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So far, existing methods for viral quasispecies assembly can be classified into reference-based approaches on the one hand and de novo (reference free) approaches on the other hand see for a recent review of related approaches. Notwithstanding the short size of virus genomes, it is still a challenge because within a viral quasispecies (i) closely related strains share plenty of near-identical genomic fragments, (ii) single strains are affected by repetitive regions, (iii) the number of strains is unknown, and (iv) the abundances of strains vary across the strains, which is further aggravated by read coverage fluctuations along the genomes.
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Further, along with strain identity-preserving sequence, accurate estimates of strain abundances are required for full quantification of infections at the RNA/DNA level. It is the general, ultimate goal of viral quasispecies assembly to reconstruct the individual, strain-specific haplotypes at their full length. To accurately account for these issues, accurate reconstruction of strain-resolved genomes can be very helpful, if not even necessary. Currently, the COVID-19 pandemic puts the necessity to monitor the outbreak of viruses, to track their evolutionary history, and to develop effective vaccines and drugs in the spotlight of greater public interest. In addition, biological functionalities or phenotypic appearance can differ substantially across different strains. Among others, it contributes to tissue tropism, virus transmission, disease progression, virulence and drug/vaccine resistance. The genetic diversity of viral quasispecies plays an important role in viral evolution. Therefore, they are characterized by high mutation rates, and commonly populate hosts as a collection of closely related strains which differ by only small amounts of variants, and which together are referred to as viral quasispecies. Viruses such as HIV, ZIKV, and Ebola lack proofreading mechanisms when they replicate themselves with RNA-dependent RNA polymerase (RdRp). The Creative Commons Public Domain Dedication waiver ( ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
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