Inter-regional study of transmission, adaptation and pathogenesis of viruses with pandemic potential in Southeast Asia and West/Central Africa

对东南亚和西非/中非具有大流行潜力的病毒的传播、适应和发病机制进行区域间研究

• 批准号: 10426422
• 负责人: Anavaj SAKUNTABHAI
• 金额: $ 45.45万
• 依托单位: INSTITUT PASTEUR
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-31 至 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10426422
• 关键词: 2019-nCoV; Acute; Africa; African; Area; Blood Circulation; Burkina Faso; COVID-19; COVID-19 patient; COVID-19 surveillance; COVID-19 vaccination; Cambodia; Cameroon; Centers for Disease Control and Prevention (U.S.); Central Africa; Cessation of life; Clinical; Communities; Coronavirus; Country; Data; Data Collection; Detection; Developed Countries; Disease; Disease Outbreaks; Disease Surveillance; Dose; Ensure; Epidemiology; Equatorial Guinea; Event; Far East; Gambia; Genetic Determinism; Genomics; Goals; Guinea; Guinea-Bissau; Health system; Incidence; Income; Ivory Coast; Knowledge; Laboratories; Laos; Madagascar; Mali; Mauritania; Medicine; Metadata; Methods; Molecular; Monitor; Niger; Patients; Population; Recording of previous events; Reporting; Reverse Transcriptase Polymerase Chain Reaction; SARS-CoV-2 B.1.1.7; SARS-CoV-2 B.1.351; SARS-CoV-2 B.1.617.2; Sampling; Senegal; Severities; Severity of illness; Societies; Source; Southeastern Asia; Symptoms; System; Thailand; Time; Timidity; Tunisia; Vaccinated; Vaccination; Vaccines; Variant; Vietnam; Viral Pathogenesis; Virus; base; detection method; genetic signature; genome sequencing; genomic data; molecular subtypes; pandemic disease; pathogen genomics; respiratory; response; sequencing platform; severe COVID-19; stem; tool; transmission process; variants of concern; virus genetics; whole genome

Project Summary/Abstract Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) has rapidly spread across the world. As of June, 2021, over 171 million laboratory-confirmed cases and greater than 3.68 million deaths have been reported globally. This increase in cases has been associated with emergence of new variants which have increased transmissibility and severity. While Southeast Asia kept COVID-19 cases under relative control in 2020. In 2021, SARS-CoV-2 began to spread rapidly and caused continuing outbreaks in the region. In Africa, the genomic surveillance gap, combined with very fragile health systems with limited management capacities, exposes the continent to possible new COVID-19 waves that could prove to be much more severe on the continent, where vaccination clearly remains at a very timid stage. The overall goal of the project is to increase sequencing capacity and add to the depth of sequencing knowledge available in South East Asia and African countries with 4 Specific Aims. 1)To increase sequencing numbers for samples from certain regions. We will focus on samples from land borders with Thailand and Vietnam and community transmission in Cambodia stemming from the February 20th “event.” These sequences will help to understand community transmission within Cambodia. In Africa, we will increase sequencing numbers from samples from African countries with very low sequencing coverage including Mali, Burkina Faso, Guinea, Côte d’Ivoire, Guinea-Bissau, Niger, Cabo-Verde, Mauritania, Tunisia, Madagascar, Cameroon, Equatorial Guinea and Central Africa Republic. We will confirm known variants of concern as well as detection of potential local new variants. 2)To increase sequencing numbers for samples from patients with atypical profiles. We will systematically collect data at epidemiological level for demographical data, clinical symptoms, COVID-19 vaccination status, history of COVID-19 in relation with patients. We will focus on re-infected patient samples, severe COVID-19 cases and post-vaccinated SARS-CoV-2 infected patients. 3) To monitor introduction and dissemination of known VOCs using molecular sub-typing tools. We will help participating countries building up molecular capacities to subtype known variants. 4) Identify viral genetic determinants of high transmissibility and disease severity. Sequences from severe cases will be analyzed in comparison to the sequences from the randomly selected group to identify viral genetic signatures associated to disease severity. Regarding the transmissibility, we will rely on circulation dynamics of the detected variants in each country as well as in all countries. Overall, the studies outlined in this proposal will rapidly add essential sequence data needed regarding COVID-19 cases in lower–middle income, least-developed countries. They will provide the basis for further study on inter-/intra-host variant emergence and vaccine escape in a unique population from a least-developed country in an understudied, but vitally important, region of the world.

项目摘要/摘要 严重的急性呼吸道冠状病毒2（SARS-COV-2），2019年冠状病毒病的病因 （COVID-19）迅速遍及世界各地。截至2021年6月，超过1.71亿个实验室确认 案件和368万例死亡人数已有报道。案件的增加是 与新变体的出现有关，这些变体的传播和严重程度增加。尽管 东南亚洲在2020年将Covid-19案件保持相对控制。2021年，SARS-COV-2开始蔓延 在非洲，基因组监视差距合并 由于管理能力有限的非常脆弱的卫生系统，可以继续进行新的 在非洲大陆上可能更为严重的covid-19波，在那里疫苗接种清楚 仍然处于非常胆小的阶段。该项目的总体目标是提高测序能力并添加到 在东南亚和非洲国家提供了4个特定目标的测序知识深度。 1）增加某些区域样品的测序数字。我们将专注于样本 与泰国和越南的土地边界以及柬埔寨的社区传播，由 2月20日“活动”。这些序列将有助于了解柬埔寨内的社区传播。 在非洲，我们将增加来自非洲国家的样本的测序数量，这些数字非常低 覆盖范围包括马里，布基纳法索，几内亚，科特迪瓦，几内亚 - 比索，尼日尔，卡波·维德， 毛里塔尼亚，突尼斯，马达加斯加，喀麦隆，赤道几内亚和中非共和国。我们将确认 已知的关注变体以及检测潜在的局部新变体。 2）增加测序 来自非典型特征患者的样品数量。我们将系统地收集数据 人口统计数据，临床症状，共同199疫苗接种状况，历史的流行病学水平 与患者相关的COVID-19。我们将专注于重新感染的患者样本，严重的Covid-19病例 和接种后的SARS-COV-2感染患者。 3）监视介绍和传播 使用分子亚型工具的已知VOC。我们将帮助参与国家建立分子 亚型已知变体的能力。 4）确定高透射率和 疾病的严重程度。与来自严重病例的序列相比将分析 随机选择的组以鉴定与疾病严重程度相关的病毒遗传特征。关于 传播性，我们将依靠每个国家和所有国家的检测变体的循环动力学 国家。总体而言，该提案中概述的研究将迅速添加所需的基本序列数据 关于中低收入收入，最不发达国家的19例案件。他们将提供基础 要进一步研究 - 宿主体内的变体出现和疫苗从独特的人群中逃脱 最不发达的国家在一个世界上的理解但至关重要的地区。