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HCV strains evolve differently in HIV-coinfected individuals, according to the results of a database analysis of HCV genetic sequences from patients monoinfected with HCV and those who were coinfected with HIV. The study compared results from 112 coinfected persons (CIPs) and 176 monoinfected persons (MIPs), according to the report published in the journal Infection, Genetics, and Evolution.
Genetic differences between intrahost variants of the HCV hypervariable region 1 (HVR1) were sampled from CIPs and MIPs, and the nucleotide sequences of intrahost HCV HVR1 variants (n = 28,622) obtained were represented using 148 physical-chemical (PhyChem) indexes of DNA nucleotide dimers. Changes of the intrahost HCV population were detected by measuring coevolution among the HVR1 site using new PhyChem properties extracted from the next-generation sequencing of HVR1 data. Small but statistically significant variances in seven of the PhyChem indexes, measured using these intrahost HVR1 variants, was shown to be strongly associated with CIPs and MIPs (P less than .0001).
“The computational models built using these new markers provide novel opportunities for development of cybermolecular diagnostics,” wrote James Lara, PhD, and his colleagues at the Centers for Disease Control and Prevention.
All HVR1 sequences used (n = 28,622) shared only 6,782 profiles of the selected calculated dinucleotide-based auto covariances of the seven PhyChem indexes. The vast majority (98%-99%) of these profiles were found to be specific to CIPs or MIPs, indicating that coevolution among HVR1 sites reflects HCV adaptation to HIV among coinfected individuals, according to the authors.
Because of the common occurrence of HIV-coinfection in high-risk groups, “HCV strains circulating in high-risk groups need to be carefully monitored for the identification of potentially new traits of clinical and public health relevance,” Dr. Lara and his colleagues concluded.
The authors reported having no conflicts of interest.
SOURCE: Lara J et al. Infection, Genetics and Evolution. 2018. 65:216-25.
HCV strains evolve differently in HIV-coinfected individuals, according to the results of a database analysis of HCV genetic sequences from patients monoinfected with HCV and those who were coinfected with HIV. The study compared results from 112 coinfected persons (CIPs) and 176 monoinfected persons (MIPs), according to the report published in the journal Infection, Genetics, and Evolution.
Genetic differences between intrahost variants of the HCV hypervariable region 1 (HVR1) were sampled from CIPs and MIPs, and the nucleotide sequences of intrahost HCV HVR1 variants (n = 28,622) obtained were represented using 148 physical-chemical (PhyChem) indexes of DNA nucleotide dimers. Changes of the intrahost HCV population were detected by measuring coevolution among the HVR1 site using new PhyChem properties extracted from the next-generation sequencing of HVR1 data. Small but statistically significant variances in seven of the PhyChem indexes, measured using these intrahost HVR1 variants, was shown to be strongly associated with CIPs and MIPs (P less than .0001).
“The computational models built using these new markers provide novel opportunities for development of cybermolecular diagnostics,” wrote James Lara, PhD, and his colleagues at the Centers for Disease Control and Prevention.
All HVR1 sequences used (n = 28,622) shared only 6,782 profiles of the selected calculated dinucleotide-based auto covariances of the seven PhyChem indexes. The vast majority (98%-99%) of these profiles were found to be specific to CIPs or MIPs, indicating that coevolution among HVR1 sites reflects HCV adaptation to HIV among coinfected individuals, according to the authors.
Because of the common occurrence of HIV-coinfection in high-risk groups, “HCV strains circulating in high-risk groups need to be carefully monitored for the identification of potentially new traits of clinical and public health relevance,” Dr. Lara and his colleagues concluded.
The authors reported having no conflicts of interest.
SOURCE: Lara J et al. Infection, Genetics and Evolution. 2018. 65:216-25.
HCV strains evolve differently in HIV-coinfected individuals, according to the results of a database analysis of HCV genetic sequences from patients monoinfected with HCV and those who were coinfected with HIV. The study compared results from 112 coinfected persons (CIPs) and 176 monoinfected persons (MIPs), according to the report published in the journal Infection, Genetics, and Evolution.
Genetic differences between intrahost variants of the HCV hypervariable region 1 (HVR1) were sampled from CIPs and MIPs, and the nucleotide sequences of intrahost HCV HVR1 variants (n = 28,622) obtained were represented using 148 physical-chemical (PhyChem) indexes of DNA nucleotide dimers. Changes of the intrahost HCV population were detected by measuring coevolution among the HVR1 site using new PhyChem properties extracted from the next-generation sequencing of HVR1 data. Small but statistically significant variances in seven of the PhyChem indexes, measured using these intrahost HVR1 variants, was shown to be strongly associated with CIPs and MIPs (P less than .0001).
“The computational models built using these new markers provide novel opportunities for development of cybermolecular diagnostics,” wrote James Lara, PhD, and his colleagues at the Centers for Disease Control and Prevention.
All HVR1 sequences used (n = 28,622) shared only 6,782 profiles of the selected calculated dinucleotide-based auto covariances of the seven PhyChem indexes. The vast majority (98%-99%) of these profiles were found to be specific to CIPs or MIPs, indicating that coevolution among HVR1 sites reflects HCV adaptation to HIV among coinfected individuals, according to the authors.
Because of the common occurrence of HIV-coinfection in high-risk groups, “HCV strains circulating in high-risk groups need to be carefully monitored for the identification of potentially new traits of clinical and public health relevance,” Dr. Lara and his colleagues concluded.
The authors reported having no conflicts of interest.
SOURCE: Lara J et al. Infection, Genetics and Evolution. 2018. 65:216-25.
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