Antigenic evolution of dengue viruses over 20 years

AbstractEnterovirus A71 (EV-A71), Coxsackievirus A16 (CV-A16) and CV-A10 are the major causative agents of hand, foot and mouth disease (HFMD). The conformational epitopes play a vital role in monitoring the antigenic evolution, predicting dominant strains and preparing vaccines. In this study, we employed a Bioinformatics-based algorithm to predict the conformational epitopes of EV-A71 and CV-A16 and compared with that of CV-A10. Prediction results revealed that the distribution patterns of conformational epitopes of EV-A71 and CV-A16 were similar to that of CV-A10 and their epitopes likewise consisted of three sites: site 1 (on the “north rim” of the canyon around the fivefold vertex), site 2 (on the “puff”) and site 3 (one part was in the “knob” and the other was near the threefold vertex). The reported epitopes highly overlapped with our predicted epitopes indicating the predicted results were reliable. These data suggested that three-site distribution pattern may be the basic distribution role of epitopes on the enteroviruses capsids. Our prediction results of EV-A71 and CV-A16 can provide essential information for monitoring the antigenic evolution of enterovirus.

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Complete genome characterization and evolutionary analysis of dengue viruses isolated during 2016–2017 in Pune, India

Infection Genetics and Evolution ◽

10.1016/j.meegid.2021.104909 ◽

2021 ◽

pp. 104909

Author(s):

Divya Tiraki ◽

Karuna Singh ◽

Shubham Shrivastava ◽

A.C. Mishra ◽

Vidya Arankalle

Keyword(s):

Complete Genome ◽

Evolutionary Analysis ◽

Genome Characterization ◽

Dengue Viruses

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Dengue viruses circulating in Indonesia: A systematic review and phylogenetic analysis of data from five decades

Reviews in Medical Virology ◽

10.1002/rmv.2037 ◽

2019 ◽

pp. e2037 ◽

Cited By ~ 8

Author(s):

Harapan Harapan ◽

Alice Michie ◽

Benediktus Yohan ◽

Pei‐Yun Shu ◽

Mudatsir Mudatsir ◽

...

Keyword(s):

Systematic Review ◽

Phylogenetic Analysis ◽

Dengue Viruses

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Genetic epidemiology of dengue viruses in phase III trials of the CYD tetravalent dengue vaccine and implications for efficacy

eLife ◽

10.7554/elife.24196 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 17

Author(s):

Maia A Rabaa ◽

Yves Girerd-Chambaz ◽

Kien Duong Thi Hue ◽

Trung Vu Tuan ◽

Bridget Wills ◽

...

Keyword(s):

Genetic Epidemiology ◽

Phase Iii ◽

Envelope Gene ◽

Dengue Vaccine ◽

Virus Genotype ◽

Pivotal Phase ◽

Dengue Viruses ◽

High Amino Acid ◽

Phase Iii Trials ◽

Trial Participants

This study defined the genetic epidemiology of dengue viruses (DENV) in two pivotal phase III trials of the tetravalent dengue vaccine, CYD-TDV, and thereby enabled virus genotype-specific estimates of vaccine efficacy (VE). Envelope gene sequences (n = 661) from 11 DENV genotypes in 10 endemic countries provided a contemporaneous global snapshot of DENV population genetics and revealed high amino acid identity between the E genes of vaccine strains and wild-type viruses from trial participants, including at epitope sites targeted by virus neutralising human monoclonal antibodies. Post-hoc analysis of all CYD14/15 trial participants revealed a statistically significant genotype-level VE association within DENV-4, where efficacy was lowest against genotype I. In subgroup analysis of trial participants age 9–16 years, VE estimates appeared more balanced within each serotype, suggesting that genotype-level heterogeneity may be limited in older children. Post-licensure surveillance is needed to monitor vaccine performance against the backdrop of DENV sequence diversity and evolution.

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Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to haemagglutinin evolution

Journal of General Virology ◽

10.1099/vir.0.043059-0 ◽

2012 ◽

Vol 93 (9) ◽

pp. 1996-2007 ◽

Cited By ~ 35

Author(s):

Kim B. Westgeest ◽

Miranda de Graaf ◽

Mathieu Fourment ◽

Theo M. Bestebroer ◽

Ruud van Beek ◽

...

Keyword(s):

Humoral Immunity ◽

Influenza A ◽

Phylogenetic Trees ◽

Influenza Viruses ◽

Genetic Maps ◽

Genetic Evolution ◽

Human Influenza ◽

Nucleotide Level ◽

Antigenic Evolution ◽

Positively Selected Sites

Each year, influenza viruses cause epidemics by evading pre-existing humoral immunity through mutations in the major glycoproteins: the haemagglutinin (HA) and the neuraminidase (NA). In 2004, the antigenic evolution of HA of human influenza A (H3N2) viruses was mapped (Smith et al., Science 305, 371–376, 2004) from its introduction in humans in 1968 until 2003. The current study focused on the genetic evolution of NA and compared it with HA using the dataset of Smith and colleagues, updated to the epidemic of the 2009/2010 season. Phylogenetic trees and genetic maps were constructed to visualize the genetic evolution of NA and HA. The results revealed multiple reassortment events over the years. Overall rates of evolutionary change were lower for NA than for HA1 at the nucleotide level. Selection pressures were estimated, revealing an abundance of negatively selected sites and sparse positively selected sites. The differences found between the evolution of NA and HA1 warrant further analysis of the evolution of NA at the phenotypic level, as has been done previously for HA.

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