Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses

Standard

Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. / Bào, Yīmíng; Amarasinghe, Gaya K.; Basler, Christopher F. et al.

In: Viruses, Vol. 9, No. 5, 106, 11.05.2017.

Research output: Contribution to journal › Article › peer-review

Harvard

Bào, Y, Amarasinghe, GK, Basler, CF, Bavari, S, Bukreyev, A, Chandran, K, Dolnik, O, Dye, JM, Ebihara, H, Formenty, P, Hewson, R, Kobinger, GP, Leroy, EM, Mühlberger, E, Netesov, SV, Patterson, JL, Paweska, JT, Smither, SJ, Takada, A, Towner, JS, Volchkov, VE, Wahl-Jensen, V & Kuhn, JH 2017, 'Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses', Viruses, vol. 9, no. 5, 106. https://doi.org/10.3390/v9050106

APA

Bào, Y., Amarasinghe, G. K., Basler, C. F., Bavari, S., Bukreyev, A., Chandran, K., Dolnik, O., Dye, J. M., Ebihara, H., Formenty, P., Hewson, R., Kobinger, G. P., Leroy, E. M., Mühlberger, E., Netesov, S. V., Patterson, J. L., Paweska, J. T., Smither, S. J., Takada, A., ... Kuhn, J. H. (2017). Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. Viruses, 9(5), [106]. https://doi.org/10.3390/v9050106

Vancouver

Bào Y, Amarasinghe GK, Basler CF, Bavari S, Bukreyev A, Chandran K et al. Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. Viruses. 2017 May 11;9(5):106. doi: 10.3390/v9050106

Author

Bào, Yīmíng ; Amarasinghe, Gaya K. ; Basler, Christopher F. et al. / Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. In: Viruses. 2017 ; Vol. 9, No. 5.

BibTeX

@article{361d0b433eab4990a2411111b9662b81,

title = "Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses",

abstract = "The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.",

keywords = "Cuevavirus, Ebola, Ebolavirus, Filoviridae, Filovirus, ICTV, Marburgvirus, Mononegavirales, Virus classification, Virus taxonomy, BATS, NAMES, marburgvirus, cuevavirus, CHINA, virus taxonomy, filovirus, FILOVIRIDAE, ebolavirus, SEQUENCE COMPARISON PASC, VIRAL GENOMES, virus classification, VIRUSES",

author = "Yīm{\'i}ng B{\`a}o and Amarasinghe, {Gaya K.} and Basler, {Christopher F.} and Sina Bavari and Alexander Bukreyev and Kartik Chandran and Olga Dolnik and Dye, {John M.} and Hideki Ebihara and Pierre Formenty and Roger Hewson and Kobinger, {Gary P.} and Leroy, {Eric M.} and Elke M{\"u}hlberger and Netesov, {Sergey V.} and Patterson, {Jean L.} and Paweska, {Janusz T.} and Smither, {Sophie J.} and Ayato Takada and Towner, {Jonathan S.} and Volchkov, {Viktor E.} and Victoria Wahl-Jensen and Kuhn, {Jens H.}",

note = "Publisher Copyright: {\textcopyright} 2017 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2017",

month = may,

day = "11",

doi = "10.3390/v9050106",

language = "English",

volume = "9",

journal = "Viruses",

issn = "1999-4915",

publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

number = "5",

}

RIS

TY - JOUR

T1 - Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses

AU - Bào, Yīmíng

AU - Amarasinghe, Gaya K.

AU - Basler, Christopher F.

AU - Bavari, Sina

AU - Bukreyev, Alexander

AU - Chandran, Kartik

AU - Dolnik, Olga

AU - Dye, John M.

AU - Ebihara, Hideki

AU - Formenty, Pierre

AU - Hewson, Roger

AU - Kobinger, Gary P.

AU - Leroy, Eric M.

AU - Mühlberger, Elke

AU - Netesov, Sergey V.

AU - Patterson, Jean L.

AU - Paweska, Janusz T.

AU - Smither, Sophie J.

AU - Takada, Ayato

AU - Towner, Jonathan S.

AU - Volchkov, Viktor E.

AU - Wahl-Jensen, Victoria

AU - Kuhn, Jens H.

PY - 2017/5/11

Y1 - 2017/5/11

N2 - The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

AB - The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

KW - Cuevavirus

KW - Ebola

KW - Ebolavirus

KW - Filoviridae

KW - Filovirus

KW - ICTV

KW - Marburgvirus

KW - Mononegavirales

KW - Virus classification

KW - Virus taxonomy

KW - BATS

KW - NAMES

KW - marburgvirus

KW - cuevavirus

KW - CHINA

KW - virus taxonomy

KW - filovirus

KW - FILOVIRIDAE

KW - ebolavirus

KW - SEQUENCE COMPARISON PASC

KW - VIRAL GENOMES

KW - virus classification

KW - VIRUSES

UR - http://www.scopus.com/inward/record.url?scp=85019189029&partnerID=8YFLogxK

U2 - 10.3390/v9050106

DO - 10.3390/v9050106

M3 - Article

C2 - 28492506

AN - SCOPUS:85019189029

VL - 9

JO - Viruses

JF - Viruses

SN - 1999-4915

IS - 5

M1 - 106

ER -

ID: 8690162