Agrima Bhatt, Rajasthan University
In the last few decades, humankind has gone through major healthcare upheavals causing a large amount of death and destruction. Epidemics, pandemics have come, some have passed with time but some have evolved to stay. And as we continue forward, scientists are already predicting the next pandemic to come soon. In the history of time, however, viral infections have continued to prevail, whether we talk about the present coronavirus or the emergence of H1N1 in 1918.
Medical research keeps on pondering the many questions that virus holds, researchers have grabbed onto very limited knowledge of it and continued to explore their physiology. This article discusses the details on viral pathogens, genome assembly of the viral strain, among other issues relevant to the same.
What is a Viral Pathogen and its Strains?
Pathogens refer to the organisms responsible for causing a disease. Different pathogens cause different diseases in the host organism. A viral pathogen can be termed as a substance that is small in size as compared to bacteria. Viral pathogens are much more infectious as they invade the host cells and reproduce in number through the process of replication. They use the host organism’s protein machinery for a continuous replication process.
What is interesting to know is that all viruses possess the ability to mutate and co-infect. The process of its mutation depends on the type of genome as a virus containing RNA can mutate faster. Co-infection strengthens the possibility of the presence of multiple related viral strains within the host. If the genomes of these viral strains could be reconstructed, we can find out the repercussions of their infections. This exploration will also increase our very limited knowledge of these viruses and their strains.
What is Haploflow?
Haploflow is one such de novo genome assembly software developed by German scientists. It uses a novel flow algorithm to reconstruct viral strain genomes. The traditional genome assembly can be a bit challenging, however, Haploflow uses the fast algorithms of the metagenome assemblers. It captures variation between different strains and combines those variants together that are not occurring twice.
After experimentation, Haploflow was found to be correct in most metrics as compared to the results of 12 other assemblers. Haploflow was able to assemble the three genomes entirely with few corrections in an HIV data set. It scored a total of 9.66 out of 10 in comparison with PredictHaplo and PEHaplo.
Applications and Future Use:
Haploflow was able to perform reconstruction on SARS-CoV-2 samples. It showed a high duplication ratio in its genome assembly when assessed with QUAST. These technologies can be a key to know more about the genetic epidemiology of viruses and genome-based viral phenotyping. This allows people to trace the disease back to its viral strains to avoid a future pandemic.
This reconstruction of genomes allows the software to perform the most complex computational biology tasks. As we move to the future, and research and development continue to soar high, scientists are eager to see if one day maybe we can perform de novo genome assembly on humans as well.
Also read: Are probiotics and prebiotics safe during pregnancy & lactation?
References:
- Fritz, A., Bremges, A., Deng, Z.-L., Lesker, T. R., Götting, J., Ganzenmueller, T., Sczyrba, A., Dilthey, A., Klawonn, F., & McHardy, A. C. (2021). Haploflow: strain- resolved de novo assembly of viral genomes. Genome Biology, 22(1). https://doi.org/10.1186/s13059-021-02426-8.
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Author’s info:
Agrima Bhatt is an undergraduate student studying BSc. Biotechnology in Jaipur, Rajasthan. She is a science and research enthusiast who also loves to write articles and short snippets.
Some of her published articles at BioXone are:
- https://bioxone.in/news/worldnews/molecular-mechanisms-underlying-virescent-mutation-in-cotton/
- https://bioxone.in/news/worldnews/multi-angle-projection-microscope-a-novel-imaging-technique/
- https://bioxone.in/news/worldnews/scientists-develop-novel-cholera-vaccine-from-rice-grains/
- https://bioxone.in/news/worldnews/ai-predicts-the-relation-between-viruses-and-mammals/
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