Recombination Analysis of Non-Poliovirus Members of the Enterovirus C Species: Restriction of Recombination Events to Members of the Same 3DPol Cluster

Q: What are the key findings of this study?

Non-polio Enterovirus C sequences exhibited 89 recombinant forms with recombination restricted within four 3DPol clusters and significant topology differences across VP1, 2C, and 3DPol.

Q: What is the clinical evidence from this study?

Population: Enterovirus C infection / genomic recombination (n=191). Intervention: Phylogenetic and segregation analysis across Enterovirus C genomic regions (VP1, 2C, 3DPol). Primary outcome: Recombination patterns, phylogenetic topology violations, and recombinant forms across VP1, 2C, and 3DPol genomic regions (p=<0.01).

Q: What does this research mean for the field?

Recombination in non-poliovirus Enterovirus C species is largely restricted to members of the same 3DPol phylogenetic cluster, likely constrained by anatomical compartmentalization and tissue tropism. Novelty: ClaimNovelty.INCREMENTAL. Consensus alignment: ConsensusAlignment.NEUTRAL.

Q: What question did this study set out to answer?

To investigate the frequency, patterns, and phylogenetic dynamics of recombination in non-poliovirus members of the species Enterovirus C.

Lieke Brouwer; Kimberley Benschop; Dung Nguyen; Everlyn Kamau; Dasja Pajkrt; Peter Simmonds; Katja C. Wolthers

doi:10.3390/v12070706

June 30, 2020VirusesOpen Access

Recombination Analysis of Non-Poliovirus Members of the Enterovirus C Species: Restriction of Recombination Events to Members of the Same 3DPol Cluster

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Key result

Non-polio Enterovirus C exhibits 89 recombinant forms with recombination restricted across specific genomic clusters.

P<0.01
n=191

Figures

Why the study?

Knowledge regarding recombination in non-polio enteroviruses within the species Enterovirus C is limited, despite frequent recombination in enteroviruses.

Key Points

To investigate the frequency, patterns, and phylogenetic dynamics of recombination in non-poliovirus members of the species Enterovirus C.
Analyzed a complete database of 191 Enterovirus C sequences, comprising 11 newly sequenced non-polio isolates and 180 sequences of more than 7000 base pairs extracted from GenBank.
Constructed maximum likelihood phylogenetic trees for VP1, 2C, and 3DPol genomic regions and compared topologies using the Shimodaira-Hasegawa test.
Conducted genome-wide segregation analysis and segregated sequences into four 3DPol clusters based on a pairwise p-distance threshold of 0.21.
Shimodaira-Hasegawa tests demonstrated that VP1, 2C, and 3DPol alignments were significantly better explained by their own topologies than those of other regions (p < 0.01), confirming frequent recombination.
Segregation dropped sharply at the boundaries of the P1 region and the beginning of the P3 region, identifying 89 distinct recombinant forms across four 3DPol clusters.
Recombination occurred readily between members of the same 3DPol cluster but was rarely detected between different clusters, corresponding to segregation between gastrointestinal and respiratory sample origins.

PICO

P

Population

191 non-polio Enterovirus C full-length genomic sequences (11 newly sequenced from stool samples and 180 from GenBank) analyzed for phylogenetic recombination patterns.

E

Exposure / Comparator

Phylogenetic and segregation analysis across Enterovirus C genomic regions (VP1, 2C, 3DPol)

O

Primary Outcome

Recombination patterns, phylogenetic topology violations, and recombinant forms across VP1, 2C, and 3DPol genomic regions, p=<0.01

Main Result

p-value: p=<0.01

Limitations

Limited amount of full-length Enterovirus C sequences available, as typing is usually performed using only partial VP1 sequences.
Available data may be biased towards specific types, geographical locations, and time points originating from laboratories that conduct full-length sequencing.

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Implication

Supports expanded enterovirus C surveillance; hypothesis-generating for recombination dynamics in human isolates.

Abstract

Enteroviruses (EVs) are highly prevalent viruses worldwide. Recombination is known to occur frequently in EVs belonging to species Enterovirus A, Enterovirus B, and Enterovirus C. Although many recombinant vaccine-derived poliovirus (VDPV) strains have been reported, our knowledge on recombination in non-polio EVs in the species Enterovirus C is limited. Here, we combined a dataset consisting of 11 newly generated full-length Enterovirus C sequences and 180 publicly available sequences to study recombination dynamics in non-polio EVs. To identify recombination patterns, maximum likelihood phylogenetic trees of different genomic regions were constructed, and segregation analyses were performed. Recombination was observed between members of the same 3DPol cluster, but was rarely observed between members of different clusters. We hypothesize that this restriction may have arisen through their different compartmentalization in respiratory and enteric tracts related to differences in cellular tropisms so that the opportunity to recombine may not be available.

Discussion

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Cite This Study

Brouwer et al. (2020) studied Enterovirus C infection / genomic recombination (n=191). Phylogenetic and segregation analysis across Enterovirus C genomic regions (VP1, 2C, 3DPol) was evaluated on Recombination patterns, phylogenetic topology violations, and recombinant forms across VP1, 2C, and 3DPol genomic regions (p=<0.01). Non-polio Enterovirus C sequences exhibited 89 recombinant forms with recombination restricted within four 3DPol clusters and significant topology differences across VP1, 2C, and 3DPol.

synapsesocial.com/papers/6a7da62010b6f5f3737d8840 https://doi.org/10.3390/v12070706

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Recombination Analysis of Non-Poliovirus Members of the Enterovirus C Species: Restriction of Recombination Events to Members of the Same 3DPol Cluster

Figures

Key Points

PICO

Main Result

Limitations

Ask about this paper

Implication

Abstract

Discussion

Cite This Study

Recombination Analysis of Non-Poliovirus Members of the Enterovirus C Species: Restriction of Recombination Events to Members of the Same 3DPol Cluster

Figures

Key Points

PICO

Main Result

Limitations

Ask about this paper

Implication

Abstract

Discussion

Cite This Study

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