Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, Institute of Nutrition and Food Safety, Campus Torribera, University of Barcelona, Barcelona, Spain.
Liver Unit, Internal Medicine Hospital Vall d'Hebron, Autonomous University of Barcelona, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain; Roche Diagnostics, S.L., Sant Cugat del Vallés, Barcelona, Spain.
EBioMedicine. 2019 Jan;39:348-357. doi: 10.1016/j.ebiom.2018.11.023. Epub 2018 Nov 22.
A huge outbreak in the men-having-sex-with-men (MSM) has hit Europe during the years 2016-2018. Outbreak control has been hampered by vaccine shortages in many countries, and to minimize their impact, reduction of antigen doses has been implemented. However, these measures may have consequences on the evolution of hepatitis A virus (HAV), leading to the emergence of antigenic variants. Cases in vaccinated MSM patients have been detected in Barcelona, opening the possibility to study HAV evolution under immune pressure.
We performed deep-sequencing analysis of ten overlapping fragments covering the complete capsid coding region of HAV. A total of 14578255 reads were obtained and used for the analysis of virus evolution in vaccinated versus non-vaccinated patients. We estimated maximum and minimum mutation frequencies, and Shannon entropy in the quasispecies of each patient. Non-synonymous (NSyn) mutations affecting residues exposed in the capsid surface were located, with respect to epitopes, using the recently described crystal structure of HAV, as an indication of its potential role in escaping to the effect of vaccines.
HAV evolution at the quasispecies level, in non-vaccinated and vaccinated patients, revealed higher diversity in epitope-coding regions of the vaccinated group. Although amino acid replacements occurring in and around the epitopes were observed in both groups, their abundance was significantly higher in the quasispecies of vaccinated patients, indicating ongoing processes of fixation.
Our data suggest positive selection of antigenic variants in some vaccinated patients, raising concerns for new vaccination polices directed to the MSM group.
2016 年至 2018 年期间，男男性行为人群（MSM）在欧洲爆发了一场大规模疫情。许多国家疫苗短缺，这对疫情控制造成了阻碍，为了将其影响降到最低，已经减少了抗原剂量。然而，这些措施可能会对甲型肝炎病毒（HAV）的演变产生影响，导致抗原变异体的出现。在巴塞罗那已经检测到接种疫苗的 MSM 患者病例，这为在免疫压力下研究 HAV 进化开辟了可能性。
我们对 HAV 完整衣壳编码区的十个重叠片段进行了深度测序分析。共获得 14578255 条reads，并用于分析接种疫苗和未接种疫苗患者的病毒进化。我们估计了每个患者准种中最大和最小突变频率以及香农熵。根据最近描述的 HAV 晶体结构，定位了影响衣壳表面暴露残基的非同义（NSyn）突变，这表明其可能在逃避疫苗作用方面具有潜在作用。
在未接种疫苗和接种疫苗的患者中，HAV 在准种水平上的进化显示，接种组的表位编码区多样性更高。尽管在两组中都观察到了发生在表位内和周围的氨基酸替换，但在接种患者的准种中，它们的丰度明显更高，表明正在进行固定过程。
我们的数据表明，一些接种疫苗的患者中出现了抗原变异的正选择，这引发了对新的针对 MSM 群体的疫苗接种政策的关注。
