重组GII.P16基因型对基于逆转录聚合酶链反应的诺如病毒基因组A区分型提出挑战。

Recombinant GII.P16 genotype challenges RT-PCR-based typing in region A of norovirus genome.

作者信息

Bonura Floriana, Urone Noemi, Bonura Celestino, Mangiaracina Leonardo, Filizzolo Chiara, Sciortino Giuseppa, Sanfilippo Giuseppa L, Martella Vito, Giammanco Giovanni M, De Grazia Simona

机构信息

Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Via del Vespro 133, Palermo I-90127, Italy.

Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy.

出版信息

J Infect. 2021 Jul;83(1):69-75. doi: 10.1016/j.jinf.2021.04.015. Epub 2021 Apr 20.

DOI:10.1016/j.jinf.2021.04.015

PMID:33887286

Abstract

OBJECTIVES

In latest years GII.4[P16] and GII.2[P16] noroviruses have become predominant in some temporal/geographical settings. In parallel with the emergence of the GII.P16 polymerase type, norovirus surveillance activity in Italy experienced increasing difficulties in generating sequence data on the RNA polymerase genomic region A, using the widely adopted JV12A/JV13B primer set. Two sets of modified primers (Deg1 and Deg2) were tested in order to improve amplification and typing of the polymerase gene.

METHODS

Amplification and typing performance of region A primers was assessed in RT-PCR on 452 GII norovirus positive samples obtained from 2194 stool samples collected in 2016-2019 from children hospitalized with acute gastroenteritis.

RESULTS

The use of Deg1 increased the rate of samples types in region A from 49.5% to 81.4% and from 21.9% to 69.7% in 2016 and 2017, respectively. The rate of Deg1 typed samples remained high in 2018 (90.1%), but sharply decreased to 11.8% in 2019. The second primers set, Deg2, was able to increase to 64.9% the rate of 2019 samples typed in region A, while typing efficiently 73.2%, 69%, and 86.4% of samples collected in 2016, 2017 and 2018, respectively.

CONCLUSIONS

The plasticity of norovirus genomes requires continuous updates of the primers used for strain characterization.

摘要

目的

近年来，GII.4[P16]和GII.2[P16]诺如病毒在某些时间/地理环境中已成为主要毒株。随着GII.P16聚合酶类型的出现，意大利的诺如病毒监测活动在使用广泛采用的JV12A/JV13B引物组生成RNA聚合酶基因组区域A的序列数据时遇到了越来越多的困难。为了提高聚合酶基因的扩增和分型效果，对两组改良引物（Deg1和Deg2）进行了测试。

方法

在RT-PCR中，对2016 - 2019年从急性胃肠炎住院儿童收集的2194份粪便样本中获得的452份GII诺如病毒阳性样本，评估区域A引物的扩增和分型性能。

结果

使用Deg1引物时，区域A样本分型率在2016年从49.5%提高到81.4%，在2017年从21.9%提高到69.7%。2018年Deg1分型样本率仍较高（90.1%），但在2019年急剧降至11.8%。第二组引物Deg2能够将2019年区域A样本分型率提高到64.9%，同时分别有效地对2016年、2017年和2018年收集的样本进行73.2%、69%和86.4%的分型。