Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing

Hare, Daniel; Meaney, Carolyn; Powell, James; Slevin, B; Brien, Breda O'; Power, Lorraine; Connell, Nuala H. O’; Gascun, Cillian F. De; Dunne, Colum P.; Stapleton, Patrick

doi:10.1016/j.jhin.2022.04.015

Cited by 10 publications

(4 citation statements)

References 32 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

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“…Overcrowded environments have been implicated to increase the risk of COVID-19 outbreaks in workplaces and hospital environments ( [50] , [51] , [52] ). Future studies may consider optimizing the routine cleaning schedule according to the ED attendance to reduce the risk of contamination.…”

Section: Discussionmentioning

confidence: 99%

A longitudinal environmental surveillance study for SARS-CoV-2 from the emergency department of a teaching hospital in Hong Kong

Yung¹,

Leung²,

Lee³

et al. 2023

Journal of Hospital Infection

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“…We assigned PANGO lineages with pangolin 9 version 3.1.17, aligned consensus sequences with MAFFT, 10 and created a phylogenetic tree via IQ-TREE2 11 and visualized it with ggtree 12 (open-source software). We measured relatedness by single-nucleotide polymorphism (SNP) differences between viral sequences, with a difference of 0 or 1 SNP indicating a close genetic relationship 13 , 14 and with larger differences suggesting less genetic relatedness.…”

Section: Methodsmentioning

confidence: 99%

“…Given SARS-CoV-2's low estimated mutation rate, 15,16 direct transmission events would typically manifest as a 0-or 1-SNP difference between sequences. 13,14 The observed 2-SNP difference could indicate direct transmission with a greater-than-expected SNP difference or independent transmission. Other available WGS data did not suggest direct transmission between case-members.…”

Section: Lessons Learnedmentioning

confidence: 98%

Investigation of SARS-CoV-2 Transmission in The Tabernacle Choir at Temple Square in the Context of Prevention Protocols, Utah, September–November 2021

et al. 2023

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Group singing and playing of wind instruments increase COVID-19 transmission risk. After a pause during the initial period of the COVID-19 pandemic, The Tabernacle Choir at Temple Square organization (hereinafter, Choir) resumed musical events in September 2021 with prevention protocols, including required vaccination and pre-event rapid antigen testing. We investigated potential SARS-CoV-2 transmission at Choir events during September 21–November 7, 2021. We interviewed COVID-19–positive members (hereinafter, case-members) and identified members exposed when a case-member attended a Choir event during his or her infectious period. We compared whole genome sequencing results to assess the genetic relatedness of available SARS-CoV-2 specimens obtained from case-members. We identified 30 case-members through pre-event testing (n = 10), self-reported positive test results (n = 18), and a review of Utah’s disease surveillance system (n = 2). All 30 case-members reported symptoms; 21 (70%) were women and 23 (77%) received a positive test result by nucleic acid amplification test. No hospitalizations or deaths were reported. We identified 176 test-eligible exposed members from 14 instances of case-members attending events during their infectious periods. All were tested at least once 2 to 14 days after exposure: 74 (42%) by rapid antigen test only (all negative) and 102 (58%) by nucleic acid amplification test (4 positive, 97 negative, and 1 equivocal). Among viral sequences available from 15 case-members, the smallest single-nucleotide polymorphism distance between 2 sequences was 2, and the next-smallest distance was 10. The lack of disease detected in most exposed members suggests that minimal, if any, transmission occurred at Choir events. When community COVID-19 incidence is high, prevention protocols might help limit SARS-CoV-2 transmission during group musical activities.

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Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing

Cited by 10 publications

References 32 publications

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

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

A longitudinal environmental surveillance study for SARS-CoV-2 from the emergency department of a teaching hospital in Hong Kong

Investigation of SARS-CoV-2 Transmission in The Tabernacle Choir at Temple Square in the Context of Prevention Protocols, Utah, September–November 2021

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