Genomic surveillance allows researchers to examine the genome sequence of the viral strains infecting the population. As the virus multiplies inside human cells, it needs to copy its genome to make more viral particles, a process called replication. Copying errors are sometimes introduced in this process because the enzyme that copies the RNA is error-prone. These copying errors introduce mutations or changes to the genomic sequence.
The changes alter the viral genes, leading to a change in the viral proteins encoded by them. Thus, though mutations arise in the normal course of viral replication, they can then get selected for their beneficial properties to the virus. Continuous monitoring of viral genome variations is very useful in tracing the path of the spread of the disease.
Such information can be very useful in containment measures and strategies. Metagenomic sequencing is most appropriate for diagnostic sequencing of unknown or poorly characterized viruses, PCR amplicon sequencing works well for short viral genomes and low diversity in primer binding sites, and target enrichment works for all pathogen sizes but is particularly advantageous for large viruses and for viruses that have diverse but well-characterized genomes. Two obvious areas of innovation currently exist: methods that can effectively deplete host DNA without affecting viral DNA, and the further development of long-read technologies to achieve the flexibility and competitive pricing of short-read technologies.
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Huang, W. Whole-genome sequence analysis reveals the enterovirus D68 isolates during the United States outbreak mainly belong to a novel clade. This provides information about what is driving the spread of the virus both locally and nationally.
This work can be made more precise if virus genomes are combined with information about where, how and when people travel locally and internationally.
Virus genome sequences can also identify unique genetic changes shared by all those infected in a single virus transmission chain. This can be used to distinguish whether two clusters of cases in the same area have arisen because one started infection in the other, or because there were two distinct and independent chains of transmission with separate, earlier origins. Virus genomes can therefore add to the information provided by patient contact tracing, which is important for tracking outbreaks in communities, hospitals and other care settings.
Many genetic changes that occur in the genome of the virus will have no significant effect on the course of infection or disease, or the impact of control measures. However, a few of the changes might be important. These need to be identified and tracked through time. In viruses such as influenza, we know that genetic changes can alter how the immune system recognises viruses, resistance to antiviral drugs, and the severity of disease. These discoveries have yet to be made for the new coronavirus.
Rapid, large-scale virus genome sequencing is a new stream of information that can contribute to the tracking of epidemics and the development of new methods of control. Their work will help shed light on how the virus evolves as it spreads and how well containment efforts are working. Share on Twitter.
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