Why is viral genome de novo sequencing important?

Viral genome de novo sequencing is crucial for advancing our understanding of viral biology. It enables researchers to identify and characterize new viral strains, track genetic mutations, and investigate viral evolution. These insights are essential for understanding how viruses interact with their hosts, monitoring outbreaks, and elucidating the molecular mechanisms of viral diseases. Mapping and analyzing viral genomes provide a foundation for addressing both emerging and existing viral threats.

What types of viruses can be sequenced using this technology?

This sequencing technology can be applied to a diverse range of viruses, including those with DNA or RNA genomes. It covers single-stranded and double-stranded DNA viruses, as well as single-stranded and double-stranded RNA viruses. The method is adaptable to various viral types, from well-characterized pathogens to newly discovered viral entities.

What sample types are required for sequencing?

For effective Viral genome de novo sequencing, suitable samples include purified viral DNA or RNA, and clinical specimens or virus cultures classified under Biosafety Level 2 (P2) or lower. Samples must be well-preserved and free from contamination to ensure accurate and reliable sequencing results.

What are the challenges associated with viral genome de novo sequencing?

A major challenge of viral genome de novo sequencing is managing the extensive data generated, which can complicate sequence assembly and analysis. Sequencing complex or low-concentration samples may require specialized techniques to avoid biases and ensure comprehensive coverage. Advanced bioinformatics tools and expertise are essential for effective data processing and accurate genome reconstruction.

Viral Genome De Novo Sequencing

Service Overview

Viruses negatively impact the health of humans, plants, and animals. The effect of viral pathogens identification can act tremendously on infectious diseases, virology and public health. Based on our viral genome de novo sequencing platform, we help you reconstruct the complete viral genomes and detect genomic mutations, virulence changes, and explore viral evolution. The availability of viral genomes enables researchers to identify unknown pathogens and track variations and diversity of known pathogens.

Our Advantages:

Comprehensive Coverage: Our services encompass complete viral genome sequencing, ensuring meticulous coverage of all genomic regions with exceptional accuracy.
High Precision: Utilizing our advanced sequencing platform, we achieve nucleotide-level resolution with an accuracy rate of up to 99.9%, guaranteeing dependable genomic data.
Customizable Solutions: We offer versatile sequencing options, adaptable to a wide array of viral genomes and sample types, thereby catering to diverse research requirements.
Expert Analysis: Our experienced bioinformatics team provides thorough genome assembly and variant detection, delivering data with 99% reliability.

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What is Viral Genome De Novo Sequencing

Viruses are microscopic pathogens composed of genetic material, either DNA or RNA, encased within a protein coat. These viruses have the capacity to infect a variety of hosts, including humans, animals, and plants. Their ability to exhibit extensive genetic diversity and rapid evolution underscores the importance of studying viruses to better understand infectious diseases.

Viral genome de novo sequencing represents an advanced methodological approach aimed at determining the complete genetic sequence of a virus de novo—meaning from the beginning, without any pre-existing knowledge of its genomic structure. This intricate process encompasses the extraction of viral nucleic acids from a given sample, followed by sequencing these nucleic acids using high-throughput technological platforms, and subsequently assembling the resulting sequences into a comprehensive genome map.

The applications of this technique are manifold: it is indispensable for the discovery of novel viruses, the study of genetic variations within viral populations, and the elucidation of viral evolutionary dynamics. By enabling a detailed and accurate construction of a viral genome, De Novo Sequencing fosters significant advancements in virology and epidemiological research, providing pivotal insights into how viruses adapt and propagate.

Applications of Viral Genome De Novo Sequencing

Virus Discovery: The technique allows for the identification and characterization of complete genomic sequences of novel viruses, thus enabling the investigation and study of previously unknown pathogens.
Mutation and Evolution Tracking: By monitoring genetic alterations over time, this tool aids in understanding viral evolution and the emergence of new strains.
Epidemiological Research: The comprehensive insights gained into the genetic diversity and dissemination of viruses are indispensable for outbreak investigations and public health responses.
Genomic Surveillance: This approach is instrumental in continuous monitoring of viral genomes, facilitating the early identification and prompt response to emerging viral threats.

Service Specifications

Introduction to Our Viral Genome De Novo Sequencing Services

At CD Genomics, our viral genome de novo sequencing service is meticulously crafted to address a wide range of research needs. We employ state-of-the-art sequencing technologies, including Illumina HiSeq, Oxford Nanopore, and PacBio SMRT, to produce high-resolution genomic data. The Illumina HiSeq platform is renowned for its high throughput and exceptional accuracy, while PacBio SMRT and Oxford Nanopore technologies excel in generating longer read lengths.

Our team of expert bioinformaticians conducts thorough analyses, encompassing genome assembly, variant identification, and evolutionary assessments. This comprehensive approach provides an in-depth understanding of viral genomes. Our services are specifically designed to support various aspects of viral research, from identifying new viral entities to detailed monitoring of genetic variations, thereby offering critical insights into viral genomics and epidemiology.

Viral Genome De Novo Sequencing Workflow

The Workflow of Viral Genome De Novo Sequencing.

Technical Parameters

Illumina 150PE/250PE, 300~500 bp, 300~500 bp
PacBio SMRT, 2 K, 100X

Note: The above content includes only a portion of the bioinformatics analysis. For more information or to customize the analysis, please contact us directly.

Bioinformatics Analysis

Our bioinformatics analysis includes: genome assembly, gene functional annotation, pathogenic microbiology, and comparative genomic analysis. We are flexible to your needs. Feel free to contact us to discuss the bioinformatics pipeline suitable for your project.

Genomic Assembly	De novo genomic assembly and outcome evaluation
	Coding/noncoding gene prediction
	Repetitive sequence analysis
Gene Functional Annotation	NR, GO, COG, KEGG, SwissProt, TrEMBL, Pfam, TCDB, SignalP, CAZy
	Protein coding gene prediction
	Non-coding RNA prediction
Comparative Genomic Analysis	Synteny analysis
	Analysis of gene family evolution
	Phylogenetic analysis
	ANI analysis

Sample Requirement

1.8 < OD260/280 < 2.0, no degradation or contamination.
Illumina platform: concentration > 20 ng, amount ≥ 1 μg.
PacBio platform: concentration > 60 ng, amount ≥ 5 μg.

Sampling kits: We provide a complete range of microbial sampling kits for clients, including microbial collection products, DNA/RNA isolation kits, and accessories for storage and mailing.

Note: If you wish to obtain more accurate and detailed information regarding sample requirements, please feel free to contact us directly.

Deliverables

Raw sequencing data
Assembled and annotated sequences
Quality-control dashboard
Customized bioinformatics report

Demo

Partial results of our viral genome de novo sequencing service are shown below:

The Bacterial Viral Genome De Novo Sequencing Results Display.

FAQs

Viral Genome De Novo Sequencing FAQ

1. Why is viral genome de novo sequencing important?
- Viral genome de novo sequencing is crucial for advancing our understanding of viral biology. It enables researchers to identify and characterize new viral strains, track genetic mutations, and investigate viral evolution. These insights are essential for understanding how viruses interact with their hosts, monitoring outbreaks, and elucidating the molecular mechanisms of viral diseases. Mapping and analyzing viral genomes provide a foundation for addressing both emerging and existing viral threats.
2. What types of viruses can be sequenced using this technology?
- This sequencing technology can be applied to a diverse range of viruses, including those with DNA or RNA genomes. It covers single-stranded and double-stranded DNA viruses, as well as single-stranded and double-stranded RNA viruses. The method is adaptable to various viral types, from well-characterized pathogens to newly discovered viral entities.
3. What sample types are required for sequencing?
- For effective Viral genome de novo sequencing, suitable samples include purified viral DNA or RNA, and clinical specimens or virus cultures classified under Biosafety Level 2 (P2) or lower. Samples must be well-preserved and free from contamination to ensure accurate and reliable sequencing results.
4. What are the challenges associated with viral genome de novo sequencing?
- A major challenge of viral genome de novo sequencing is managing the extensive data generated, which can complicate sequence assembly and analysis. Sequencing complex or low-concentration samples may require specialized techniques to avoid biases and ensure comprehensive coverage. Advanced bioinformatics tools and expertise are essential for effective data processing and accurate genome reconstruction.

Please feel free to reach out if you have any further inquiries or require additional information.

Case Study

Biological Characteristics of Infectious Laryngotracheitis Viruses Isolated in China
Journal: Viruses
Impact factor: 5.818
Published: 31 May 2022

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Backgrounds

Avian infectious laryngotracheitis virus (ILTV), or Gallid herpesvirus 1, is a herpesvirus causing severe respiratory disease in chickens with high economic impact. First found in the USA and later in China, it can cause significant mortality. The virus has a 150 kb DNA genome encoding about 80 proteins. Despite some identified virulence factors, key details remain unknown. This study compares the genomes and pathogenicity of three recent ILTV strains from China.

Methods

Sample preparation:

LMH cells
ILTV
DNA extraction

Method:

Whole-genome sequencing
Illumina MiSeq sequencing platform

Data Analysis:

Sequence assembly
Synteny analysis
Sequence alignment
Phylogenetic analysis
Statistical analysis

Results

The complete genomes of three ILTV strains—SH2016, SH2017, and GD2018—were sequenced and deposited in GenBank. The genomes are nearly identical, with SH2017 and GD2018 sharing 99.9% similarity, while SH2016 is 99.7% similar to the others. All strains have 82 ORFs, with 31 proteins being identical. Notably, SH2016 differs from SH2017 and GD2018 in eight specific proteins.

Figure 1. Protein profile of three ILTV isolates. (Wu M et al., 2022) Figure 1. Diagram of proteins of three ILTVs.

Phylogenetic analysis of 20 ILTV strains reveals that SH2016, SH2017, and GD2018 fall into distinct sub-lineages. SH2016 clusters with Russian and Australian vaccine strains, indicating possible evolution from these vaccines. SH2017 and GD2018, showing 99.9% similarity, are closely related to U.S. vaccine strains, suggesting a different evolutionary path.

Figure 2. Phylogenetic relationship among ILTV isolates. (Wu M et al., 2022) Figure 2. Phylogenetic tree of ILTVs

Conclusions

Three ILTV isolates, despite high genomic similarity, exhibit notable differences in replication and pathogenicity. SH2016 is more virulent, while SH2017 and GD2018 cause milder symptoms. Variations in specific viral proteins likely account for these differences.

References

Kosuri S, Church G M. Large-scale de novo DNA synthesis: technologies and applications. Nature methods, 2014, 11(5): 499.
Marston D A, McElhinney L M, Ellis R J, et al. Next generation sequencing of viral RNA genomes. BMC genomics, 2013, 14(1): 444.
Wu M, Zhang Z, Su X, et al. Biological characteristics of infectious laryngotracheitis viruses isolated in China. Viruses. 2022 May 31;14(6):1200.

* For research purposes only, not intended for clinical diagnosis, treatment, or individual health assessments.