human rotavirus strains from children with diarrhea in the Philippines

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Accepted Manuscript First detection of DS-1-like G1P[8] human rotavirus strains from children with diarrhea in the Philippines Dai Yamamoto, Amado Tandoc, III, Edelwisa Mercado, Frederick Quicho, Socorro Lupisan, Mariko Saito, Michiko Okamoto, Akira Suzuki, Raita Tamaki, Lydia Sombrero, Remigio Olveda, Hitoshi Oshitani PII:

S2052-2975(17)30031-8

DOI:

10.1016/j.nmni.2017.04.001

Reference:

NMNI 319

To appear in:

New Microbes and New Infections

Received Date: 23 November 2016 Revised Date:

5 April 2017

Accepted Date: 5 April 2017

Please cite this article as: Yamamoto D, Tandoc III A, Mercado E, Quicho F, Lupisan S, Saito M, Okamoto M, Suzuki A, Tamaki R, Sombrero L, Olveda R, Oshitani H, First detection of DS-1-like G1P[8] human rotavirus strains from children with diarrhea in the Philippines, New Microbes and New Infections (2017), doi: 10.1016/j.nmni.2017.04.001. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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First detection of DS-1-like G1P[8] human rotavirus strains from

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children with diarrhea in the Philippines

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Dai Yamamoto1,2*, Amado Tandoc III3, Edelwisa Mercado3, Frederick Quicho4 , Socorro

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Lupisan3, Mariko Saito1,2, Michiko Okamoto2, Akira Suzuki2, Raita Tamaki2, Lydia

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Sombrero3, Remigio Olveda3, Hitoshi Oshitani2

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Author affiliations:

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Tohoku-RITM Collaborating Research Center for Emerging and Reemerging Infectious

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Diseases, RITM Compound, FCC, Alabang, Muntinlupa City, Metro Manila,

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Philippines 1781 2

Seiryo-machi, Aoba-ku, Sendai, Japan, 980-8575

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Department of Virology, Tohoku University Graduate School of Medicine, 2-1,

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Research Institute for Tropical Medicine, RITM Compound, FCC, Alabang, Muntinlupa

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City, Metro Manila, Philippines 1781

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Ospital ng Palawan, 220 Malvar Street, City of Puerto Princesa, Palawan, Philippines

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* Corresponding author

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Dai Yamamoto Kushiro City General Hospital 1-12, Shunkodai, Kushiro, 085-0822, Japan Tel: +81-154-41-6121 e-mail: [email protected]

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To the Editor: The majority of human rotavirus A are classified into two genetic groups, which have distinct genotype constellations of all the 11 gene segments encoding viral proteins (G,

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P, I, R, C, M, A, N, T, E and H) represented by prototype strains Wa and DS-1,

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respectively(Table) [1]. In nature, genotype constellations are stably maintained, and

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reassortment between them has rarely been described. However, recently in Japan and

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Thailand, the G1P[8] human rotavirus on the DS-1-like genotype constellation, in which

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the outer-capsid proteins were replaced with those of the Wa-like virus with the DS-1-like

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genotype background, was reported [2,3,4,5] We also identified DS-1-like G1P[8]

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rotaviruses in the Philippines and genetically analyzed them to elucidate their relatedness

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to previously reported rotaviruses and locally circulating rotaviruses to gain insights into

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their origin and evolutionary pathway.

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Stool specimens were collected from 45 children admitted with acute diarrhea in Palawan, Philippines in 2012. Rotaviruses were detected and genotyped using RT-PCR [6]

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. 25 specimens (56%) were rotavirus-positive, including seven G1P[8] and 11 G2P[4].

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Four G1P[8] and two G2P[4] specimens were subjected to direct sequencing for all gene

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segments. Sequence data were phylogenetically analyzed(Figure a-d), and pairwise

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sequence identity were obtained. Our results revealed that all the rotavirus strains,

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including G1P[8], had a DS-1-like genotype constellation. Four DS-1-like G1P[8] strains

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were found to be genetically diverse (Table). Strain TGO12-016 had identical gene

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sequences to strain TGO12-004, except for the VP3 gene. Several genes of TGO12-016

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(VP7, VP4, VP3, NSP1, and NSP3-NSP5) showed high sequence identities (>99%) to

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those of TGO12-045 and TGO12-012(except for NSP3 and NSP5 genes), as well as to

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DS-1-like G1P[8] strains identified in other countries, whereas other genes, such as VP6,

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VP1, VP2, and NSP2, exhibited lower identities. Strains TGO12-012 and TGO12-045 were

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ACCEPTED MANUSCRIPT considered identical to strains HC12016 and PCB-180. VP6, VP1, VP2, and NSP2 genes

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of strains TGO12-016 and TGO12-004 showed >99% identity to those of G2P[4] strain

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TGO12-003, suggesting that these gene segments of DS-1-like G1P[8] strains might have

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been derived from a locally circulating G2P[4] strain. In contrast, none of the gene

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segments of strains TGO12-012 and TGO12-045 clustered with those of local G2P[4]

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strain TGO12-003.

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We identified three distinct types, suggesting that various reassortants were

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generated in Palawan. Six genes of all DS-1-like G1P[8] strains had high sequence identity,

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implying that they had possibly originated from the same rotavirus. Although genetic

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information was not sufficient because only limited number of rotavirus strains were

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analyzed in the present study, two possibilities are conceivable for the diversity in

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DS-1-like G1P[8] viruses in the Philippines: 1) various intergenogroup reassortants were

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generated in the Philippines, and a single strain has spread to other Asian countries; 2) a

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single DS-1-like G1P[8] rotavirus strain was transmitted from any other Asian country to

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Palawan, where further reassortment occurred between this strain and local G2P[4] viruses.

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Although the origin is still not clear, intergenogroup reassortment has been more frequently

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reported in developing countries [7,8,9]. Therefore, it may be easily speculated that the

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DS-1-like G1P[8] rotavirus was generated in one of the Southeast Asian countries,

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including the Philippines, and was subsequently spread to other Asian countries.

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Continuous monitoring is necessary to identify the emergence and spread of novel

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reassortant viruses.

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Acknowledgements

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The work was supported in part by the Grant-in-Aid for Scientific Research (KAKENHI)

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(Grant no. 23890016) and The Japan Initiative for Global Research Network on Infectious

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Diseases from the Ministries of Education, Culture, Sports, Science, and Technology,

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Japan.

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Conflicts of interest

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None to declare.

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References

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Ozaki T, Katayama K, Nakagomi O. Spread and predominance in Japan of novel

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4. Kuzuya M, Fujii R, Hamano M, Kida K, Mizoguchi Y, Kanadani T, Nishimura K,

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Kishimoto T. Prevalence and molecular characterization of G1P[8] human rotaviruses

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possessing DS-1-like VP6, NSP4, and NSP5/6 in Japan. J Med Virol.

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2014;86(6):1056-64.

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5. Komoto S, Tacharoenmuang R, Guntapong R, Ide T, Haga K, Katayama K, Kato T,

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Ouchi Y, Kurahashi H, Tsuji T, Sangkitporn S, Taniguchi K. Emergence and

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Characterization of Unusual DS-1-Like G1P[8] Rotavirus Strains in Children with

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Diarrhea in Thailand. PLoS One. 2015;10(11):e0141739.

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Figure Legends

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Fig. a-d

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Phylogenetic dendrograms(a-d) of

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respectively) constructed by neighbor-joining methods with MEGA.5 program. Variation

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scale is described at the bottom. Percent bootstrap support is indicated at each node(the

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values 99% is shaded.

The nucleotide sequences determined in this study were deposited in the Genbank database under accession numbers KP007144-KP007211 Two genes(NSP3 and NSP5) of TGO12-012 were not determined due to the lack of sample

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(a) VP7 RVA/Human-wt/JPN/OH3385/2012/G1P[8] RVA/Human-wt/JPN/HC12016/2012/G1P[8] RVA/Human-wt/JPN/OH3493/2012/G1P[8]

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DS-1-like G1P[8] strains

RVA/Human-wt/JPN/OH3506/2012/G1P[8] 99 RVA/Human-wt/JPN/OH3625/2012/G1P[8]

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RVA/Human-wt/PHI/TGO12-045/2012/G1P[8] RVA/Human-wt/PHI/TGO12-016/2012/G1P[8]

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RVA/Human-wt/PHI/TGO12-012/2012/G1P[8] RVA/Human-wt/PHI/TGO12-004/2012/G1P[8]

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RVA/Human-wt/JPN/91TA984/1991/G1P[8] RVA/Human-wt/JPN/OH3514/2012/G1P[8]

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RVA/Human-wt/JPN/OH3592/2012/G1P[8] 100

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RVA/Vaccine/USA/Rotarix-A41CB052A/1988/G1P1A[8] RVA/Human-wt/PHI/TGE12-045/2012/G1P[8]

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RVA/Human-wt/PHI/TGP12-005/2012/G1P[8]

RVA/Human-tc/USA/Wa/1974/G1P[8]

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100 RVA/Vaccine/USA/RotaTeq-WI79-9/1992/G1P7[5] RVA/Human-tc/USA/DS-1/1976/G2P1B[4] 100

RVA/Human-wt/CHI/TB-Chen/1996/G2P[4] RVA/Human-wt/AUS/WAPC703/2010/G2P[4] 99

RVA/Human-wt/PHI/TGO12-003/2012/G2P[4] RVA/Human-wt/PHI/TGO12-007/2012/G2P[4] RVA/Avian/PO-13/G18P[17] (out group)

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(b) VP6

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RVA/Human-wt/JPN/OH3625/2012/G1P[8] RVA/Human-wt/JPN/HC12016/2012/G1P[8]

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RVA/Human-wt/JPN/OH3493/2012/G1P[8]

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DS-1-like G1P[8] strains

RVA/Human-wt/JPN/OH3506/2012/G1P[8]

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RVA/Human-wt/PHI/TGO12-012/2012/G1P[8] 88

RVA/Human-wt/PHI/TGO12-045/2012/G1P[8]

RVA/Human-wt/AUS/WAPC703/2010/G2P[4]

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RVA/Human-wt/PHI/TGO12-003/2012/G2P[4]

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RVA/Human-wt/PHI/TGO12-007/2012/G2P[4]

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RVA/Human-wt/PHI/TGO12-016/2012/G1P[8]

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RVA/Human-wt/PHI/TGO12-004/2012/G1P[8] RVA/Human-wt/BGD/RV161/2000/G12P[6] RVA/Human-wt/COD/DRC88/2003/G8P[8] RVA/Human-wt/CHI/TB-Chen/1996/G2P[4]

RVA/Human-tc/USA/DS-1/1976/G2P1B[4] RVA/Human-wt/JPN/OH3514/2012/G1P[8]

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RVA/Human-wt/JPN/OH3592/2012/G1P[8] RVA/Avian/PO-13/G18P[17] (out group)

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(c) VP3

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RVA/Human-wt/PHI/TGO12-016/2012/G1P[8] RVA/Human-wt/PHI/TGO12-045/2012/G1P[8]

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RVA/Human-wt/PHI/TGO12-012/2012/G1P[8]

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RVA/Human-wt/JPN/HC12016/2012/G1P[8]

DS-1-like G1P[8] strains

RVA/Human-wt/COD/DRC88/2003/G8P[8] 99

RVA/Human-wt/AUS/WAPC703/2010/G2P[4]

RVA/Human-wt/BGD/RV161/2000/G12P[6]

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RVA/Human-wt/CHI/TB-Chen/1996/G2P[4] RVA/Human-wt/PHI/TGO12-004/2012/G1P[8]

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RVA/Human-wt/PHI/TGO12-007/2012/G2P[4] RVA/Human-wt/PHI/TGO12-003/2012/G2P[4]

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RVA/Human-tc/USA/DS-1/1976/G2P1B[4] RVA/Avian/PO-13/G18P[17] (out group)

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(d) NSP2

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RVA/Human-wt/PHI/TGO12-004/2012/G1P[8] 81

RVA/Human-wt/PHI/TGO12-016/2012/G1P[8]

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RVA/Human-wt/PHI/TGO12-003/2012/G2P[4]

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RVA/Human-wt/PHI/TGO12-007/2012/G2P[4]

DS-1-like G1P[8] strains

RVA/Human-wt/AUS/WAPC703/2010/G2P[4] RVA/Human-wt/PHI/TGO12-045/2012/G1P[8]

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RVA/Human-wt/JPN/HC12016/2012/G1P[8]

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RVA/Human-wt/PHI/TGO12-012/2012/G1P[8]

RVA/Human-wt/BGD/RV161/2000/G12P[6]

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RVA/Human-wt/COD/DRC88/2003/G8P[8]

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RVA/Human-wt/CHI/TB-Chen/1996/G2P[4] RVA/Human-tc/USA/DS-1/1976/G2P1B[4] RVA/Avian/PO-13/G18P[17] (out group)

N2