Molecular characterization of the 2022 Sudan virus disease outbreak in Uganda.
Molecular characterization of the 2022 Sudan virus disease outbreak in Uganda.
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DOI：
10.1128/jvi.00590-23
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发表时间：
2023-10-31
影响因子：
5.4
通讯作者：
Klena, John D.
中科院分区：
文献类型：
--
作者：
Balinandi, Stephen;Whitmer, Shannon;Mulei, Sophia;Nassuna, Charity;Pimundu, Godfrey;Muyigi, Tonny;Kainulainen, Markus;Shedroff, Elizabeth;Krapiunaya, Inna;Scholte, Florine;Nyakarahuka, Luke;Tumusiime, Alex;Kyondo, Jackson;Baluku, Jimmy;Kiconco, Jocelyn;Harris, Julie R.;Ario, Alex R.;Kagirita, Atek;Bosa, Henry K.;Ssewanyana, Isaac;Nabadda, Susan;Mwebesa, Henry G.;Aceng, Jane R.;Atwine, Diana;Lutwama, Julius J.;Shoemaker, Trevor R.;Montgomery, Joel M.;Kaleebu, Pontiano;Klena, John D.
从2000年到2021年，乌干达经历了由本迪布乔病毒(n=1)和苏丹病毒(SUDV)(n=4)引起的五次埃博拉疫情。2022年9月20日，乌干达宣布在穆本德地区爆发第五起苏丹病毒病疫情，截至2023年1月11日疫情宣布结束时，已有142例确诊病例和22例疑似病例。通过回溯性病例调查，最早确定的病例于2022年8月初发病。在14 2例确诊病例中，我们进行了无偏(Illumina)和SUDV扩增特异性(Minion)高通量测序，获得了12 0例SUDV基因组和编码全序列，占95.4%(10 4/10 9)的确诊病例在可测序范围(CT≤30)内，10个基因组序列在可测序范围内，6个基因组序列重复。对新出现的Mubende变异体的核苷酸遗传亲缘关系的比较表明，它与2011年的Nakisamata SUDV序列关系最密切，代表了一种可能的新的人畜共患病溢出事件，并显示出与以前暴发一致的暴发间和暴发内替换率。Mubende变体的最新共同祖先估计发生在2021年10月和11月。与1976年以来的SUDV株相比，Mubende变异株的糖蛋白氨基酸序列具有99.7%的相似性，最大相似性为96.1%。将遗传序列和流行病学数据纳入应对活动产生了对疫情的广泛概述，从而能够快速核实已确定的患者之间的流行病学联系。埃博拉病(EBOD)是一种高病死率的公共卫生威胁。大多数EBOD疫情都发生在偏远地区，但2013-2016年西非的疫情表明，当EBOD到达城市人口时，它可能是多么具有破坏性。在这里，总结了2022年在乌干达Mubende区爆发的苏丹病毒病(SVD)，并评估了新变种的遗传相关性。Mubende变异体与20世纪70年代历史上的SUDV序列显示出96%的氨基酸相似性，并在整个疫情期间保持高度保守，这对正在进行的诊断非常重要，对未来的治疗开发也非常有希望。在Mubende SVD暴发期间发现的病毒之间的遗传差异与流行病学数据联系在一起，以更好地解释病毒传播和接触者追踪链。应该使用这种方法来更好地整合离散的流行病学和序列数据，以应对未来的病毒暴发。
Uganda experienced five Ebola disease outbreaks caused by Bundibugyo virus (n = 1) and Sudan virus (SUDV) (n = 4) from 2000 to 2021. On 20 September 2022, Uganda declared a fifth Sudan virus disease outbreak in the Mubende district, resulting in 142 confirmed and 22 probable cases by the end of the outbreak declaration on 11 January 2023. The earliest identified cases, through retrospective case investigations, had onset in early August 2022. From the 142 confirmed cases, we performed unbiased (Illumina) and SUDV-amplicon-specific (Minion) high-throughput sequencing to obtain 120 SUDV genome-and coding-complete sequences, representing 95.4% (104/109) of SVD-confirmed individuals within a sequence-able range (Ct ≤30) and 10 genome sequences outside of this range and 6 duplicate genome sequences. A comparison of the nucleotide genetic relatedness for the newly emerged Mubende variant indicated that it was most closely related to the Nakisamata SUDV sequence from 2011, represented a likely new zoonotic spillover event, and exhibited an inter- and intra-outbreak substitution rate consistent with previous outbreaks. The most recent common ancestor for the Mubende variant was estimated to have occurred in October and November 2021. The Mubende variant glycoprotein amino acid sequences exhibited 99.7% similarity altogether and a maximum of 96.1% glycoprotein similarity compared to historical SUDV strains from 1976. Integrating the genetic sequence and epidemiological data into the response activities generated a broad overview of the outbreak, allowing for quick fact-checking of epidemiological connections between the identified patients. Ebola disease (EBOD) is a public health threat with a high case fatality rate. Most EBOD outbreaks have occurred in remote locations, but the 2013–2016 Western Africa outbreak demonstrated how devastating EBOD can be when it reaches an urban population. Here, the 2022 Sudan virus disease (SVD) outbreak in Mubende District, Uganda, is summarized, and the genetic relatedness of the new variant is evaluated. The Mubende variant exhibited 96% amino acid similarity with historic SUDV sequences from the 1970s and a high degree of conservation throughout the outbreak, which was important for ongoing diagnostics and highly promising for future therapy development. Genetic differences between viruses identified during the Mubende SVD outbreak were linked with epidemiological data to better interpret viral spread and contact tracing chains. This methodology should be used to better integrate discrete epidemiological and sequence data for future viral outbreaks.
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影响因子：
82.9
作者：
Kinganda-Lusamaki E;Black A;Mukadi DB;Hadfield J;Mbala-Kingebeni P;Pratt CB;Aziza A;Diagne MM;White B;Bisento N;Nsunda B;Akonga M;Faye M;Faye O;Edidi-Atani F;Matondo-Kuamfumu M;Mambu-Mbika F;Bulabula J;Di Paola N;Pauthner MG;Andersen KG;Palacios G;Delaporte E;Sall AA;Peeters M;Wiley MR;Ahuka-Mundeke S;Bedford T;Tamfum JM
通讯作者：
Tamfum JM
影响因子：
3.7
作者：
Albarino, C. G.;Shoemaker, T.;Stroeher, U.
通讯作者：
Stroeher, U.
影响因子：
3.8
作者：
Kuhn, Jens H.;Amarasinghe, Gaya K.;Orton, Richard J.
通讯作者：
Orton, Richard J.
影响因子：
5.2
作者：
Kawuki, J.;Musa, T. H.;Yu, X.
通讯作者：
Yu, X.
DOI：
10.1126/science.1259657
发表时间：
2014-09-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gire SK;Goba A;Andersen KG;Sealfon RS;Park DJ;Kanneh L;Jalloh S;Momoh M;Fullah M;Dudas G;Wohl S;Moses LM;Yozwiak NL;Winnicki S;Matranga CB;Malboeuf CM;Qu J;Gladden AD;Schaffner SF;Yang X;Jiang PP;Nekoui M;Colubri A;Coomber MR;Fonnie M;Moigboi A;Gbakie M;Kamara FK;Tucker V;Konuwa E;Saffa S;Sellu J;Jalloh AA;Kovoma A;Koninga J;Mustapha I;Kargbo K;Foday M;Yillah M;Kanneh F;Robert W;Massally JL;Chapman SB;Bochicchio J;Murphy C;Nusbaum C;Young S;Birren BW;Grant DS;Scheiffelin JS;Lander ES;Happi C;Gevao SM;Gnirke A;Rambaut A;Garry RF;Khan SH;Sabeti PC
通讯作者：
Sabeti PC