Whole genome amplicon sequencing and phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from lineage B.1.36.27 isolated in Hong Kong

Tsang, Hin Fung; Yu, Allen Chi Shing; Wong, Heong Ting; Leung, Wai Ming; Chiou, Jiachi; Wong, Yin Kwan; Yim, Aldrin Kay Yuen; Tsang, Dnc; Tsang, Alan K.L.; Wong, Wing Tak; Wong, Sze Chuen Cesar; Cho, William C.

doi:10.1080/14737159.2022.2015330

Cited by 2 publications

(1 citation statement)

References 22 publications

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“…Bioinformatic analysis. Sequencing data was analyzed using DRAGEN COVID Lineage (version 3.5.9; Illumina Inc., USA) and method as described previously [11,12]. In brief, sequencing reads of human origin were removed using NCBI Human Read Scrubber algorithm.…”

Section: Whole Viral Genome Sequencingmentioning

confidence: 99%

The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis

Tsang

Yu²,

Yim³

et al. 2023

PLoS ONE

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Pediatric population was generally less affected clinically by SARS-CoV-2 infection. Few pediatric cases of COVID-19 have been reported compared to those reported in infected adults. However, a rapid increase in the hospitalization rate of SARS-CoV-2 infected pediatric patients was observed during Omicron variant dominated COVID-19 outbreak. In this study, we analyzed the B.1.1.529 (Omicron) genome sequences collected from pediatric patients by whole viral genome amplicon sequencing using Illumina next generation sequencing platform, followed by phylogenetic analysis. The demographic, epidemiologic and clinical data of these pediatric patients are also reported in this study. Fever, cough, running nose, sore throat and vomiting were the more commonly reported symptoms in children infected by Omicron variant. A novel frameshift mutation was found in the ORF1b region (NSP12) of the genome of Omicron variant. Seven mutations were identified in the target regions of the WHO listed SARS-CoV-2 primers and probes. On protein level, eighty-three amino acid substitutions and fifteen amino acid deletions were identified. Our results indicate that asymptomatic infection and transmission among children infected by Omicron subvariants BA.2.2 and BA.2.10.1 are not common. Omicron may have different pathogenesis in pediatric population.

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Section: Whole Viral Genome Sequencingmentioning

confidence: 99%

The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis

Tsang

Yu²,

Yim³

et al. 2023

PLoS ONE

Self Cite

View full text Add to dashboard Cite

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Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases

Pei

Yeung

Wong

et al. 2023

Cells

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The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.

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Whole genome amplicon sequencing and phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from lineage B.1.36.27 isolated in Hong Kong

Cited by 2 publications

References 22 publications

The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis

The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis

Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases

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