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Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses

Chien YS, Chen FJ, Wu HC, Lin CH, Chang WC, Perera D, et al.

Microbiol Spectr, 2023 Oct 13.
PMID: 37831475 DOI: 10.1128/spectrum.02507-23

Enteroviruses (EVs) are a group of viruses that cause various human illnesses. While the CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) method can generate VP1 gene fragments for enterovirus genotyping, it is unable to detect recombinant strains. Recent advances in viral genome sequencing using next-generation sequencing technologies have enabled comprehensive analyses. However, the high cost poses a challenge for widespread adoption. To address this issue, this study proposes a cost-effective approach for generating complete enterovirus genome sequences using the Oxford Nanopore MinION sequencer. This protocol not only facilitates the generation of accurate genome sequences for various enterovirus strains but also allows for the differentiation of co-infections from viral isolates. In addition, the method can generate polyprotein sequences as well as peptide sequences of the upstream ORF (uORF) whose expression can impact virus infection. Through the analysis of complete enterovirus genomes, this study successfully identified seven enterovirus A71 isolates obtained during the 2018 enterovirus outbreak in Malaysia and Taiwan as recombinants between enterovirus A71 and coxsackievirus A2. Furthermore, our study has made a significant discovery by establishing a strong correlation between uORF trees and the epidemics of EVA71. This finding highlights the potential of uORF sequences as valuable indicators for monitoring and understanding the spread of EVA71 infections. We also identified notable amino acid changes in the transmembrane domain of the uORF protein within a newly identified lineage. These findings provide crucial insights into the molecular characteristics and evolutionary dynamics of EVA71, offering valuable information for future research and intervention strategies. IMPORTANCE By employing a cost-effective approach for complete genome sequencing, the study has enabled the identification of novel enterovirus strains and shed light on the genetic exchange events during outbreaks. The success rate of genome sequencing and the scalability of the protocol demonstrate its practical utility for routine enterovirus surveillance. Moreover, the study's findings of recombinant strains of EVA71 and CVA2 contributing to epidemics in Malaysia and Taiwan emphasize the need for accurate detection and characterization of enteroviruses. The investigation of the whole genome and upstream ORF sequences has provided insights into the evolution and spread of enterovirus subgenogroups. These findings have important implications for the prevention, control, and surveillance of enteroviruses, ultimately contributing to the understanding and management of enterovirus-related illnesses.
Fulltext A Quality Improvement Approach to Reduce 30-day Readmissions and Mortality in Patients with Acute Decompensated Heart Failure

Hoo YY, Mazlan-Kepli W, Hasan WNHW, Chen FJ, Devadas P, Chow YY, et al.

J Saudi Heart Assoc, 2021;33(2):149-156.
PMID: 34183912 DOI: 10.37616/2212-5043.1247

Objectives: Heart failure [HF] hospital readmissions are a continued challenge in the care of HF patients, which contribute substantially to the high costs of the disease and high mortality rate in lower to middle income country. We implemented a quality improvement project to improve patient outcomes and resource utilization.
Methods: This study was a prospective cohort design with a historical comparison group. It was conducted to assess the difference in 30-day readmissions and mortality and to assess compliance rate with HF guideline between the historical pre-intervention audit 1 cohort and prospective post-intervention audit 2 cohorts. Audit 1 cohort were recruited from January to February 2019, whereas, audit 2 cohort which received the bundled intervention program were recruited from July to December 2019. Clinical outcomes were compared between cohorts using 30-day readmissions and mortality.
Results: A total of 50 and 164 patients were included in audit 1 and audit 2 cohort, respectively. Patients in the audit 2 cohort were younger [63.0 ± 14.5 in audit 1 vs 56.5 ± 12.7 in audit 2, p = 0.003] and majority were male [50.0% in audit 1 vs 72.0% in audit2, p = 0.004]. Thirty-day readmissions were significantly different [36.0% audit 1 vs. 22.0% audit 2, p = 0.045], but the mortality rates were similar [4.0%% audit 1 vs. 5.5% audit 2, p = 0.677] between two cohorts.
Conclusion: A significant decrease in 30-day readmissions was observed in the post-intervention audit 2 cohort in our setting. Further study in larger population and prolong study follow-up is warranted.

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