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. 2017 Jun 15:2:41.
doi: 10.12688/wellcomeopenres.11558.2. eCollection 2017.

Enterovirus D68 in Viet Nam (2009-2015)

Nguyen Thi Han Ny  1   2 , Nguyen To Anh  1 , Vu Thi Ty Hang  1 , Lam Anh Nguyet  1 , Tran Tan Thanh  1 , Do Quang Ha  1 , Ngo Ngoc Quang Minh  3 , Do Lien Anh Ha  4 , Angela McBride  1 , Ha Manh Tuan  5 , Stephen Baker  1   6 , Pham Thi Thanh Tam  1 , Tran My Phuc  1 , Dang Thao Huong  1 , Tran Quoc Loi  7 , Nguyen Tran Anh Vu  7 , Nguyen Van Hung  8 , Tran Thi Thuy Minh  8 , Nguyen Van Xang  9 , Nguyen Dong  9 , Ho Dang Trung Nghia  1   10 , Nguyen Van Vinh Chau  11 , Guy Thwaites  1   6 , H Rogier van Doorn  1   6 , Catherine Anscombe  1 , Tan Le Van  1 ; VIZIONS Consortium
Affiliations

Enterovirus D68 in Viet Nam (2009-2015)

Nguyen Thi Han Ny et al. Wellcome Open Res. .

Abstract

Background: Since 1962, enterovirus D68 (EV-D68) has been implicated in multiple outbreaks and sporadic cases of respiratory infection worldwide, but especially in the USA and Europe with an increasing frequency between 2010 and 2014. We describe the detection, associated clinical features and molecular characterization of EV-D68 in central and southern Viet Nam between 2009 and 2015.

Methods: Enterovirus/rhinovirus PCR positive respiratory or CSF samples taken from children and adults with respiratory/central nervous system infections in Viet Nam were tested by an EV-D68 specific PCR. The included samples were derived from 3 different observational studies conducted at referral hospitals across central and southern Viet Nam between 2009 and 2015. Whole-genome sequencing was carried out using a MiSeq based approach. Phylogenetic reconstruction and estimation of evolutionary rate and recombination were carried out in BEAST and Recombination Detection Program, respectively.

Results: EV-D68 was detected in 21/625 (3.4%) enterovirus/rhinovirus PCR positive respiratory samples but in none of the 15 CSF. All the EV-D68 patients were young children (age range: 11.8 - 24.5 months) and had moderate respiratory infections. Phylogenetic analysis suggested that the Vietnamese sequences clustered with those from Asian countries, of which 9 fell in the B1 clade, and the remaining sequence was identified within the A2 clade. One intra sub-clade recombination event was detected, representing the second reported recombination within EV-D68. The evolutionary rate of EV-D68 was estimated to be 5.12E -3 substitutions/site/year. Phylogenetic analysis indicated that the virus was imported into Viet Nam in 2008.

Conclusions: We have demonstrated for the first time EV-D68 has been circulating at low levels in Viet Nam since 2008, associated with moderate acute respiratory infection in children. EV-D68 in Viet Nam is most closely related to Asian viruses, and clusters separately from recent US and European viruses that were suggested to be associated with acute flaccid paralysis.

Keywords: Enterovirus D68; VIZIONS; Vietnam; next generation sequencing; respiratory infections.

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Conflict of interest statement

Competing interests: No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Recombination analysis of EVD68-VN9.
( A) Similarity plot analysis of EVD68-VN5 against the two heterogenic parents, EVD68-VN3 (blue) and EVD68-VN7 (purple). The x-axis indicates the number of nucleotides along the alignment, the y-axis indicates percentage similarity. ( B) Bootscan plot analysis supporting for the recombination event of EVD68-VN5 detected by similarity plot analysis in ( A). The y-axis indicates the percentage of bootstrap values. ( C) Phylogenetic analyses of nonrecombinant fragments of representatives of clade B1; the putative recombinant strain is in red.
Figure 2.
Figure 2.. MCC tree from Bayesian timescale phylogenetic analysis based on complete VP1 nucleotide sequence (927nt) of EV-D68 including Vietnamese strains obtained from this study (dark blue) and global representatives retrieved from GenBank.
Figure 3.
Figure 3.. MCC tree from Bayesian timescale phylogenetic analysis based on complete genomes of EV-D68 including Vietnamese strains obtained from this study (dark blue) and global representatives retrieved from GenBank.
See this image and copyright information in PMC

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