Genomic surveillance with NGS can track infectious disease transmission and identify novel strains of coronavirus and other emerging pathogens. With near complete sequence data of pathogen genomes, we can implement effective infectious disease surveillance strategies to prevent further transmission and infection.
Infectious disease surveillance with next-generation sequencing (NGS) can:
Genomic surveillance helps public health officials track the path of an epidemic, perform contact tracing, determine the rate of pathogen evolution, and understand if a pathogen is changing in ways that could impact diagnostic or therapeutic effectiveness.
NGS is a valuable technology for genomic surveillance of infectious diseases such as COVID-19. Not only can it track the prevalence of coronavirus mutant strains, NGS can also identify novel coronavirus mutations, unlike PCR technology. Using NGS, scientists can detect low-frequency minority variants, multiple polymorphisms, and novel mutations.
As the coronavirus mutates, new strains evolve such as B.1.1.7 (Alpha variant, UK), B.1.351 (Beta variant, S. Africa), P1 (Gamma variant, Brazil), and B.1.617.2 (Delta variant, India). Surveillance and monitoring are critical because mutations can result in greater transmissibility or infectiousness. These coronavirus mutations can potentially make vaccines less effective/protective or even evade test diagnosis.
Genome-wide strain typing with NGS can help epidemiologists identify and characterize mutations quickly to prevent further spread. Strain-level tracing can support identification of outbreak clusters and transmission routes.
In contrast, PCR is designed to detect specific regions of the pathogen genome; it will not identify new mutations across rapidly evolving pathogen genomes. Furthermore, PCR performance can suffer if mutations occur in the primer or probe binding regions.
Starting at minute 52:31, Dr. Charles Chiu, authority on infections and the implications of coronavirus mutations, discusses viral variants. These include the B.1.1.7 strain causing a surge in the UK; and B.1.351, first reported in South Africa.View Video
NGS has broad applicability for responding to the SARS-CoV-2 pandemic, from initial detection and characterization to monitoring, surveillance, and diagnostic detection.View Webinar
Join change-makers, thought leaders, and industry shapers for a discussion about the role of genomics in infectious disease surveillance.View Webinar
Earlier and more comprehensive detection of infectious pathogens and antimicrobial resistance (AMR) markers can help optimize patient management and treatment.View Webinar
Reagent kits for the NovaSeq 6000 System provide ready-to-use cartridge-based reagents for cluster generation and SBS.
The flexible NextSeq 550 System offers a seamless transition between high-throughput sequencing and array scanning.
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Up to 75% of new or emerging infectious diseases are estimated to have zoonotic origins.1,2 We now know that zoonotic reservoirs are significant in the spread of pathogens. With NGS, it is possible to screen reservoir animals such as bats to predict and prevent viral pathogen outbreaks.
Infectious disease surveillance with NGS-based target enrichment or metagenomics can help us understand interspecies transmission, how zoonotic diseases emerge, spread and become resistant to common therapies, and enable us to better contain, treat and prevent disease outbreaks.
Targeted enrichment sequencing can be scaled up to monitor zoonotic pathogens, while genomic surveillance with metagenomics allows for unbiased, culture-free detection and identification of a broad number of pathogens. Metagenomics also helps us understand the relationship between our microbiome and pathogen interactions, which is important when designing measures to control infectious diseases.
Learn more about:Target Enrichment
Microbial whole-genome sequencing can access all the genetic variant information of a pathogen as it spreads from food to humans. The more variants we can describe, the higher the probability of finding the sources of infections and routes of transmission.
Target enrichment uses hybridization to capture genomic regions of interest. This method can provide the high sensitivity needed to detect a virus and provide information about its epidemiology and evolution.
These panels offer targeted enrichment sequencing solutions for respiratory pathogen and respiratory virus detection and characterization, including COVID-19 and flu.
Shotgun metagenomics enables sequencing of DNA from the complete microbial community in zoonotic samples, including both novel and known species. The sequencing reads can be used to understand the emergence, evolution, and transmission of AMR gene and/or species distributions.
NGS-based bacterial genome sequencing paired with user-friendly bioMérieux software allows comprehensive isolate discrimination and characterization.
NGS can characterize SARS-CoV-2 and other respiratory pathogens, identify novel pathogens, and more. Compare NGS methods for common coronavirus studies.
Software tools to detect and identify viral sequences, examine COVID-19 host responses, and contribute findings to shared databases.
Methods to interrogate host genetic variation and profile the molecular mechanisms that drive immune responses.