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Viral Quasispecies Inference from Single Observations—Mutagens as Accelerators of Quasispecies Evolution [PDF]

Microorganisms
RNA virus populations exist as quasispecies-complex, dynamic clouds of closely related but genetically diverse variants generated by high mutation rates during replication. Assessing quasispecies structure and diversity is crucial for understanding viral
Josep Gregori, Miquel Salicrú, Marta Ibáñez-Lligoña, Sergi Colomer-Castell, Carolina Campos, Alvaro González-Camuesco, Josep Quer   +6 more
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SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants

Microbiology Spectrum, 2021
The dynamics of quasispecies afford RNA viruses a great fitness on cell tropism and host range. To study the quasispecies features and the intra-host evolution of SARS-CoV-2, we collected nine confirmed patients and sequenced the haplotypes of spike gene
Fengming Sun, Xiuhua Wang, Shun Tan, Yunjie Dan, Yanqiu Lu, Juan Zhang, Junli Xu, Zhaoxia Tan, Xiaomei Xiang, Yi Zhou, Weiwei He, Xing Wan, Wei Zhang, Yaokai Chen, Wenting Tan, Guohong Deng   +15 more
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PacBio high-fidelity near full-length genome sequencing for HIV-1 quasispecies: methodological framework and validation [PDF]

Frontiers in Microbiology
This study aimed to develop an optimized sequencing workflow for HIV-1 near full-length genome (NFLG) quasispecies, integrating the PacBio Revio platform with a streamlined bioinformatics pipeline to enable precise characterization of the genetic ...
Bo Zhu, Bo Zhu, Xiaorui Wang, Xiaorui Wang, Hanping Li, Yongjian Liu, Lei Jia, Xiaolin Wang, Jingyun Li, Bohan Zhang, Jingwan Han, Wei Ma, Lin Li   +12 more
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Association of Liver Damage and Quasispecies Maturity in Chronic HCV Patients: The Fate of a Quasispecies [PDF]

Microorganisms
Viral diversity and disease progression in chronic infections, and particularly how quasispecies structure affects antiviral treatment, remain key unresolved issues.
Josep Gregori, Marta Ibañez-Lligoña, Sergi Colomer-Castell, Carolina Campos, Damir García-Cehic, Josep Quer   +5 more
doaj   +2 more sources

Near extinction of the HBV quasispecies driven by the hard selective sweep in chronic hepatitis B [PDF]

mBio
The viral quasispecies play an important role in pathogenesis. However, little is known about the nature of hepatitis B virus (HBV) quasispecies and its impact on the outcomes of chronic hepatitis B.
Daiqiang Lu, Andong He, Guichan Liao, Renyu Zhou, Zichun Cheng, Ka Cheuk Yip, Xiufang Wang, Wei Cao, Jiaojiao Peng, Ruiman Li, Jie Peng, Feng Gao   +11 more
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Quasispecies theory and the behavior of RNA viruses.

PLoS Pathogens, 2010
A large number of medically important viruses, including HIV, hepatitis C virus, and influenza, have RNA genomes. These viruses replicate with extremely high mutation rates and exhibit significant genetic diversity.
Adam S Lauring, Raul Andino
doaj   +3 more sources

Molecular characterization of HIV-1 near-full-length proviral quasispecies in monocytes from patients across different virological responses [PDF]

Frontiers in Microbiology
IntroductionLow-level viremia (LLV) in HIV infection, defined as detectable but low plasma viral load, is associated with an increased risk of virological failure (VF); however, the mechanisms underlying LLV remain unclear.
Jian Li, Jian Li, Chuyu Zhang, Chuyu Zhang, Zhenyi Zou, Zhenyi Zou, Yawen Liang, Yawen Liang, Peng Ma, Yun Lan, Yun Lan, Quanmin Li, Qian Kong, Qian Kong, Ruiying He, Ruiying He, Linghua Li, Weilie Chen, Weilie Chen   +18 more
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Investigation of Natural Resistance to Fostemsavir and Lenacapavir in Naïve Primary Infections by Ultra-Deep Sequencing of near Full-Length HIV-1 Genomes [PDF]

Viruses
Next-generation sequencing (NGS) of near full-length HIV genomes was performed to investigate natural resistance to Fostemsavir (FTR) and Lenacapavir (LEN) at the quasispecies level in nine naïve primary HIV infections harboring different HIV subtypes ...
Elisabetta Lazzari, Gabriella Rozera, Roberta Gagliardini, Valentina Mazzotta, Lavinia Fabeni, Federica Forbici, Giulia Berno, Cristian Cosentino, Enrico Girardi, Andrea Antinori, Fabrizio Maggi, Isabella Abbate   +11 more
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Quasispecies Nature of RNA Viruses: Lessons from the Past

Vaccines, 2023
Viral quasispecies are distinct but closely related mutants formed by the disparity in viral genomes due to recombination, mutations, competition, and selection pressure.
Kiran Singh, Deepa Mehta, Shaurya Dumka, Aditya Singh Chauhan, Sachin Kumar   +4 more
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Quasispecies theory and emerging viruses: challenges and applications [PDF]

npj Viruses
Quasispecies theory revolutionized our understanding of viral evolution by describing viruses as dynamic populations of genetically diverse variants constantly adapting. This article explores the theory’s role in virus-host interactions, including immune
Josep Sardanyés, Celia Perales, Esteban Domingo, Santiago F. Elena   +3 more
doaj   +2 more sources