Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification

Souza, Juliana Vanessa Cavalcante; Santos, Hazerral de Oliveira; Leite, Anderson Brandão; Giovanetti, Marta; Bezerra, Rafael dos Santos; Carvalho, Enéas; Bernardino, Jardelina de Souza Todão; Viala, Vincent Louis; Haddad, Rodrigo; Ciccozzi, Massimo; Alcântara, Luiz Carlos Júnior; Sampaio, Sandra Coccuzzo; Covas, Dimas Tadeu; Kashima, Simone; Elias, Maria Carolina; Slavov, Svetoslav Nanev

doi:10.3390/v14091933

Cited by 10 publications

(4 citation statements)

References 15 publications

(17 reference statements)

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“…Single Primer Amplification (SISPA) [50] Chikungunya Dengue, Zika virus Viral metagenomics was found to be a potent method for the identification of emerging arboviruses. Illumina NextSeq 2000 [60] Avian influenza virus (H7N9) Viral infection surveillance in poultry farms. Ion Torrent PGM [61] Influenza virus Diagnostic test, insights on transmission, evolution, and drug resistance.…”

Section: Nanopore-based Sequence-independentmentioning

confidence: 99%

Genomics for Emerging Pathogen Identification and Monitoring: Prospects and Obstacles

Vashisht,

Mondal

et al. 2023

BioMedInformatics

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Emerging infectious diseases (EIDs) pose an increasingly significant global burden, driven by urbanization, population explosion, global travel, changes in human behavior, and inadequate public health systems. The recent SARS-CoV-2 pandemic highlights the urgent need for innovative and robust technologies to effectively monitor newly emerging pathogens. Rapid identification, epidemiological surveillance, and transmission mitigation are crucial challenges for ensuring public health safety. Genomics has emerged as a pivotal tool in public health during pandemics, enabling the diagnosis, management, and prediction of infections, as well as the analysis and identification of cross-species interactions and the categorization of infectious agents. Recent advancements in high-throughput DNA sequencing tools have facilitated rapid and precise identification and characterization of emerging pathogens. This review article provides insights into the latest advances in various genomic techniques for pathogen detection and tracking and their applications in global outbreak surveillance. We assess methods that leverage pathogen sequences and explore the role of genomic analysis in understanding the epidemiology of newly emerged infectious diseases. Additionally, we address technical challenges and limitations, ethical and legal considerations, and highlight opportunities for integrating genomics with other surveillance approaches. By delving into the prospects and obstacles of genomics, we can gain valuable insights into its role in mitigating the threats posed by emerging pathogens and improving global preparedness in the face of future outbreaks.

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Section: Nanopore-based Sequence-independentmentioning

confidence: 99%

Genomics for Emerging Pathogen Identification and Monitoring: Prospects and Obstacles

Vashisht,

Mondal

et al. 2023

BioMedInformatics

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“…This method has been used to identify arboviruses in patients with undiagnosed encephalitis/meningitis and in patients with symptoms consistent with arboviral infection but yielding inconclusive RT-PCR data [ 5 , 44 , 45 , 46 ]. NGS has proved to be a useful tool to analyze strains of Orthomyxoviridae obtained from different geographical areas, resulting in the classification and separation of these viruses into two major clades, namely the Thogoto-like and Dhori-like viruses [ 47 ].…”

Section: Arbovirus Diagnostic Approachesmentioning

confidence: 99%

Latest Advances in Arbovirus Diagnostics

2023

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Arboviruses are a diverse family of vector-borne pathogens that include members of the Flaviviridae, Togaviridae, Phenuviridae, Peribunyaviridae, Reoviridae, Asfarviridae, Rhabdoviridae, Orthomyxoviridae and Poxviridae families. It is thought that new world arboviruses such as yellow fever virus emerged in the 16th century due to the slave trade from Africa to America. Severe disease-causing viruses in humans include Japanese encephalitis virus (JEV), yellow fever virus (YFV), dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), Crimean–Congo hemorrhagic fever virus (CCHFV), severe fever with thrombocytopenia syndrome virus (SFTSV) and Rift Valley fever virus (RVFV). Numerous methods have been developed to detect the presence of these pathogens in clinical samples, including enzyme-linked immunosorbent assays (ELISAs), lateral flow assays (LFAs) and reverse transcriptase–polymerase chain reaction (RT-PCR). Most of these assays are performed in centralized laboratories due to the need for specialized equipment, such as PCR thermal cyclers and dedicated infrastructure. More recently, molecular methods have been developed which can be performed at a constant temperature, termed isothermal amplification, negating the need for expensive thermal cycling equipment. In most cases, isothermal amplification can now be carried out in as little as 5–20 min. These methods can potentially be used as inexpensive point of care (POC) tests and in-field deployable applications, thus decentralizing the molecular diagnosis of arboviral disease. This review focuses on the latest developments in isothermal amplification technology and detection techniques that have been applied to arboviral diagnostics and highlights future applications of these new technologies.

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“…Their study resulted in the discovery of two novel RNA and DNA viruses namely grapevine umbra-like virus (GULV) and grapevine pararetrovirus (GPRV), respectively. Application of metagenomics in clinical specimen vector-borne viruses 5,6 , respiratory viral infections 7 , and blood-borne viruses have been studied before 8 . However, despite the potential of metagenomics studies in the discovery of novel viruses and revealing the hiding nods of the viral evolution, its robustness for surveillance on emerging and reemerging viral outbreaks, and bioterrorism remain mostly untouched.…”

Section: Introductionmentioning

confidence: 99%

A metagenomic survey on Solanum tuberosum virome revealed environmental contamination of a laboratory-developed strain of SARS-CoV-2

Hassanpour

Mohebbi

2023

Preprint

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Metagenomics is a promising approach to discovering viral sequences in environmental samples. We used recently published RNA-Seq data of Solanum tuberosum (S. tuberosum) from China for a metavirome study. Several environmentally related non-intact viruses read from forest animals, moths, bacteria, and amoeba were detected. Further investigation resulted in non-indigenous sequences of SARS-CoV-2 genomes of lineage B with novel substitutions. Three substitutions, including A22D and A36V in the envelope protein and Q498H in the spike glycoprotein that were recently reported from a laboratory strain virus with enhanced virulence, were detected in all samples. Further substitutions at ORF1ab were also uncovered. These were L1457V, D4553N, W6538S, I1525T, D1585Y, D6928G, N3414K, T3432S. Two unexpected frameshifts, ORF1a:2338–4401 and ORF1a:3681–4401, were noticed within the ORF1ab. The genomic evidence and geographical evidence of lab leaks are also provided. The findings of the presented study highlight the threats of the emerged potentially severe genotypes bearing substitutions that are not yet clinically reported. More studies are warranted to uncover the role of the novel substitutions in the severity of SARS-coV-2

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Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification

Cited by 10 publications

References 15 publications

Genomics for Emerging Pathogen Identification and Monitoring: Prospects and Obstacles

Genomics for Emerging Pathogen Identification and Monitoring: Prospects and Obstacles

Latest Advances in Arbovirus Diagnostics

A metagenomic survey on Solanum tuberosum virome revealed environmental contamination of a laboratory-developed strain of SARS-CoV-2

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