pathways and spread these genes in the microbial community. These mobile systems could be engineered to enhance OMP degradation in WWTPs, and this review aims to summarize and better understand the role that MGEs might play in the degradation and wastewater treatment process. Available data about the presence of catabolic MGEs in WWTPs are reviewed, and current methods used to identify and measure MGEs in environmental samples are critically evaluated. Finally, examples of how these MGEs could be used to improve micropollutant degradation in WWTPs are outlined. In the near future, advances in the use of MGEs will hopefully enable us to apply selective augmentation strategies to improve OMP conversion in WWTPs.

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Section: Methods For Mobile Genetic Elements Analysis In Environmentamentioning

confidence: 99%

Section: Catabolic Mobile Genetic Elements In Wastewater Treatment Plmentioning

confidence: 99%

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

2020

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“…Undoubtedly, detection of novel virus variants and species has been facilitated by the dramatic progress in whole-genome sequencing [46][47][48][49][50][51], thanks to the advent of a number of next-generation sequencing methods allowing full-length sequencing at a fraction of the time and cost required for traditional Sanger sequencing [52].…”

Section: Sequence Of Target Rna Virusesmentioning

confidence: 99%

Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge

et al. 2020

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The RNA-dependent RNA polymerase (RdRp) is an essential enzyme for the viral replication process, catalyzing the viral RNA synthesis using a metal ion-dependent mechanism. In recent years, RdRp has emerged as an optimal target for the development of antiviral drugs, as demonstrated by recent approvals of sofosbuvir and remdesivir against Hepatitis C virus (HCV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respectively. In this work, we overview the main sequence and structural features of the RdRp of emerging RNA viruses such as Coronaviruses, Flaviviruses, and HCV, as well as inhibition strategies implemented so far. While analyzing the structural information available on the RdRp of emerging RNA viruses, we provide examples of success stories such as for HCV and SARS-CoV-2. In contrast, Flaviviruses’ story has raised attention about how the lack of structural details on catalytically-competent or ligand-bound RdRp strongly hampers the application of structure-based drug design, either in repurposing and conventional approaches.

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“…Through this proof-reading function, the CoVs appear to have overcome the limitation, which in most RNA viruses, during process of replication, lead to the non-viable virions rapidly outnumbering the viable ones, leading to a loss of itness and/ or viral extinction. In addition, the CoVs, like other RNA viruses can resort to RNA viral evolution through recombination (synthesis of chimeric RNA molecules from two different progeny genomes) and reassortment (the packaging within a single virion of genomic segments from different progeny viruses) [17].…”

Section: Future Prospects Of Covid-19mentioning

confidence: 99%

COVID-19 pandemic, recurrent outbreaks and prospects for assimilation of hCoV-19 into the human genome

Nikhra¹

2020

Int J Clin Virol

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The outbreaks and resurgence: The disease which reportedly began in the Chinese city Wuhan in November-December 2019, soon spread to various parts of the world, and was named and declared a pandemic disease by WHO. While the European countries were recovering from the epidemic, the disease took hold in the USA, the South American countries, Arabian countries, and South Asian countries, predominantly affecting Brazil, Peru, Iran, and India. Presently, many European countries are witnessing a resurgence and recurrent outbreaks of COVID-19. Spread and evolving new insights: Whereas there is workplace-related infection rise as people are returning to their offices, in other places the outbreaks are related to the people crowding and meeting care-freely and trying to resort back to their earlier way of life. The reopening of the educational facilities across the continents may make matters worse. Impact on health and healthcare: Most cases of COVID-19 infections go unnoticed and are followed by self-recovery. But what may appear good from the clinical perspective, appears to complicate epidemiological efforts to contain the outbreak. With the evolving information about the disease, there seem to be certain possible outcomes such as control and containment, or the persistence of the disease as global endemic accompanied with outbreaks and resurgent episodes. Gnetic factors linked to disease severity: With the COVID-19 pandemic, not all infected patients develop a severe respiratory illness. Further, there is a large variation in disease severity, which may be due to the genetic factors underlying the variable response to the virus. It is becoming clear that apart from the advanced age and pre-existing conditions, certain genetic constituent factors render some patients more vulnerable to the more severe forms of the diseases. Integration of virus into human genome: A significant part of the human genome is derived from viruses especially the RNA viruses. In fact, about 8 percent of the human genome is made up of endogenous retroviruses (ERVs), which are viral gene sequences that have become a permanent part of the human lineage after they infected our ancient ancestors. With this background, a novel concept emerging that if COVID-19 persists for several generations, its genetic material is projected to be integrated or assimilated into human genome. The involved mechanisms are conceptualized through the transposons or transposable elements of the SARS-CoV-2.

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High-throughput sequencing (HTS) for the analysis of viral populations

Cited by 51 publications

References 306 publications

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge

COVID-19 pandemic, recurrent outbreaks and prospects for assimilation of hCoV-19 into the human genome

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