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. 2024 Oct;29(44):2400221.
doi: 10.2807/1560-7917.ES.2024.29.44.2400221.

Enhanced echovirus 11 genomic surveillance in neonatal infections in Spain following a European alert reveals new recombinant forms linked to severe cases, 2019 to 2023

Maria Dolores Fernandez-Garcia  1   2 , Nerea Garcia-Ibañez  1 , Juan Camacho  1 , Almudena Gutierrez  3   4 , Laura Sánchez García  3   4 , Cristina Calvo  3   4   5 , Antonio Moreno-Docón  6 , Ana Isabel Menasalvas  6 , Antonio Medina  7 , Mercedes Perez-Ruiz  7 , Maria Carmen Nieto Toboso  8 , Carmen Muñoz-Almagro  9   2   10 , Cristian Launes  2   10 , Carla Berengua  11 , María Cabrerizo  1   2   4 ; Spanish study group for Enterovirus and Parechovirus infections (PI22CIII-00035)  12 ; Spanish study group for Enterovirus and Parechovirus infections
Collaborators, Affiliations

Enhanced echovirus 11 genomic surveillance in neonatal infections in Spain following a European alert reveals new recombinant forms linked to severe cases, 2019 to 2023

Maria Dolores Fernandez-Garcia et al. Euro Surveill. 2024 Oct.

Abstract

BackgroundIn 2023, a European alert was issued regarding an increase in severe enterovirus (EV) neonatal infections associated with echovirus 11 (E11) new lineage 1.AimTo analyse E11-positive cases between 2019 and 2023 to investigate whether the new lineage 1 circulated in Spain causing severe neonatal infections.MethodsEV-positive samples from hospitalised cases are sent for typing to the National Reference Enterovirus Laboratory. Available samples from 2022-23 were subjected to metagenomic next-generation sequencing.ResultsOf 1,288 samples genotyped, 103 were E11-positive (98 patients: 6 adults, 33 neonates, 89 children under 6 years; male to female ratio 1.9). E11 detection rate was similar before and after detection of the new lineage 1 in Spain in June 2022 (9.7% in 2019 vs 10.6% in 2023). The proportion of E11-infected ICU-admitted neonates in 2019-2022 (2/7) vs 2022-2023 (5/12) did not significantly differ (p = 0.65). In severe neonatal infections, 4/7 E11 strains were not linked to the new lineage 1. The three novel E11 recombinant genomes were associated with severe (n = 2) and non-severe (n = 1) cases from 2022-2023 and clustered outside the new lineage 1. Coinfecting pathogenic viruses were present in four of 10 E11-positive samples.ConclusionThe emergence of the new lineage 1 is not linked with an increase in incidence or severity of neonatal E11 infections in Spain. The detection of two novel E11 recombinants associated with severe disease warrants enhancing genomic and clinical surveillance.

Keywords: Enterovirus; echovirus 11; genomic surveillance; international alert; neonatal infection; new variant; recombinant.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Echovirus 11 detection in enterovirus samples, Spain, January 2019–December 2023 (n = 1,288)
Figure 2
Figure 2
Phylogenetic tree of partial (395 bp) 3´-VP1 coding sequences of 88 echovirus 11 study strains and sequences from previously described echovirus 11 strains extracted from GenBank (n = 46), including new lineage1 variant strains detected in France, Germany Italy, and the United Kingdom, 2013–2023
Figure 3
Figure 3
Phylogenetic tree of complete VP1 coding sequences of 10 echovirus 11 study strains and sequences from previously described echovirus 11 strains extracted from GenBank (n = 98), worldwide countriesa
Figure 4
Figure 4
Heatmap analysis showing virus diversity in echovirus 11-positive study samples, Spain, 2022‒2023 (n = 10 samples)
Figure 5
Figure 5
Plot of similarity of whole genome nt sequences of echovirus 11 study strains for (A) query SPA1, (B) query SPA7 and (C) query SPA4 with E11 strains from the National Center for Biotechnology Information
See this image and copyright information in PMC

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