在巴西亚马逊地区贝伦市的儿童腹泻样本中检测到的小核糖核酸病毒的多样性（1982-2019 年）。

Diversity of picornaviruses detected in diarrheal samples from children in Belém, Brazilian Amazon (1982-2019).

机构信息

Programa de Pós-graduação em Biologia Parasitária na Amazônia, Universidade do Estado do Pará-UEPA, Belém, Pará, Brazil.

Laboratório de Bioinformática-BIOINFO, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil.

出版信息

J Med Virol. 2023 Jun;95(6):e28873. doi: 10.1002/jmv.28873.

DOI:10.1002/jmv.28873

PMID:37349989

Abstract

In this investigation, fecal specimens from children with diarrhea were collected from four community studies conducted between 1982 and 2019 in Belém, Brazilian Amazon. A total of 234 samples were tested by quantitative reverse transcription polymerase chain reaction (RT-qPCR) to detect infections by picornaviruses of the Enterovirus (EV), Parechovirus (HPeV), Cosavirus (HCoSV), Kobuvirus (Aichivirus - AiV) and Salivirus (SalV) genera. The positive samples were subjected to different amplification protocols of the VP1 region of the genome, such as nested PCR or snPCR, and were subsequently genotyped by sequencing VP1 and VP3 of the viral genome. Positivity was observed in 76.5% (179/234) of the samples tested using RT-qPCR for at least one virus, and co-infection was observed in 37.4% (67/179) of the cases. EV was detected in 50.8% (119/234), HPeV in 29.9% (70/234), HCoSV in 27.3% (64/234), and AiV/SalV in 2.1% (5/234) of the specimens tested by RT-qPCR. Using nested PCR and/or snPCR techniques, the positivity rates were 94.11% (112/119) for EV, 72.85% (51/70) for HPeV, and 20.31% (13/64) for HCoSV. It was not possible to amplify the samples that were positive for AiV/SalV. Sequencing revealed 67.2% (80/119) EV, 51.4% (36/70) HPeV, and 20.31% (13/64) HCoSV. Forty-five different types of EV were found among species A, B, and C; HCoSV identified five species, including a possible recombinant strain; all HPeV were identified as belonging to species A, in two samples a possible recombination involving three different strains was verified. This study demonstrated the high circulation and diversity of different types of picornaviruses in fecal samples, including those collected more than 30 years ago. This endorsed the evaluation of important points in the epidemiology of these viruses, such as the presence of co-infection and the possibility of knowing more about these agents, considering that some were recently described; therefore, their detection in older samples can provide more data about their ancestry.

摘要

在这项研究中，从 1982 年至 2019 年在巴西亚马逊州贝伦进行的四项社区研究中收集了腹泻儿童的粪便标本。共有 234 个样本通过定量逆转录聚合酶链反应 (RT-qPCR) 进行了检测，以检测肠道病毒 (EV)、小核糖核酸病毒 (HPeV)、柯萨病毒 (HCoSV)、嵌杯样病毒 (Aichivirus - AiV) 和唾液病毒 (SalV) 属的病毒感染。阳性样本通过基因组 VP1 区的不同扩增方案进行了检测，例如嵌套 PCR 或 snPCR，随后通过测序 VP1 和 VP3 对病毒基因组进行了基因分型。使用 RT-qPCR 对至少一种病毒进行检测，在 234 个测试样本中观察到 76.5%（179/234）的阳性，在 37.4%（67/179）的病例中观察到了合并感染。EV 在 50.8%（119/234）的样本中被检测到，HPeV 在 29.9%（70/234）的样本中被检测到，HCoSV 在 27.3%（64/234）的样本中被检测到，而 AiV/SalV 在 2.1%（5/234）的样本中被检测到。使用嵌套 PCR 和/或 snPCR 技术，EV 的阳性率为 94.11%（112/119），HPeV 的阳性率为 72.85%（51/70），HCoSV 的阳性率为 20.31%（13/64）。不可能扩增到 AiV/SalV 阳性的样本。测序显示，EV 为 67.2%（80/119），HPeV 为 51.4%（36/70），HCoSV 为 20.31%（13/64）。在 A、B 和 C 种中发现了 45 种不同类型的 EV；HCoSV 鉴定了 5 种，包括一种可能的重组株；所有 HPeV 均被鉴定为属于 A 种，在两个样本中，验证了涉及三种不同菌株的可能重组。这项研究表明，在粪便样本中存在多种不同类型的小核糖核酸病毒的高循环和多样性，包括 30 多年前采集的样本。这证实了对这些病毒流行病学的重要方面进行评估的必要性，例如合并感染的存在以及更多了解这些病毒的可能性，因为其中一些病毒是最近才被描述的；因此，在较老的样本中检测到这些病毒可以提供更多关于其起源的信息。