Phylogenomic tracing of asymptomatic transmission in a COVID-19 outbreak

Zhang, Ju; Ding, Nan; Song, Yangzi; Song, Rui; Pan, Yang; Wang, Linghang; Yan, Shuo; Wang, Qi; Ma, Shan-Fang; Wei, Lirong; Yu, Fang; Lu, Lian-he; Zhang, Fujie; Chen, Chen; Zeng, Hui

doi:10.1016/j.xinn.2021.100099

Cited by 4 publications

(3 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another important aspect of asymptomatic viral circulation is the critical role that it can play in the emergence of new genetic variants. 26 This link needs to be studied further.…”

Section: Discussionmentioning

confidence: 98%

SARS-CoV-2 RT-PCR positivity in relation to clinical and demographic characteristics in residents of border quarantine centres, Khyber Pakhtunkhwa, Pakistan: a prospective cohort study

Imran

Uddin

Ambade

et al. 2022

Transactions of the Royal Society of Tropical Medicine and Hygiene

View full text Add to dashboard Cite

Background As international travellers were the primary source of sever acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, border checkpoints became an important tool to isolate cases. We determined the period prevalence and SARS-CoV-2 reverse transcription polymerase chain reaction positivity in relation to clinical and demographic characteristics in healthy travellers quarantined at the Pakistan–Afghanistan border. Methods The study was conducted from 15 to 25 April 2020. Period prevalence was calculated and the association between positivity and individuals’ age, sex and occupation were assessed using χ2 and Mantel–Haenszel tests. Logistic regression was used to calculate adjusted odds ratios (ORs) for each age group. Time-to-event (TTE) analysis was conducted to check the difference in positivity among various groups. Results In a total of 708 individuals, 71 tested positive (10%). Compared with those ≤20 y of age, the sex- and occupation-adjusted odds of testing positive were less among the older age group (41–60 y; OR 0.26, p=0.008). Taxi drivers had higher odds of testing positive (OR 4.08, p<0.001). Kaplan–Meier curves and hazard ratios (0.32, p<0.01) showed that the positivity period differed significantly across the pre-symptomatic vs asymptomatic group (26 vs 14 d). Conclusions The cases who were likely to acquire infection through occupational exposure largely remained asymptomatic. For effective control of transmission and the emergence of new variants, testing capacities should be revamped with effective isolation measures.

show abstract

“…Another important aspect of asymptomatic viral circulation is the critical role that it can play in the emergence of new genetic variants. 26 This link needs to be studied further.…”

Section: Discussionmentioning

confidence: 98%

SARS-CoV-2 RT-PCR positivity in relation to clinical and demographic characteristics in residents of border quarantine centres, Khyber Pakhtunkhwa, Pakistan: a prospective cohort study

Imran

Uddin

Ambade

et al. 2022

Transactions of the Royal Society of Tropical Medicine and Hygiene

View full text Add to dashboard Cite

show abstract

“…Since the Delta variant had a much higher fatality compared to its predecessor, Alpha, more severe NPIs were advised to accommodate the rise in cases [ 254 ]. Relatedly, Zhang et al [ 255 ] were able to use SARS-CoV-2 genomes recovered via HC and subsequent phylogeny reconstructions to find evidence of transmission and trace the spread of the virus in asymptomatic patients, which is often overlooked in models calculating the reproductive number (R 0 ) but crucial for understanding the spread of the disease [ 256 , 257 ]. Indeed, HC was extensively employed in tracing outbreak patterns during COVID-19 ( Figure 2 ; Table S1 ), enhancing our understanding of the pandemic’s evolutionary dynamics, virulence, and management.…”

Section: Case Study: Sars-cov-2mentioning

confidence: 99%

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Quek,

2024

Pathogens

View full text Add to dashboard Cite

High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens—bacteria, fungi, parasites and viruses—including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.

show abstract

“…Unprecedented large-scale PCR screening and routine PCR testing in high-risk regions has identified large numbers of patients that had positive viral nucleic Ivyspring International Publisher acid tests but were found to exhibit no concomitant clinical signs nor typical COVID-19 computed tomography (CT) images in their full course of infection [1], which made these cases distinct from symptomatic infections [2,3]. The occurrence of asymptomatic infections in patients who had tested positive for SARS-CoV-2 has varied from study to study [4][5][6][7][8][9][10]. For example, an early study of the SARS-CoV-2 outbreak on the Diamond Princess cruise ship in Japan indicated that 17.9% of the 634 infected passengers were asymptomatic [11].…”

Section: Introductionmentioning

confidence: 99%

Dysregulation of Innate and Adaptive Immune Responses in Asymptomatic SARS-CoV-2 Infection with Delayed Viral Clearance

Cao¹,

Zhang²,

Liu³

et al. 2022

Int. J. Biol. Sci.

View full text Add to dashboard Cite

Phylogenomic tracing of asymptomatic transmission in a COVID-19 outbreak

Cited by 4 publications

References 43 publications

SARS-CoV-2 RT-PCR positivity in relation to clinical and demographic characteristics in residents of border quarantine centres, Khyber Pakhtunkhwa, Pakistan: a prospective cohort study

SARS-CoV-2 RT-PCR positivity in relation to clinical and demographic characteristics in residents of border quarantine centres, Khyber Pakhtunkhwa, Pakistan: a prospective cohort study

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Dysregulation of Innate and Adaptive Immune Responses in Asymptomatic SARS-CoV-2 Infection with Delayed Viral Clearance

Contact Info

Product

Resources

About