Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review

Hare, Daniel; Dembicka, Kornelia Maria; Brennan, Carol; Campbell, C.; Sutton-Fitzpatrick, Una; Stapleton, Patrick; Gascun, Cillian F. De; Dunne, Colum P.

doi:10.1016/j.jhin.2023.08.002

Cited by 3 publications

(1 citation statement)

References 120 publications

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“…On the other hand, NGS methods have emerged as valuable tools for rapidly and efficiently generating complete genome sequences (Batista et al, 2020; Lee et al, 2023; Zufan et al, 2024). Particularly, their relevance was highlighted during the COVID-19 pandemic, when several specialized laboratories had access to this technology enabling the rapid sequencing of complete SARS-CoV-2 genomes for variant surveillance (Hare et al, 2023; Pisano et al, 2022). Despite its costliness, the widespread adoption of NGS during the pandemic paved the way for equipment acquisition, reagent availability, and professional training, thereby enabling its application for sequencing other viral genomes.…”

Section: Discussionmentioning

confidence: 99%

Hepatitis A virus whole genome sequencing strategy using NGS/Illumina technology

Sicilia,

Fantilli,

Cuba

et al. 2024

Preprint

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Background: Molecular epidemiology of hepatitis A virus (HAV) plays a critical role in identifying outbreak origin and conducting surveillance. Although it is mostly carried out using short partial VP1/2A genomic sequences, utilizing whole-genome sequences (WGS) provides more accurate and robust information. Objective: we aimed to develop an amplicon-based next-generation sequencing (NGS) strategy to obtain complete HAV genomes utilizing the COVIDSeq Test (Illumina), available in surveillance laboratories after the COVID19 pandemic. Study design: 25 primer pairs were designed and used to amplify partial genomic fragments (400bp) that comprise the entire HAV genome sequence from 16 HAV previously positive serum and stool samples from Argentina. The DNA library was prepared using the Illumina COVIDSeq Test and sequenced in a MiSeq equipment. Phylogenetic analyses were performed with IQ-Tree using WGS and VP1/2A partial sequences of 1084pb and 422pb. Results: 11 samples could be successfully amplified and sequenced, with horizontal coverage between 79.3%-100% (>90% in 9 samples). Individual RT-PCRs and Sanger sequencing with specific primers had to be performed in 6 samples to cover gaps of Ns. Phylogenetic analyses of WGS and VP1/2A partial sequences yielded similar results (clustering with genotype IA), although 422pb fragments showed low accurate grouping definition. Conclusion: the amplicon-based NGS whole genome sequencing tool developed by adapting the COVIDSeq test to HAV, proved to be efficient in generating new complete and near-complete viral sequences. The study of the 1084bp fragment of the VP1/2A region would constitute a useful alternative option for outbreak investigation with public health impact.

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Section: Discussionmentioning

confidence: 99%

Hepatitis A virus whole genome sequencing strategy using NGS/Illumina technology

Sicilia,

Fantilli,

Cuba

et al. 2024

Preprint

View full text Add to dashboard Cite

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SARS-CoV-2 surveillance in a hospital and control of an outbreak on a geriatric ward using whole genome sequencing

Schmidt,

Lemmermann,

Linke

et al. 2024

Infection Prevention in Practice

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Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance

Struelens,

Ludden,

Werner

et al. 2024

Front. Sci.

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This article advocates for mobilizing pathogen genomic surveillance to contain and mitigate health threats from infectious diseases and antimicrobial resistance (AMR), building upon successes achieved by large-scale genome sequencing analysis of SARS-CoV-2 variants in guiding COVID-19 monitoring and public health responses and adopting a One Health approach. Capabilities of laboratory-based surveillance and epidemic alert systems should be enhanced by fostering (i) universal access to real-time whole genome sequence (WGS) data of pathogens to inform clinical practice, infection control, public health policies, and vaccine and antimicrobial drug research and development; (ii) integration of diagnostic microbiology data, data from testing asymptomatic individuals, pathogen sequence data, clinical data, and epidemiological data into surveillance programs; (iii) stronger cross-sectorial collaborations between healthcare, public health, animal health, and environmental surveillance and research using One Health approaches, toward understanding the ecology and transmission pathways of pathogens and AMR across ecosystems; (iv) international collaboration and interconnection of surveillance networks, harmonization of laboratory methods, and standardization of surveillance methods for global reporting, including on pathogen genomic variant or strain nomenclature; (v) responsible data sharing between surveillance networks, databases, and platforms according to FAIR (findability, accessibility, interoperability, and reusability) principles; and (vi) research on genomic surveillance system implementation and its cost-effectiveness for different pathogens and AMR threats across different settings. Regional and global One Health policies and governance initiatives should foster the concerted development and efficient utilization of pathogen genomic surveillance to protect the health of humans, animals, and the environment.

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Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review

Cited by 3 publications

References 120 publications

Hepatitis A virus whole genome sequencing strategy using NGS/Illumina technology

Hepatitis A virus whole genome sequencing strategy using NGS/Illumina technology

SARS-CoV-2 surveillance in a hospital and control of an outbreak on a geriatric ward using whole genome sequencing

Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance

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