Toward a global virus genomic surveillance network

Hill, Verity; Githinji, George; Vogels, Chantal B.F.; Bento, Ana I.; Chaguza, Chrispin; Carrington, Christine V. F.; Grubaugh, Nathan D.

doi:10.1016/j.chom.2023.03.003

Cited by 32 publications

(48 citation statements)

References 79 publications

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“…Enabling broader access to information from genomic surveillance for emerging and re-emerging pathogens has been and will remain a global health priority 12,17,19,[39][40][41][42] . In addition to the crucial work of building global sequencing capacity, methodological advances in how sequences are analyzed can address gaps in the surveillance landscape 12 .…”

Section: Discussionmentioning

confidence: 99%

Leveraging global genomic sequencing data to estimate local variant dynamics

Susswein

Johnson

Kassa

et al. 2023

Preprint

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Accurate, reliable, and timely estimates of pathogen variant risk are essential for informing effective public health responses to infectious diseases. Despite decades of use for influenza vaccine strain selection and PCR-based molecular diagnostics, data on pathogen variant prevalence and growth advantage has only risen to its current prominence during the SARS-CoV-2 pandemic. However, such data are still often sparse: novel variants are initially rare or a region has limited sequencing. To ensure real-time estimates of risk are available in these types of data-sparse conditions, we develop a hierarchical modeling approach that estimates variant fitness advantage and prevalence by pooling data across geographic regions. We apply this method to estimate SARS-CoV-2 variant dynamics at the country-level and assess its stability with retrospective validation. Our results show that more stable and robust estimates can be obtained even when sequencing data are sparse, as compared to established, single-country estimation approaches. We discuss how this method can inform risk assessment of novel emerging variants and provide situational awareness on currently circulating variants, for a range of pathogens and use-cases.

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Section: Discussionmentioning

confidence: 99%

Leveraging global genomic sequencing data to estimate local variant dynamics

Susswein

Johnson

Kassa

et al. 2023

Preprint

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“…The PrimalSeq protocol uses a series of overlapping PCR amplicons generated with primers designed using PrimalScheme (https://primalscheme.com) to efficiently sequence virus genomes directly from clinical specimens [8,9]. Here, we used PrimalScheme to develop primer schemes for all four serotypes of dengue virus, which can be used with the amplicon-based sequencing protocols widely established during the COVID-19 pandemic [14]. We selected genetically diverse genomes within each of the dengue virus serotypes and then used PrimalScheme to generate four serotype-specific primer schemes ( Fig.…”

Section: Resultsmentioning

confidence: 99%

DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus

Vogels,

Hill,

Breban

et al. 2023

Preprint

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BackgroundThe increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes.ResultsWe developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 101-102RNA copies/μL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments.ConclusionsDengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance.

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“…The key transmission pathways and distributions of specific genetic lineages remains unknown (Gyawali et al, 2019). Nonetheless, there is increasing awareness of the crucial nature of molecular xeno-monitoring in response to the emergence and re-emergence of neglected arboviruses (Hill et al, 2023; Laiton-Donato et al, 2023). This is of particular significance on the Australian continent where a large number of ecosystems, at huge geographic scales, are under constant environmental disturbance potentially favoring arbovirus emergence and dispersal through dynamic changes in mosquito vector populations, reservoir distribution, and human proximity to those reservoirs and vectors.…”

Section: Discussionmentioning

confidence: 99%

“…The COVID-19 pandemic has highlighted the utility of genomic surveillance in tracking and monitoring the spread of viruses, detecting new variants, and informing public health interventions (Hill et al, 2023;Zeghbib et al, 2023). However, adapting routine sequencing into public health investigations will require additional programmatic investment in expertise and resources.…”

Section: The Role Of Xeno-monitoring Coupled With Metatranscriptomics...mentioning

confidence: 99%

Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and metatranscriptomics

Julia S. P. Vieira,

Onn,

Shivas

et al. 2024

Preprint

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Arbovirus surveillance of wild-caught mosquitoes is an affordable and sensitive means of monitoring virus transmission dynamics at various spatial-temporal scales, and emergence and re-emergence during epidemic and interepidemic periods. A variety of molecular diagnostics for arbovirus screening of mosquitoes (known as xeno-monitoring) are available, but most provide limited information about virus diversity. PCR-based screening coupled with metatranscriptomics is an increasingly affordable and sensitive pipeline for integrating complete viral genome sequencing into surveillance programs. This enables large-scale, high-throughput arbovirus screening from diverse samples. We collected mosquitoes in CO2-baited light traps from five urban parks in Brisbane from March 2021 to May 2022. Mosquito pools of ≤200 specimens were screened for alphaviruses and orthoflaviviruses using virus genus-specific primers and reverse transcription quantitative PCR (qRT-PCR). A subset of virus-positive samples was then processed using a mosquito-specific ribosomal RNA depletion method and then sequenced on the Illumina NextSeq. Overall, 54,670 mosquitoes, representing 26 species were screened in 382 pools. Thirty detections of arboviruses were made in 28 pools. Twenty of these positive pools were further characterised using meta-transcriptomics generating 18 full-length genomes. These full-length sequences belonged to four medically relevant arboviruses: Barmah Forest, Ross River, Sindbis-like and Stratford viruses. Phylogenetic and evolutionary analyses revealed the evolutionary progression of arbovirus lineages over the last 100 years, highlighting long-distance dispersal across the Australian continent and continuous circulation characterised by constant turnover of virus lineages.

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Toward a global virus genomic surveillance network

Cited by 32 publications

References 79 publications

Leveraging global genomic sequencing data to estimate local variant dynamics

Leveraging global genomic sequencing data to estimate local variant dynamics

DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus

Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and metatranscriptomics

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