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Identification of a Novel Astrovirus (Astrovirus VA1) Associated with an Outbreak of Acute Gastroenteritis
Open accessAbstract
The etiology of a large proportion of gastrointestinal illness is unknown. In this study, random Sanger sequencing and pyrosequencing approaches were used to analyze fecal specimens from a gastroenteritis outbreak of unknown etiology in a child care center. Multiple sequences with limited identity to known astroviruses were identified. Assembly of the sequences and subsequent reverse transcription-PCR (RT-PCR) and rapid amplification of cDNA ends generated a complete genome of 6,586 nucleotides. Phylogenetic analysis demonstrated that this virus, named astrovirus VA1 (AstV-VA1), is highly divergent from all previously described astroviruses. Based on RT-PCR, specimens from multiple patients in this outbreak were unequivocally positive for Ast-VA1.
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“Astroviruses have a broad host range (Donato and Vijaykrishna 2017) and are frequently detected in the faeces of mammals, birds, and humans with gastroenteritis (Finkbeiner et al. 2009; De Benedictis et al. 2011).”
From Red fox viromes in urban and rural landscapes (2020) · cites this paper as Finkbeiner et al. 2009
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Self-citationThe Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses
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“A study in the USA revealed the high level of co-infections in pigs (13.9%), revealing the frequent opportunity for recombination, especially between viruses of different lineages [61].”
BackgroundInfluentialAstrovirus Biology and Pathogenesis.
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Self-citationHigh Throughput Sequencing for Detection of Foodborne Pathogens
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“The second clade contains VA1, VA2 and VA3 (also known as HMO-A, HMO-B and HMO-C).”
BackgroundInfluentialSelf-citationKarlsson, E., Small, C. T., Freiden, P., Feeroz, M., Matsen, F., San, S., Hasan, M., Wang, D., Jones-Engel, L., & Schultz-Cherry, S. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1005225 · Cited by 80
“In contrast to bat AstVs, NHP AstVs are distributed throughout the Astroviridae family Based on the high prevalence rate and genetic diversity of AstV detected in bats compared to other species, bats have been proposed as a pimary natural reservoir for AstVs and possibly as host of the most recent conmon ancestor of t…”
BackgroundInfluentialSelf-citationAdaptive Immunity Restricts Replication of Novel Murine Astroviruses
Yokoyama, C. C., Loh, J., Zhao, G.-Y., Stappenbeck, T., Wang, D., Huang, H. V., Virgin, H., & Thackray, L. B. (2012) · Journal of Virology · doi:10.1128/jvi.02018-12 · Cited by 80
“Human astrovirus 1 (HAstV1) to HAstV8 are an important cause of gastroenteritis in pediatric inpatients and outpatients, HIV-infected and immunocompromised populations, and the elderly (9, 10, 12, 16, 21, 22, 24, 28, 39, 44, 48, 53, 63).”
BackgroundSelf-citationBurbelo, P., Ching, K. H., Esper, F. L., Iadarola, M., Delwart, E., Lipkin, W., & Kapoor, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022576 · Cited by 79
Human Parvovirus 4 as Potential Cause of Encephalitis in Children, India
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“The raw sequence reads were deconvoluted on the basis of the barcode and then processed through a standardized bioinformatic pipeline (2).”
Self-citationObservational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study
Lambert, S., Ware, R., Cook, A., Maguire, F. A., Whiley, D., Bialasiewicz, S., Mackay, I., Wang, D., Sloots, T., Nissen, M., et al. (2012) · BMJ Open · doi:10.1136/bmjopen-2012-002134 · Cited by 69
Self-citationApplication of High-Throughput DNA Sequencing in Phytopathology
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Astrovirus MLB1 Is Not Associated with Diarrhea in a Cohort of Indian Children
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“Since 2008, five highly divergent astroviruses have been discovered in human diarrhea specimens: MLB1 [8], astrovirus MLB2 (MLB2) [9], astrovirus VA1 (VA1) [10], astrovirus VA2 (VA2) [9], and astrovirus VA3 (VA3) [9].”
BackgroundSelf-citationEvidence of a Recombinant Wild-Type Human Astrovirus Strain from a Kenyan Child with Gastroenteritis
Wolfaardt, M., Kiulia, N., Mwenda, J., & Taylor, M. B. (2010) · Journal of Clinical Microbiology · doi:10.1128/jcm.01093-10 · Cited by 63
Metagenomic Analysis of Viruses in Feces from Unsolved Outbreaks of Gastroenteritis in Humans
Moore, N., Wang, J., Hewitt, J., Croucher, D., Williamson, D., Paine, S., Yen, S., Greening, G., & Hall, R. J. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.02029-14 · Cited by 60
“A more tenable explanation could be a “diagnostic gap,” a theory also suggested by others (5, 13, 30).”
BackgroundDetection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses
Laurin, M., Dastor, M., & L'Homme, Y. (2011) · Archives of Virology · doi:10.1007/s00705-011-1088-7 · Cited by 57
Molecular characterization of a porcine astrovirus strain in China
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“In humans, eight classical human astroviruses (HAstV) are known [6, 25], and novel genotypes have continuously emerged in recent years [7, 8, 12].”
BackgroundUse of Illumina Deep Sequencing Technology To Differentiate Hepatitis C Virus Variants
Ninomiya, M., Ueno, Y., Funayama, R., Nagashima, T., Nishida, Y., Kondo, Y., Inoue, J., Kakazu, E., Kimura, O., Nakayama, K., et al. (2011) · Journal of Clinical Microbiology · doi:10.1128/jcm.05715-11 · Cited by 50
“NS3 Patient 1 3426 7 S gCC A 3447 14 L (C/t/g)TT L/F/V (67 [89]/6 [8]/2 [3]) 3495 30 D GAg E 3513 36 L gTt V 3588 61 S (T/g)CG S/A (48 [71]/20 [29]) 3591 62 K AgG R 3618 71 I gTC V 3645 80 Q CtG L 3663 86 P CaG Q 3747 114 V aTc I 3801 132 I gTC V 3855 150 V GcT A 3915 170 I gT(A/g) V 4149 248 I gTC V 4152 249 E GAc D…”
Reuter, G., Pankovics, P., & Boros, Á. (2018) · Clinical Microbiology Reviews · doi:10.1128/cmr.00040-18 · Cited by 49
“Finally, the MAstV9 species includes astrovirus clades VA1 (or HMO-C) (23) and VA3 (or HMO-B) (19, 21, 24).”
InfluentialIdentification and characterization of deer astroviruses.
Smits, S., van Leeuwen, M., Kuiken, T., Hammer, A., Simon, J., & Osterhaus, A. (2010) · Journal of General Virology · doi:10.1099/vir.0.024067-0 · Cited by 49
“The phylogenetic topology determined in this study is largely in agreement with previous analyses of astrovirus phylogeny (Finkbeiner et al., 2008, 2009a, b, c; Kapoor et al., 2009; Rivera et al., 2010).”
ResultRed fox viromes in urban and rural landscapes
Campbell, S. J., Ashley, W., Gil-Fernandez, M., Newsome, T. M., Di Giallonardo, F., Ortiz-Baez, A. S., Mahar, J. E., Towerton, A. L., Gillings, M., Holmes, E. C., et al. (2020) · Virus Evolution · doi:10.1093/ve/veaa065 · Cited by 47
Viral gastroenteritis in children in Colorado 2006–2009
Osborne, C. M., Montano, A., Robinson, C., Schultz-Cherry, S., & Dominguez, S. (2015) · Journal of Medical Virology · doi:10.1002/jmv.24022 · Cited by 47
“…and the four known endemic humans coronavirus (order: Nidovirales, family: Coronaviridae, genus: Alphacoronavirus species: human coronavirus 229E and NL63; genus: Betacoronavirus, species: human coronavirus HKU1 and OC43) [Kuypers et al., 2007; Dominguez et al., 2009; Finkbeiner et al., 2009a,b].”
BackgroundPropagation of Astrovirus VA1, a Neurotropic Human Astrovirus, in Cell Culture
Janowski, A. B., Bauer, I. K., Holtz, L. R., & Wang, D. (2017) · Journal of Virology · doi:10.1128/jvi.00740-17 · Cited by 45
“Stool samples positive for VA1 by PCR (CDC_B and CDC_C) from the originally described outbreak of VA1-associated gastroenteritis in Virginia, USA, were used as the initial inoculum (23).”
BackgroundMethodInfluentialSelf-citationPérot, P., Lecuit, M., & Eloit, M. (2017) · Viruses · doi:10.3390/v9010010 · Cited by 43
“After the discovery of distant HAstV strains, MLB [16,63] and VA1/HMO-C [17], additional”
BackgroundBat Astroviruses: Towards Understanding the Transmission Dynamics of a Neglected Virus Family
Fischer, K., dos Reis, V. P., & Balkema-Buschmann, A. (2017) · Viruses · doi:10.3390/v9020034 · Cited by 42
“In a study where fecal samples from pigs and humans from several Colombian regions were collected, the authors assumed that recombination between the porcine and the human astroviruses within the variable region of ORF2 had occurred [59].”
BackgroundInfluentialA Systematic Approach to Novel Virus Discovery in Emerging Infectious Disease Outbreaks
Sridhar, S., To, K., Chan, J., Lau, S., Woo, P. C. Y., & Yuen, K. Y. (2015) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2014.12.002 · Cited by 42
New astrovirus in human feces from Burkina Faso
Phan, T., Nordgren, J., Ouermi, D., Simporé, J., Nitiéma, L., Deng, X.-T., & Delwart, E. (2014) · Journal of Clinical Virology · doi:10.1016/j.jcv.2014.03.024 · Cited by 42
“The fourth human astrovirus species (mamastrovirus 9), also described in 2009, includes strains VA1 [5], VA3 [6], HMO-B and HMO-C [4].”
BackgroundPorcine astrovirus viremia and high genetic variability in pigs on large holdings in Croatia.
Brnić, D., Prpić, J., Keros, T., Roić, B., Starešina, V., & Jemeršić, L. (2013) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2012.12.027 · Cited by 42
Identification of a second encephalitis-associated astrovirus in cattle
Seuberlich, T., Wüthrich, D., Selimovic-Hamza, S., Drögemüller, C., Oevermann, A., Bruggmann, R., & Bouzalas, I. (2016) · Emerging Microbes and Infections · doi:10.1038/emi.2016.5 · Cited by 40
Martella, V., Pinto, P., Tummolo, F., Grazia, S. D., Giammanco, G., Medici, M., Ganesh, B., L'Homme, Y., Farkas, T., Jakab, F., et al. (2014) · Archives of Virology · doi:10.1007/s00705-014-2153-9 · Cited by 40
“A number of unusual HAstVs discovered recently are genetically more closely related to animal AstVs than to ‘‘canonical’’ HAstVs [3, 16, 17, 26, 28, 39].”
BackgroundPativada, M., Nataraju, S. M., Ganesh, B., Rajendran, K., Ramamurthy, T., Ganguly, S., Bhattacharya, M., Ghosh, M., Kobayashi, N., & Krishnan, T. (2012) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2012.07.018 · Cited by 38
Novel Astroviruses in Children, Egypt
Ahmed, S. F., Sebeny, P., Klena, J., Pimentel, G., Mansour, A., Naguib, A., Bruton, J., Young, S. Y., Holtz, L. R., & Wang, D. (2011) · Emerging Infectious Diseases · doi:10.3201/eid1712.110909 · Cited by 38
Self-citationHata, A., Kitajima, M., Haramoto, E., Lee, S., Ihara, M., Gerba, C., & Tanaka, H. (2018) · Scientific Reports · doi:10.1038/s41598-018-30217-y · Cited by 37
Khamrin, P., Thongprachum, A., Okitsu, S., Hayakawa, S., Maneekarn, N., & Ushijima, H. (2016) · Journal of Medical Virology · doi:10.1002/jmv.24337 · Cited by 37
“After the discovery of novel astroviruses MLB and VA clades, the viruses have been reported as occurring in acute gastroenteritis pediatric patients globally, including several countries in Asia [Finkbeiner et al., 2008b, 2009b; Matsumoto et al., 2013].”
BackgroundMethodResultInfluentialHigh evolutionary rate of human astrovirus.
Babkin, I., Tikunov, A., Zhirakovskaia, E., Netesov, S., & Tikunova, N. (2012) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2012.01.019 · Cited by 37
Isolation and phylogenetic characterization of bat astroviruses in southern China
Xiao, J.-P., Li, J., Hu, G., Chen, Z., Wu, Y., Chen, Y., Chen, Z., Liao, Y., Zhou, J., Ke, X., et al. (2011) · Archives of Virology · doi:10.1007/s00705-011-1011-2 · Cited by 37
“Recently, two new astroviruses, astrovirus MLB1 and astrovirus VA1, were detected in patients with diarrhea [7, 8].”
BackgroundThe Expanding Field of Mammalian Astroviruses: Opportunities and Challenges in Clinical Virology.
Boujon, C. L., Koch, M., & Seuberlich, T. (2017) · Advances in Virus Research · doi:10.1016/bs.aivir.2017.07.002 · Cited by 37
Cordey, S., Brito, F., Vu, D., Turin, L., Kilowoko, M., Kyungu, E., Genton, B., Zdobnov, E., D'Acremont, V., & Kaiser, L. (2016) · Emerging Microbes and Infections · doi:10.1038/emi.2016.98 · Cited by 35
Update on SARS research and other possibly zoonotic coronaviruses
Anderson, L., & Tong, S. (2010) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2010.06.016 · Cited by 34
“Various other molecular tools have been developed and applied to samples from humans, and a number of novel viruses have been detected, including novel coronaviruses [54] [55] [56] , parvoviruses [57, 58] , polyomaviruses [59, 60] , astroviruses [61] and rhinoviruses [62] .”
BackgroundSelf-citationSurveillance of Human Astrovirus Infection in Brazil: The First Report of MLB1 Astrovirus
Xavier, M. D. P. T. P., Costa, F. A. C., Rocha, M., de Andrade, J. D. S. R., Diniz, F. B., de Andrade, T. R., Miagostovich, M., Leite, J. P., & Volotão, E. D. M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135687 · Cited by 33
From orphan virus to pathogen: the path to the clinical lab
Li, L., & Delwart, E. (2011) · Current Opinion in Virology · doi:10.1016/j.coviro.2011.07.006 · Cited by 29
“Viral metagenomics was initially used to analyze environmental samples using Sanger shotgun sequencing [4], and has rapidly expanded to include samples such as human and animal feces [5–11], blood [12,13], tissues [14–17] and respiratory secretions [18–20] often using next generation sequencing.”
MethodBeyond the Gastrointestinal Tract: The Emerging and Diverse Tissue Tropisms of Astroviruses
Janowski, A. B. (2021) · Viruses · doi:10.3390/v13050732 · Cited by 35
Kumthip, K., Khamrin, P., Ushijima, H., & Maneekarn, N. (2018) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2018.08.024 · Cited by 32
Astrovirus infection in hospitalized children: Molecular, clinical and epidemiological features.
Siqueira, J. A., Oliveira, D. D. S., Carvalho, T. C. D. D., Portal, T. M., Justino, M. C., da Silva, L. D., Resque, H. R., & Gabbay, Y. (2017) · Journal of Clinical Virology · doi:10.1016/j.jcv.2017.07.014 · Cited by 32
The Diversity of Human RNA Viruses
Woolhouse, M. E. J., & Adair, K. (2013) · Future Virology · doi:10.2217/fvl.12.129 · Cited by 42
Full-genome based molecular characterization of encephalitis-associated bovine astroviruses.
Bouzalas, I., Wüthrich, D., Selimovic-Hamza, S., Drögemüller, C., Bruggmann, R., & Seuberlich, T. (2016) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2016.06.052 · Cited by 31
“Some of them, such as HAstV MLB (MAstV 6), HAstV HMO-A (MAstV 8) and HAstV VA1 (MAstV 9) are novel genotype species and form previously unknown phylogenetic clades (Finkbeiner et al., 2008; Finkbeiner et al., 2009).”
BackgroundHata, A., Katayama, H., Kitajima, M., & Furumai, H. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.00563-15 · Cited by 31
“On the basis of the background presented above, we performed the present study to investigate the occurrence and genetic diversity of classic HAstVs as well as novel AstVs in wastewater in Japan.”
BackgroundInfluentialA Novel Astrovirus-Like RNA Virus Detected in Human Stool
Munnink, B. O., Cotten, M., Canuti, M., Deijs, M., Jebbink, M., van Hemert, F. V., Phan, M. V. T., Bakker, M., Farsani, S. M. J., Kellam, P., et al. (2016) · Virus Evolution · doi:10.1093/ve/vew005 · Cited by 29
“Two new clades of astroviruses have been described in stool samples from patients with diarrhoea (Finkbeiner, Kirkwood, and Wang 2008; Finkbeiner et al. 2009b).”
BackgroundA novel astrovirus from dromedaries in the Middle East.
Woo, P. C. Y., Lau, S., Teng, J. L. L., Tsang, A. K. L., Joseph, S., Xie, J., Jose, S., Fan, R. Y. Y., Wernery, U., & Yuen, K. Y. (2015) · Journal of General Virology · doi:10.1099/jgv.0.000233 · Cited by 29
“Novel human and animal AstVs have been discovered in recent years (Atkins et al., 2009; Chu et al., 2010; Finkbeiner et al., 2008, 2009; Hu et al., 2014; Kapoor et al., 2009; Luo et al., 2011; Martella et al., 2011a, b; Rivera et al., 2010; Smits et al., 2010; Stenglein et al., 2012).”
BackgroundDefining the Etiology of Diarrhea: Novel Approaches
Operario, D., & Houpt, E. (2011) · Current Opinion in Infectious Diseases · doi:10.1097/qco.0b013e32834aa13a · Cited by 29
Zhao, G.-Y., Droit, L., Tesh, R., Popov, V., Little, N. S., Upton, C., Virgin, H., & Wang, D. (2011) · Journal of Virology · doi:10.1128/jvi.00637-11 · Cited by 29
Self-citationAfrad, M. H., Karmakar, P. C., Das, S., Matthijnssens, J., Ahmed, F., Nahar, S., Faruque, A. G., Rahman, M. Z., Rahman, M., & Azim, T. (2013) · Journal of Clinical Virology · doi:10.1016/j.jcv.2013.09.028 · Cited by 28
Environmental assessment reveals the presence of MLB‐1 human astrovirus in Uruguay
Lizasoain, A., Tort, L., García, M., Gómez, M. M., Leite, J. P. G., Miagostovich, M., Cristina, J., Colina, R., & Victoria, M. (2015) · Journal of Applied Microbiology · doi:10.1111/jam.12856 · Cited by 27
“Screening of the recently identified HAstV was carried out amplifying a 409 bp segment of the ORF1b region of the AstV genome with primers SF0073 and SF0076 designed with a bias for the detection of highly divergent HAstV (MLB and VA) (Finkbeiner et al. 2009c).”
BackgroundMethodInfluentialFirth, A., & Atkins, J. (2010) · Virology Journal · doi:10.1186/1743-422x-7-17 · Cited by 27
“[11] [12] [13] [14] for recent phylogenetic trees).”
Health conditions in rural areas with high livestock density: Analysis of seven consecutive years
van Dijk, C. E., Zock, J., Baliatsas, C., Smit, L. A. M., Borlée, F., Spreeuwenberg, P. M. M., Heederik, D. J. J., & Yzermans, J. C. (2016) · Environmental Pollution · doi:10.1016/j.envpol.2016.12.023 · Cited by 25
Advanced techniques for detection and identification of microbial agents of gastroenteritis.
Dunbar, S., Zhang, H., & Tang, Y.-W. (2013) · Clinics in Laboratory Medicine · doi:10.1016/j.cll.2013.03.003 · Cited by 26
Recently Identified Novel Human Astroviruses in Children with Diarrhea, China
Wang, Y.-X., Li, Y., Jin, Y., Li, D.-D., Li, X., & Duan, Z. (2013) · Emerging Infectious Diseases · doi:10.3201/eid1908.121863 · Cited by 26
Self-citationPhylogenetically diverse TT virus viremia among pregnant women.
Bzhalava, D., Ekström, J., Lysholm, F., Hultin, E., Faust, H., Persson, B., Lehtinen, M., de Villiers, E., & Dillner, J. (2012) · Virology · doi:10.1016/j.virol.2012.06.022 · Cited by 26
Neurotropic Astroviruses in Animals
Wildi, N., & Seuberlich, T. (2021) · Viruses · doi:10.3390/v13071201 · Cited by 25
“The HMO clade originally contained newly discovered astrovirus strains from humans (HuAstV VA1) [58] and mink feces samples (MiAstV, MAstV 10), which showed genetic similarity to OvAstV 1 (MAstV 13).”
BackgroundInfluentialYuan, X.-Y., Meng, K., Zhang, Y.-X., Qi, L.-H., Ai, W., & Wang, Y.-L. (2018) · Msphere · doi:10.1128/msphere.00380-18 · Cited by 23
Metadata
- Authors
- Finkbeiner, S. R., Li, Y., Ruone, S., Conrardy, C., Gregoricus, N., Toney, D., Virgin, H. W., Anderson, L. J., Vinjé, J., Wang, D., & Tong, S.
- Affiliations
- Washington University in St. Louis (US)
- Centers for Disease Control and Prevention (US)
- Commonwealth of Virginia (US)
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333
- Corresponding author
- Wang, David
- Tong, Suxiang
- Venue
- Journal of Virology
- Publisher
- American Society for Microbiology
- Published
- 2009-10-15
- Volume
- 83
- Issue
- 20
- Pages
- 10836-10839
- ISSN
- 0022-538X (ISSN-L)
- 1098-5514
- PMC
- PMC2753140
- OpenAlex
- W2117058366
- Cited by
- 224
- References
- 0
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 10 · 2023: 6 · 2022: 10 · 2021: 9 · 2020: 7 · 2019: 14 · 2018: 13 · 2017: 14 · 2016: 19 · 2015: 20 · 2014: 14 · 2013: 12 · 2012: 26
- FWCI
- 15.36
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Virology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Burroughs Wellcome Fund
- National Institutes of Health (AI057160)
- Centers for Disease Control and Prevention
- National Institute of Allergy and Infectious Diseases (U54AI057160)
- Topics
- Health Sciences › Medicine › Infectious Diseases › Viral gastroenteritis research and epidemiology
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Health Sciences › Medicine › Epidemiology › Respiratory viral infections research
- Keywords
- astrovirus, acute gastroenteritis, gastroenteritis outbreak, daycare centers, viral etiology, viral genome, phylogenetic analysis, fecal samples, RNA viruses
- MeSH terms
- Adult, Animals, Mamastrovirus, Child Day Care Centers, Child, Preschool, Disease Outbreaks, Feces, Female, Gastroenteritis, Genotype, Humans, Infant, Male, Molecular Sequence Data, Phylogeny, Species Specificity, Polymerase Chain Reaction, Sequence Analysis, DNA, Astroviridae Infections
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