Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts.

Coxsackievirus A16 (CVA16) is a major pathogen that causes hand, foot, and mouth disease (HFMD). The recombination form (RF) shifts and global transmission dynamics of CVA16 remain unknown. In this retrospective study, global sequences of CVA16 were retrieved from the GenBank database and analyzed using comprehensive phylogenetic inference, RF surveys, and population structure. A total of 1,663 sequences were collected, forming a 442-sequences dataset for VP1 coding region analysis and a 345-sequences dataset for RF identification. Based on the VP1 coding region used for serotyping, three genotypes (A, B, and D), two subgenotypes of genotype B (B1 and B2), and three clusters of subgenotype B1 (B1a, B1b, and B1c) were identified. Cluster B1b has dominated the global epidemics, B2 disappeared in 2000, and D is an emerging genotype dating back to August 2002. Globally, four oscillation phases of CVA16 evolution, with a peak in 2013, and three migration pathways were identified. Europe, China, and Japan have served as the seeds for the global transmission of CVA16. Based on the 3D coding region of the RFs, five clusters of RFs (RF-A to -E) were identified. The shift in RFs from RF-B and RF-C to RF-D was accompanied by a change in genotype from B2 to B1a and B1c and then to B1b. In conclusion, the evolution and population dynamics of CVA16, especially the coevolution of 3D and VP1 genes, revealed that genotype evolution and RF replacement were synergistic rather than stochastic.

Consolidation treatment needed for sustained HBsAg-negative response induced by interferon-alpha in HBeAg positive chronic hepatitis B patients.

Hepatitis B surface antigen (HBsAg) clearance is considered as functional cure in patients with chronic hepatitis B (CHB). This study aimed to assess the durability of HBsAg clearance achieved by interferon-based therapies in patients with CHB who were originally positive for hepatitis B envelope antigen (HBeAg). In this prospective study, HBeAg-positive CHB patients with confirmed HBsAg loss under interferon-based therapies were enrolled within 12 weeks from end of treatment and followed up for 48 weeks. Virological markers, biochemical indicators, and liver imaging examinations were observed every 3-6 months. Sustained functional cure was analysed as primary outcome. Factor associated with sustained HBsAg loss or reversion was also investigated. The rate of HBsAg loss sustainability was 91.8% (212/231). Patients receiving consolidation treatment for 12-24 weeks or ≥ 24 weeks had higher rates of sustained HBsAg negativity than those receiving consolidation treatment for < 12 weeks (98.3% and 91.2% vs. 86.7%, P â€‹= â€‹0.068), and the former groups had significantly higher anti-HBs levels than the later (P â€‹< â€‹0.05). The cumulative incidence of HBsAg reversion and HBV DNA reversion was 8.2% and 3.9%, respectively. Consolidation treatment of ≥ 12 weeks [odd ratio (OR) 3.318, 95% confidence interval (CI) 1.077-10.224, P â€‹= â€‹0.037) was a predictor of sustained functional cure, and HBeAg-positivity at cessation of treatment (OR 12.271, 95% CI 1.076-139.919, P â€‹= â€‹0.043) was a predictor of HBsAg reversion. Interferon-alpha induced functional cure was durable and a consolidation treatment of ≥ 12-24 weeks was needed after HBsAg loss in HBeAg-positive CHB patients.

Comparing Enterovirus 71 with Coxsackievirus A16 by analyzing nucleotide sequences and antigenicity of recombinant proteins of VP1s and VP4s.

BACKGROUND: Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) are two major etiological agents of Hand, Foot and Mouth Disease (HFMD). EV71 is associated with severe cases but not CA16. The mechanisms contributed to the different pathogenesis of these two viruses are unknown. VP1 and VP4 are two major structural proteins of these viruses, and should be paid close attention to. RESULTS: The sequences of vp1s from 14 EV71 and 14 CA16, and vp4s from 10 EV71 and 1 CA16 isolated in this study during 2007 to 2009 HFMD seasons were analyzed together with the corresponding sequences available in GenBank using DNAStar and MEGA 4.0. Phylogenetic analysis of complete vp1s or vp4s showed that EV71 isolated in Beijing belonged to C4 and CA16 belonged to lineage B2 (lineage C). VP1s and VP4s from 4 strains of viruses expressed in E. coli BL21 cells were used to detect IgM and IgG in human sera by Western Blot. The detection of IgM against VP1s of EV71 and CA16 showed consistent results with current infection, while none of the sera were positive against VP4s of EV71 and CA16. There was significant difference in the positive rates between EV71 VP1 and CA16 VP1 (χ(2) = 5.02, P < 0.05) as well as EV71 VP4 and CA16 VP4 (χ(2) = 15.30, P < 0.01) in the detection of IgG against recombinant proteins with same batch of serum samples. The sera-positive rate of IgG against VP1 was higher than that against VP4 for both EV71 (χ(2) = 26.47, P < 0.01) and CA16 (χ(2) = 16.78, P < 0.01), which might be because of different positions of VP1 and VP4 in the capsid of the viruses. CONCLUSIONS: EV71 and CA16 were highly diverse in the nucleotide sequences of vp1s and vp4s. The sera positive rates of VP1 and VP4 of EV71 were lower than those of CA16 respectively, which suggested a less exposure rate to EV71 than CA16 in Beijing population. Human serum antibodies detected by Western blot using VP1s and VP4s as antigen indicated that the immunological reaction to VP1 and VP4 of both EV71 and CA16 was different.

Early Serum HBsAg Kinetics as Predictor of HBsAg Loss in Patients with HBeAg-Negative Chronic Hepatitis B after Treatment with Pegylated Interferonα-2a.

Hepatitis B surface antigen (HBsAg) loss is an ideal treatment endpoint for patients with chronic hepatitis B (CHB). We investigated the predictive value of on-treatment HBsAg levels for HBsAg loss in hepatitis B e antigen (HBeAg)-negative CHB patients who received 120-week PEG-IFNα-2a treatment. Serum HBV DNA, HBsAg, and anti-HBs levels were assayed at baseline and every 3 months during the treatment. Of 81 patients, 12 achieved HBsAg loss, 20 achieved HBsAg < 100 IU/mL, and 49 maintained HBsAg ≥ 100 IU/mL. HBsAg loss rate was only 3.7% at 48 weeks, while it reached to 11.1% and 14.8% after treatment of 96 weeks and 120 weeks. The cutoff HBsAg levels at 12 weeks predicting HBsAg loss at 96 weeks and 120 weeks of treatment were 400 IU/mL and 750 IU/mL, with AUC 0.725 and 0.722, positive predictive value (PPV) 29.41% and 30.56%, and negative predictive value (NPV) 93.75% and 97.78%, respectively. The cutoff HBsAg levels at 24 weeks predicting HBsAg loss at 96 weeks and 120 weeks of treatment were 174 IU/mL and 236 IU/mL respectively, with AUC 0.925 and 0.922, PPV 40.0% and 46.15%, and both NPV 100%. The predictive ability of the cutoff HBsAg levels at 24 weeks was better than that at 12 weeks for HBsAg loss at either 96 or 120 weeks (χ2 = 3.880, P = 0.049 and χ2 = 4.412, P = 0.036). These results indicate that extended therapy is critical to HBsAg loss in HBeAg-negative CHB patients during PEG-IFN treatment, and the HBsAg level at 24 weeks can be used to predict HBsAg loss during tailoring PEG-IFN therapy.

Molecular epidemiology of coxsackievirus A16 circulating in children in Beijing, China from 2010 to 2019.

BACKGROUND: Coxsackievirus A16 (CVA16) is one of the major etiological agents of hand, foot and mouth disease (HFMD). This study aimed to investigate the molecular epidemiology and evolutionary characteristics of CVA16. METHODS: Throat swabs were collected from children with HFMD and suspected HFMD during 2010-2019. Enteroviruses (EVs) were detected and typed by real-time reverse transcription-polymerase chain reaction (RT-PCR) and RT-PCR. The genotype, evolutionary rate, the most recent common ancestor, population dynamics and selection pressure of CVA16 were analyzed based on viral protein gene (VP1) by bioinformatics software. RESULTS: A total of 4709 throat swabs were screened. EVs were detected in 3180 samples and 814 were CVA16 positive. More than 81% of CVA16-positive children were under 5 years old. The prevalence of CVA16 showed obvious periodic fluctuations with a high level during 2010-2012 followed by an apparent decline during 2013-2017. However, the activities of CVA16 increased gradually during 2018-2019. All the Beijing CVA16 strains belonged to sub-genotype B1, and B1b was the dominant strain. One B1c strain was detected in Beijing for the first time in 2016. The estimated mean evolutionary rate of VP1 gene was 4.49 × 10-3 substitution/site/year. Methionine gradually fixed at site-23 of VP1 since 2012. Two sites were detected under episodic positive selection, one of which (site-223) located in neutralizing linear epitope PEP71. CONCLUSIONS: The dominant strains of CVA16 belonged to clade B1b and evolved in a fast evolutionary rate during 2010-2019 in Beijing. To provide more favorable data for HFMD prevention and control, it is necessary to keep attention on molecular epidemiological and evolutionary characteristics of CVA16.

Sub-genotype change and recombination of coxsackievirus A6s may be the cause of it being the predominant pathogen for HFMD in children in Beijing, as revealed by analysis of complete genome sequences.

OBJECTIVES: To investigate why coxsackievirus A6 (CVA6) has replaced enterovirus A71 (EV71) and coxsackievirus A16 (CVA16), which used to be the most predominant etiological agents, for hand, foot and mouth disease (HFMD) in children in Beijing, China. METHODS: Sixty-four CVA6-positive samples were identified from 2010 to 2016 and selected for whole genome sequence amplification and analysis. RESULTS: It was demonstrated that the whole genome sequences of CVA6s in this study were 7432-7435 nucleotides in length, and the different lengths were only in the 5'UTR region. The phylogenetic tree analysis of the full-length VP1 region of CVA6s indicated that the prevalent CVA6s in Beijing changed from the previous D2 sub-genotype to the D3 sub-genotype in 2013. In this study, two recombinant forms (RFs)- RF-C and RF-D - of CVA6 mainly appeared in 2010 and 2011. Since 2013, three recombinant CVA6 variants - RF-A, J and L - have been prevalent in children with HFMD in Beijing. The recombination region of RF-J was located at the 2C region, while RF-L had a new recombination point in the 3D region. The recombination of prevalent CVA6s in Beijing from 2013 to 2016 occurred within non-capsid regions of the genome, especially the P2 and P3 regions. CONCLUSIONS: The sub-genotype change and recombination of CVA6s indicated from this study may explain why CVA6 has become the predominant pathogen causing HFMD since 2013.

[Analysis on the change of genotype of enteroviruses associated hand, foot and mouth disease in Beijing during 2013 to 2014].

OBJECTIVE: To analyze the genotype, epidemic pattern and the characteristics of the disease of enteroviruses during the epidemic season of hand, foot and mouth disease (HMFD) in children from 2013 to 2014 in Beijing to provide the scientific evidence for prevention and treatment of HFMD. METHOD: During April to September in 2013 and March to October in 2014, a total of 977 throat swabs were collected from children who visited the Children's Hospital Affiliated to Capital Institute of Pediatrics, including 147 from patients with HFMD in 2013, 343 with HFMD, 201 with atypical HFMD, 83 with herpangina, 25 with fever with convulsions, 64 fever with rash and 114 with rash in 2014. Enteroviruses universal type (EV), Enteroviruses type 71 (EV71) and Coxsackievirus group A 16 (CA16) were detected by real-time RT-PCR respectively. The nucleic acid of specimens which were identified with non-EV71, non-CA16 was tested by nested PCR and analyzed by VP1 sequencing. The detection rate and epidemic pattern of different genotypes of enterovirus were analyzed among different age groups and between 2013 and 2014. RESULT: Of 977 throat swabs, 80. 1% samples were detected positive for enteroviruses. The positive rates of CA16, EV71, CA6, CA10, CA4 and other EVs were 25. 6% (250/977), 18. 9% (185/977), 20. 0% (195/977), 5. 0% (49/977), 1.5% (15/977) and 9.1% (89/977), respectively. Twenty six of the 89 other EVs included CA2, CA5, CA8, CA9, CA12, CA14, CB2, CB5, E6, E9 and E25, each genotype of which was no more than 3. The nucleotide homologies shared among CA6, CA10 and CA4 strains between 2013 and 2014 were 94. 3% - 100%, 93. 8% - 99. 1% and 92.7% - 99. 8%, respectively. The positive rates of ≤1 year group were 71. 1% (106/149), which was lower than that of other age groups (all P <0. 05), but similar to that of >5 year group (χ2 =1. 181,P = 0. 277). In 2013, the positive rate of EV was 85. 7% (126/147) and the predominant genotype was CA6 54. 8% (69/126), followed by CA16 20. 6% (26/126) and EV71 11. 9% (15/126). In 2014, the positive rate of EV was 85. 4% (293/343) in the 343 children with HFMD, the predominant genotypes were CA16 with the positive rate of 42. 7% (125/293), EV71 with 38. 2% (112/293) and CA6 with only 11. 3% (33/293). In 2014, the positive rates of EV in 201 atypical HFMD, 83 herpangina, 25 fever with convulsions, 64 fever with rash and 114 rash were 83. 6% (168/201), 80. 7% (67/83), 76. 0% (19/25), 64. 1% (41/64) and 60. 5% (69/114), respectively. All genotypes of enteroviruses peaked mainly during May to August every year, but there were no obvious epidemiological pattern about each genotype. CONCLUSION: CA6 became the main causative agent of HFMD in 2013, however, CA16 and EV71 predominated again in 2014 in Beijing. The clinical manifestations caused by CA6, CA10, CA4 and other genotype of enteroviruses differed from EV71 and CA16. Besides EV71 and CA16, more attention should be paid to CA6, CA10, CA4 and other type of enteroviruses.

[Sequence and antigenicity analysis for VP4s of EV71 strains isolated from Children in Beijing].

In order to learn about the correlation between the sequences of VP4 of EV71 and clinical symptoms of patients and analyze the antigenicity of VP4 of EV71, as well as the cross-reactivity with VP4 of CA16, the sequences of VP4 gene from 10 EV71 strains isolated from infants and children with hand, foot and mouth diseases (HFMD) during 2007 to 2009 were determined through standard molecular cloning protocols, and the results were analyzed by EditSeq and MegAlign of DNAStar. Full-length genes of VP4s of EV71 and CA16 were amplified from virus isolates and expressed in E. coli. Then the expressed VP4s were used as antigens to detect IgG antibody in 189 sera samples from people taking health check up and patients of non-HFMD by Western-Blot. They were also used to detect IgM antibody in 14 of sera samples from infants and children with EV71 infection and 12 of sera samples from those with CA16 infection. The nucleotides identities among these 10 sequences of VP4s isolated in our lab were 94.20% - 100.00% and the deduced amino acids were identical. There was no consistent divergence between the sequences of serious cases and those from general HFMD cases. Phylogenetic analysis based on VP4s indicated that these 10 VP4s of EV71 belonged to C4. The nucleotide identities between EV71 VP4 (s67) and CA16 VP4 (s401) was 69.60% and the deduced amino acids identities was 78.60%. In the detection of IgG, the sera-positive rate for EV71 VP4 was 38.10% and the sera-positive rate of CA16 VP4 was 58.20%. The difference in the sera-positive rate between them was significant (chi2 = 15.30, P < 0.01), suggesting that the expressed VP4s of EV71 and CA16 were of good antigenicity and not cross-reactive. There was no positive reaction detected for IgM against VP4s for EV71 or CA16. The data from this study reveal important information for the further study of EV71.

[Study on the association of hand, foot and mouth disease and enterovirus 71/CA16 among children in Beijing, 2007].

OBJECTIVE: To reveal the etiological agent of hand, foot and mouth disease in children in Beijing. METHODS: Throat swabs were collected from 6 infants and young children with hand, foot and mouth disease who visited the affiliated Children's Hospital from May to June 2007. Aspirated fluid from tracheal intubatton, serum and cerebral spinal fluid (CSF) were collected from a 9 years old girl (No.4243) having central neural system complication of severe hand, foot and mouth disease and admitted to the hospital from the Emergency Department. Throat swab and aspirated fluid were inoculated into the cell lines Hep-2, MDCK and Vero for virus isolation. RNAs were extracted by Trizol from 6 throat swab specimens and aspirated fluid, serum while CSF was from that severe case (No.4243). The gene fragment from 5' UTR of enterovirus was amplified from throat swabs and aspirated fluid by reverse transcription-polymerase chain reaction (RT-PCR) with the primer pairs located at the untranslated region of all enterovirus. EV71 was identified by RT-PCR with the 2 and half primer pairs located at different parts of VP1 gene of EV71. The PCR products for VP1 encoding gene of EV71 from the specimens were sequenced and sequence analysis was performed by comparing those published VP1 genes of EV71. EV71 and CA16 specific primers were used to identify the isolates by RT-PCR and the sequences were directly determined from PCR products. RESULTS: Gene fragments with expected molecular weight were amplified from all 6 throat swabs and the aspirate by the primer pairs universal for the 5' UTR of enterovirus, suggesting that these patients with hand, foot and mouth disease were infected by entorovirus. Out of these 7 specimens, 2 throat swabs and the aspirate were also showing positive for the VP1 of the EV71 by different primer sets. Sequence analysis revealed that the sequences for the amplicons from 1 throat swab (No. F4211) and the aspirate shared highest homology with those published EV71, indicating that these specimens were truly positive for EV71. The sequences amplified from these specimens shared 100% and 98.9% homology to each other and were closer to the sequences of EV71 identified from Zhejiang province than those from Taiwan and strain BrCr. Gene fragments for 5' UTR of enterovirus were obtained by RT-PCR after CPE appeared in 6 out of 7 inoculations including that aspirate fluid in Vero cell, indicating that enteroviruses were isolated from these specimens. Virus isolates from one throat swab (No. F4211) and the aspirate (No. 4243) were positive by RT-PCR with the primer pairs for EV71, which was consistent with RT-PCR amplification directly from specimens. Virus isolates from other 4 specimens were CA16 by RT-PCR and sequence analysis. CONCLUSION: These data suggested that hand, foot and mouth disease recently appeared in children in Beijing was related with EV71 and CA16. EV71 could cause severe clinical manifestations with central nerve system complications even in the child older than 5 years.