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Hazan G, Goldstein Y, Greenberg D, Khalde F, Mahajna R, Keren-Naos A, Hershkovitz E, Faingelernt Y, Givon-Lavi N, Danino D. Comparing single versus multiple virus detection in pediatric acute gastroenteritis postimplementation of routine multiplex RT-PCR diagnostic testing. J Med Virol 2024; 96:e29344. [PMID: 38149453 DOI: 10.1002/jmv.29344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Utilizing multiplex real time polymerase chain reaction (RT-PCR) for rapid diagnosis of gastroenteritis, enables simultaneous detection of multiple pathogens. A comparative analysis of disease characteristics was conducted between cases with single and multiple viruses. Rotavirus vaccine was introduced in 2010, reaching a 70% coverage in 2 years. All rectal swabs collected from diarrheic children (<5 years) between December 2017 and March 2022 were included. Detection of the same viruses within 2 months was considered a single episode. Episodes with positive stool bacterial PCR were excluded. A total of 5879 samples were collected, revealing 86.9% (1509) with single virus detection and 13.1% (227) with multiple viruses. The most frequent combination was rotavirus and norovirus (27.8%), these infections followed a winter-spring seasonality akin to rotavirus. Children with multivirus infections exhibited higher immunodeficiency (OR 2.06) rates, but lower food allergy (OR 0.45) and prematurity rates (OR 0.55) compared to single infections. Greater disease severity, evaluated by the Vesikari score, was observed in multivirus episodes (p < 0.001, OR 1.12). Multivirus infections accounted for 13.1% of symptomatic cases in hospitalized young children. Despite vaccination efforts, rotavirus remained prominent, frequently in co-infections with norovirus. Overall, multivirus infections were linked to more severe diseases than single virus cases.
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Affiliation(s)
- Guy Hazan
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Pulmonary Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Yoav Goldstein
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - David Greenberg
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Firas Khalde
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Rofaida Mahajna
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Ayelet Keren-Naos
- Clinical Virology Laboratory, Soroka University Medical Center, Beer Sheva, Israel
| | - Eli Hershkovitz
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Yaniv Faingelernt
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Gastroenterology Hepatology and Nutrition Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Noga Givon-Lavi
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Dana Danino
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
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Zhiyanov A, Shkurnikov M, Nersisyan A, Hui C, Baranova A, Tonevitsky A. The signature of SARS-CoV-2 evolution reflects selective pressures within human guts. J Med Virol 2023; 95:e28996. [PMID: 37515485 DOI: 10.1002/jmv.28996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/09/2023] [Accepted: 07/16/2023] [Indexed: 07/31/2023]
Abstract
In somatic cells, microRNAs (miRNAs) bind to the genomes of RNA viruses and influence their translation and replication. In London and Berlin samples represented in GISAID database, we traced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages and divided these sequenced in two groups, "Ancestral variants" and "Omicrons," and analyzed them through the prism of the tissue-specific binding between host miRNAs and viral messenger RNAs. We demonstrate a significant number of miRNA-binding sites in the NSP4 region of the SARS-CoV-2 genome, with evidence of evolutionary pressure within this region exerted by human intestinal miRNAs. Notably, in infected cells, NSP4 promotes the formation of double-membrane vesicles, which serve as the scaffolds for replication-transcriptional complexes and protect viral RNA from intracellular destruction. In 3 years of selection, the loss of many miRNA-binding sites in general and those within the NSP4 in particular has shaped the SARS-CoV-2 genomes. With that, the descendants of the BA.2 variants were promoted as dominant strains, which define current momentum of the pandemics.
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Affiliation(s)
- Anton Zhiyanov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Ashot Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Cai Hui
- Department of Nanoengineering, Sun Yat-Sen University, Shenzhen, China
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, Virginia, USA
- Research Centre for Medical Genetics, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Art Photonics GmbH, Berlin, Germany
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