Genetic characterization of a novel G3P[14] rotavirus strain causing gastroenteritis in 12year old...
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1 3 Genetic characterization of a novel G3P[14] rotavirus strain causing 4 gastroenteritis in 12 year old Australian child 5 6 7 Celeste M. Donato a,b,⇑,1 Q1 , Nicholas M. Manuelpillai a,c,1 , Daniel Cowley a , Susie Roczo-Farkas a , 8 Jim P. Buttery d,e,f , Nigel W. Crawford d,g,h , Carl D. Kirkwood a,b,h 9 a Enteric Virus Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia 10 b Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia 11 c School of Medicine, University of Notre Dame, Sydney, New South Wales, Australia 12 d SAEFVIC, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia 13 e Department of Infectious Diseases, Monash Children’s Hospital, Melbourne, Victoria, Australia 14 f Department of Paediatrics, Monash University, Melbourne, Victoria, Australia 15 g Department of General Medicine, Royal Children’s Hospital, Melbourne, Victoria, Australia 16 h Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia 17 18 20 article info 21 Article history: 22 Received 21 February 2014 23 Received in revised form 7 April 2014 24 Accepted 10 April 2014 25 Available online xxxx 26 Keywords: 27 Rotavirus 28 Zoonotic transmission 29 Whole genome sequencing 30 Gastroenteritis 31 Bovine 32 Bat 33 34 abstract 35 A genotype G3P[14] rotavirus strain was identified in a 12 year old child presenting to the Emergency 36 Department of the Royal Children’s Hospital, Melbourne, with gastroenteritis. G3P[14] strains have been 37 previously identified in rabbits in Japan, China, the USA and Italy and a single lapine-like strain from a 38 child in Belgium. 39 Full genome sequence analysis of RVA/Human-wt/AUS/RCH272/2012/G3P[14] (RCH272) revealed that 40 the strain contained the novel genome constellation G3-P[14]-I2-R3-C3-M3-A9-N2-T6-E2-H3. The gen- 41 ome was genetically divergent to previously characterized lapine viruses and the genes were distantly 42 related to a range of human bovine-like strains and animal strains of bovine, bat and canine/feline char- 43 acteristics. The VP4, VP6, NSP2, NSP3, NSP4 and NSP5 genes of RCH272 clustered within bovine lineages 44 in the phylogenetic analysis and shared moderate genetic similarity with an Australian bovine-like 45 human strain RVA/Human-tc/AUS/MG6/1993/G6P[14]. Bayesian coalescent analysis suggested these 46 genes of RCH272 and RVA/Human-tc/AUS/MG6/1993/G6P[14] were derived from a population of rela- 47 tively homogenous bovine-like ancestral strains circulating between 1943 and 1989. The VP7, VP1, 48 VP2 and NSP1 genes shared moderate genetic similarity with the Chinese strain RVA/Bat-tc/CHN/ 49 MSLH14/2011/G3P[3] and the VP3 gene clustered within a lineage comprised of canine and feline strains. 50 This strain may represent the direct transmission from an unknown host species or be derived via mul- 51 tiple reassortment events between strains originating from various species. The patient lived in a house- 52 hold containing domesticated cats and dogs and in close proximity to a colony of Gray-headed Flying- 53 foxes. However, without screening numerous animal populations it is not possible to determine the ori- 54 gins of this strain. 55 Ó 2014 Elsevier B.V. All rights reserved. 56 57 58 59 1. Introduction 60 Group A rotavirus infection causes 114 million episodes of diar- 61 rhea annually, resulting in 24 million clinic visits and 2.4 million 62 hospitalizations (Glass et al., 2006). The majority of the 453,000 63 annual deaths due to rotavirus infection occur in developing coun- 64 tries of Asia and sub-Saharan Africa (Tate et al., 2012). 65 Rotavirus (Reoviridae virus family) is a non-enveloped virus 66 with a genome comprised of 11 segments of double stranded 67 RNA (dsRNA), encoding six structural viral proteins (VP1-4, VP6, 68 VP7) and six non-structural proteins (NSP1-5/6) (Estes and 69 Kapikian, 2007). Rotavirus strains can be classified into eight 70 groups (Group A–H) based on genetic characteristics of the inner 71 capsid protein (VP6), with group A strains the most common cause 72 of symptomatic disease in humans (Matthijnssens et al., 2012). A 73 whole genome classification system assigns genotypes to each http://dx.doi.org/10.1016/j.meegid.2014.04.009 1567-1348/Ó 2014 Elsevier B.V. All rights reserved. ⇑ Corresponding author at: Murdoch Childrens Research Institute, Royal Chil- dren’s Hospital, Flemington Road, Parkville, Victoria 3052, Australia. Tel.: +61 3 8341 6444; fax: +61 3 8341 6449. Q2 E-mail address: [email protected] (C.M. Donato). 1 C.M.D. and N.M.M contributed equally to this work. Infection, Genetics and Evolution xxx (2014) xxx–xxx Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid MEEGID 1932 No. of Pages 13, Model 5G 30 April 2014 Please cite this article in press as: Donato, C.M., et al. Genetic characterization of a novel G3P[14] rotavirus strain causing gastroenteritis in 12 year old Australian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid.2014.04.009
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Infection, Genetics and Evolution xxx (2014) xxx–xxx
MEEGID 1932 No. of Pages 13, Model 5G
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Contents lists available at ScienceDirect
Infection, Genetics and Evolution
journal homepage: www.elsevier .com/locate /meegid
Genetic characterization of a novel G3P[14] rotavirus strain causinggastroenteritis in 12 year old Australian child
http://dx.doi.org/10.1016/j.meegid.2014.04.0091567-1348/� 2014 Elsevier B.V. All rights reserved.
⇑ Corresponding author at: Murdoch Childrens Research Institute, Royal Chil-dren’s Hospital, Flemington Road, Parkville, Victoria 3052, Australia. Tel.: +61 38341 6444; fax: +61 3 8341 6449.
E-mail address: [email protected] (C.M. Donato).1 C.M.D. and N.M.M contributed equally to this work.
Please cite this article in press as: Donato, C.M., et al. Genetic characterization of a novel G3P[14] rotavirus strain causing gastroenteritis in 12 yAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid.2014.04.009
Celeste M. Donato a,b,⇑,1, Nicholas M. Manuelpillai a,c,1, Daniel Cowley a, Susie Roczo-Farkas a,Jim P. Buttery d,e,f, Nigel W. Crawford d,g,h, Carl D. Kirkwood a,b,h
a Enteric Virus Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australiab Department of Microbiology, La Trobe University, Melbourne, Victoria, Australiac School of Medicine, University of Notre Dame, Sydney, New South Wales, Australiad SAEFVIC, Murdoch Childrens Research Institute, Melbourne, Victoria, Australiae Department of Infectious Diseases, Monash Children’s Hospital, Melbourne, Victoria, Australiaf Department of Paediatrics, Monash University, Melbourne, Victoria, Australiag Department of General Medicine, Royal Children’s Hospital, Melbourne, Victoria, Australiah Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
a r t i c l e i n f o a b s t r a c t
35363738394041424344454647
Article history:Received 21 February 2014Received in revised form 7 April 2014Accepted 10 April 2014Available online xxxx
Keywords:RotavirusZoonotic transmissionWhole genome sequencingGastroenteritisBovineBat
484950515253545556
A genotype G3P[14] rotavirus strain was identified in a 12 year old child presenting to the EmergencyDepartment of the Royal Children’s Hospital, Melbourne, with gastroenteritis. G3P[14] strains have beenpreviously identified in rabbits in Japan, China, the USA and Italy and a single lapine-like strain from achild in Belgium.
Full genome sequence analysis of RVA/Human-wt/AUS/RCH272/2012/G3P[14] (RCH272) revealed thatthe strain contained the novel genome constellation G3-P[14]-I2-R3-C3-M3-A9-N2-T6-E2-H3. The gen-ome was genetically divergent to previously characterized lapine viruses and the genes were distantlyrelated to a range of human bovine-like strains and animal strains of bovine, bat and canine/feline char-acteristics. The VP4, VP6, NSP2, NSP3, NSP4 and NSP5 genes of RCH272 clustered within bovine lineagesin the phylogenetic analysis and shared moderate genetic similarity with an Australian bovine-likehuman strain RVA/Human-tc/AUS/MG6/1993/G6P[14]. Bayesian coalescent analysis suggested thesegenes of RCH272 and RVA/Human-tc/AUS/MG6/1993/G6P[14] were derived from a population of rela-tively homogenous bovine-like ancestral strains circulating between 1943 and 1989. The VP7, VP1,VP2 and NSP1 genes shared moderate genetic similarity with the Chinese strain RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] and the VP3 gene clustered within a lineage comprised of canine and feline strains.
This strain may represent the direct transmission from an unknown host species or be derived via mul-tiple reassortment events between strains originating from various species. The patient lived in a house-hold containing domesticated cats and dogs and in close proximity to a colony of Gray-headed Flying-foxes. However, without screening numerous animal populations it is not possible to determine the ori-gins of this strain.
� 2014 Elsevier B.V. All rights reserved.
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1. Introduction
Group A rotavirus infection causes 114 million episodes of diar-rhea annually, resulting in 24 million clinic visits and 2.4 millionhospitalizations (Glass et al., 2006). The majority of the 453,000
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annual deaths due to rotavirus infection occur in developing coun-tries of Asia and sub-Saharan Africa (Tate et al., 2012).
Rotavirus (Reoviridae virus family) is a non-enveloped viruswith a genome comprised of 11 segments of double strandedRNA (dsRNA), encoding six structural viral proteins (VP1-4, VP6,VP7) and six non-structural proteins (NSP1-5/6) (Estes andKapikian, 2007). Rotavirus strains can be classified into eightgroups (Group A–H) based on genetic characteristics of the innercapsid protein (VP6), with group A strains the most common causeof symptomatic disease in humans (Matthijnssens et al., 2012). Awhole genome classification system assigns genotypes to each
ear old
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gene. The nomenclature Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hxrepresents the genotypes of the genes encoding VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 respectively. Cur-rently 27 G, 37 P, 17 I, 9 R, 9 C, 8 M, 18 A, 10 N, 12 T, 15 E and11 H genotypes have been described (Guo et al., 2012; Jere et al.,2013; Papp et al., 2012; Trojnar et al., 2013). The genotype classi-fication system based on the two outer capsid proteins VP7 andVP4, is the most widely used scheme in molecular epidemiologyand surveillance programs (Estes and Kapikian, 2007).
Zoonotic transmission increases the genetic diversity within thepopulation of rotavirus strains causing human infection and thesegmented rotavirus genome facilitates reassortment betweenstrains (Ramig and Ward, 1991; Taniguchi and Urasawa, 1995).Strains bearing mixed genome constellations derived from bothhuman and animal viruses are detected more commonly thanstrains possessing a genome only derived from animal viruses, sug-gesting a better adaption to the human host (Martella et al., 2010;Matthijnssens et al., 2011).
The Australian Rotavirus Surveillance Program (ARSP) has mon-itored the diversity and distribution of genotypes identified in chil-dren hospitalized with severe gastroenteritis since 1999 (Kirkwoodet al., 2011a). In 2012, the ARSP identified a G3P[14] strain causingacute gastroenteritis in a child. Genotype G3 strains have a broadhost range, including buffalo, cats, cows, dogs, horses, humans,pigs, rabbits, sheep, monkeys and bats in association with numer-ous P genotypes (Matthijnssens et al., 2011). Genotype P[14]strains are predominantly bovine-like, generally associated withVP7 genotype G10, G6 and G8 (Matthijnssens et al., 2011). In Aus-tralia, G10P[14] (n = 6), G8P[14] (n = 4) and G6P[14] zoonotictransmission strains have been identified exhibiting bovine charac-teristics (Cowley et al., 2013; Matthijnssens et al., 2008; Swiateket al., 2010). Seven G3P[14] strains have been reported worldwide,six were identified in rabbits in Japan, China, the USA and Italy(Guo et al., 2012). A human G3P[14] strain identified from a Bel-gian child exhibited an exclusively lapine-like genome constella-tion, suggesting a direct zoonotic transmission (Matthijnssenset al., 2006).
This study describes the full genome characterization of aG3P[14] rotavirus strain identified in a 12 year old Australian childwho presented to hospital with gastroenteritis and milddehydration.
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2. Materials and methods
2.1. Ethics statement
The collection and analysis of fecal samples by the ARSP isexempt from ethics approval. Informed consent was obtained fromthe patient’s parents prior to the characterization of the strain,acquisition of the patient’s medical history and demographicdetails.
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2.2. Clinical history
A 12 year old male presented to the Emergency Department ofthe Royal Children’s Hospital, Melbourne, Victoria, Australia, with a5 day history of acute gastroenteritis. He had non-bloody diarrheawith intermittent emesis. He was afebrile and mildly dehydratedon clinical assessment and was treated with oral fluids and ananti-emetic (ondansetron). No underlying medical conditions werereported; the patient had not been vaccinated against rotavirusand had no history of significant underlying medical conditions.The patient lived in metropolitan Melbourne and had recently trav-elled to regional Western Australia on a family camping holidayprior to disease onset. No family members reported symptoms of
Please cite this article in press as: Donato, C.M., et al. Genetic characterizationAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid
gastroenteritis. The family reported cats and dogs in the familyhome and a colony of Gray-headed Flying-foxes (Pteropus polio-cephalus) present on the property. No contact with cows or rabbitswas reported either at home or whilst camping. Although no directcontact was reported, there was an abundance of wallabies andkangaroos in the campsite.
2.3. Pathology testing
A fecal sample was collected and aliquots were used by the bac-teriology, virology and parasitology pathology testing servicesensuring the optimal detection of pathogens. The sample wastested for the presence of rotavirus antigen by enzyme immunoas-say (RIDASCREEN� (R-biopharm AG)) and was also screened for thepresence of other enteric pathogens including Adenovirus, Enterovi-rus, ova, cysts, parasites, Salmonella, Shigella, Campylobacter, Yer-sinia, Vibrio and shiga-like toxin producing Escherichia coli by thepathology services at the Royal Children’s Hospital.
2.4. Amplification of 11 rotavirus genes
Fecal suspensions (20% wt/vol) were prepared and RNAextracted using the QIAamp� Viral RNA Mini Kit (QIAGEN, Inc., Hil-den, Germany) as previously described (Cowley et al., 2013). The11 genes were reverse transcribed and amplified by PCR usingthe PrimerScript High Fidelity RT-PCR Kit (Takara, Japan). Briefly,3–5 ll of RNA was denatured at 97 �C for 3 min and quenched onice. RNA was reverse transcribed at 50 �C for 30 min, followed bydenaturation at 94 �C for 2 min. Forty cycles comprised of denatur-ation at 98 �C for 10 s, annealing conditions were dependent onprimer melting temperature (Tm�). For primers with aTm� P 55 �C, 55 �C for 5 s was used, and for primers with aTm� < 55 �C, 50 �C for 15 s was used. An extension at 72 �C for5 min was followed by a final extension of 5 min at 72 �C. The oli-gonucleotide primers used in the amplification of the 11 gene seg-ments are detailed in Supplementary Table 1.
2.5. Nucleotide sequencing
PCR amplicons were excised and purified via gel extraction andspin column purification using the Wizard SV Gel or PCR Clean-UpSystem (Promega, USA) according to the manufacturer’s protocol.Purified DNA together with oligonucleotide primers (detailed inSupplementary Table 1), were sent to the Australian GenomeResearch Facility, Melbourne, and sequenced using an ABI PRISMBigDye Terminator Cycle Sequencing Reaction Kit (Applied Biosys-tems, Foster City, CA, USA) in an Applied Biosystems 3730xl DNAAnalyzer (Applied Biosystems, Foster City, CA, USA). Primer walk-ing was employed to cover the complete sequence of each gene.
2.6. Phylogenetic analysis
The generated electropherograms were visually analyzed andcontiguous DNA sequence files constructed utilizing the Sequen-cher� Software program (version 5.0.1, Gene Codes Corp Inc., AnArbor, MI, USA). Nucleotide similarity searches were performedusing the BLAST server on the GenBank database at the NationalCenter for Biotechnology Information, USA (www.ncbi.nlm.nih.gov). The nucleotide and amino acid sequences of each gene werecompared with sequences available in GenBank possessing theentire open reading frame (ORF). Multiple nucleotide and aminoacid alignments were constructed using the MUSCLE algorithm inthe MEGA5.20 program (Edgar, 2004; Tamura et al., 2011). Nucle-otide and amino acid distance matrixes were calculated using thep-distance algorithm in MEGA5.20 (Tamura et al., 2011). Theoptimal evolutionary model was selected based upon the Akaike
of a novel G3P[14] rotavirus strain causing gastroenteritis in 12 year old.2014.04.009
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Table 1Genome constellation and nucleotide similarities of RVA/Human-1 wt/AUS/RCH272/2012/G3P[14] to global G3P[14] strains and global human and strains with 2 highest nucleotide similarity.
⁄Strains within each genotype with the highest nucleotide similarity to RVA/Human-wt/AUS/RCH272/2012/G3P[14].aPreviously characterized Australian G10P[14] strain.VP, viral protein; NSP, non-structural protein.Shaded cells indicate strains with the same genotype as RVA/Human-wt/AUS/RCH272/2012/G3P[14].NA – genotype known but no sequence data available for analysis.
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Human and Porcine strains
RVA/Simian-tc/ZAF/SA11-N2/1958/G3P2 JN827253 RVA/Vaccine/CHN/ZTR-5/XXXX/G3P2 JF896470 RVA/Simian-tc/ZAF/SA11-H96/1958/G3P5 DQ838620
RVA/Human-tc/KEN/B10/1987/G3P2 HM627558 RVA/Horse-wt/IND/Erv105/XXXX/G3PX DQ981479
RVA/Cow-wt/IND/PTN P-970/2009/G3PX HQ199897 RVA/Human-wt/IND/HR B54/2010/G3P8 JF720882 RVA/Cow-wt/IND/UKD/2009/G3P9 JF689845 RVA/Human-wt/IND/UP H2/2009/G3P11 JF742651 RVA/Cow-wt/IND/RUBV3/XXXX/G3P3 EF200549 RVA/Buffalo-wt/IND/B-46/2008/G3PX HM235510
RVA/Cow-wt/IND/MF10/2010/G3PX JF689835 RVA/Human-wt/IND/MP B100/2008/G3PX JF831944 RVA/Cow-xx/IND/B31/XXXX/G3PX DQ487203 RVA/Cow-xx/IND/Hisar/XXXX/G3PX DQ478582 RVA/Horse-wt/IND/Erv80/XXXX/G3PX DQ981477
RVA/Cow-wt/IND/J63/XXXXX/G3PX AF386914 RVA/Bat-tc/CHN/MSLH14/2011/G3P3 KC960624
RVA/Human-wt/AUS/RCH272/2012/G3P14 KF690130 RVA/Horse-wt/ARG/E3198/2008/G3P3 JX036370
RVA/Bat-tc/CHN/MYAS33/2013/G3P10 KF649188 RVA/Human-wt/THA/CMH079/2005/G3P10 EU791924 RVA/Human-wt/THA/CMH222/XXXX/G3PX AY707792 RVA/Rabbit-tc/CHN/N5/1992/G3P14 JQ423907
RVA/Simian-tc/USA/RRV/1975/G3P3 AF295303 RVA/Human-tc/ITA/PA260-97/1997/G3P3 HQ661117 RVA/Dog-tc/ITA/RV52-96/1996/G3P3 AF271090
RVA/Dog-wt/KOR/KS05/2005/G3P3 FJ669131 RVA/Rabbit-wt/ITA/160-01/2001/G3P22 AF528202 RVA/Rabbit-wt/ITA/229-01/2001/G3P22 AF528203
RVA/Rabbit-wt/ITA/308-01/2001/G3P22 AF528201 RVA/Rabbit-tc/ITA/30-96/1996/G3P14 AF528204 RVA/Human-wt/BEL/B4106/2000/G3P14 AY456382
RVA/Rabbit-tc/USA/BAP-2/1989/G3P14 U62153 RVA/Dog-tc/ITA/RV198-95/1995/G3P3 HQ661139 RVA/Human-tc/ISR/Ro1845/1985/G3P3 EU708895 RVA/Dog-tc/AUS/K9/1981/G3P3 EU708928 RVA/Cat-tc/AUS/Cat97/1984/G3P3 EU708950 RVA/Human-tc/USA/HCR3A/1984/G3P3 L21666
RVA/Dog-tc/USA/A79-10/1979/G3P3 EU708939 RVA/Dog-tc/USA/CU-1/1982/G3P3 EU708917
RVA/Human-wt/MEX/7177-1042/XXXX/G3PX AJ488587
Equine strains
Outgroup RVA/Human-tc/USA/DS-1/1976/G2P4 AB118023
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0.1
(a) VP7
Fig. 1. Phylogenetic tress constructed from the nucleotide sequences of (a) VP7, (b) VP4 genes of rotavirus strain RCH272 with other group A rotavirus strains. The position ofstrain RCH272 is indicated by a � symbol and in bold. Bootstrap values P70% are shown. Scale bar shows number substitutions per site. The nomenclature of all the rotavirusstrains indicates the rotavirus group, species isolated from, country of strain isolation, the common name, year of isolation, and the genotypes for genome segment 9 and 4 asproposed by the Rotavirus Classification Working Group.
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Please cite this article in press as: Donato, C.M., et al. Genetic characterization of a novel G3P[14] rotavirus strain causing gastroenteritis in 12 year oldAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid.2014.04.009
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RVA/Human-tc/GBR/A64/1987/G10P[14] EF672563 RVA/Sheep-tc/ESP/OVR762/2002/G8P[14] EF554151
RVA/Antelope-wt/ZAF/RC-18-08/2008/G6P[14] FJ495129 RVA/Human-wt/AUS/WAG8.1/2002/G8P[14] GQ398013
RVA/Human-tc/AUS/MG6/1993/G6P[14] EF554096 RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690128
RVA/Guanaco-wt/ARG/Chubut/1999/G8P[14] FJ347103 RVA/Human-wt/BEL/B10925/1997/G6P[14] EF554118
RVA/Human-tc/ITA/PA169/1988/G6P[14] EF554129 RVA/Human-wt/HUN/Hun5/1997/G6P[14] EF554107 RVA/Human-wt/ITA/111-05-27/2005/G6P[14] EF554140 RVA/Cow-wt/IND/68/2007/G8P[14] GU984754 RVA/Cow-wt/IND/86/2007/G8P[14] GU984756 RVA/Cow-wt/IND/79/2007/G8P[14] GU984755 RVA/Human-wt/AUS/D355/2011/G10P[14] JX567754 RVA/Human-wt/AUS/SA175/2011/G10P[14] JX567758 RVA/Human-wt/AUS/V585/2011/G10P[14] JX567755 RVA/Human-wt/AUS/WDP280/2011/G10P[14] JX567757 RVA/Human-wt/AUS/V582/2011/G10P[14] JX567756 RVA/Human-wt/AUS/SA179/2011/G10P[14] JX567759 RVA/Human-tc/THA/Mc35/1987-9/G10P[14] D14032
RVA/Cow-tc/JPN/Sun9/2000/G8P[14] AB158430 RVA/Human-wt/FIN/HAL 1166/1986/G8P[14] L20875
RVA/Human-wt/HUN/BP1879/2003/G6P[14] FN665680 RVA/Human-wt/HUN/BP1062/2004/G8P[14] FN665691
RVA/Rabbit-tc/JPN/R-2/XXXX/G3P[14] U62152 RVA/Rabbit-tc/CHN/N5/1992/G3P[14] JQ423905 RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] DQ205224
RVA/Human-wt/BEL/B4106/2000/G3P[14] AY740738 RVA/Rabbit-tc/USA/BAP-2/1989/G3P[14] U62152
RVA/Rabbit-tc/USA/C-11/XXXX/G3P[14] U62150 RVA/Rabbit-tc/USA/ALA/XXXX/G3P[14] U62149
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Fig. 1 (continued)
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information criterion (corrected) (AICc) ranking implemented injModelTest (Darriba et al., 2012; Guindon and Gascuel, 2003). Max-imum likelihood phylogenetic trees using the selected models ofnucleotide substitution GTR + GG4 + I (VP1, VP2, VP3, VP6, NSP1,NSP2 and VP7), GTR + GG4 (VP4 and NSP3), HKY + GG4 (NSP4) andTrN + GG4 + I (NSP5) were generated using MEGA5.20 (Tamuraet al., 2011). The robustness of branches was assessed by bootstrapanalysis using 1000 pseudoreplicate runs.
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2.7. Determination of time to most recent common ancestor
The time to most common recent ancestor (tMRCA) was calcu-lated using the Bayesian Markov Chain Monte Carlo (MCMC)method in the BEAST package (version 1.7.5) (Drummond et al.,2012). Initially, all sequences of the relevant genotype availablein GenBank that possessed the entire ORF were selected for analy-sis. The VP1 (R3), VP2 (C3), VP3 (M3) and NSP1 (A9) gene geno-types comprised a limited number of highly diverse sequenceswhich were not suitable for tMRCA analysis. With the exceptionof VP4, identical sequences were removed. Due to the excessivenumber of sequences in the VP7, NSP2 and NSP4 gene analysis,strains with >99.9% nt similarity from over-represented locationswere removed. The strains comprising each gene dataset aredetailed in Supplementary Data for the VP4 (n = 27, 1986–2012),VP6 (n = 112, 1958–2012), VP7 (n = 151, 1958–2012), NSP2(n = 100, 1965–2012), NSP3 (n = 41, 1965–2012), NSP4 (n = 135,
Please cite this article in press as: Donato, C.M., et al. Genetic characterizationAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid
1973–2012) and NSP5 (n = 60, 1967–2012) genes. The data wasanalyzed utilizing an uncorrelated lognormal relaxed clock usingthe models TN93 + GG4 + I (VP6, NSP5), TN93 + GG4 (VP7, NSP3,NSP4) and GTR + GG4 (NSP2, VP4) determined by AICc ranking injModelTest (Darriba et al., 2012; Drummond et al., 2006;Guindon and Gascuel, 2003; Posada, 2008). A coalescent GaussianMarkov random field (GMRF) Bayesian Skyride tree was used todescribe the demographic history (Drummond et al., 2002; Mininet al., 2008). The MCMC chain was run for 100 million generationswith sampling every 10,000 generations for all genes analyzed,except VP6 and VP7 which were run for 200 million generationswith sampling every 20,000 generations. Convergence wasassessed using the program Tracer (version 1.5.0) (http://tree.bio.ed.ac.uk/software/tracer/), with an effective sample size of at least200 after the first 10% of chain lengths were discarded as burn-in.The maximum clade credibility was obtained using TreeAnnotator(version 1.7.5) removing the initial 10% of trees as burn-in. Thetime-ordered maximum clade credibility trees were viewed inthe FigTree (version 1.4.0) (http://tree.bio.ed.ac.uk/software/figtree).
2.8. Assignment of genotypes
The genotypes of each of the 11 genome segments were deter-mined using the online RotaC rotavirus genotyping tool (v2.0,http://rotac.regatools.be).
of a novel G3P[14] rotavirus strain causing gastroenteritis in 12 year old.2014.04.009
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RVA/Human-tc/THA/T152/1998/G12P[9] DQ146699 RVA/Human-wt/THA/CU365-KK/2008/G3P[9] JN706445
RVA/Human-tc/ITA/PA260-97/1997/G3P[3] HQ661112 RVA/Human-tc/JPN/AU-1/1982/G3P[9] DQ490533
RVA/Horse-wt/ARG/E3198/2008/G3P[3] JX036365 RVA/Rhesus-tc/USA/TUCH/2002/G3P[24] EF583010
RVA/Human-tc/JPN/K8/1977/G1P[9] JQ713645 RVA/Rabbit-tc/CHN/N5/1992/G3P[14] JQ423902
RVA/Human-tc/CHN/L621/2006/G3P[9] JX946159 RVA/Human-wt/CHN/E2451/2011/G3P[9] JX946168
RVA/Dog-tc/ITA/RV198-95/1995/G3P[3] HQ661134 RVA/Dog-tc/ITA/RV52-96/1996/G3P[3] HQ661123 RVA/Human-tc/ISR/Ro1845/1985/G3P[3] EU708890
RVA/Cat-tc/AUS/Cat97/1984/G3P[3] EU708945 RVA/Cat-tc/AUS/Cat2/1984/G3P[9] EU708956 RVA/Dog-tc/AUS/K9/1981/G3P[3] EU708923 RVA/Human-tc/USA/HCR3A/1984/G3P[3] EU708901 RVA/Dog-tc/USA/CU-1/1982/G3P[3] EU708912 RVA/Dog-tc/USA/A79-10/1979/G3P[3] EU708934
RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690125 RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] KC960619
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RVA/Human-wt/THA/CU365-KK/2008/G3P[9] JN706480 RVA/Human-tc/CHN/L621/2006/G3P[9] JX946160
RVA/Human-tc/JPN/K8/1977/G1P[9] JQ713646 RVA/Horse-wt/ARG/E3198/2008/G3P[3] JX036366 RVA/Simian-tc/USA/RRV/1975/G3P[3] EF583007
RVA/Rabbit-tc/CHN/N5/1992/G3P[14] JQ423903 RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690126
RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] KC960620 RVA/Rhesus-tc/USA/TUCH/2002/G3P[24] EF583011
RVA/Human-tc/JPN/AU-1/1982/G3P[9] DQ490536 RVA/Human-tc/ITA/PA260-97/1997/G3P[3] HQ661113
RVA/Human-tc/THA/T152/1998/G12P[9] DQ146700 RVA/Human-wt/CHN/E2451/2011/G3P[9] JX946169
Outgroup RVA/Human-tc/USA/Wa/1974/G1P[8] X14942
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RVA/Simian-tc/USA/RRV/1975/G3P[3] EF583008 RVA/Rabbit-tc/CHN/N5/1992/G3P[14] JQ423904 RVA/Horse-wt/ARG/E3198/2008/G3P[3] JX036367 RVA/Human-wt/CHN/E2451/2011/G3P[9] JX946170 RVA/Human-tc/CHN/L621/2006/G3P[9] JX946161
RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] KC960621 RVA/Human-tc/JPN/AU-1/1982/G3P[9] DQ490537
RVA/Human-tc/JPN/K8/1977/G1P[9] JQ713647 RVA/Human-wt/THA/CU365-KK/2008/G3P[9] JN706508
RVA/Human-tc/THA/T152/1998/G12P[9] DQ146701 RVA/Dog-tc/ITA/RV52-96/1996/G3P[3] HQ661125 RVA/Dog-tc/ITA/RV198-95/1995/G3P[3] HQ661136 RVA/Human-tc/ITA/PA260-97/1997/G3P[3] HQ661114
RVA/Rhesus-tc/USA/TUCH/2002/G3P[24] EF583012 RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] DQ205223
RVA/Human-wt/BEL/B4106/2000/G3P[14] AY740739 RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690127
RVA/Dog-tc/USA/A79-10/1979/G3P[3] EU708936 RVA/Cat-tc/AUS/Cat97/1984/G3P[3] EU708947 RVA/Human-tc/ISR/Ro1845/1985/G3P[3] EU708892 RVA/Cat-tc/AUS/Cat2/1984/G3P[9] EU708958 RVA/Dog-tc/USA/CU-1/1982/G3P[3] EU708914 RVA/Human-tc/USA/HCR3A/1984/G3P[3] EU708903
RVA/Dog-tc/AUS/K9/1981/G3P[3] EU708925 RVA/Horse-wt/ARG/E4040/2008/G14P[12] JN872867
RVA/Horse-wt/ARG/E30/1993/G3P[12] JF712568 RVA/Horse-wt/IRL/04V2024/2004/G14P[12] JN903523 RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] JQ345491
RVA/Horse-wt/IRL/03V04954/2003/G3P[12] JN903524 RVA/Horse-tc/JPN/OH-4/1982/G6P[5] KC815682
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Fig. 2. Maximum likelihood phylogenetic tress constructed from the nucleotide sequences of (a) VP1, (b) VP2, (c) VP3, (d) VP6 and (e) NSP1 genes of rotavirus strain RCH272with other group A rotavirus strains. The position of strain RCH272 is indicated by a � symbol and in bold. Bootstrap values P70% are shown. Scale bar shows numbersubstitutions per site. The position of strain RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] is indicated by a j symbol and in bold. The position of strain RVA/Human-tc/AUS/MG6/1993/G6P[14] is indicated by a d symbol and in bold. The nomenclature of all the rotavirus strains indicates the rotavirus group, species isolated from, country of strainisolation, the common name, year of isolation, and the genotypes for genome segment 9 and 4 as proposed by the Rotavirus Classification Working Group.
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Human strains
RVA/Cow-wt/ZAF/1603/2007/G6P[5] JN831213 RVA/Horse-tc/JPN/R-22/1984/G10P[11] AB040055 RVA/Human-tc/IND/69M/1980/G8P[10] EF583016
RVA/Human-wt/ITA/PAI58/1996/G3P[9] GU296429 RVA/Human-wt/AUS/V585/2011/G10P[14] JX567763 RVA/Human-wt/IND/N155/2003/G10P[11] EU200797
RVA/Human-tc/IND/I321/XXXX/G10P[11] X94618 RVA/Guanaco-wt/ARG/Chubut/1999/G8P[14] FJ347104 RVA/Guanaco-wt/ARG/Rio_Negro/1998/G8P[1] FJ347126
RVA/Antelope-wt/ZAF/RC-18-08/G6P[14] FJ495131 RVA/Cow-wt/ZAF/1604/2007/G8P[1] JN931224 RVA/Sheep-tc/ESP/OVR762/2002/G8P[14] EF554152 RVA/Human-wt/ZAF/2371WC/2008/G9P[8] JN014002 RVA/Human-wt/BEL/B10925/1997/G6P[14] EF554119
RVA/Cow-wt/IND/68/2007/G8P[14] GU984757 RVA/Cow-wt/IND/86/2007/G8P[14] GU984759 RVA/Cow-wt/IND/79/2007/G8P[14] GU984758 RVA/Cow-xx/IND/M-1/2009/G3P[X] HM235508
RVA/Cow-xx/IND/I2/2009/GXP[X] HQ171911 RVA/Pig-wt/IND/HP113/1987/G6P[23] GQ003294 RVA/Pig-wt/IND/HP140/1987/G6P[13] DQ003295 RVA/Human-wt/HUN/BP1062/2004/G8P[14] FN665693
RVA/Human-tc/GBR/A64/1987/G10P[14] EF583020 RVA/Rhesus-tc/USA/PTRV/1990/G8P[1] FJ422136
RVA/Human-wt/HUN/BP1879/2003/G6P[14] FN665682
Bovine strains
RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690129 RVA/Human-tc/AUS/MG6/1993/G6P[14] EF554097
RVA/Human-wt/BEL/B4106/2000/G3P[14] AY740737 RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] DQ205226 RVA/Human-tc/JPN/KF17/2010/G6P[9] JF421979
RVA/Human-tc/KEN/D205/1989/G2P[4] JF304919 RVA/Human-wt/HUN/Hun5/1997/G6P[14] EF554108 RVA/Cow-wt/IND/RUBV51/2001-5/G15P[21] EF200567 RVA/Human-wt/ITA/PAH136/1996/G3P[9] GU296428
RVA/Simian-tc/ZAF/SA11 H96/1958/G3P[2] JF791806 RVA/Cow-wt/IND/RUBV117/2001-5/G15P[21] EF200569 RVA/Cow-wt/IND/RUBV51/2001-5/G15P[21]
RVA/Cow-wt/ARG/B383/1998/G15P[11] FJ347115 RVA/Human-tc/KEN/AK26/1982/G2P[4] JF304930 RVA/Human-tc/PHL/L26/1987/G12P[4] DQ146695 RVA/Human-tc/USA/DS-1/1976/G2P[4] DQ870507 RVA/Human-tc/JPN/S2/1980/G2P[4] DQ870488 RVA/Human-wt/CHN/TB-Chen/1996/G2P[4] AY787645
Outgroup RVA/Human-tc/USA/Wa/1974/G1P[8] K02086100
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Fig. 2 (continued)
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2.9. Accession numbers
The nucleotide sequences of the 11 gene segments of RVA/Human-wt/AUS/RCH272/2012/G3P[14] were deposited in Gen-Bank under the accession numbers KF690125–KF690135.
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3. Results
3.1. Sample characterization
The fecal sample tested positive for rotavirus and no otherenteric pathogens were identified. The rotavirus strain was desig-nated RVA/Human-wt/AUS/RCH272/2012/G3P[14], subsequently
Please cite this article in press as: Donato, C.M., et al. Genetic characterizationAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid
referred to as RCH272. Sequence analysis derived the genome con-stellation G3-P[14]-I2-R3-C3-M3-A9-N2-T6-E2-H3 which differsfrom the constellation observed in previously characterizedG3P[14] strains (Table 1).
3.2. Phylogenetic and tMRCA analysis of VP7 and VP4 genes
Analysis of the time-ordered maximum clade credibility treesobtained from the Bayesian coalescent analysis matched thetopography of the Maximum Likelihood trees for all genes ana-lyzed except VP7 where minor branching differences were noteddue to the removal of strains without dates of collection (datanot shown).
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RVA/Horse-wt/ARG/E3198/2008/G3P[3] JX036371 RVA/Simian-tc/USA/RRV/1975/G3P[3] EU636928 RVA/Rabbit-tc/CHN/N5/1992/G3P[14] JQ423897
RVA/Rhesus-tc/USA/TUCH/2002/G3P[24] DQ838651 RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] KC960625
RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690131 RVA/Human-wt/BEL/B4106/2000/G3P[14] AY740735
RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] DQ205225 RVA/Rabbit-tc/USA/ALA/XXXX/G3P[14] AF084549
RVA/Rabbit-tc/USA/C-11/XXXX/G3P[14] AF084550 RVA/Rabbit-tc/USA/BAP-2/1989/G3P[14] AF084551
RVA/Dog-tc/ITA/RV52-96/1996/G3P[3] HQ661129 RVA/Dog-tc/ITA/RV198-95/1995/G3P[3] HQ661140 RVA/Human-tc/USA/HCR3A/1984/G3P[3] EU708907
RVA/Dog-tc/USA/A79-10/1979/G3P[3] EU708940 RVA/Dog-tc/AUS/K9/1981/G3P[3] EU708929 RVA/Cat-tc/AUS/Cat97/1984/G3P[3] EU708951 RVA/Dog-tc/USA/CU-1/1982/G3P[3] EU708918 RVA/Human-tc/ISR/Ro1845/1985/G3P[3] EU708896 RVA/Cat-wt/JPN/FRV64/1989/G3P[3] D78362
Outgroup RVA/Horse-wt/ARG/E30/1993/G3P[12] JF712572
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Fig. 2 (continued)
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The VP7 gene of RCH272 shared 78.4–89.2% nucleotide (nt) and87.4–97.8% amino acid (aa) similarity to global G3 strains and washighly divergent to the majority of global human G3 strains.RCH272 was most closely related to the Chinese strain RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] (Table 1). The 151 VP7 G3 genesincluded in the tMRCA analysis were isolated between 1958–2012 and shared a common ancestral strain circulating in 1924(95% higher posterior density (HPD) 1904–1943) and the majorityof human and animal strains diverged at this point. RCH272 clus-tered within a bovine-like lineage comprised of Indian human,equine and bovine strains and RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] and these strains shared a common ancestor circulatingin 1959 (95% HPD: 1937–1984) (Fig. 1(a)).
The VP4 gene of RCH272 shared 80.4–96.9% nt and 92.3–98.6%aa similarity to global P[14] strains. RCH272 shared the highestnucleotide similarity to a previously characterized Australianstrain RVA/Human-tc/AUS/MG6/1993/G6P[14] (Table 1). Analysisof partial VP4 ORFs from four Australian G8P[14] strains(RVA/Human-wt/AUS/VG8/2002/G8P[14], RVA/Human-tc/AUS/DG8/1996/G8P[14], RVA/Human-wt/AUS/NTG8/2007/G8P[14] andRVA/Human-wt/AUS/WAG8.2/2003/G8P[14]) identified 94.7–95.7%nt and 95.1–98.7% aa similarity. The 27 VP4 P[14] genes includedin the tMRCA analysis (isolated 1986–2012) shared an commonancestral strain circulating in 1867 (95% HPD 1782–1945). Thelarge range is reflective of the small number of diverse sequencesobtained; suggesting the progenitor strains of some lineages maynot have been identified. RCH272 clustered within a lineagepredominantly comprised of human bovine-like strains(Fig. 1(b)). The VP4 gene of RCH272 shared an ancestor strain withtwo Australian strains, RVA/Human-tc/AUS/MG6/1993/G6P[14](1989, 95% HPD 1984–1992) and RVA/Human-wt/AUS/WAG8.1/2002/G8P[14] (1984, 95% HPD 1976–1990). The VP4 gene of theAustralian G10P[14] strains identified in the Northern Territoryand RCH272 shared a common ancestor strain circulating in1928 (95% HPD: 1887–1965). The European lapine P[14] strainsformed a distinct lineage that diverged from the other P[14] strainsin 1867 (95% HPD 1782–1945).
3.3. Phylogenetic and tMRCA analysis of structural genes VP1, VP2, VP3& VP6
RCH272 was distantly related to the strains comprising thesmall, diverse VP1 R3 (83.4–94.9% nt and 94.9–98.1% aa similarity)
Please cite this article in press as: Donato, C.M., et al. Genetic characterizationAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid
and VP2 C3 (86.5–88.3% nt and 97.3–98.4% aa similarity) geno-types. RCH272 VP1 and VP2 genes shared the highest geneticsimilarity to RVA/Bat-tc/CHN/MSLH14/2011/G3P[3], these strainsformed distinct lineages in the VP1 and VP2 trees that clusteredclosest to sub-lineages predominantly comprised of humanG3P[3], and G3P[9] strains (Table 1, Fig. 2a and b). The VP3 geneshared 81.8–91.9% nt and 88.5–96.3% aa similarity to strainscomprising the M3 genotype; exhibiting the highest genetic iden-tity to RVA/Human-tc/ISR/Ro1845/1985/G3P[3] (Table 1). RCH272formed a sub-lineage with canine, feline and human zoonoticstrains of canine and feline origins, closely related to a sub-lineagecomprised of a lapine strain and a human lapine-like zoonoticstrain. RVA/Human-tc/CHN/MSLH14/2011/G3P3 clustered withina separate lineage of the M3 tree (Fig. 2c). The VP6 gene shared amoderate degree of genetic relatedness to strains comprising theI2 genotype (84.7–97.1% nt and 96.2–99.7% aa similarity), exhibit-ing the highest genetic relatedness to RVA/Human-tc/AUS/MG6/1993/G6P[14] (Table 1). RCH272 and RVA/Human-tc/AUS/MG6/1993/G6P[14] formed a discrete node clustering closest to a sub-lineage predominantly comprised of bovine strains and humanbovine-like zoonotic strains (Fig. 2d). The VP6 gene of RCH272and RVA/Human-tc/AUS/MG6/1993/G6P[14] shared an ancestorstrain circulating in 1974 (95% HPD: 1949–1991).
3.4. Phylogenetic and tMRCA analysis of non-structural genes NSP1-NSP5
RCH272 shared moderate degrees of genetic relatedness to thestrains comprising the A9 (80.4–86.8% nt and 87.2–93.3% aa), N2(84.0–95.7% nt and 92.4–99.1% aa), T6 (87.1–98.1% nt and 92.0–98.7% aa), E2 (80.3–96.0% nt and 85.6–89.9% aa) and H3 (90.1–97.6% nt and 91.4–99.0% aa) genotypes. RCH272 formed a discretenode in the NSP1 A9 tree, clustering within a lineage comprised ofG3P[3], G3P[14] and G3P[24] strains from various animal speciesincluding RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] (Fig. 2e) andshared the highest degree of genetic relatedness to RVA/Simian-tc/USA/RRV/1975/G3P[3] (Table 1). The NSP2 gene of RCH272shared the highest genetic identity to RVA/Human-tc/AUS/MG6/1993/G6P[14]. In the NSP2 N2 tree, these strains shared a discretenode within a large sub-lineage predominantly comprised ofbovine strains, bovine-like human zoonotic strains and a smallnumber of canine, feline and lapine origins and human zoonoticstrains (Fig. 3a). The NSP3, NSP4 and NSP5 genes of RCH272 shared
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Human and Equine strains
RVA/Cow-tc/BGR/UK/1973/G6P[5] J02420 RVA/Cow-wt/ZAF/1603/2007/G6P[5] JN831205
Human strains
RVA/Human-tc/AUS/MG6/1993/G6P[14] EF554100 RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690132
RVA/Human-tc/USA/Se584/1998/G6P[9] EF672608 RVA/Dog-tc/ITA/RV198-95/1995/G3P[3] HQ661141
RVA/Human-tc/ITA/PA260-97/1997/G3P[3] HQ661119 RVA/Dog-tc/ITA/RV52-96/1996/G3P[3] HQ661130
RVA/Human-wt/JPN/KF17/2010/G6P[9] JF421982 RVA/Human-wt/RUS/O211/2007/G3P[9] KC020028
RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] DQ205227 RVA/Human-wt/BEL/B4106/2000/G3P[14] AY740734 RVA/Human-wt/ITA/PAI58/1996/G3P[9] GU296413
RVA/Guanaco-wt/ARG/Chubut/1999/G8P[14] FJ347107 RVA/Vicuna-wt/ARG/C75/2010/G8P[14] JX070053
RVA/Cow-tc/ZAF/O Agent/1965/G8P[1] DQ838597 RVA/Vaccine/CHN/ZTR-5/XXXX/G3P[2] JF896472 RVA/Cow-wt/ARG/B383/1998/G15P[11] FJ347118 RVA/Cow-wt/ZAF/1604/2007/G8P[1] JN831216
RVA/Macaque-tc/USA/PTRV/1990/G8P[1] JF422139 RVA/Simian-tc/USA/RRV/1975/G3P[3] EU636931
RVA/Cow-tc/CHN/DQ-75/2008/G10P[11] GU384196 RVA/Cow-tc/USA/WC3/1981/G6P[5] EF990700 RVA/Cow-tc/JPN/BRV106/1983/G6P[1] AB748594
RVA/Cow-tc/VEN/BRV033/1990/G6P[1] EF990704 RVA/Cow-tc/JPN/BRV105/1983/G6P[1] AB748593 RVA/Human-tc/ISR/Ro8059/1995/G6P[1] AB748596 RVA/Cow-tc/FRA/RF/1982/G6P[1] Z21640 RVA/Cow-tc/USA/NCDV/1971/G6P[1] JF693032 RVA/Cow-tc/IND/CR231/39/1994-1997/G6P[1] AB748595 RVA/Cow-tc/JPN/BRV101/1985-1986/G6P[1] AB748592
Bovine, Canine, Feline and Human strains
Outgroup RVA/Simian-tc/ZAF/SA11-H96/1958/G3P[2] DQ838615
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Fig. 3. Maximum likelihood phylogenetic tress constructed from the nucleotide sequences of (a) NSP2, (b) NSP3, (c) NSP4 and (d) NSP5 genes of rotavirus strain RCH272 withother group A rotavirus strains. The position of strain RCH272 is indicated by a � symbol and in bold. The position of strain RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] is indicatedby a j symbol and in bold. The position of strain RVA/Human-tc/AUS/MG6/1993/G6P[14] is indicated by a d symbol and in bold. Bootstrap values P70% are shown. Scale barshows number substitutions per site. The nomenclature of all the rotavirus strains indicates the rotavirus group, species isolated from, country of strain isolation, the commonname, year of isolation, and the genotypes for genome segment 9 and 4 as proposed by the Rotavirus Classification Working Group.
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the highest genetic relatedness to the strains RVA/Cow-tc/FRA/RF/1982/G6P[1], RVA/Human-tc/AUS/MG6/1993/G6P[14] and RVA/Human-wt/BEL/B10925/1997/G6P[14] and clustered within largelineages in the T6, E2 and H3 genotypes. These lineages were pre-dominantly comprised of bovine strains and human bovine-likezoonotic strains and RCH272 clustered closely to RVA/Human-tc/AUS/MG6/1993/G6P[14] (Fig. 3b–d).
For the NSP2, NSP3, NSP4 and NSP5 gene analysis, the strainsharing a most recent common ancestor with RCH272 was RVA/Human-tc/AUS/MG6/1993/G6P[14]. The tMRCA values obtainedvaried and had large confidence intervals; NSP2 (1976, HPD:1960–1988) NSP3 (1943, 95% HPD: 1892–1982), NSP4 (1950, 95%HPD: 1987–1902), and NSP5 (1944, 95% HPD: 1893–1985).
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4. Discussion
A G3P[14] strain was identified from a 12 year old Australianchild following a week long history of gastroenteritis. Sequenceanalysis of the strain RCH272 identified a previously unreportedG3-P[14]-I2-R3-C3-M3-A9-N2-T6-E2-H3 genome constellation.Only seven G3P[14] strains have been reported worldwide, six iden-tified in rabbits in Japan, China, the USA and Italy and a humanlapine-like strain (Guo et al., 2012; Matthijnssens et al., 2006). Com-pared to the three complete G3P[14] genomes, RCH272 shared 8/11genotypes with RVA/Human-wt/BEL/B4106/2000/G3P[14] andRVA/Rabbit-tc/ITA/30-96/1996/G3P[14], and 6/11 genotypes withRVA/Rabbit-tc/CHN/N5/1992/G3P[14]. Despite possessing a
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RVA/Cow-tc/USA/WC3/1981/G6P[5] EF990701 RVA/Vaccine/USA/RotaTeq-BrB-9/1996/G4P[5] GU565093
RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690133 RVA/Rhesus-tc/USA/PTRV/1990/G8P[1] FJ422137
RVA/Human-tc/AUS/MG6/1993/G6P[14] EF554101 RVA/Cow-tc/USA/NCDV/1967/G6P[1] X81429
RVA/Cow-tc/VEN/BRV033/1990/G6P[1] EF99075 RVA/Cow-tc/FRA/RF/1982/G6P[1] Z21639
RVA/Cow-xx/KOR/KJ19-2/XXXX/GXP[X] FJ206167 RVA/Cow-xx/KOR/KJ69-1/XXXX/GXP[X] FJ206180
RVA/Human-tc/ITA/PA169/1988/G6P[14] EF554134 RVA/Cow-tc/ZAF/OAgent/1965/G8P[1] JF693043
RVA/Guanaco-wt/ARG/Chubut/1999/G8P[14] FJ347108 RVA/Human-wt/KEN/B12/1987/G8P[1] HM627550
RVA/Human-wt/ITA/PAI58/1996/G3P[9] GU296414 RVA/Human-wt/ITA/PAH136/1996/G3P[9] GU296415 RVA/Human-wt/TUN/17237/2008/G6P[9] JX271009
RVA/Giraffe-wt/IRL/GirRV/2007/G10P[11] GQ428138 RVA/Cow-wt/ZAF/1605/2007/G6P[5] JN831228 RVA/Cow-wt/ZAF/1603/2007/G6P[5] JN831206 RVA/Human-wt/AUS/V585/2011/G10P[14] JX567766 RVA/Cow-wt/CHN/DQ-75/2008/G10P[11] GU384197
RVA/Goat-xx/CHN/XL/2010/G10P[15] JQ004978 RVA/Sheep-wt/CHN/CC0812-1/2008/G10P[15] HQ834204 RVA/Sheep-tc/CHN/Lamb-NT/2007/G10P[15] FJ031021
Bovine Strains
RVA/Human-tc/BGD/GO34/1999/G6P[1] GU937885 RVA/Cow-wt/IND/B85/2010/GXP[X] JF720880
RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] DQ205228 RVA/Human-wt/BEL/B4106/2000/G3P[14] AY740733
RVA/Guanaco-wt/ARG/Rio_Negro/1998/G8P[1] FJ347130 RVA/Cow-wt/ARG/B383/1998/G15P[11] FJ347119
RVA/Antelope-wt/ZAF/RC-18-08/2008/G6P[14] FJ495132 RVA/Cow-wt/ZAF/1604/2007/G8P[1] JN831217
RVA/Sheep-tc/ESP/OVR762/2002/G8P[14] EF554156 RVA/Human-wt/ITA/111-05-27/2005/G6P[14] EF554145 RVA/Human-wt/BEL/B10925/1997/G6P[14] EF554123
Outgroup RVA/Human-tc/USA/DS-1/1976/G2P[4] EF136660
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Fig. 3 (continued)
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predominantly lapine-like genome constellation, RCH272 sharedrelatively low genetic relatedness to the lapine strains, with theexception of the VP3 and NSP1 genes. Whilst it is unlikely that thestrain RCH272 possesses recent lapine origins it cannot be entirelyruled out as Australian lapine strains are not available forcomparison.
It is possible that RCH272 was derived by multiple reassort-ment events between strains originating in various animal species.The VP7, VP1, VP2 and NSP1 genes shared a moderate genetic rela-tionship with the recently described bat strain, RVA/Bat-tc/CHN/MSLH14/2011/G3P[3], isolated from a lesser horseshoe bat (Rhinol-ophus hipposideros) in China (He et al., 2013). The VP3 gene pos-sessed canine/feline characteristics and may have originated inanother parental strain. However, numerous genes of RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] possess canine/feline characteristicsand the VP3 gene may have been derived from the same strainas the bat-like genes.
Bats are an important reservoir for numerous, highly patho-genic, viruses capable of zoonotic transmission including Nipahvirus, Ebola virus, Hendra virus and Lyssaviruses (Smith andWang, 2013). Three diverse rotavirus strains have been identifiedfrom bats, thus it is unknown if they represent true bat strains orinterspecies transmissions (Esona et al., 2010; He et al., 2013; Xiaet al., 2013). The recent identification of two G8P[6] strains in Bra-zilian Indian children which exhibited bovine-like VP7 and VP6
Please cite this article in press as: Donato, C.M., et al. Genetic characterizationAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid
genes and a VP4 gene most similar to the strain RVA/Bat-wt/KEN/KE4852/2007/G25P[6] isolated from a African straw-coloredfruit bat (Eidolon helvum) suggests bats may readily transmitbovine rotavirus strains facilitating reassortment events (Esonaet al., 2010; Luchs and Timenetsky Mdo, 2014).
The VP4, VP6, NSP2, NSP3, NSP4 and NSP5 genes of RCH272were possibly derived from a population of strains related to pre-viously characterized Australian bovine strains and bovine-likehuman zoonotic strains. G6P[14] and G8P[14] strains have beensporadically identified in Australian children during the past twodecades, however, due to the limited sequence data of these strainsit is unknown if they are direct transmissions or reassortant strains(Matthijnssens et al., 2008; Swiatek et al., 2010). The frequentidentification of P[14] rotavirus animal-human zoonotictransmission events, suggests P[14] genes are endemic in the ani-mal rotavirus population and circulating Australia-wide. A recentexample is the artiodactyl-like zoonotic G10P[14] strain detectedin 2012 in the Northern Territory region of Australia (Cowleyet al., 2013). The G10P[14] strain possessed 6/11 genes belongingto the same genotype as RCH272 (Table 1), however, these geneswere genetically divergent suggesting there is a heterogenouspopulation of animal strains circulating in Australia capable ofzoonotic transmission.
Whilst rotavirus strains typically exhibit a degree of hostspecies restriction, P[14] strains are often reported as zoonotic
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Human strains
RVA/Human-tc/GBR/A64/1987/G10P[14] EF672568 RVA/Human-xx/XXX/A28/XXXX/GXP[X] D10771 RVA/Human-tc/IND/I321/XXXX/G10P[11] AF165066
RVA/Cow-tc/FRA/RF/1982/G6P[1] AY116593 RVA/Cow-wt/DNK/DK12011/2007/G6P[5] JN248456 RVA/Human-wt/KEN/D205/1989/G2P[4] JF304924
RVA/Human-wt/AUS/WAPC703/2010/G2P[4] JX965154 RVA/Human-tc/AUS/MG6/1993/G6P[14] EF554102 RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690134 RVA/Human-wt/BEL/B10925/1997/G6P[14] EF554124
RVA/Human-wt/HUN/Hun5/1997/G6P[14] EF554113 RVA/Cow-wt/IND/RUBV189/2001-5/G3P[3] EF592592 RVA/Human-wt/ITA/111-05-27/2005/G6P[14] EF554146
RVA/Human-wt/IND/048348/2004/G2P[4] GU929444 RVA/Human-wt/BFA/265-BF/2010/G6P[6] JN116551 RVA/Human-wt/USA/0537/2002/G3P[9] JF805008 RVA/Buffalo-tc/ITA/10733/2001/G6P[3] AY293829
RVA/Human-tc/KEN/B10/1987/G3P[2] HM627562 RVA/Human-wt/ITA/Pa5 89/XXXX/G6P[14] EU659855
RVA/Cow-wt/ZAF/1604/2007/G8P[1] JN831218 RVA/Human-wt/THA/CMH028/2007/GXP[X] JQ043301
RVA/Human-wt/BRA/12482_06BA/2006/G2P[4] HM066168 RVA/Human-wt/BRA/13438_07RJ/2007/G2P[4] HM123858
RVA/Human-wt/ITA/PAI58/1996/G3P[9] GU296417 RVA/Horse-xx/XXX/H-2/XXXX/GXP[X] AF144801
RVA/Human-wt/ITA/PAH136/1996/G3P[9] GU296416 RVA/Human-wt/RUS/Omsk 04/XXXX/GXP[X] DQ270101
Human and Bovine strains
Human, Ovine and Bovine strains RVA/Cow-xx/IND/UKD IVRI M-1/2009/GXP[X] HM363563
RVA/Horse-tc/USA/FI-14/1981/G3P[12] AF144803 RVA/Rabbit-tc/JPN/R-2/XXXX/G3P[14] AF144794
RVA/Cow-tc/USA/B223/XXXX/G10P[11] AF144805 RVA/Horse-wt/IRE/CM1/2008/G14P[X] GQ463194
Outgroup RVA/Horse-tc/GBR/L338/1991/G13P[18] JF712564
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Fig. 3 (continued)
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transmissions (Matthijnssens et al., 2006). Recent structural stud-ies suggest the P[14] glycoprotein is able to bind to the humanA-type histo-blood group antigen (HBGA), potentially enablingP[14] strains to cross species barrier into humans expressing thecognate HBGA antigen (Hu et al., 2012). Whilst the HBGA statusof this patient is unknown, possessing the A-type HBGA may pre-dispose individuals to infection with P[14] strains.
RCH272 is the first report of a G3P[14] strain that does not exhi-bit lapine-like characteristics and the unique genetic composition
Please cite this article in press as: Donato, C.M., et al. Genetic characterizationAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid
of the strain may have resulted in infectivity of an older child.There was no reported transmission of the strain from the childto any close contacts and the strain may not be highly transmissi-ble between humans. It is likely this strain was contracted via zoo-notic transmission and possibly derived via reassortment eventsbetween strains originating from various host species. It is alsopossible the strain represents a direct interspecies transmissionfrom an unidentified host species, possibly a bat given the charac-terized bat strains RVA/Bat-tc/CHN/MSLH14/2011/G3P[3] and
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RVA/Cow-tc/FRA/RF/1982/G6P[1] AF188126 RVA/Human-tc/ISR/Ro8059/1995/G6P[1] AB748611
RVA/Cow-tc/VEN/BRV033/1990/G6P[1] EF990706 RVA/Cow-xx/KOR/KJ69-1/XXXX/G6P[7] FJ206081
RVA/Cow-tc/USA/NCDV/1967/G6P[1] GU937876 RVA/Cow-tc/USA/WC3/1981/G6P[5] EF990702 RVA/Human-wt/AUS/CK20039/2008/G2P[4] KC443597
RVA/Cow-tc/JPN/AzuK-1/2006/G21P[29] AB573086 RVA/Cat-tc/AUS/Cat2/1984/G3P[9] EU708966 RVA/Human-tc/USA/Se584/1998/G6P[9] EF672611
RVA/Antelope-wt/ZAF/RC-18-08/G6P[14] FJ495136 RVA/Rhesus-tc/USA/PTRV/1990/G8P[1] FJ422141
RVA/Human-tc/AUS/MG6/1993/G6P[14] EF554103 RVA/Human-wt/AUS/RCH272/2012/G3P[14] KF690135
RVA/Human-wt/BEL/B10925/1997/G6P[14] EF554125 RVA/Cow-tc/JPN/Dai-10/2008/G24P[33] AB573078 RVA/Human-tc/KEN/B12/1987/G8P[1] HM627552
RVA/Cow-tc/KOR/KJ19-2/2004/G8P[7] FJ206054 RVA/Human-tc/ITA/PA169/1988/G6P[14] EF554136
RVA/Buffalo-xx/ITA/10733/XXXX/G6P[3] EU659853 RVA/Human-wt/ITA/111-05-27/2005/G6P[14] EF554147 RVA/Sheep-tc/ESP/OVR762/2002/G8P[14] EF554158
RVA/Human-tc/GBR/A64/1987/G10P[14] EF672569 RVA/Human-wt/DEN/06S3744b/GXP[14] JX008870
RVA/Human-wt/RUS/O1180/2011/G3P[9] KC020048 RVA/Human-wt/ITA/PAI58/1996/G3P[9] GU296419 RVA/Human-wt/TUN/17237/2008/G6P[9] JX271011 RVA/Human-wt/USA/0537/2002/G3P[9] JF805009
RVA/Cow-wt/ARG/B383/1998/G15P[11] FJ347121 RVA/Human-wt/HUN/BP1879/2003/G6P[14] FN665687 RVA/Human-wt/HUN/Hun5/1997/G6P[14] EF554114
RVA/Cow-wt/ZAF/1603/2007/G6P[5] JN831208 RVA/Cow-wt/ZAF/1604/2007/G8P[1] JN831219
RVA/Giraffe-wt/IRE/GirRV/2007/G10P[11] GQ428140 RVA/Human-wt/ITA/PAH136/1996/G3P[9] GU296418
RVA/Human-wt/BRA/RV10109/2008/G3P[9] JQ715680 RVA/Cat-wt/ITA/BA222/2005/G3P[9] GU827416 RVA/Human-wt/JPN/KF17/2010/G6P[9] JF421985
RVA/Human-wt/EGY/Egy3399/2004/G6P[14] HM113524
Bovine and Human strains
RVA/Human-wt/BEL/B4106/2000/G3P[14] AY740731 RVA/Rabbit-tc/ITA/30-96/1996/G3P[14] DQ205231
RVA/Guanaco-wt/ARG/Rio_Negro/1998/G8P[1] FJ347132 RVA/Human-wt/AUS/V585/2011/G10P[14] JX567768
Bovine and Human strains
Outgroup RVA/Human-tc/USA/DS-1/1976/G2P[4] M33608
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Fig. 3 (continued)
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RVA/Bat-wt/KEN/KE4852/2007/G25P[6] possess genes of bovineand canine/feline origins (Esona et al., 2010; He et al., 2013). With-out screening a number of animal populations it is impossible toaccurately determine the host species of this strain. The familyreported cats and dogs in the family home and a colony of batspresent on the property, representing possible sources oftransmission.
There has been an increase in the detection of rare or unusualrotavirus strains in the vaccine-era in Australia (Kirkwood et al.,2011b). The efficacy of Rotarix� has been demonstrated againstfully heterotypic G2P[4] and G9P[4] strains in some settings,however, no efficacy has been shown for Rotarix� or RotaTeq�
against fully heterotypic strains of non-human origins (De Voset al., 2009; Yen et al., 2011). The sustained circulation of strains
Please cite this article in press as: Donato, C.M., et al. Genetic characterizationAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid
that are antigenically distinct to the vaccine strains may challengethe efficacy of vaccination programs in Australia and elsewhere. Ifunusual rotavirus strains become more prevalent in younger chil-dren they may lead to reduced vaccine efficacy. Therefore, contin-ued identification and characterization of novel or unusualgenotypes is vital to ensure an effective vaccine program.
Acknowledgements
We would like to acknowledge the assistance of Alissa McMinn,Research Nurse, SAEFVIC Unit, Murdoch Childrens Research Insti-tute, Melbourne, Victoria, Australia, for collection and supply ofpatient information. We gratefully acknowledge Dr Nicole Donkerfor critical review of the manuscript and helpful discussions.
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C.M. Donato et al. / Infection, Genetics and Evolution xxx (2014) xxx–xxx 13
MEEGID 1932 No. of Pages 13, Model 5G
30 April 2014
C.D. Kirkwood is a codeveloper of an investigational rotavirusvaccine. C.D. Kirkwood is director of Australian Rotavirus Surveil-lance Program, which is supported by research grants from vaccinemanufacturers CSL, GSK and Merck. This work was supported bygrants from the National Health and Medical Research Council ofAustralia [1031473]; Australian Commonwealth Department ofHealth; GSK Biologicals (Melbourne, Australia); and CSL (Mel-bourne, Australia). CD Kirkwood is supported by a Career Develop-ment Award from the National Health and Medical ResearchCouncil of Australia [607347].
NW Crawford and JP Buttery have acted as chief investigatorsfor epidemiological and safety studies sponsored by vaccine man-ufacturers (CSL) and have had serological testing supported(Merck). All payments, including for sitting on advisory boardsare paid directly to an administrative fund held by Murdoch Child-rens Research Institute.
This study was supported by the Victorian Government’s Oper-ational Infrastructure Support Program.
Appendix A. Supplementary data
Supplementary data associated with this article can be found, inthe online version, at http://dx.doi.org/10.1016/j.meegid.2014.04.009.
References
Cowley, D., Donato, C.M., Roczo-Farkas, S., Kirkwood, C.D., 2013. Novel G10P[14]rotavirus strain, Northern Territory, Australia. Emerg. Infect. Dis. 19, 1324–1327.
Darriba, D., Taboada, G.L., Doallo, R., Posada, D., 2012. JModelTest 2: more models,new heuristics and parallel computing. Nat. Methods 9, 772.
De Vos, B., Han, H.H., Bouckenooghe, A., Debrus, S., Gillard, P., Ward, R., Cheuvart, B.,2009. Live attenuated human rotavirus vaccine, RIX4414, provides clinicalprotection in infants against rotavirus strains with and without shared G and Pgenotypes: integrated analysis of randomized controlled trials. Pediatr. Infect.Dis. J. 28, 261–266.
Drummond, A.J., Ho, S.Y., Phillips, M.J., Rambaut, A., 2006. Relaxed phylogeneticsand dating with confidence. PLoS Biol. 4, e88.
Drummond, A.J., Nicholls, G.K., Rodrigo, A.G., Solomon, W., 2002. Estimatingmutation parameters, population history and genealogy simultaneously fromtemporally spaced sequence data. Genetics 161, 1307–1320.
Drummond, A.J., Suchard, M.A., Xie, D., Rambaut, A., 2012. Bayesian phylogeneticswith BEAUti and the BEAST 1.7. Mol. Biol. Evol..
Edgar, R.C., 2004. MUSCLE: multiple sequence alignment with high accuracy andhigh throughput. Nucleic Acids Res. 32, 1792–1797.
Esona, M.D., Mijatovic-Rustempasic, S., Conrardy, C., Tong, S., Kuzmin, I.V.,Agwanda, B., Breiman, R.F., Banyai, K., Niezgoda, M., Rupprecht, C.E., Gentsch,J.R., Bowen, M.D., 2010. Reassortant group A rotavirus from straw-colored fruitbat (Eidolon helvum). Emerg. Infect. Dis. 16, 1844–1852.
Estes, M.K., Kapikian, A.Z., 2007. Fields Virology, fifth ed. Lippincott Williams &Wilkins, Philadelphia.
Glass, R.I., Parashar, U.D., Bresee, J.S., Turcios, R., Fischer, T.K., Widdowson, M.-A.,Jiang, B., Gentsch, J.R., 2006. Rotavirus vaccines: current prospects and futurechallenges. Lancet 368, 323–332.
Guindon, S., Gascuel, O., 2003. A Simple, fast, and accurate algorithm to estimatelarge phylogenies by maximum likelihood. Syst. Biol. 52, 696–704.
Guo, D., Liu, J., Lu, Y., Sun, Y., Yuan, D., Jiang, Q., Lin, H., Li, C., Si, C., Qu, L., 2012. Fullgenomic analysis of rabbit rotavirus G3P[14] strain N5 in China: identificationof a novel VP6 genotype. Infect. Genet. Evol. 12, 1567–1576.
He, B., Yang, F., Yang, W., Zhang, Y., Feng, Y., Zhou, J., Xie, J., Feng, Y., Bao, X., Guo, H.,Li, Y., Xia, L., Li, N., Matthijnssens, J., Zhang, H., Tu, C., 2013. Characterization of anovel G3P[3] rotavirus isolated from a lesser horseshoe bat: a distant relative offeline/canine rotaviruses. J. Virol. 87, 12357–12366.
Hu, L., Crawford, S.E., Czako, R., Cortes-Penfield, N.W., Smith, D.F., Le Pendu, J., Estes,M.K., Prasad, B.V.V., 2012. Cell attachment protein VP8⁄ of a human rotavirus
Please cite this article in press as: Donato, C.M., et al. Genetic characterizationAustralian child. Infect. Genet. Evol. (2014), http://dx.doi.org/10.1016/j.meegid
specifically interacts with A-type histo-blood group antigen. Nature 485, 256–259.
Jere, K.C., Esona, M.D., Ali, Y.H., Peenze, I., Roy, S., Bowen, M.D., Saeed, I.K., Khalafalla,A.I., Nyaga, M.M., Mphahlele, J., Steele, D., Seheri, M.L., 2013. Novel NSP1genotype characterised in an African camel G8P[11] rotavirus strain. Infect.Genet. Evol. 21C, 58–66.
Kirkwood, C.D., Boniface, K., Barnes, G.L., Bishop, R.F., 2011a. Distribution ofrotavirus genotypes after introduction of rotavirus vaccines, Rotarix(R) andRotaTeq(R), into the National Immunization Program of Australia. Pediatr.Infect. Dis. J. 30, S48–S53.
Kirkwood, C.D., Roczo, S., Boniface, K., Bishop, R.F., Barnes, G.L., 2011b. Australianrotavirus surveillance program annual report, 2010/11. Commun. Dis. Intell. 35,281–287.
Luchs, A., Timenetsky Mdo, C., 2014. G8P[6] rotaviruses isolated from Amerindianchildren in Mato Grosso do Sul, Brazil, during 2009: close relationship of the Gand P genes with those of bovine and bat strains. J. Gen. Virol. 95, 627–641.
Martella, V., Banyai, K., Matthijnssens, J., Buonavoglia, C., Ciarlet, M., 2010. Zoonoticaspects of rotaviruses. Vet. Microbiol. 140, 246–255.
Matthijnssens, J., Ciarlet, M., Heiman, E., Arijs, I., Delbeke, T., McDonald, S.M.,Palombo, E.A., Iturriza-Gomara, M., Maes, P., Patton, J.T., Rahman, M., Van Ranst,M., 2008. Full genome-based classification of rotaviruses reveals a commonorigin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J. Virol. 82, 3204–3219.
Matthijnssens, J., Ciarlet, M., McDonald, S.M., Attoui, H., Banyai, K., Brister, J.R.,Buesa, J., Esona, M.D., Estes, M.K., Gentsch, J.R., Iturriza-Gomara, M., Johne, R.,Kirkwood, C.D., Martella, V., Mertens, P.P., Nakagomi, O., Parreno, V., Rahman,M., Ruggeri, F.M., Saif, L.J., Santos, N., Steyer, A., Taniguchi, K., Patton, J.T.,Desselberger, U., Van Ranst, M., 2011. Uniformity of rotavirus strainnomenclature proposed by the Rotavirus Classification Working Group(RCWG). Arch. Virol. 156, 1397–1413.
Matthijnssens, J., Otto, P.H., Ciarlet, M., Desselberger, U., Van Ranst, M., Johne, R.,2012. VP6-sequence-based cutoff values as a criterion for rotavirus speciesdemarcation. Arch. Virol. 157, 1177–1182.
Matthijnssens, J., Rahman, M., Martella, V., Xuelei, Y., De Vos, S., De Leener, K.,Ciarlet, M., Buonavoglia, C., Van Ranst, M., 2006. Full genomic analysis of humanrotavirus strain B4106 and lapine rotavirus strain 30/96 provides evidence forinterspecies transmission. J. Virol. 80, 3801–3810.
Minin, V.N., Bloomquist, E.W., Suchard, M.A., 2008. Smooth skyride through a roughskyline: Bayesian coalescent-based inference of population dynamics. Mol. Biol.Evol. 25, 1459–1471.
Papp, H., Al-Mutairi, L.Z., Chehadeh, W., Farkas, S.L., Lengyel, G., Jakab, F., Martella,V., Szucs, G., Banyai, K., 2012. Novel NSP4 genotype in a camel G10P[15]rotavirus strain. Acta Microbiol. Immunol. Hung. 59, 411–421.
Posada, D., 2008. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25,1253–1256.
Ramig, R.F., Ward, R.L., 1991. Genomic segment reassortment in rotavirus and otherreoviridae. Adv. Virus Res. 39, 163–207.
Smith, I., Wang, L.F., 2013. Bats and their virome: an important source of emergingviruses capable of infecting humans. Curr. Opin. Virol. 3, 84–91.
Swiatek, D.L., Palombo, E.A., Lee, A., Coventry, M.J., Britz, M.L., Kirkwood, C.D., 2010.Characterisation of G8 human rotaviruses in Australian children withgastroenteritis. Virus Res. 148, 1–7.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., 2011. MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28,2731–2739.
Taniguchi, K., Urasawa, S., 1995. Diversity in rotavirus genomes. Semin. Virol. 6,123–131.
Tate, J.E., Burton, A.H., Boschi-Pinto, C., Steele, A.D., Duque, J., Parashar, U.D., 2012.2008 estimate of worldwide rotavirus-associated mortality in children youngerthan 5 years before the introduction of universal rotavirus vaccinationprogrammes: a systematic review and meta-analysis. Lancet Infect. Dis. 12,136–141.
Trojnar, E., Sachsenroder, J., Twardziok, S., Reetz, J., Otto, P.H., Johne, R., 2013.Identification of an avian group A rotavirus containing a novel VP4 gene with aclose relationship to those of mammalian rotaviruses. J. Gen. Virol. 94, 136–142.
Xia, L.L., He, B., Hu, T.S., Zhang, W.D., Wang, Y.Y., Xu, L., Li, N., Qiu, W., Yu, J., Fan, Q.S.,Zhang, F.Q., Tu, C.C., 2013. Isolation and characterization of rotavirus from bat.Bing Du Xue Bao 29, 632–637.
Yen, C., Figueroa, J.R., Uribe, E.S., Carmen-Hernandez, L.D., Tate, J.E., Parashar, U.D.,Patel, M.M., Richardson Lopez-Collado, V., 2011. Monovalent rotavirus vaccineprovides protection against an emerging fully heterotypic G9P[4] rotavirusstrain in Mexico. J. Infect. Dis. 204, 783–786.
of a novel G3P[14] rotavirus strain causing gastroenteritis in 12 year old.2014.04.009
