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1. Whole Genome Sequences of the Wildtype AU-1 Rotavirus A Strain: The Prototype of the AU-1-like Genotype Constellation.

Author

Agbemabiese, Chantal Ama, Dennis, Francis Ekow, Lartey, Belinda Larteley, Damanka, Susan Afua, Nakagomi, Toyoko, Nakagomi, Osamu, and Armah, George Enyimah

Subjects
WHOLE genome sequencing, VIRAL genomes, ROTAVIRUSES, GENOMES, GENOTYPES
Abstract

Most human rotaviruses belong to the Wa-like, DS-1-like, or AU-1-like genotype constellation. The AU-1-like constellation, albeit minor, captured attention because its prototype strain AU-1 originated from feline rotavirus, leading to the concept of interspecies transmission of rotavirus. The AU-1 genome sequence determined by various laboratories over the years has documented two conflicting VP7 sequences in the GenBank. As culture-adaptation may introduce changes in the viral genome, the original fecal (wild-type) and the seed stock of culture-adapted AU-1 genomes were sequenced using the Illumina's MiSeq platform to determine the authentic AU-1 sequence and to identify what mutational changes were selected during cell-culture adaptation. The wild-type and culture-adapted AU-1 genomes were identical except for one VP4-P475L substitution. Their VP7 gene was 99.9% identical to the previously reported AU-1 VP7 under accession number AB792641 but only 92.5% to that under accession number D86271. Thus, the wild-type sequences determined in this study (accession numbers OR727616-OR727626) should be used as the reference. The VP4-P475L mutation was more likely incidental than inevitable during cell-culture adaptation. This was the first study in which the whole genomes of both wild-type and cultured RVA strains were simultaneously determined by deep sequencing. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Reassortment of human rotavirus gene segments into G11 rotavirus strains

Author

Matthijnssens, Jelle, Rahman, Mustafizur, Ciarlet, Max, Zeller, Mark, Heylen, Elisabeth, Nakagomi, Toyoko, Uchida, Ryuichi, Hassan, Zahid, Azim, Tasnim, Nakagomi, Osamu, and Van Ranst, Marc

Subjects
Rotavirus infections -- Research -- Genetic aspects, Rotaviruses -- Research -- Genetic aspects, Health
Abstract

Group A rotaviruses are the most frequently detected viral cause of diarrhea in children worldwide and cause [approximately equal to] 600,000 deaths in children A nucleotide sequence-based classification and nomenclature [...]

Published
2010
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21. Healthcare-associated viral gastroenteritis among children in a large pediatric hospital, United Kingdom

Author

Cunliffe, Nigel A., Booth, J. Angela, Elliot, Claire, Lowe, Sharon J., Sopwith, Will, Kitchin, Nick, Nakagomi, Osamu, Nakagomi, Toyoko, Hart, C. Anthony, and Regan, Martyn

Subjects
Children -- Diseases, Gastroenteritis -- Risk factors -- Prevention -- Demographic aspects -- Research, Viral vaccines -- Health aspects, Health
Abstract

Enteric viruses are major etiologic agents of acute gastroenteritis (AGE) among infants and young children worldwide (1). Rotavirus is the most common single cause of severe diarrhea leading to dehydration [...]

Published
2010
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22. Serotype G12 rotaviruses, Lilongwe, Malawi

Author

Cunliffe, Nigel A., Ngwira, Bagrey M., Dove, Winifred, Nakagomi, Osamu, Nakagomi, Toyoko, Perez, Arantza, Hart, C. Anthony, Kazembe, Peter N., and Mwansambo, Charles C.V.

Subjects
Gastroenteritis -- Diagnosis, Rotaviruses -- Research, Rotaviruses -- Health aspects
Abstract

To assess diversity of rotavirus strains in Lilongwe, Malawi, we conducted a cross-sectional study of children with acute gastroenteritis, July 2005-June 2007. Serotype G12 was identified in 30 (5%) of [...]

Published
2009

24. Rotavirus

Author

Nakagomi, Osamu, primary, Nakagomi, Toyoko, additional, and Cunliffe, Nigel A, additional

Published
2013
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25. Sapovirus

Author

Nakagomi, Osamu, primary, Nakagomi, Toyoko, additional, and Cunliffe, Nigel A, additional

Published
2013
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26. List of Contributors

Author

Acuin, Jose M, primary, Adam, Rodney D, additional, Agbenyega, Tsiri, additional, Ahmed, AM Shamsir, additional, Ahmed, Tahmeed, additional, Ali, S Asad, additional, Anstead, Gregory M, additional, Armah, George E, additional, Aston, Stephen J, additional, Ballard, Ronald C, additional, Barnett, Elizabeth D, additional, Bates, Imelda, additional, Beadling, Charles W, additional, Beeching, Nicholas J, additional, Bennish, Michael L, additional, Bern, Caryn, additional, Bia, Frank J, additional, Bird, Brian H, additional, Bloom, Allyson K, additional, Bodeker, Gerard, additional, Bradsher, Robert W, additional, Broek, Nynke van den, additional, Brooker, Simon, additional, Brooks, John T, additional, Brooks, W Abdullah, additional, Brouqui, Philippe, additional, Brown, Michael, additional, Bruschi, Fabrizio, additional, Bundy, Donald AP, additional, Bunnag, Danai, additional, Caballero, Benjamin, additional, Callahan, Michael V, additional, Camerlin, Aulasa J, additional, Campbell, Grant L, additional, Carapetis, Jonathan R, additional, Carrol, Enitan D, additional, Caumes, Eric, additional, Charrel, Remi N, additional, Checkley, Anna M, additional, Chhabra, Mala, additional, Chher, Tepirou, additional, Chiong, Charlotte M, additional, Chisti, M Jobayer, additional, Christiani, David C, additional, Connor, Bradley A, additional, Cooper, Edward S, additional, Cooper, Philip J, additional, Coughlin, R Richard, additional, Cross, John H, additional, Cunliffe, Nigel N, additional, Danta, Mark, additional, Day, Nicholas PJ, additional, Dekumyoy, Paron, additional, deSilva, Nilanthi, additional, Deye, Gregory, additional, Dillingham, Rebecca, additional, Doorn, H Rogier van, additional, Doudier, Barbara, additional, Drancourt, Michel, additional, Dromer, Françoise, additional, Eddleston, Michael, additional, El-Kamary, Samer S, additional, Farrar, Jeremy, additional, Fawzi, Wafaie, additional, Feasey, Nicholas A, additional, Field, Vanessa, additional, Fischer, Marc, additional, Fisher-Hoch, Susan, additional, Forsyth, Kevin, additional, Fox, LeAnne M, additional, Friedlander, Arthur M, additional, Galdos-Cardenas, Gerson, additional, Garcia, Hector H, additional, Garcia, Lynne S, additional, Geretti, Anna-Maria, additional, Gikas, Achilleas, additional, Gilman, Robert H, additional, Gonzalez, Victor Javier Sanchez, additional, Gordon, Melita A, additional, Gosselin, Richard A, additional, Graham, Stephen M, additional, Grant, Alison D, additional, Gray, James J, additional, Graybill, John R, additional, Graz, Bertrand, additional, Green, Stephen, additional, Griffiths, Jeffrey K, additional, Gryseels, Bruno, additional, Gubler, Duane J, additional, Guhadasan, Rathi, additional, Hall, Aron J, additional, Hamer, Davidson, additional, Harley, David, additional, Harris, Jason B, additional, Hartman, Amy L, additional, Hassall, Oliver, additional, Hay, Roderick J, additional, Heyns, Chris F, additional, Hill, David R, additional, Hobdell, Martin H, additional, Hoed, Caroline M den, additional, Holtz, Meredith L, additional, Hossain, M Iqbal, additional, Hotez, Peter J, additional, Houpt, Eric R, additional, Howard, Cynthia R, additional, Hung, Chien-Ching, additional, Islam, Munirul, additional, Joekes, Elizabeth, additional, Johnston, Victoria, additional, Kampondeni, Sam, additional, Kang, Gagandeep, additional, Kazanjian, Powel, additional, Keystone, Jay S, additional, Khan, Wasif Ali, additional, Kim, Arthur Y, additional, King, Christopher L, additional, Klion, Amy D, additional, Knight, Richard, additional, Krause, Peter James, additional, Krishna, Sanjeev, additional, Kuipers, Ernst J, additional, LaBeaud, Angelle D, additional, Lalloo, David G, additional, Lamballerie, Xavier De, additional, Lambert, Saba, additional, LaRocque, Regina C, additional, Lawrenson, John, additional, Levine, Myron M, additional, Libraty, Daniel H, additional, Lockwood, Diana NJ, additional, Lommerse, Kinke M, additional, Lortholary, Olivier, additional, López-Vélez, Rogelio, additional, Lopman, Benjamin A, additional, Mabey, David, additional, Magill, Alan J., additional, Maguiña, Ciro, additional, Mahmood, Syed Faisal, additional, Maitland, Kathryn, additional, Manji, Hadi, additional, Marston, Barbara J, additional, Mathew, Anu, additional, Mathews, Christine E, additional, Maurin, Max, additional, Maurtua-Neumann, Paola J, additional, Mayaud, Philippe, additional, Mayosi, Bongani M, additional, McCormick, Joseph B, additional, McKew, Stephen, additional, McLellan, Susan LF, additional, McMinn, Peter C, additional, Mega, Joseph D, additional, Meier, Donald E, additional, Million, Matthieu, additional, Mittal, Veena, additional, Molyneux, Elizabeth M, additional, Montgomery, Susan P, additional, Morera, Pedro, additional, Moro, Pedro L, additional, Moss, William J, additional, Murrell, K Darwin, additional, Nakagomi, Osamu, additional, Nakagomi, Toyoko, additional, Nanda, Neha, additional, Nataro, James P, additional, Navaro, Eileen E, additional, Neafie, Ronald C, additional, Negroni, Ricardo, additional, Nelson, Ann M, additional, Newton, Paul N, additional, Newton, Robert, additional, Nichol, Stuart T, additional, Norman, Francesca F, additional, Nunes, Marcio RT, additional, Nutman, Thomas B, additional, Oberhelman, Richard A, additional, Oldfield, Edward C, additional, Ordaya, Eloy E, additional, Paddock, Christopher D, additional, Paessler, Slobodan, additional, Papanikolaou, Ilias C, additional, Pappas, Georgios, additional, Paris, Luc, additional, Parola, Philippe, additional, Parry, Christopher M, additional, Patel, Manish M, additional, Peacock, Sharon J, additional, Peeling, Rosanna, additional, Persson, Hans, additional, Peters, Philip J, additional, Phillips, Jonathan J, additional, Phillips, Richard O, additional, Qamar, Farah Naz, additional, Rahman, Atif, additional, Rajab, Jamilla, additional, Raoult, Didier, additional, Rein, Michael F, additional, Renvoisé, Aurélié, additional, Reynes, Jean-Marc, additional, Richards, Frank O, additional, Richens, John, additional, Rimoin, Anne W, additional, Riviello, Robert, additional, Rodrigues, Ema G, additional, Ronald, Allan R, additional, Rosenthal, Benjamin M, additional, Rosmarin, David, additional, Ruiz-Tiben, Ernesto, additional, Ryan, Edward T, additional, Saha, Debasish, additional, Saavedra, Arturo, additional, Schantz, Peter M, additional, Schountz, Tony, additional, Schumacher, Sandra K, additional, Sejvar, James J, additional, Sethi, Aisha, additional, Seung, Kwonjune J, additional, Sharma, Om Prakash, additional, Sharp, Trueman W, additional, Shankar, Anuraj H, additional, Shin, Sonya S, additional, Shlim, David R, additional, Sickels, Nicholas J van, additional, Sitas, Freddy, additional, Snelling, Thomas L, additional, Socolovschi, Cristina, additional, Solomon, Tom, additional, Staples, J Erin, additional, Stewart, Robert C, additional, Stich, August, additional, Strickland, G Thomas, additional, Suh, Kathryn N, additional, Suhrbier, Andreas, additional, Supparatpinyo, Khuanchai, additional, Sutcliffe, Catherine G, additional, Swierczewski, Brett E, additional, Tarpley, John L, additional, Taylor, Hugh R, additional, Taylor, Terrie, additional, Thomas, Harry J, additional, Thwaites, C Louise, additional, Thwaites, Guy E, additional, Tiwari, Tejpratap SP, additional, Tu, Phan Van, additional, Turner, Angus W, additional, Vannier, Edouard, additional, Vasconcelos, Pedro FC, additional, Vega-López, Fransisco, additional, Velarde, Jorge J, additional, Vietri, Nicholas J, additional, Visvesvara, Govinda S, additional, Vyas, Keyur S, additional, Wakeham, Katie, additional, Walsh, Thomas J, additional, Wansbrough-Jones, Mark H, additional, Warrell, David A, additional, Warrell, Mary J, additional, Warraich, Haider J, additional, Watt, George, additional, Wattanagoon, Yupaporn, additional, Watthanakulpanich, Dorn, additional, Weaver, Scott C, additional, Webman, Rachel B, additional, Weidle, Paul J, additional, Weiss, Louis M, additional, White, Nicholas J, additional, Whitty, Christopher JM, additional, Woodhall, Dana M, additional, Wright, Stephen G, additional, Xavier, Ramnik J, additional, Xiao, Lihua, additional, Yu, Hongjie, additional, and Zaidi, Anita KM, additional

Published
2013
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31. Detection of three independently-generated DS-1-like G9P[8] reassortant rotavirus A strains during the G9P[8] dominance in Vietnam, 2016–2018

Author

Hoa-Tran, Thi Nguyen, primary, Nakagomi, Toyoko, additional, Vu, Hung Manh, additional, Nguyen, Trang Thu Thi, additional, Takemura, Taichiro, additional, Hasebe, Futoshi, additional, Dao, Anh Thi Hai, additional, Anh, Pham Hong Quynh, additional, Nguyen, Anh The, additional, Dang, Anh Duc, additional, and Nakagomi, Osamu, additional

Published
2020
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37. Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains

Author

Agbemabiese, Chantal Ama, Nakagomi, Toyoko, Damanka, Susan Afua, Dennis, Francis Ekow, Lartey, Belinda Larteley, Armah, George Enyimah, Nakagomi, Osamu, Agbemabiese, Chantal Ama, Nakagomi, Toyoko, Damanka, Susan Afua, Dennis, Francis Ekow, Lartey, Belinda Larteley, Armah, George Enyimah, and Nakagomi, Osamu

Abstract

Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A (RVA)strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship.However, within a genotype, there is lack of a consensus lineage designation framework and a set of common sequences that can serve as references. Phylogenetic analyses were carried out on over 8,500 RVA genotype 2 genes systematically retrieved from the rotavirus database within the NCBI Virus Variation Resource. In line with previous designations, using pairwise comparison of cogent nucleotide sequences and stringent bootstrap support, reference lineages were defined. This study proposes a lineage framework and provides a dataset ranging from 34 to 145 sequences for each genotype 2 gene for orderly lineage designation of global genotype 2 genes of RVAs detected in human and animals. The framework identified five to 31 lineages depending on the gene.The least number of lineages (five to seven) were observed in genotypes A2 (NSP1), T2 (NSP3) and H2 (NSP5) which are limited to human RVA whereas the most number of lineages (31) was observed in genotype E2 (NSP4). Sharing of the same lineage constellations of the genotype 2 backbone genes between recently-emerging, unusual G1P[8], G3P[8], G8P[8] and G9P[4] reassortants and many contemporary G2P[4] strains provided strong support to the hypothesis that unusual genotype 2 strains originated primarily from reassortment events in the recent past involving contemporary G2P[4] strains as one parent and ordinary genotype 1 strains or animal RVA strains as the other. The lineage framework with selected reference sequences will help researchers to identify the lineage to which a given genotype 2 strain belongs, and trace the evolutionary history of common and unusual genotype 2 strains in circulation., PLoS ONE, 14(5), art.no.e0217422; 2019

Published
2019

39. Rotavirus P[4]G2 in a vaccinated population, Brazil

Author

Patel, Manish M., de Oliveira, Lucia Helena, Bispo, Ana Maria, Gentsch, Jon, Parashar, Umesh D., Linhares, Alexandre C., Velazquez, F. Raul, Gurgel, Ricardo Queiroz, Vieira, Sarah Cristina Fontes, Barros, Vanessa Cristiane Farias, Fontes, Paula Brandao, Salustino, Eduardo F., Nakagomi, Osamu, Nakagomi, Toyoko, Dove, Winifred, Cunliffe, Nigel A., and Cuevas, Luis E.

Abstract

To the Editor: Gurgel et al. provide an early examination of postmarketing surveillance data from Brazil, one of the first countries to implement routine childhood immunization with Rotarix vaccine (I). [...]

Published
2008

41. Predominance of rotavirus P[4]G2 in a vaccinated population, Brazil

Author

Gurgel, Ricardo Q., Cuevas, Luis E., Vieira, Sarah C.F., Barros, Vanessa C.F., Fontes, Paula B., Salustino, Eduardo F., Nakagomi, Osamu, Nakagomi, Toyoko, Dove, Winifred, Cunliffe, Nigel, and Hart, Charles A.

Subjects
Vaccination -- Health aspects, Infection -- Health aspects
Abstract

We identified 21 rotaviruses in 129 patients with diarrhea in a Brazilian city with high rotavirus vaccine coverage, All rotaviruses were genotype P[4]G2 with 1 mixed infection with P[NT]G9. Although [...]

Published
2007

42. Detection of G12 human rotaviruses in Nepal

Author

Pun, Sher Bahadur, Nakagomi, Toyoko, Sherchand, Jeevan Bahadur, Pandey, Basu Dev, Cuevas, Luise E., Cunliffe, Nigel A., Hart, C.A., and Nakagomi, Osamu

Subjects
Rotaviruses -- Diagnosis, Rotaviruses -- Research, Diarrhea in children -- Causes of, Diarrhea in children -- Diagnosis, Enzyme-linked immunosorbent assay -- Usage, Polymerase chain reaction -- Usage
Abstract

Of 731 stool specimens collected from children with diarrhea in Kathmandu, Nepal, from August 2004 through July 2005, 170 (23.3%) tested positive for rotavirus. Reverse transcription-PCR, including a revised G12-specific [...]

Published
2007

43. Whole genome characterization of feline-like G3P[8] reassortant rotavirus A strains bearing the DS-1-like backbone genes detected in Vietnam, 2016

Author

Hoa-Tran, Thi Nguyen, primary, Nakagomi, Toyoko, additional, Vu, Hung Manh, additional, Kataoka, Chikako, additional, Nguyen, Trang Thi Thu, additional, Dao, Anh Thi Hai, additional, Nguyen, Anh The, additional, Takemura, Taichiro, additional, Hasebe, Futoshi, additional, Dang, Anh Duc, additional, and Nakagomi, Osamu, additional

Published
2019
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48. Japanese Society of Tropical Medicine

Author

Hashizume, Masahiro, Nakagomi, Toyoko, and Nakagomi, Osamu

Subjects
Rotavirus, fluids and secretions, Impact, Surveillance, viruses, Time-series analysis, virus diseases, Vaccine, Gastroenteritis
Abstract

Rotavirus is a leading cause of severe acute gastroenteritis in children worldwide, and globally licensed vaccines are available. To expedite the introduction of rotavirus vaccines in the national immunisation programme, a simple, ecological method to monitor changes in the burden of rotavirus disease may be of great help. Here, we report an application of a time-series analysis on a publicly-available dataset in Japan on the weekly number of laboratory-confirmed rotavirus-positive samples over the last 5 year period between the 36th week of 2009 and the 35th week of 2014 during which rotavirus vaccines became marketed in Japan and presumed to reach an uptake rate of at least 39% as a national average. Compared with the expected number of rotavirus detection based on the preceding four rotavirus seasons, the number of rotavirus detection during the 2013?2014 season was 42.9% (95% CI: 38.6, 47.8). This suggests that the use of rotavirus vaccine had a positive impact on reducing the burden of rotavirus diarrhoea in Japan. This method, because of its simplicity and little cost, should be applicable to early detection of the impact of rotavirus vaccine even in resource-poor countries where the World Health Organization funded and implemented the sentinel surveillance programmes of laboratory-confirmed rotavirus cases.

Published
2015

50. Free-Chlorine Disinfection as a Selection Pressure on Norovirus

Author

0000-0002-3133-5917, Rachmadi, Andri Taruna, Kitajima, Masaaki, Watanabe, Kozo, Yaegashi, Sakiko, Serrana, Joeselle, Nakamura, Arata, 1000040155693, Nakagomi, Toyoko, 1000070143047, Nakagomi, Osamu, Katayama, Kazuhiko, 1000010253816, Okabe, Satoshi, 1000080550368, Sano, Daisuke, 0000-0002-3133-5917, Rachmadi, Andri Taruna, Kitajima, Masaaki, Watanabe, Kozo, Yaegashi, Sakiko, Serrana, Joeselle, Nakamura, Arata, 1000040155693, Nakagomi, Toyoko, 1000070143047, Nakagomi, Osamu, Katayama, Kazuhiko, 1000010253816, Okabe, Satoshi, 1000080550368, and Sano, Daisuke

Abstract

Human noroviruses are excreted in feces from infected individuals and included in wastewater. It is critical to remove/inactivate them in wastewater treatment processes, particularly in the disinfection step, before release to aquatic environments. However, the high mutation rates of human noroviruses raise concerns about the emergence of strains that are less susceptible to disinfectants and can survive even after wastewater treatment. This study aimed to demonstrate the strain-dependent susceptibility of norovirus to free chlorine. A population originated from the murine norovirus strain S7-PP3, a surrogate for human noroviruses in environmental testing, was exposed to free chlorine and then propagated in a host cell. This cycle of free chlorine exposure followed by propagation in cells was repeated 10 times, and populations with lower susceptibility to free chlorine were obtained from two independent trials of chlorine exposure cycles. Open reading frame 2 (ORF2) and ORF3 of the murine norovirus genome were analyzed by next-generation sequencing, and a unique nonsynonymous mutation (corresponding to a change from phenylalanine to serine) at nucleotide (nt) 7280 in ORF3, which encodes the minor capsid protein VP2, was found in chlorine-exposed populations from both trials. It was confirmed that all of the clones from the chlorine-treated population had lower susceptibility to free chlorine than those from the control population. These results indicate that exposure to free chlorine and dilution exert different driving forces to form murine norovirus (MNV) quasispecies, and that there is a selective force to form MNV quasispecies under free chlorine exposure. IMPORTANCE This study showed that free chlorine disinfection exerted a selection pressure for murine norovirus (MNV). The strain-dependent viral susceptibility to the disinfectant elucidated in this study highlights the importance of employing less susceptible strains as representative viruses in disinfection

Published
2018

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