Sustainability of surveillance systems for SARS-CoV-2

Adlhoch, Cornelia; Gomes, Helena de Carvalho

doi:10.1016/s1473-3099(22)00174-8

Cited by 6 publications

(9 citation statements)

References 6 publications

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“…This technique is proving to be important for understanding transmission patterns and potential host-virus interactions. These analyzes cannot be performed with the diagnostic technique of Realtime-PCR or CRISPR (218,219).…”

Section: Genomic Surveillance Overviewmentioning

confidence: 99%

“…Universal access to vaccines, variations in surveillance systems, virological diagnostic tests, and a combination of measures to protect vulnerable groups have managed to keep the number of SARS-CoV-2 cases at an affordable level for hospitals and health institutions. The effect of these policies allowed a decrease in the circulation of other respiratory viruses in the first months of the pandemic, reducing the overload of health systems (218,238,239,240).…”

Section: Future Projections Of Hadv Study In the 21st Centurymentioning

confidence: 99%

“…To avoid a HAdV pandemic, all the groups described above are required to act together, using the tools acquired by the recent COVID-19 pandemic. The development of vaccines, genomic surveillance in sentinel centers, web pages with scientific dissemination in real time, free access to genomic sequences and multisectoral coordination, to recognize early unusual increase in cases of infection that could be important for human health and zoonosis control (123,218).…”

Section: Future Projections Of Hadv Study In the 21st Centurymentioning

confidence: 99%

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An Old Acquaintance. Could Adenovirus be our Next Pandemic Threat?

Saint-Pierre¹,

Conei²,

Lizama³

et al. 2022

Preprint

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Human adenoviruses are one of the most important pathogens detected in acute respiratory diseases in pediatrics and immunocompromised patients. In 1953, Wallace Rowe described it for the first time in oropharyngeal lymphatic tissue. To date, more than 85 types of HAdV have been described, with different cellular tropisms. They can cause respiratory and gastrointestinal symptoms, even urinary tract inflammation, although most infections are asymptomatic. However, there is a population at risk that can develop serious and even lethal conditions. These viruses have a double-stranded DNA genome, 25-48 kbp, 90 nm in diameter, without a mantle, stable in the environment, and resistant to fat-soluble detergents. Currently the diagnosis is made with lateral flow immunochromatography or molecular biology through a polymerase chain reaction. The objective of this review is to recognize the variability of HAdV, the pandemic potential that a recombinant could present between HAdV-3 and 7 viral types, known to produce aggressive outbreaks in health facilities. The review determined the characteristics of HAdV, from the infection to treatment, vaccine development and the evaluation of the social determinants of health associated with HAdV, guiding the necessary measures for future sanitary control, and preventing disasters such as the SARS-CoV-2 pandemic.

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Section: Genomic Surveillance Overviewmentioning

confidence: 99%

Section: Future Projections Of Hadv Study In the 21st Centurymentioning

confidence: 99%

Section: Future Projections Of Hadv Study In the 21st Centurymentioning

confidence: 99%

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An Old Acquaintance. Could Adenovirus be our Next Pandemic Threat?

Saint-Pierre¹,

Conei²,

Lizama³

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents ongoing risks and threats to natural and vaccine-induced immunity and the effectiveness of diagnostics and therapeutics ( 1 – 3 ). With the rapidly increasing volume of SARS-CoV-2 genomes, leveraging this wealth of data for variant surveillance quickly becomes intractable due to a daunting computational hurdle of using gold-standard phylogenetic approaches ( 4 ).…”

Section: Introductionmentioning

confidence: 99%

Early detection of SARS-CoV-2 variants through dynamic co-mutation network surveillance

Huang

Qiu

Bible

et al. 2023

Front. Public Health

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BackgroundPrecise public health and clinical interventions for the COVID-19 pandemic has spurred a global rush on SARS-CoV-2 variant tracking, but current approaches to variant tracking are challenged by the flood of viral genome sequences leading to a loss of timeliness, accuracy, and reliability. Here, we devised a new co-mutation network framework, aiming to tackle these difficulties in variant surveillance.MethodsTo avoid simultaneous input and modeling of the whole large-scale data, we dynamically investigate the nucleotide covarying pattern of weekly sequences. The community detection algorithm is applied to a co-occurring genomic alteration network constructed from mutation corpora of weekly collected data. Co-mutation communities are identified, extracted, and characterized as variant markers. They contribute to the creation and weekly updates of a community-based variant dictionary tree representing SARS-CoV-2 evolution, where highly similar ones between weeks have been merged to represent the same variants. Emerging communities imply the presence of novel viral variants or new branches of existing variants. This process was benchmarked with worldwide GISAID data and validated using national level data from six COVID-19 hotspot countries.ResultsA total of 235 co-mutation communities were identified after a 120 weeks' investigation of worldwide sequence data, from March 2020 to mid-June 2022. The dictionary tree progressively developed from these communities perfectly recorded the time course of SARS-CoV-2 branching, coinciding with GISAID clades. The time-varying prevalence of these communities in the viral population showed a good match with the emergence and circulation of the variants they represented. All these benchmark results not only exhibited the methodology features but also demonstrated high efficiency in detection of the pandemic variants. When it was applied to regional variant surveillance, our method displayed significantly earlier identification of feature communities of major WHO-named SARS-CoV-2 variants in contrast with Pangolin's monitoring.ConclusionAn efficient genomic surveillance framework built from weekly co-mutation networks and a dynamic community-based variant dictionary tree enables early detection and continuous investigation of SARS-CoV-2 variants overcoming genomic data flood, aiding in the response to the COVID-19 pandemic.

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“…1 These policy changes were reflected in the number of COVID-19 cases reported in England. Cornelia Adlhoch and Helena de Carvalho Gomes 2 discussed how surveillance systems for SARS-CoV-2 need to be representative to ensure the provision of high-quality information to understand the ongoing impact of COVID-19.…”

mentioning

confidence: 99%