Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods

Kamelian, Kimia; Montoya, Vincent; Olmstead, Andrea D.; Dong, Winnie; Harrigan, Richard; Morshed, Muhammad; Joy, Jeffrey B.

doi:10.1038/s41598-019-52613-8

Cited by 4 publications

(1 citation statement)

References 42 publications

(48 reference statements)

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“…The development of NGS techniques has led to a huge amount of genomic sequence data [3]. As it was shown for emerging infectious diseases, such as SARS, MERS, Zika, and Ebola, whole-genome sequencing (WGS) metagenomics SARS-CoV-2 Variant Surveillance in Genomic Medicine Era DOI: http://dx.doi.org/10.5772/intechopen.107137 technique offers the possibility to rapidly obtain the full sequence of pathogen genomes, tracing origins, spread and transmission chains of outbreaks, and monitoring the pathogen evolution [24][25][26][27][28].…”

Section: Sars-cov-2 Variants -Two Years Aftermentioning

confidence: 99%

SARS-CoV-2 Variant Surveillance in Genomic Medicine Era

Diaconu¹,

Pitica²,

Chivu‐Economescu³

et al. 2023

Infectious Diseases

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In the genomic medicine era, the emergence of SARS-CoV-2 was immediately followed by viral genome sequencing and world-wide sequences sharing. Almost in real-time, based on these sequences, resources were developed and applied around the world, such as molecular diagnostic tests, informed public health decisions, and vaccines. Molecular SARS-CoV-2 variant surveillance was a normal approach in this context yet, considering that the viral genome modification occurs commonly in viral replication process, the challenge is to identify the modifications that significantly affect virulence, transmissibility, reduced effectiveness of vaccines and therapeutics or failure of diagnostic tests. However, assessing the importance of the emergence of new mutations and linking them to epidemiological trend, is still a laborious process and faster phenotypic evaluation approaches, in conjunction with genomic data, are required in order to release timely and efficient control measures.

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Section: Sars-cov-2 Variants -Two Years Aftermentioning

confidence: 99%

SARS-CoV-2 Variant Surveillance in Genomic Medicine Era

Diaconu¹,

Pitica²,

Chivu‐Economescu³

et al. 2023

Infectious Diseases

View full text Add to dashboard Cite

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The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents

Timsit,

Armand-Lefèvre,

Le Goff

et al. 2024

Infectious Diseases Now

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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

Chiara

D’Erchia

Gissi

et al. 2020

Briefings in Bioinformatics

157

131

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Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our ‘ vademecum ’ for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.

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Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods

Cited by 4 publications

References 42 publications

SARS-CoV-2 Variant Surveillance in Genomic Medicine Era

SARS-CoV-2 Variant Surveillance in Genomic Medicine Era

The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

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