Perspective Chapter: Molecular Diagnostics in Viral Outbreak Surveillance

IntechOpen eBooks, Journal Year: 2025, Volume and Issue: unknown

Published: April 16, 2025

Understanding and adopting various methods for monitoring viral outbreaks is required pathogen surveillance. Accurate diagnosis can play a significant role in the safe effective treatment prescribed. Africa remains burdened with host of infectious diseases, which challenges healthcare systems proper management diseases. Surveillance are implemented some parts that have infrastructure funding to perform routine testing screening. However, not all this continent equipped necessary tools support. With travel, tourism goods exchange, diseases spread across borders rapidly, posing threat global health, emphasising unified need efforts prevent, detect, act on disease through improved access vaccinations treatments. Effective response depends several elements, including laboratory capacity, skilled health staff, surveillance detect limit illnesses rapidly. Traditional molecular such as genotyping polymerase chain reaction (PCR)-based detection now being complemented like next-generation sequencing clustered regularly interspaced short palindromic repeats (CRISPR). This book chapter aims summarise current broadly describes issue climate change its impact outbreaks.

Language: Английский

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Genomic surveillance of SARS-CoV-2 variants using pooled WGS

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 22, 2025

This study presents the development and validation of a genomic surveillance strategy using Whole Genome Sequencing (WGS) on normalized pooled samples to detect monitor SARS-CoV-2 variants. A bioinformatics pipeline was designed specifically for analyzing WGS data validated simulated datasets, reference materials, clinical collected during key periods Delta Omicron variant emergence. The approach evaluated its accuracy in estimating abundance at both Phylogenetic Assignment Named Global Outbreak (PANGO) lineage level World Health Organization (WHO) level. From simulation method achieved an overall sensitivity 99.1% positive predictive value (PPV) 99.9% detecting variants WHO At PANGO level, it 82.8% PPV 77.4% when predicted considered accurate if shared more than 90% markers with any true present sample. estimation further materials. Analysis showed results consistent national epidemiological trends, particularly emergence Korea. WGS-based offers scalable economical solution monitoring variants, providing public health authorities valuable tool tracking pandemic dynamics enabling timely responses.

Language: Английский

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Genomic, socio-environmental, and sequencing capability patterns in the surveillance of SARS-CoV-2 in Latin America and the Caribbean up to 2023

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 26, 2025

Latin America and the Caribbean (LAC) have been one of most strongly impacted regions by Coronavirus disease 2019 (COVID-19) emergency, with more than 83 million reported infections 1.7 deaths until December 2023, intensifying economic social inequalities. This study aimed to provide information regional SARS-CoV-2 surveillance programs determining genomic, socio-environmental, sequencing capacity patterns associated circulation virus in up 2023. Data from 24 countries LAC were analyzed using public databases A sampling sequences cases region enabled a phylogenomic elucidate temporal distribution various variants concern (VOCs), mutations, recombinants. Also, we identified differences capabilities LAC. Additionally, correlation generalized linear model (GLM) analyses conducted explore potential associations between 89 socio-environmental variables five COVID-19 indicators at country level. The revealed diversity predominance some during specific periods, mainly VOCs recombinant cases, mutation rate 8.39 × 10-4 substitutions per site year, which are line other world. Besides, low (on average 0.7% cases) incomplete several identified. In analysis indicators, correlations 9 four deaths, diagnostic tests related region, although not for percentages. provides about development terms viral genome, capabilities, region's complex conditions. Therefore, emphasis must be placed on implementing an integrated epidemiological approach strengthen health infrastructure improve cooperation preparedness future affecting this region.

Language: Английский

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Genomics-based approach for detection and characterization of SARS-CoV-2 co-infections and diverse viral populations

Microbiology Spectrum, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Due to the continuous genetic diversification of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) over time, co-circulation two different lineages in same region may lead co-infections within a host, situation known contribute emergence hybrid viral populations through genomic recombination. The aim this study was use genomics-based approach identify distinct SARS-CoV-2 patients with disease 2019 (COVID-19), as an indicator potential and recombination events. cohort included 41,224 serial nasopharyngeal swabs positive for RNA, prospectively collected between January 2021 April 2022 part French national surveillance program. Full-length genomes were sequenced by next-generation sequencing (COVIDseq). Intra-host single nucleotide variants (iSNVs) identified, synthetic generated establish thresholds co-infection detection. Eight hundred sixty-one samples iSNV ratios above threshold considered "potential co-infections." Peaks prevalence occurred during periods variants. Co-infection Variants Concern (VoC) confirmed 103 cases, including Alpha-Beta 12 Alpha-Delta 15 Gamma-Delta 4 Delta-Omicron 35 Omicron BA.1-BA.2 37 cases. In conclusion, our suggests higher variant/subvariant events than that previously reported using conventional approaches, particularly characterized multiple lineages, creating increased risk Our results support premise importance approaches detect virus-infected populations, closely related lineages. We implement innovative monitor diversity human population, circulation VOCs. This focused on detecting highly diverse which are facilitate can potentially new recombinant novel characteristics. Monitoring characterizing cases outbreak is key strategy better understanding evolution, especially epidemic periods. However, challenging, their often underestimated. study, we developed be implemented programs applied large datasets. Concern.

Language: Английский

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Estimating the deferred value of pathogen genomic data for secondary use

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: May 13, 2025

The COVID-19 pandemic has illuminated the utility of pathogen genomics and highlighted roadblocks to international data sharing. This article describes deferred value for secondary use using a set 10,110 assembled genomes Vibrio cholerae shared via repositories between 2010 2024 as an illustrative representation disease. Trends in quality, representativeness, timeliness sharing well increasing role microbiology services genomic providers resulting from gradually improving access sequencing technologies countries with high burden disease were identified. individual aggregated was tracked over time mapped geographical hot spots cholera. lag collection samples V. cultures submission genome database remained eight years on average. assessment described here paves way mobilization quality microbial global health knowledge discovery.

Language: Английский

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SARS-CoV-2 genomics and impact on clinical care for COVID-19

Journal of Antimicrobial Chemotherapy, Journal Year: 2023, Volume and Issue: 78(Supplement_2), P. ii25 - ii36

Published: Nov. 1, 2023

Abstract The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated adaptation rapid deployment viral WGS analysis techniques that had been previously applied on a more limited basis to other pathogens, such as HIV influenza viruses. need for was driven in part by low mutation rate SARS-CoV-2, which measuring variation along entire genome sequence effectively differentiate lineages characterize evolution. Several approaches designed maximize throughput accuracy were quickly adopted surveillance labs around world. These broad-based genomic sequencing efforts revealed ongoing evolution virus, highlighted successive new variants throughout course pandemic. insights instrumental characterizing effects mutations transmissibility, immune escape tropism, turn helped guide public health policy, use monoclonal antibody therapeutics vaccine development strategies. As direct-acting antivirals treatment became widespread, potential antiviral resistance has delineate monitor global databases their emergence. Given critical role genomics international effort combat pandemic, coordinated should be made expand capacity infrastructure towards anticipation prevention future pandemics.

Language: Английский

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Viral sequencing to inform the global elimination of dog-mediated rabies - a systematic review

One Health & Implementation Research, Journal Year: 2024, Volume and Issue: 4(2), P. 15 - 37

Published: May 31, 2024

Background: Rabies is a fatal zoonotic disease, present in almost 150 countries. The “Zero by 30” initiative aims to eliminate human deaths from dog-mediated rabies globally 2030. This systematic review investigates how viral sequencing can contribute achieving the goal improving understanding of circulation and impact control measures. Methods: A comprehensive search bibliographic databases was conducted focusing on research regions with endemic published between 2000 2023, adhering Preferred Reporting Items for Systematic Reviews Meta-Analyses (PRISMA) guidelines. Data were extracted synthesised provide recommendations further application support control. Results: 220 studies identified have documented virus (RABV) sequences 94 countries, primarily using first-generation technology produce partial genomes predominantly overseas rather than in-country. Dogs be primary RABV reservoir these regions, although some more localised wildlife reservoirs. Clade classifications commonly based host association or geographical location, however, lack standardised methods nomenclature classifying lineages limited comparison at higher resolution. Cross-species transmission, both local long-distance transmission identified, quantitative inference limited. Sequence data particularly useful identifying transboundary spread incursions, investigating shifts, tracing sources rabies, endemicity typically characterised identification multiple co-circulating lineages. Conclusion: There an urgent need classification phylogeny-based RABVs, improved capacity including proficiency bioinformatics phylogenetics. Our findings emphasise critical foster international cooperation coordinate efforts reduce spread, limit reintroductions maintain progress towards 2030 target.

Language: Английский

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Update on the Phylodynamic and Genetic Variability of Marburg Virus

Viruses, Journal Year: 2023, Volume and Issue: 15(8), P. 1721 - 1721

Published: Aug. 11, 2023

The COVID-19 pandemic has not only strained healthcare systems in Africa but also intensified the impact of emerging and re-emerging diseases. Specifically Equatorial Guinea, mirroring situation other African countries, unique zoonotic outbreaks have occurred during this challenging period. One notable resurgence is Marburg virus disease (MVD), which further burdened already fragile system. re-emergence amid believed to stem from a probable spill-over, although precise transmission routes remain uncertain. Given gravity situation, addressing existing challenges paramount. Though genome sequences current outbreak were available for study, we analyzed all whole pathogen advocate shift towards active surveillance. This essential ensure successful containment any potential Guinea wider context. presents an update on phylodynamics genetic variability MARV, confirmed existence at least two distinct patterns viral spread. pattern demonstrates slower continuous recurring circulation, while exhibits faster yet limited episodic These results highlight critical need strengthen genomic surveillance region effectively curb pathogen’s dissemination. Moreover, study emphasizes importance prompt alert management, comprehensive case investigation analysis, contact tracing, searching. steps are vital support system’s response health crisis. By implementing these strategies, can better arm ourselves against posed by infectious

Language: Английский

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Integration of individualized and population-level molecular epidemiology data to model COVID-19 outcomes

Cell Reports Medicine, Journal Year: 2024, Volume and Issue: 5(1), P. 101361 - 101361

Published: Jan. 1, 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility and immune escape have emerged periodically throughout the disease 2019 (COVID-19) pandemic, but impact of these on severity has remained unclear. In this single-center, retrospective cohort study, we examined association between SARS-CoV-2 clade patient outcome over a two-year period in Chicago, Illinois. Between March 2020 2022, 14,252 residual diagnostic specimens were collected from SARS-CoV-2-positive inpatients outpatients alongside linked clinical demographic metadata, which 2,114 processed for viral whole-genome sequencing. When controlling demographics vaccination status, several clades associated risk hospitalization, was negated by inclusion population-level confounders, including case count, sampling bias, shifting standards care. These data highlight importance integrating non-virological factors into models accurate assessment risk.

Language: Английский

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Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Viruses, Journal Year: 2024, Volume and Issue: 16(3), P. 430 - 430

Published: March 11, 2024

Genomic sequencing of clinical samples to identify emerging variants SARS-CoV-2 has been a key public health tool for curbing the spread virus. As result, an unprecedented number genomes were sequenced during COVID-19 pandemic, which allowed rapid identification genetic variants, enabling timely design and testing therapies deployment new vaccine formulations combat variants. However, despite technological advances deep sequencing, analysis raw sequence data generated globally is neither standardized nor consistent, leading vastly disparate sequences that may impact Here, we show both Illumina Oxford Nanopore platforms, downstream bioinformatic protocols used by industry, government, academic groups resulted in different virus from same sample. These workflows produced consensus with differences single nucleotide polymorphisms, inclusion exclusion insertions, and/or deletions, using as input datasets. compared characterized such discrepancies propose specific suite parameters should be adopted across field. Consistent results are fundamental future pathogen surveillance efforts, including pandemic preparation, allow data-driven response.

Language: Английский

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