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Impact of the SARS-CoV-2 Pandemic on the Prevalence and Incidence of Gastrointestinal Viruses in Children up to Five Years Old: a Retrospective Cohort Study

Maldonado-Barrueco, Alfredo ; García-Rodríguez, Julio ; Yániz-Ramirez, Jorge ; [et al.]

American Society for Microbiology ; 2022

In: Microbiology Spectrum Vol. 10, No. 3 ( 2022-06-29)

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In: Microbiology Spectrum, American Society for Microbiology, Vol. 10, No. 3 ( 2022-06-29)

Abstract: The aim is determining the impact of non-pharmaceutical measures (NPIs) against SARS-CoV-2 in the incidence and prevalence of gastrointestinal viruses (GV) in children. Demographic, analytical, and clinical data of children from which samples were received at the Hospital Universitario La Paz (Madrid, Spain) and that had a gastrointestinal infection with a positive sample through multiplex-PCR for GV were collected. The time periods included were prepandemic (P1): March 14, 2019 to March 14, 2020 and pandemic (P2): March 15, 2020 to March 15, 2021. The global prevalence, relative incidence (RI, per 1,000 admissions) and absolute incidence (AI, per 100,000 population) of GV were compared for both time periods. The prevalence of GV versus SARS-CoV-2 was determined for P2. Seven-hundred and 50 out of 2,547 children analyzed in P1 and 106 out of 1,368 in P2 were positive by PCR for GV (46.3% decrease in P2). Prevalence and RI of GV declined in P2, except for the RI of rotavirus. Adenovirus showed the largest decreased of prevalence and RI (100%), followed by sapovirus. Astrovirus reduction was less pronounced (3.1% versus 0.4%). Norovirus was the most frequent virus in both time periods and its prevalence and RI also decreased in P2 (15.2% versus 4.7% and 3.40 versus 1.74, respectively). Rotavirus had the smallest decrease in prevalence (2.6% versus 2.5%), and its RI increased during P2 from 0.7 to 0.93. After removing the rotavirus vaccine strains from the analysis, the prevalence and RI decreased during P2 (2.1% to 0.7% and 0.5 to 0.3, respectively). The AI decreased during P2 in all GV, and the prevalence of SARS-CoV-2 and GV was inversely proportional over time. Prevalence and incidence of GV have decreased during the pandemic, probably due to the implementation of NPIs against this virus and the reduction of health care attention to infections other than COVID-19. The differences in the decrease of prevalence and incidence for each virus may be explained by differences in the transmission and the resistance in the environment. Prevalence and RI of rotavirus might be biased since the PCR used detects both the infecting and the vaccine strains. IMPORTANCE Our original article contains an analysis of the impact of the measures applied against SARS-CoV-2 on the prevalence and incidence of GV in children. The small number of studies published to date that analyze the impact of these measures individually on each of the GV makes our study of great interest at this time.

Type of Medium: Online Resource

ISSN: 2165-0497

URL: Article

DOI: 10.1128/spectrum.02669-21

Language: English

Publisher: American Society for Microbiology

Publication Date: 2022

detail.hit.zdb_id: 2807133-5

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Genome-wide analyses of human noroviruses provide insights on evolutionary dynamics and evidence of coexisting viral populations evolving under recombination constraints

Tohma, Kentaro ; Lepore, Cara J. ; Martinez, Magaly ; [et al.]

Public Library of Science (PLoS) ; 2021

In: PLOS Pathogens Vol. 17, No. 7 ( 2021-7-13), p. e1009744-

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In: PLOS Pathogens, Public Library of Science (PLoS), Vol. 17, No. 7 ( 2021-7-13), p. e1009744-

Abstract: Norovirus is a major cause of acute gastroenteritis worldwide. Over 30 different genotypes, mostly from genogroup I (GI) and II (GII), have been shown to infect humans. Despite three decades of genome sequencing, our understanding of the role of genomic diversification across continents and time is incomplete. To close the spatiotemporal gap of genomic information of human noroviruses, we conducted a large-scale genome-wide analyses that included the nearly full-length sequencing of 281 archival viruses circulating since the 1970s in over 10 countries from four continents, with a major emphasis on norovirus genotypes that are currently underrepresented in public genome databases. We provided new genome information for 24 distinct genotypes, including the oldest genome information from 12 norovirus genotypes. Analyses of this new genomic information, together with those publicly available, showed that (i) noroviruses evolve at similar rates across genomic regions and genotypes; (ii) emerging viruses evolved from transiently-circulating intermediate viruses; (iii) diversifying selection on the VP1 protein was recorded in genotypes with multiple variants; (iv) non-structural proteins showed a similar branching on their phylogenetic trees; and (v) contrary to the current understanding, there are restrictions on the ability to recombine different genomic regions, which results in co-circulating populations of viruses evolving independently in human communities. This study provides a comprehensive genetic analysis of diverse norovirus genotypes and the role of non-structural proteins on viral diversification, shedding new light on the mechanisms of norovirus evolution and transmission.

Type of Medium: Online Resource

ISSN: 1553-7374

URL: Article

DOI: 10.1371/journal.ppat.1009744

DOI: 10.1371/journal.ppat.1009744.g001

DOI: 10.1371/journal.ppat.1009744.g002

DOI: 10.1371/journal.ppat.1009744.g003

DOI: 10.1371/journal.ppat.1009744.g004

DOI: 10.1371/journal.ppat.1009744.g005

DOI: 10.1371/journal.ppat.1009744.g006

DOI: 10.1371/journal.ppat.1009744.g007

DOI: 10.1371/journal.ppat.1009744.g008

DOI: 10.1371/journal.ppat.1009744.g009

DOI: 10.1371/journal.ppat.1009744.g010

DOI: 10.1371/journal.ppat.1009744.g011

DOI: 10.1371/journal.ppat.1009744.t001

DOI: 10.1371/journal.ppat.1009744.t002

DOI: 10.1371/journal.ppat.1009744.s001

DOI: 10.1371/journal.ppat.1009744.s002

DOI: 10.1371/journal.ppat.1009744.s003

DOI: 10.1371/journal.ppat.1009744.s004

DOI: 10.1371/journal.ppat.1009744.s005

DOI: 10.1371/journal.ppat.1009744.s006

DOI: 10.1371/journal.ppat.1009744.s007

DOI: 10.1371/journal.ppat.1009744.s008

DOI: 10.1371/journal.ppat.1009744.s009

DOI: 10.1371/journal.ppat.1009744.s010

DOI: 10.1371/journal.ppat.1009744.s011

DOI: 10.1371/journal.ppat.1009744.s012

DOI: 10.1371/journal.ppat.1009744.s013

DOI: 10.1371/journal.ppat.1009744.s014

DOI: 10.1371/journal.ppat.1009744.s015

DOI: 10.1371/journal.ppat.1009744.s016

DOI: 10.1371/journal.ppat.1009744.s017

DOI: 10.1371/journal.ppat.1009744.s018

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2021

detail.hit.zdb_id: 2205412-1

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Detection of novel GII.17 norovirus in Argentina, 2015

Degiuseppe, Juan I. ; Gomes, Karina A. ; Hadad, María F. ; [et al.]

Elsevier BV ; 2017

In: Infection, Genetics and Evolution Vol. 47 ( 2017-01), p. 121-124

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In: Infection, Genetics and Evolution, Elsevier BV, Vol. 47 ( 2017-01), p. 121-124

Type of Medium: Online Resource

ISSN: 1567-1348

URL: Article

DOI: 10.1016/j.meegid.2016.11.026

Language: English

Publisher: Elsevier BV

Publication Date: 2017

detail.hit.zdb_id: 2057622-5

SSG: 12

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Recombinant Nontypeable Genotype II Human Noroviruses in the Americas

Tohma, Kentaro ; Lepore, Cara J. ; Degiuseppe, Juan I. ; [et al.]

Centers for Disease Control and Prevention (CDC) ; 2020

In: Emerging Infectious Diseases Vol. 26, No. 1 ( 2020-01), p. 157-159

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In: Emerging Infectious Diseases, Centers for Disease Control and Prevention (CDC), Vol. 26, No. 1 ( 2020-01), p. 157-159

Type of Medium: Online Resource

ISSN: 1080-6040 , 1080-6059

URL: Article

DOI: 10.3201/eid2601.190626

Language: English

Publisher: Centers for Disease Control and Prevention (CDC)

Publication Date: 2020

detail.hit.zdb_id: 2004375-2

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Increased frequency of rotavirus G3P[8] and G12P[8] in Argentina during 2008–2009: Whole-genome characterization of emerging G12P[8] strains

Stupka, Juan A. ; Degiuseppe, Juan I. ; Parra, Gabriel I.

Elsevier BV ; 2012

In: Journal of Clinical Virology Vol. 54, No. 2 ( 2012-06), p. 162-167

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In: Journal of Clinical Virology, Elsevier BV, Vol. 54, No. 2 ( 2012-06), p. 162-167

Type of Medium: Online Resource

ISSN: 1386-6532

URL: Article

DOI: 10.1016/j.jcv.2012.02.011

Language: English

Publisher: Elsevier BV

Publication Date: 2012

detail.hit.zdb_id: 1499932-8

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Shifting Hierarchies of Interleukin-10-Producing T Cell Populations in the Central Nervous System during Acute and Persistent Viral Encephalomyelitis

Puntambekar, Shweta S. ; Bergmann, Cornelia C. ; Savarin, Carine ; [et al.]

American Society for Microbiology ; 2011

In: Journal of Virology Vol. 85, No. 13 ( 2011-07), p. 6702-6713

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In: Journal of Virology, American Society for Microbiology, Vol. 85, No. 13 ( 2011-07), p. 6702-6713

Abstract: Interleukin-10 (IL-10) mRNA is rapidly upregulated in the central nervous system (CNS) following infection with neurotropic coronavirus and remains elevated during persistent infection. Infection of transgenic IL-10/green fluorescent protein (GFP) reporter mice revealed that CNS-infiltrating T cells were the major source of IL-10, with minimal IL-10 production by macrophages and resident microglia. The proportions of IL-10-producing cells were initially similar in CD8 + and CD4 + T cells but diminished rapidly in CD8 + T cells as the virus was controlled. Overall, the majority of IL-10-producing CD8 + T cells were specific for the immunodominant major histocompatibility complex (MHC) class I epitope. Unlike CD8 + T cells, a large proportion of CD4 + T cells within the CNS retained IL-10 production throughout persistence. Furthermore, elevated frequencies of IL-10-producing CD4 + T cells in the spinal cord supported preferential maintenance of IL-10 production at the site of viral persistence and tissue damage. IL-10 was produced primarily by the CD25 + CD4 + T cell subset during acute infection but prevailed in CD25 − CD4 + T cells during the transition to persistent infection and thereafter. Overall, these data demonstrate significant fluidity in the T-cell-mediated IL-10 response during viral encephalitis and persistence. While IL-10 production by CD8 + T cells was limited primarily to the time of acute effector function, CD4 + T cells continued to produce IL-10 throughout infection. Moreover, a shift from predominant IL-10 production by CD25 + CD4 + T cells to CD25 − CD4 + T cells suggests that a transition to nonclassical regulatory T cells precedes and is retained during CNS viral persistence.

Type of Medium: Online Resource

ISSN: 0022-538X , 1098-5514

URL: Article

DOI: 10.1128/JVI.00200-11

Language: English

Publisher: American Society for Microbiology

Publication Date: 2011

detail.hit.zdb_id: 1495529-5

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Detection of human rotavirus G9P[8] strains circulating in Argentina: Phylogenetic analysis of VP7 and NSP4 genes

Stupka, Juan A. ; Parra, Gabriel I. ; Gómez, Jorge ; [et al.]

Wiley ; 2007

In: Journal of Medical Virology Vol. 79, No. 6 ( 2007-06), p. 838-842

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In: Journal of Medical Virology, Wiley, Vol. 79, No. 6 ( 2007-06), p. 838-842

Abstract: During the surveillance of rotavirus strains that were circulating in Argentinean children from 2000 to 2004, seven rotaviruses were detected bearing the genotype combination G9P[8]. The molecular characterization of the VP7 and NSP4 genes and the RNA migration patterns support the hypothesis that rotaviruses G9 could have been reintroduced into Argentina as a novel G9P[8] strain, rather than represent VP7 gene reassortants from G9P[6] strains that had been circulating previously in this country. J. Med. Virol. 79: 838–842, 2007. © 2007 Wiley‐Liss, Inc.

Type of Medium: Online Resource

ISSN: 0146-6615 , 1096-9071

URL: Issue

URL: Article

DOI: 10.1002/jmv.v79:6

DOI: 10.1002/jmv.20841

RVK:

XA 10000

Language: English

Publisher: Wiley

Publication Date: 2007

detail.hit.zdb_id: 752392-0

detail.hit.zdb_id: 1475090-9

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Molecular characterization of calicivirus strains detected in outbreaks of gastroenteritis in Argentina

Gomes, Karina A. ; Stupka, Juan A. ; Gómez, Jorge ; [et al.]

Wiley ; 2007

In: Journal of Medical Virology Vol. 79, No. 11 ( 2007-11), p. 1703-1709

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In: Journal of Medical Virology, Wiley, Vol. 79, No. 11 ( 2007-11), p. 1703-1709

Type of Medium: Online Resource

ISSN: 0146-6615 , 1096-9071

URL: Issue

URL: Journal

URL: Article

DOI: 10.1002/jmv.v79:11

DOI: 10.1002/(ISSN)1096-9071

DOI: 10.1002/jmv.20989

RVK:

XA 10000

Language: English

Publisher: Wiley

Publication Date: 2007

detail.hit.zdb_id: 752392-0

detail.hit.zdb_id: 1475090-9

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Vesicle-Cloaked Virus Clusters Are Optimal Units for Inter-organismal Viral Transmission

Santiana, Marianita ; Ghosh, Sourish ; Ho, Brian A. ; [et al.]

Elsevier BV ; 2018

In: Cell Host & Microbe Vol. 24, No. 2 ( 2018-08), p. 208-220.e8

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In: Cell Host & Microbe, Elsevier BV, Vol. 24, No. 2 ( 2018-08), p. 208-220.e8

Type of Medium: Online Resource

ISSN: 1931-3128

URL: Article

DOI: 10.1016/j.chom.2018.07.006

Language: English

Publisher: Elsevier BV

Publication Date: 2018

detail.hit.zdb_id: 2276339-9

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Identification of Human Junctional Adhesion Molecule 1 as a Functional Receptor for the Hom-1 Calicivirus on Human Cells

Sosnovtsev, Stanislav V. ; Sandoval-Jaime, Carlos ; Parra, Gabriel I. ; [et al.]

American Society for Microbiology ; 2017

In: mBio Vol. 8, No. 1 ( 2017-03-08)

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In: mBio, American Society for Microbiology, Vol. 8, No. 1 ( 2017-03-08)

Abstract: Vesiviruses, such as San Miguel sea lion virus and feline calicivirus, are typically associated with infection in animal hosts. Following the accidental infection of a laboratory worker with San Miguel sea lion virus, a related virus was isolated in cell culture and named Hom-1. In this study, we found that Hom-1 could be propagated in a number of human cell lines, making it the first calicivirus to replicate efficiently in cultured human cells. Screening of a library of human cell surface membrane proteins showed that the virus could utilize human junctional adhesion molecule 1 as a receptor to enter cells and initiate replication. The Hom-1 virus presents a new system for the study of calicivirus biology and species specificity.

Type of Medium: Online Resource

ISSN: 2161-2129 , 2150-7511

URL: Article

DOI: 10.1128/mBio.00031-17

Language: English

Publisher: American Society for Microbiology

Publication Date: 2017

detail.hit.zdb_id: 2557172-2

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