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The 2023 South Sudanese Outbreak of Hepatitis E Emphasizes Ongoing Circulation of Genotype 1 in North, Central, and East Africa

INFECTION GENETICS AND EVOLUTION(2024)

Abbott Labs | Abbott Pandem Def Coalit | Uganda Virus Res Inst | Univ Glasgow | MRC UVRI & LSHTM Uganda Res Unit | Minist Hlth | WHO | US Ctr Dis Control

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Abstract
In April 2023, an outbreak of acute hepatitis was reported amongst internally displaced persons in the Nazareth community of South Sudan. IgM serology-based screening suggested the likely etiologic agent to be Hepatitis E virus (HEV). In this study, plasma specimens collected from anti-HEV IgM-positive cases were subjected to additional RT-qPCR testing and sequencing of extracted nucleic acids, resulting in the recovery of five full and eight partial HEV genomes. Maximum likelihood phylogenetic reconstruction confirmed the genomes belong to HEV genotype 1. Using distance-based methods, we show that genotype 1 is best split into three sub-genotypes instead of the previously proposed seven, and that these sub-genotypes are geographically restricted. The South Sudanese sequences confidently cluster within sub-genotype 1e, endemic to northeast, central, and east Africa. Bayesian Inference of phylogeny incorporating sampling dates shows that this new outbreak is not directly descended from other recent local outbreaks for which sequence data is available. However, the analysis suggests that sub-genotype 1e has been consistently and cryptically circulating locally for at least the past half century and that the known outbreaks are often not directly descended from one another. The ongoing presence of HEV, combined with poor sanitation and hygiene in the conflict-affected areas in the region, place vulnerable populations at risk for infection and its more serious effects, including progression to fulminant hepatitis.
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Key words
Hepatitis E virus,Acute hepatitis,South Sudan,Internally displaced people,Outbreak,Next-generation sequencing
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要点】:2023年南苏丹爆发的戊型肝炎疫情表明,戊型肝炎病毒(HEV)基因型1在北非、中非和东非持续流行,该研究揭示了基因型1的地理限制性亚型及其长期隐秘传播特点。

方法】:研究通过RT-qPCR测试和测序,对HEV IgM阳性病例的血浆样本进行分析,并进行最大似然系统发育重建和贝叶斯推断法来确定病毒基因型和传播历史。

实验】:实验中收集了南苏丹纳泽雷社区抗HEV IgM阳性病例的血浆样本,并从中恢复了五个完整的和八个部分的HEV基因组,使用距离法对基因型1进行了亚型划分,发现该疫情与东北、中、东非流行的亚型1e密切相关,且该亚型在当地至少隐秘传播了半个世纪。