Inter- and intra-host viral diversity in a large seasonal DENV2 outbreak.
BACKGROUND
High genetic diversity at both inter- and intra-host level are hallmarks of RNA viruses due to the error-prone nature of their genome replication. Several groups have evaluated the extent of viral variability using different RNA virus deep sequencing methods. Although much of this effort has been dedicated to pathogens that cause chronic infections in humans, few studies investigated arthropod-borne, acute viral infections.


RESULTS
We deep sequenced the complete genome of ten DENV2 isolates from representative classical and severe cases sampled in a large outbreak in Brazil using two different approaches. Analysis of the consensus genomes confirmed the larger extent of the 2010 epidemic in comparison to a previous epidemic caused by the same viruses in another city two years before (genetic distance = 0.002 and 0.0008 respectively). Analysis of viral populations within the host revealed a high level of conservation. After excluding homopolymer regions of 454/Roche generated sequences, we found 10 to 44 variable sites per genome population at a frequency of >1%, resulting in very low intra-host genetic diversity. While up to 60% of all variable sites at intra-host level were non-synonymous changes, only 10% of inter-host variability resulted from non-synonymous mutations, indicative of purifying selection at the population level.


CONCLUSIONS
Despite the error-prone nature of RNA-dependent RNA-polymerase, dengue viruses maintain low levels of intra-host variability.
Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias (LIMHC), Universidade de São Paulo, São Paulo, Brazil. cmromano@usp.br
Camila Malta
CM
Romano
Michael
M
Lauck
Felipe S
FS
Salvador
Célia Rodrigues
CR
Lima
Lucy S
LS
Villas-Boas
Evaldo Stanislau A
ES
Araújo
José Eduardo
JE
Levi
Claudio Sergio
CS
Pannuti
David
D
O'Connor
Esper Georges
EG
Kallas
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D003715:Dengue / Q000453:epidemiology / Q000235:genetics / Q000821:virology*; D003716:Dengue Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D004196:Disease Outbreaks; D005260:Female; D014644:Genetic Variation / Q000235:genetics*; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics*
D012367:RNA, Viral; D012324:RNA-Dependent RNA Polymerase