Global phylodynamics of Echovirus 30 revealed differential behavior among viral lineages

Lema, Cristina; Torres, Carolina; Sanden, Sabine van der; Cisterna, Daniel; Freire, María Cecilia; Gómez, Ricardo Martín

doi:10.1016/j.virol.2019.02.012

Cited by 28 publications

(25 citation statements)

References 48 publications

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“…Additionally, nucleotide sequences of clinical isolates-which were obtained from AM cases reported in different locations of Argentina between 1998 and 2012 [13]-were retrieved from GenBank nucleotide database for a genetic comparison with strains detected in wastewater by this study. Comparisons were performed through a matrix of nucleotide identity constructed in BioEdit software v7.2.5 [38].…”

Section: Backgrounds Of Human Enteroviruses Detection In Argentina Link Between Environmental and Clinical Isolatesmentioning

confidence: 99%

“…South America has been identified as being among the regions of the world with less available information about the genetic diversity of its circulating EVs strains [10]. In particular, Argentina has extensively studied the molecular epidemiology of echovirus 30, a member of EV-B related with AM [11][12][13]. Additionally, there are some reports regarding outbreaks of different diseases caused by EVs [14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Environmental Surveillance through Next-Generation Sequencing to Unveil the Diversity of Human Enteroviruses beyond the Reported Clinical Cases

Lizasoain

Mir

Masachessi

et al. 2021

Viruses

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The knowledge about circulation of Human Enteroviruses (EVs) obtained through medical diagnosis in Argentina is scarce. Wastewater samples monthly collected in Córdoba, Argentina during 2011–2012, and then in 2017–2018 were retrospectively studied to assess the diversity of EVs in the community. Partial VP1 gene was amplified by PCR from wastewater concentrates, and amplicons were subject of next-generation sequencing and genetic analyses. There were 41 EVs detected, from which ~50% had not been previously reported in Argentina. Most of the characterized EVs (60%) were detected at both sampling periods, with similar values of intratype nucleotide diversity. Exceptions were enterovirus A71, coxsackievirus B4, echovirus 14, and echovirus 30, which diversified in 2017–2018. There was a predominance of types from EV-C in 2017–2018, evidencing a common circulation of these types throughout the year in the community. Interestingly, high genetic similarity was evidenced among environmental strains of echovirus 30 circulating in 2011–2012 and co-temporal isolates obtained from patients suffering aseptic meningitis in different locations of Argentina. This study provides an updated insight about EVs circulating in an important region of South America, and suggests a valuable role of wastewater-based epidemiology in predicting outbreaks before the onset of cases in the community.

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Section: Backgrounds Of Human Enteroviruses Detection In Argentina Link Between Environmental and Clinical Isolatesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Environmental Surveillance through Next-Generation Sequencing to Unveil the Diversity of Human Enteroviruses beyond the Reported Clinical Cases

Lizasoain

Mir

Masachessi

et al. 2021

Viruses

View full text Add to dashboard Cite

show abstract

“…In general, 25% of the genome difference of enterovirus is used as the criteria for serotyping, while 15% of the genome difference is used as the criteria for genotyping; this is widely accepted for serotyping and genotyping of enterovirus, such as EV-A71, CV-A16, and CV-A6 (Brown et al, 1999;Oberste et al, 1999a,b;Mizuta et al, 2005;Zhang et al, 2010aZhang et al, , 2013Song et al, 2017). We refer to the published genotyping criteria of EV-A71, CV-A16, and CV-A6 and combined with the latest research progress of E-30 (Lema et al, 2019;Maruo et al, 2019;Mauri et al, 2019;Sousa et al, 2019). In addition to being able to better represent the E-30 sequences in the world, we also avoid the redundancy sequences of E-30 for genotyping, which leads to the confusion and divergence of enterovirus genotyping.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

A Large-Scale Outbreak of Echovirus 30 in Gansu Province of China in 2015 and Its Phylodynamic Characterization

Chen

Han

et al. 2020

Front. Microbiol.

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Background: Echovirus 30 (E-30) has been investigated and reported worldwide and is closely associated with several infectious diseases, including encephalitis; myocarditis; and hand, foot, and mouth disease. Although many E-30 outbreaks associated with encephalitis have been reported around the world, it was not reported in northwest China until 2015. Methods: The clinical samples, including the feces, serum, throat swabs, and cerebrospinal fluid, were collected for this study and were analyzed for diagnosis. E-30 was isolated and processed according to the standard procedures. The epidemiological and phylogenetic analysis were performed to indicate the characteristics of E-30 outbreaks and phylodynamics of E-30 in China. Results: The E-30 outbreaks affected nine towns of Gansu Province in 2015, starting at a school of Nancha town and spreading to other towns within 1 month. The epidemiological features showed that children aged 6-15 years were more susceptible to E-30 infection. The genotypes B and C cocirculated in the world, whereas the latter dominated the circulation of E-30 in China. The genome sequences of this outbreak present 99.3-100% similarity among these strains, indicating a genetic-linked aggregate outbreak of E-30 in this study. Two larger genetic diversity expansions and three small fluctuations of E-30 were observed from 1987 to 2016 in China, which revealed the oscillating patterns of E-30 in China. In addition, the coastal provinces of China, such as Zhejiang, Fujian, and Shandong, were initially infected, followed by other parts of the country. The E-30 strains isolated from mainland of China may have originated from Taiwan of China in the last century. Conclusion: The highly similar E-30 genomes in this outbreak showed an aggregate outbreak of E-30, with nine towns affected. Our results suggested that, although the genetic diversity of E-30 oscillates, the dominant lineages of E-30 in China has complex

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“…The phylogenetic analysis of VP1 gene in the present study has been widely used for typing EVs and molecular epidemiological investigations. Some EV serotypes (e.g., E6, E11, E18, E30 and CVB5) are still causing global epidemic outbreaks, while others (e.g., CVA9, E5 and E20) are primarily endemic infections [18,47,48,49,50,51]. E18 has caused many aseptic meningitis outbreaks in Germany, the United States, Japan, Korea, and other countries or regions [50,52,53,54,55,56].…”

Section: Discussionmentioning

confidence: 99%

Analysis of Enterovirus Genotypes in Cerebrospinal Fluid of Children Associated with Aseptic Meningitis in Liaocheng, China, from 2018 to 2019

Wang

Meng

et al. 2021

Preprint

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Background: Aseptic meningitis is the most common viral infection caused by human enteroviruses, but enteroviruses associated with aseptic meningitis in Liaocheng have not been reported yet. The aim of this study was to determine prevalence and genetic characteristics of enteroviruses causing aseptic meningitis in children in Liaocheng. Methods: We reviewed the epidemiological and clinical characteristics of 504 pediatric cases with aseptic meningitis in Liaocheng from 2018 to 2019, and analyzed the phylogeny of the predominant enterovirus (EV) types causing this disease. Results: A total of 107 children were positive for EV by the nested-PCR in cerebrospinal fluid samples. Most of the positive patients were children within 13 years old, had symptoms such as fever, headache and vomiting (P<0.05). The most prevalent seasons of EV-positive cases accurred in summer and autumn. The 107 EV sequences belonged to 8 serotypes, and echovirus types 18, 6 and 11 were the three dominant serotypes in Liaocheng during the 2-year period. Phylogentic analyses demonstrated that E18 and E6 isolates belonged to subgenotype C2, while E11 isolates belonged to subgenotype D5. The VP1 analysis suggested that only one lineage of these three types were co-circulating in Liaocheng region. Conclusions: This study demonstrated the diversified enterovirus genotypes attributing to the large outbreak of aseptic meningitis in Liaocheng. Therefore, the large-scale surveillance is required to the epidemiology of enteroviruses associated with aseptic meningitis, and is important for diagnosis and treatment of aseptic meningitis in Liaocheng.

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Global phylodynamics of Echovirus 30 revealed differential behavior among viral lineages

Cited by 28 publications

References 48 publications

Environmental Surveillance through Next-Generation Sequencing to Unveil the Diversity of Human Enteroviruses beyond the Reported Clinical Cases

Environmental Surveillance through Next-Generation Sequencing to Unveil the Diversity of Human Enteroviruses beyond the Reported Clinical Cases

A Large-Scale Outbreak of Echovirus 30 in Gansu Province of China in 2015 and Its Phylodynamic Characterization

Analysis of Enterovirus Genotypes in Cerebrospinal Fluid of Children Associated with Aseptic Meningitis in Liaocheng, China, from 2018 to 2019

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