Genome Sequences of 16 Enterovirus Isolates from Environmental Sewage in Guatemala, 2019 to 2021

Harrington, Chelsea; Sayyad, Leanna; Castro, Christina J.; Hill, Jamaica; Jeffries-Miles, Stacey; Belgasmi, Hanen; Rey-Benito, Gloria; Prillwitz, María Linda Mendoza; Signor, Leticia Castillo; Gerloff, Nancy

doi:10.1128/mra.00562-22

Cited by 2 publications

(3 citation statements)

References 15 publications

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“…All sequences were confirmed by VP1 cluster analysis as described in 1.6 above. The 5 additional EV genomes, presented in Table 2 , constitute the new genome submissions included in this publication [ 40 ].…”

Section: Resultsmentioning

confidence: 99%

“…For these EVs, either partial or complete capsid genes were resolved with genome lengths between 7,132 to 7,395 nucleotides (and near-complete genomes 7,015–7,143 nucleotides). The successful isolation and genomic typing of a diverse range of EVs, including echoviruses 1, 3, 6, 7, 11, 13, 18, 19, 25, 29; CVA-13, B2, and B5; EV-C99, EVB; and PVs (Sabin 1 and 3), from both RD and HLF cell lines confirms the effectiveness of incorporating the additional cell line into the testing algorithm [ 40 ]. The HLF cell line demonstrated its specificity by exclusively capturing echovirus 13 (E13), Coxsackievirus A13 (CVA-13), and enterovirus C99 (EV-C99) that were not found in other cell lines tested.…”

Section: Discussionmentioning

confidence: 96%

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Molecular epidemiology of enteroviruses from Guatemalan wastewater isolated from human lung fibroblasts

Sayyad,

Harrington,

Castro

et al. 2024

PLoS ONE

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The Global Specialized Polio Laboratory at CDC supports the Global Poliovirus Laboratory Network with environmental surveillance (ES) to detect the presence of vaccine strain polioviruses, vaccine-derived polioviruses, and wild polioviruses in high-risk countries. Environmental sampling provides valuable supplementary information, particularly in areas with gaps in surveillance of acute flaccid paralysis (AFP) mainly in children less than 15 years. In collaboration with Guatemala’s National Health Laboratory (Laboratorio Nacional de Salud Guatemala), monthly sewage collections allowed screening enterovirus (EV) presence without incurring additional costs for sample collection, transport, or concentration. Murine recombinant fibroblast L-cells (L20B) and human rhabdomyosarcoma (RD) cells are used for the isolation of polioviruses following a standard detection algorithm. Though non-polio-Enteroviruses (NPEV) can be isolated, the algorithm is optimized for the detection of polioviruses. To explore if other EV’s are present in sewage not found through standard methods, five additional cell lines were piloted in a small-scale experiment, and next-generation sequencing (NGS) was used for the identification of any EV types. Human lung fibroblast cells (HLF) were selected based on their ability to isolate EV-A genus. Sewage concentrates collected between 2020–2021 were isolated in HLF cells and any cytopathic effect positive isolates used for NGS. A large variety of EVs, including echoviruses 1, 3, 6, 7, 11, 13, 18, 19, 25, 29; coxsackievirus A13, B2, and B5, EV-C99, EVB, and polioviruses (Sabin 1 and 3) were identified through genomic typing in NGS. When the EV genotypes were compared by phylogenetic analysis, it showed many EV’s were genomically like viruses previously isolated from ES collected in Haiti. Enterovirus occurrence did not follow a seasonality, but more diverse EV types were found in ES collection sites with lower populations. Using the additional cell line in the existing poliovirus ES algorithm may add value by providing data about EV circulation, without additional sample collection or processing. Next-generation sequencing closed gaps in knowledge providing molecular epidemiological information on multiple EV types and full genome sequences of EVs present in wastewater in Guatemala.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 96%

Molecular epidemiology of enteroviruses from Guatemalan wastewater isolated from human lung fibroblasts

Sayyad,

Harrington,

Castro

et al. 2024

PLoS ONE

Self Cite

View full text Add to dashboard Cite

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“…Furthermore, it has also been shown 45, 46, 47 that samples considered negative for EVs because no isolate could be recovered on RD cell line, have an abundance of EV-Cs. Hence, studies showing an overabundance of EV-Bs 47, 48, 49, 50 in any population but in which EV isolation was based on RD cell line should be interpreted with caution as it might only be reflective of RD cell line bias for EVBs and not necessarily representative of EV diversity in such populations. How much cell culture bias has influenced the perception that EV-Bs are the most abundant EV type in the USA 39, 40, 41 remains to be determined.…”

Section: Discussionmentioning

confidence: 99%

Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology

Faleye

Skidmore

Elyaderani

et al. 2022

Preprint

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The use of wastewater-based epidemiology (WBE) for early detection of virus circulation and response during the SARS-CoV-2 pandemic increased interest in and use of virus concentration protocols that are quick, scalable, and efficient. One such protocol involves sample clarification by size fractionation using either low-speed centrifugation to produce a clarified supernatant or membrane filtration to produce an initial filtrate depleted of solids, eukaryotes and bacterial present in wastewater (WW), followed by concentration of virus particles by ultrafiltration of the above. While this approach has been successful in identifying viruses from WW, it assumes that majority of the viruses of interest should be present in the fraction obtained by ultrafiltration of the initial filtrate, with negligible loss of viral particles and viral diversity. We used WW samples collected in a population of ~700,000 in southwest USA between October 2019 and March 2021, targeting three non-enveloped viruses (enteroviruses [EV], canine picornaviruses [CanPV], and human adenovirus 41 [Ad41]), to evaluate whether size fractionation of WW prior to ultrafiltration leads to appreciable differences in the virus presence and diversity determined. We showed that virus presence or absence in WW samples in both portions (filter trapped solids [FTS] and filtrate) are not consistent with each other. We also found that in cases where virus was detected in both fractions, virus diversity (or types) captured either in FTS or filtrate were not consistent with each other. Hence, preferring one fraction of WW over the other can undermine the capacity of WBE to function as an early warning system and negatively impact the accurate representation of virus presence and diversity in a population.

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Genome Sequences of 16 Enterovirus Isolates from Environmental Sewage in Guatemala, 2019 to 2021

Abstract: Enteroviruses can cause human infectious disease. We report 16 near-complete genome sequences of enteroviruses that were isolated through environmental surveillance of wastewater in Guatemala.

Cited by 2 publications

References 15 publications

Molecular epidemiology of enteroviruses from Guatemalan wastewater isolated from human lung fibroblasts

Molecular epidemiology of enteroviruses from Guatemalan wastewater isolated from human lung fibroblasts

Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology

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