Application of deep sequencing methods for inferring viral population diversity

Huang, Sheng Wen; Hung, Su Jhen; Wang, Jen Ren

doi:10.1016/j.jviromet.2019.01.013

Cited by 10 publications

(3 citation statements)

References 74 publications

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“…The results suggest that there may be a correlation between the phylogenetic grouping and the levels of genetic diversity observed in these viruses. However, additional studies would be needed to determine the genetic diversity inside and outside of the different hosts that tick-borne viruses occupy to further understand the evolution of the MTBFs [ 33 ].…”

Section: Discussionmentioning

confidence: 99%

Differences in Genetic Diversity of Mammalian Tick-Borne Flaviviruses

Carpio

Thompson

Widen

et al. 2023

Viruses

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The genetic diversities of mammalian tick-borne flaviviruses are poorly understood. We used next-generation sequencing (NGS) to deep sequence different viruses and strains belonging to this group of flaviviruses, including Central European tick-borne encephalitis virus (TBEV-Eur), Far Eastern TBEV (TBEV-FE), Langat (LGTV), Powassan (POWV), Deer Tick (DTV), Kyasanur Forest Disease (KFDV), Alkhurma hemorrhagic fever (AHFV), and Omsk hemorrhagic fever (OHFV) viruses. DTV, AHFV, and KFDV had the lowest genetic diversity, while POWV strains LEIV-5530 and LB, OHFV, TBEV-Eur, and TBEV-FE had higher genetic diversities. These findings are compatible with the phylogenetic relationships between the viruses. For DTV and POWV, the amount of genetic diversity could be explained by the number of tick vector species and amplification hosts each virus can occupy, with low diversity DTV having a more limited vector and host pool, while POWV with higher genetic diversities has been isolated from different tick species and mammals. It is speculated that high genetic diversity may contribute to the survival of the virus as it encounters these different environments.

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Section: Discussionmentioning

confidence: 99%

Differences in Genetic Diversity of Mammalian Tick-Borne Flaviviruses

Carpio

Thompson

Widen

et al. 2023

Viruses

View full text Add to dashboard Cite

show abstract

“…The reason why the Sanger sequencing was not used here was its inability to quantify the complexity of mutant spectra. Alternatively, the NGS, capable of generating a large dataset to identify SNMs in viral genomes ( Huang et al., 2019 ; Lu et al., 2020 ), was used in this study.…”

Section: Discussionmentioning

confidence: 99%

Rescuing eGFP-Tagged Canine Distemper Virus for 40 Serial Passages Separately in Ribavirin- and Non-Treated Cells: Comparative Analysis of Viral Mutation Profiles

Liu

Wang

Lin

et al. 2021

Front. Cell. Infect. Microbiol.

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Due to lacking a proofreading mechanism in their RNA-dependent RNA polymerases (RdRp), RNA viruses generally possess high mutation frequencies, making them evolve rapidly to form viral quasispecies during serial passages in cells, especially treated with mutagens, like ribavirin. Canine distemper virus (CDV) belongs to the genus Morbillivirus. Its L protein functions as an RdRp during viral replication. In this study, a recombinant enhanced green fluorescence protein-tagged CDV (rCDV-eGFP) was rescued from its cDNA clone, followed by viral identification and characterization at passage-7 (P7). This recombinant was independently subjected to extra 40 serial passages (P8 to 47) in ribavirin- and non-treated cells. Two viral progenies, undergoing passages in ribavirin- and non-treated VDS cells, were named rCDV-eGFP-R and -N, respectively. Both progenies were simultaneously subjected to next-generation sequencing (NGS) at P47 for comparing their quasispecies diversities with each other. The rCDV-eGFP-R and -N showed 62 and 23 single-nucleotide mutations (SNMs) in individual antigenomes, respectively, suggesting that the ribavirin conferred a mutagenic effect on the rCDV-eGFP-R. The spectrum of 62 SNMs contained 26 missense and 36 silent mutations, and that of 23 SNMs was composed of 17 missense and 6 silent mutations. Neither the rCDV-eGFP-R nor -N exhibited nonsense mutation in individual antigenomes. We speculate that the rCDV-eGFP-R may contain at least one P47 sub-progeny characterized by high-fidelity replication in cells. If such a sub-progeny can be purified from the mutant swarm, its L protein would elucidate a molecular mechanism of CDV high-fidelity replication.

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“…The major reason why the conventional Sanger sequencing was not used in this study was its limited ability or inability to identify low-frequency mutations, seriously reducing its applicability to quantify the complexity of mutant spectra. In contrast, the NGS, because capable of generating a large dataset for identification of SNMs in viral genomes, has been widely used to analyze quantitatively the rich diversity of viral quasispecies ( 18 , 25 , 26 ).…”

Section: Discussionmentioning

confidence: 99%

Mutation Profiles of eGFP-Tagged Small Ruminant Morbillivirus During 45 Serial Passages in Ribavirin-Treated Cells

Liu

Zou

et al. 2021

Front. Vet. Sci.

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Small ruminant morbillivirus (SRMV), formerly known as peste-des-petits-ruminants virus, classified into the genus Morbillivirus in the family Paramyxoviridae. Its L protein functions as the RNA-dependent RNA polymerases (RdRp) during viral replication. Due to the absence of efficient proofreading activity in their RdRps, various RNA viruses reveal high mutation frequencies, making them evolve rapidly during serial passages in cells, especially treated with a certain mutagen, like ribavirin. We have previously rescued a recombinant enhanced green fluorescence protein-tagged SRMV (rSRMV-eGFP) using reverse genetics. In this study, the rSRMV-eGFP was subjected to serial passages in ribavirin-treated cells. Due to the ribavirin-exerted selective pressure, it was speculated that viral progenies would form quasispecies after dozens of passages. Viral progenies at passage-10, -20, -30, -40, and -50 were separately subjected to next-generation sequencing (NGS), consequently revealing a total of 34 single-nucleotide variations, including five synonymous, 21 missense, and one non-sense mutations. The L sequence was found to harbor eight missense mutations during serial passaging. It was speculated that at least one high-fidelity variant was present in viral quasispecies at passage-50. If purified from the population of viral progenies, this putative variant would contribute to clarifying a molecular mechanism in viral high-fidelity replication in vitro.

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Application of deep sequencing methods for inferring viral population diversity

Cited by 10 publications

References 74 publications

Differences in Genetic Diversity of Mammalian Tick-Borne Flaviviruses

Differences in Genetic Diversity of Mammalian Tick-Borne Flaviviruses

Rescuing eGFP-Tagged Canine Distemper Virus for 40 Serial Passages Separately in Ribavirin- and Non-Treated Cells: Comparative Analysis of Viral Mutation Profiles

Mutation Profiles of eGFP-Tagged Small Ruminant Morbillivirus During 45 Serial Passages in Ribavirin-Treated Cells

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