Whole-genome sequencing of SARS-CoV-2 in Uganda: implementation of the low-cost ARTIC protocol in resource-limited settings

Mboowa, Gerald; Mwesigwa, Savannah; Kateete, David Patrick; Wayengera, Misaki; Nasinghe, Emmanuel; Katagirya, Eric; Katabazi, Ashaba Fred; Kigozi, Edgar; Kirimunda, Samuel; Kamulegeya, Rogers; Kabahita, Jupiter Marina; Luutu, Moses Nsubuga; Nabisubi, Patricia; Kanyerezi, Stephen; Bagaya, Bernard S.; Joloba, Moses

doi:10.12688/f1000research.53567.1

Cited by 11 publications

(7 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…97%. This relatively lower performance of the ARTIC V4 scheme with Nextera XT, particularly in samples with higher Cvalues τ , aligns with the findings of Mboowa et al ., who reported that the ARTIC SARS-CoV-2 sequencing protocol on the Illumina MiSeq platform was sensitive and accurate to C τ of 24 in Ugandan settings [29]. This context highlights the importance of selecting appropriate sequencing protocols based on the characteristics of the samples being analysed.…”

Section: Resultsmentioning

confidence: 99%

Bridging genomic gaps: A versatile SARS-CoV-2 benchmark dataset for adaptive laboratory workflows

Zufan,

Judd,

Walsh

et al. 2024

Preprint

View full text Add to dashboard Cite

Genomic sequencing’s adoption in public health laboratories (PHLs) for pathogen surveillance is innovative yet challenging, particularly in the realm of bioinformatics. Low- and middle-income countries (LMICs) face increased difficulties due to supply chain volatility, workforce training, and unreliable infrastructure such as electricity and internet services. These challenges also extend to high-income countries (HICs) where bioinformatics is nascent in PHLs and hampered by a lack of specialized skills and computational infrastructure. This underlines the urgency for flexible and resource-aware strategies in genomic sequencing to improve global pathogen surveillance. In response to these challenges, the present research was conducted to identify and analyse key variables influencing the quality and accuracy of amplicon sequence data. An extensive benchmark dataset was developed that encompassed a diverse collection of isolates, viral loads, primer schemes, library preparation methods, sequencing technologies, and basecalling models, totalling 750 sequences. This dataset was analysed with bioinformatic workflows selected for varying levels of technical capacity. The evaluation focused on quality metrics, consensus accuracy, and common genomic epidemiological indicators. The analysis uncovers complex interactions between multiple parameters in laboratory and bioinformatic processes. emphasising resource-constrained PHLs, practical guidelines are proposed. Insights from the benchmark dataset aim to guide the establishment of specific laboratory and bioinformatics protocols for amplicon sequencing in these settings. The findings can also be used to guide the creation of specialised training curricula, further advancing genomic equity. The benchmark dataset itself allows laboratories to customise and evaluate workflows, catering to their distinct requirements and capacities. Such a holistic approach is imperative to build the capacity to monitor pathogens worldwide.Author summaryThis study marks a step toward equity in the field of pathogen genomics, especially for resource-constrained PHLs. It develops and evaluates a comprehensive amplicon sequencing benchmark dataset, offering vital insights for PHLs engaged in genomic surveillance. In particular, the study finds that the choice of basecaller model has a minimal impact on the quality and accuracy of consensus sequences derived from ONT data, which is crucial for labs with limited computational resources. It also highlights the effectiveness of longer amplicons in ensuring consistent coverage and reducing amplicon dropouts at higher viral loads. While Illumina remains a gold standard for data quality, the combination of the Midnight primer scheme with ONT’s Rapid library preparation is shown to be a viable alternative, reducing costs, procedural complexity, and hands-on time. The study synthesises these findings into practical guidelines to aid in the development of amplicon sequencing workflows for SARS-CoV-2 with implications for other pathogens.

show abstract

Section: Resultsmentioning

confidence: 99%

Bridging genomic gaps: A versatile SARS-CoV-2 benchmark dataset for adaptive laboratory workflows

Zufan,

Judd,

Walsh

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…coronavirus disease 2019 (COVID-19), malaria, or even cancer) for surveillance, antimicrobial resistance control and research [9][10][11]. The lessons learnt from the COVID-19 pandemic response could inform TB sequencing technologies and inform local and regional stakeholders on the best strategies to implement [9,12,13].…”

Section: Possible Solutionsmentioning

confidence: 99%

Implementing molecular tuberculosis diagnostic methods in limited-resource and high-burden countries

Vasiliù

Saktiawati

Duarte

et al. 2022

Breathe

View full text Add to dashboard Cite

Tuberculosis (TB) is one of the deadliest infectious diseases in the world with more than a million people dying of TB each year. Accurate and timely TB diagnosis has the potential to alleviate the global TB burden; therefore, one of the pillars of the End TB Strategy developed by the World Health Organization (WHO) is the early diagnosis of TB, including universal drug-susceptibility testing (DST). The WHO emphasises the importance of DST before treatment initiation, using molecular WHO-recommended rapid diagnostic tests (mWRDs). Currently available mWRDs are nucleic acid amplification tests, line probe assays, whole genome sequencing, and targeted next-generation sequencing. However, implementing the sequencing mWRDs in routine laboratories in low-income countries is constrained by the existing infrastructure, high cost, the specialised skills needed, data storage, and the current delay in results compared with other routine methods. These limitations are pronounced in resource-limited settings, which often have a high TB burden and need for innovative TB diagnostic technologies. In this article we propose several possible solutions, like adapting infrastructure capacity to needs, advocating for lowering costs, building bioinformatics and laboratory capacity, and increasing the use of open-access resources for software and publications.

show abstract

“…Despite the importance of this technique for the identification of new variants, it is often tedious (requiring multiple steps, including overlapping primer design, amplicon sequencing, reading merging, sorting reads by amplicon, read clustering, assembly, etc.) [6] , expensive (about US$87 per COVID-19 genome) [7] , [8] , and time-consuming (at least three to five days) [9] . PCR-based methods (e.g.…”

Section: Introductionmentioning

confidence: 99%

Interference reduction isothermal nucleic acid amplification strategy for COVID-19 variant detection

Wang

et al. 2023

Sensors and Actuators B: Chemical

View full text Add to dashboard Cite

Whole-genome sequencing of SARS-CoV-2 in Uganda: implementation of the low-cost ARTIC protocol in resource-limited settings

Cited by 11 publications

References 19 publications

Bridging genomic gaps: A versatile SARS-CoV-2 benchmark dataset for adaptive laboratory workflows

Bridging genomic gaps: A versatile SARS-CoV-2 benchmark dataset for adaptive laboratory workflows

Implementing molecular tuberculosis diagnostic methods in limited-resource and high-burden countries

Interference reduction isothermal nucleic acid amplification strategy for COVID-19 variant detection

Contact Info

Product

Resources

About