RNA virus genomics: a world of possibilities

Holmes, Edward C.

doi:10.1172/jci38050

Cited by 76 publications

(52 citation statements)

References 88 publications

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“…1 In fact, it has been proposed that A/H3N2 genetic diversity in temperate regions is due to continual importation of different viral lineages from a tropical source, and not the expansive evolution of a single lineage. 1,11 The principal limitations of this study are its relatively small sample size obtained from a single geographical origin over a short period of time and the sequencing of a single gene. Nevertheless, our findings contribute to a better understanding of the genetic and antigenic evolution of influenza A/H3N2 viruses.…”

Section: Discussionmentioning

confidence: 99%

Molecular and antigenic evolution of human influenza A/H3N2 viruses in Quebec, Canada, 2009–2011

Ann

Papenburg

Bouhy

et al. 2012

Journal of Clinical Virology

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Section: Discussionmentioning

confidence: 99%

Molecular and antigenic evolution of human influenza A/H3N2 viruses in Quebec, Canada, 2009–2011

Ann

Papenburg

Bouhy

et al. 2012

Journal of Clinical Virology

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“…No RNA viruses infecting archaea have been described. Eukaryotic RNA viruses are a dominant viral form: they are numerous, diverse, and widespread, found to infect animals, plants, and many unicellular forms (17,28,38,40,70). Only two narrow groups of bacterial RNA viruses are known, and these do not show a close relationship with the viruses infecting eukaryotes (38,40).…”

mentioning

confidence: 99%

Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs

Bolduc

Shaughnessy

Wolf

et al. 2012

J Virol

112

106

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There are no known RNA viruses that infect Archaea . Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic Archaea . A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya . However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of Eukarya and Bacteria . Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.

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“…DENV can be classified into four serotypes, each of which includes several genotypes (Holmes and Burch, 2000;Holmes, 2009). Similar to other RNA viruses, mutations frequently occur during the viral replication process in DENV because viral RNA polymerase lacks a proofreading mechanism, and resulting in endemic disease.…”

Section: Discussionmentioning

confidence: 99%

Epidemiological and etiological investigation of dengue fever in the Fujian province of China during 2004–2014

Wang

Chen

Huang

et al. 2016

Sci. China Life Sci.

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Dengue fever (DF) is a vector-borne disease and a tremendous socioeconomic burden on tropical and subtropical countries worldwide. To explore the characteristics of DF epidemic in the Fujian province, information of DF cases in Fujian during 2004-2014 was collected and analyzed. The complete E genes of 48 viral isolates were amplified and sequenced for phylogenetic analysis. A total of 733 cases was reported, of which 612 (83.5%) occurred during the peak period from August to October. Additionally, 76% (190/250) of imported cases originated from Southeast Asia countries, by the epidemiological investigation. Phylogenetic analysis of the 48 viral isolates revealed that three genotypes (I, IV, V) of DENV1, and one genotype each of DENV2 (cosmopolitan) and DENV3 (I) circulated in Fujian during [2004][2005][2006][2007][2008][2009][2010][2011][2012][2013][2014]. Similar to the results of the epidemiological investigations, the source of most of the viral isolates, including imported and indigenous cases, may be Southeast Asia countries; however, importation from adjacent provinces was also observed in recent years. Overall, DF is considered an imported epidemic disease in Fujian. Increasing diversity of the viral source and geographic expansion of the area affected by DF in recent years highlights the necessity for strengthening surveillance of the DF epidemic and developing strategies for DF prevention and control in Fujian.dengue virus, E gene, phylogenetic tree, epidemiology, etiology Citation:

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RNA virus genomics: a world of possibilities

Cited by 76 publications

References 88 publications

Molecular and antigenic evolution of human influenza A/H3N2 viruses in Quebec, Canada, 2009–2011

Molecular and antigenic evolution of human influenza A/H3N2 viruses in Quebec, Canada, 2009–2011

Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs

Epidemiological and etiological investigation of dengue fever in the Fujian province of China during 2004–2014

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