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These data suggest that the rZH501-M847-A-type virus probably represented the major virus population in the patient.
These data unambiguously demonstrated that rZH501-M847-A-type virus became the major virus population in rZH501-M847-G-infected mice.
Alternatively, rZH501-M847-A-type virus was generated by a point mutation at M847 of the M segment in the rZH501-M847-G-infected mice and became a major virus population as early as 2 days p.i.
Accumulation of rZH501-M847-A-type virus was detected in the liver of a single mouse as early as 2 days p.i. and rZH501-M847-A-type virus became the major virus population in livers, spleens and brains from day 5 to 8 p.i.
We did not observe the accumulation of rZH501-M847A-type virus after 5 passages of rZH501-M847-G in both cell types (data not shown), demonstrating that the rZH501-M847-A-type virus did not emerge after passages of rZH501-M847-G in cultured cells but it became the major virus population in mice that were infected with rZH501-M847-G.
Remarkably, as early as 2 days postinfection with rZH501-M847-G, the viruses carrying A at M847 emerged and became the major virus population thereafter, while replicating viruses retained the input A residue at M847 in rZH501-M847-A-infected mice.
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The present study revealed that wt RVFV ZH501 stock, which was originally isolated from a patient during the 1977 outbreak of RVFV in Egypt, was made up of two major virus populations with single nucleotide substitution within the Gn gene and that a single nucleotide difference in the Gn gene of wt RVFV substantially affected viral mouse virulence.
This trend in virus replication in vitro pointed to the possibility that the rZH501-M847-G-type virus that was present as a minor virus population in the patient could have amplified in cell culture to become a major viral subpopulation in the ZH501 virus stock that was generated in vitro.
Before the initiation of an optimized treatment, a genotype of the main (major) patients' virus populations (only virus species present at >20 30% are detected and therefore analysed) is assessed.
Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines.
However, virologists using HTS technologies for the purpose of rare variant detection, face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies (Archer et al., 2012a; Watson et al., 2013; Wright et al., 2011).
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