Coxsackievirus group A (CV-A) strains are important pathogens of hand, foot, and mouth disease and herpangina. We report here the near-complete genome sequences of 12 CV-A strains isolated from infants and children with different clinical diseases.
ABSTRACT
Coxsackievirus group A (CV-A) strains are important pathogens of hand, foot, and mouth disease and herpangina. We report here the near-complete genome sequences of 12 CV-A strains isolated from infants and children with different clinical diseases. The presented data will be very useful for future genome-based epidemiological studies.
ANNOUNCEMENT
Coxsackievirus group A (CV-A) strains belong to the genus Enterovirus in the family Picornaviridae (http://www.picornaviridae.com/enterovirus/enterovirus.htm). Enteroviruses (EVs) are a group of naked positive single-stranded RNA viruses, and their genome comprises a 5′ untranslated region (UTR), four capsid proteins (VP1 to VP4), seven nonstructural proteins (2A to 2C and 3A to 3D), and a 3′ UTR (1). EVs are associated with various human diseases, such as hand, foot, and mouth disease (HFMD), herpangina (HA), encephalitis, myelitis, upper and lower respiratory diseases, conjunctivitis, and gastroenteritis (2). Coxsackievirus A2 (CV-A2), CV-A6, CV-A10, and CV-A16 strains were frequently associated with HFMD and HA outbreaks and sporadic infections worldwide over the years (3–7).
In recent years, emerging CV-A2, CV-A6, and CV-A10 strains were frequently detected in HFMD and HA patients in Shenzhen, China. In order to investigate the genetic characteristics of these strains, a total of 12 CV-A strains associated with different clinical diseases, collected between 2012 and 2015, were selected for amplification of the genome sequences. Detailed epidemiological data for these strains (listed in Table 1) demonstrate that CV-A strains display considerable phenotypic variation. Viral RNA was extracted directly from fecal samples or anal swab specimens using a High Pure viral RNA kit (Roche). These strains were typed by real-time reverse transcription (RT)-PCR and seminested RT-PCR (8). Then, a pair of universal primers, EVA-F30 (5′-TTAAAACAGCCTGTGGGTTGTACCCACCCA-3′) and EVA-R36 (5′-GCTATTCTGGTTATAACAAATTTACCCCCACCAGTC-3′), targeting the 5′ UTR and 3′ UTR of the enterovirus A strains, respectively, were used to amplify near-complete genomes of these strains by a one-step RT-PCR method, as described previously (9). The genome sequence of each strain was amplified independently, and a DNA product of ∼7,400 bp was determined using a primer-walking method (TaKaRa, Dalian, China) (10). Contigs of ∼800 bp sequenced by the Sanger method were assembled into a genome sequence using the program Sequencher version 4.9.
TABLE 1.
Epidemiological data and genome sequence information for 12 coxsackievirus group A strains from this study
| Isolate | Sex | Age (mo) | Clinical manifestations | GenBank accession no. | Length in nt (% GC content)a | Closest strain (% nt identity) |
|---|---|---|---|---|---|---|
| CVA2/Shenzhen50/CHN/2012 | Male | 36 | Fever, herpangina, lethargy, tachypnea | KX595281 | 7,400 (48.9) | CVA2/Shenzhen133/CHN/2013 (98.8) |
| CVA2/Shenzhen133/CHN/2013 | Female | 10 | Fever, vesicles on mouth, herpangina | KX595282 | 7,400 (48.8) | CVA2/Shenzhen50/CHN/2012 (98.8) |
| CVA2/Shenzhen143/CHN/2013 | Male | 8 | Fever, vesicles on mouth, herpangina, coughing, rhinorrhea, pharyngalgia | KX595283 | 7,400 (48.8) | 431306 (98.7) |
| CVA2/Shenzhen21/CHN/2015 | Male | 15 | Fever, rash, vesicles on hand, foot, and mouth, myoclonic jerk | KX595284 | 7,312 (49.1) | BJ13-53/BJ/CHN/2013 (97.7) |
| CVA6/Shenzhen87/CHN/2014 | Male | 9 | Vesicles on hand, mouth, elbow, and knees, pharyngalgia | KX595285 | 7,434 (47.0) | SHAPHC5298/SH/CHN/14 (98.7) |
| CVA6/Shenzhen94/CHN/2014 | Male | 13 | Fever, rash, vesicles on hand, foot, mouth, elbow, knees, and buttock | KX595286 | 7,434 (47.1) | Hyogo9205 (97.2) |
| CVA6/sHFMD14/Shenzhen/2015 | Male | 27 | Fever, rash, vesicles on hand, foot, mouth, elbow, knees, and buttock, pharyngalgia, herpangina, tachypnea, aseptic encephalitis | MH716144 | 7,434 (47.4) | Weifang/SD/CHN/2014 (98.0) |
| CVA10/Shenzhen152/CHN/2013 | Male | 4 | Fever, rash, vesicles on hand, foot, and mouth | KX595287 | 7,411 (47.7) | FY05/AH/CHN/2013 (97.0) |
| CVA10/Shenzhen18/CHN/2014 | Male | 16 | Fever, rash, vesicles on hand, foot, and mouth, pharyngalgia, limb shaking | KX595288 | 7,411 (47.5) | CV-A10/P911/2013/China (99.1) |
| CVA10/Shenzhen180/CHN/2014 | Female | 8 | Fever, vesicles on mouth, herpangina | KX595289 | 7,411 (47.9) | FY05/AH/CHN/2013 (97.7) |
| CVA10/Shenzhen10/CHN/2015 | Female | 13 | Fever, rash, vesicles on hand, foot, mouth, and buttock, myoclonic jerk | KX595290 | 7,411 (47.6) | CV-A10/P670/2013/China (98.1) |
| CVA16/Shenzhen179/CHN/2014 | Female | 24 | Fever, rash, vesicles on hand and foot | KX595295 | 7,409 (47.4) | YN10-02 (97.9) |
nt, nucleotide.
The genome length, GC content, and most closely related strain in GenBank of the 12 CV-A strains of this study are summarized in Table 1. The four CV-A2 strains of this study show 1.2% to 3.6% nucleotide (nt) differences across the entire genome and 0.6% to 1.1% amino acid (aa) differences across the entire polyprotein. A neighbor-joining phylogenetic tree constructed by using the program MEGA7.0.26 (11), based on the complete VP1 gene of the four CV-A2 strains of this study and CV-A2 reference strains retrieved from GenBank, indicated that the four CV-A2 strains of the study clustered to genogroup D according to the genotyping method proposed by Yang et al. (12). The three CV-A6 strains from this study show 3.5% to 7.4% nt differences and 0.9% to 1.7% aa differences from each other. Phylogenetic analysis based on the complete VP1 sequence showed that these three CV-A6 strains belong to subgenogroup D3 (13). The four CV-A10 strains of the study show 3.7% to 4.8% nt differences and 0.9% to 1.4% aa differences from each other. These four CV-A10 strains belong to subgenogroup C2 based on phylogenetic analysis of the VP1 gene (14). The CV-A16 strain CVA16/Shenzhen179/CHN/2014 was assigned to subgenotype B1b based on phylogenetic analysis of the VP1 gene (15).
Data availability.
The near-complete genome sequences of 12 coxsackievirus group A strains from the present study have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1.
ACKNOWLEDGMENTS
This research was supported by Longhua District Social Science Projects (201802), the Longhua District Science and Technology Innovation Project (2017024), the Sanming Project of Medicine in Shenzhen (SZSM201611064), and special funds for the surveillance of HFMD from the Shenzhen CDC.
The views and conclusions from this report are those of the authors and do not necessarily represent the official opinion of the Shenzhen CDC or Longhua CDC.
We are grateful to the pediatricians who are from the sentinel surveillance system for HFMD in Shenzhen, China.
We declare no conflicts of interest.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The near-complete genome sequences of 12 coxsackievirus group A strains from the present study have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1.