Using genomics to improve preparedness and response of future epidemics or pandemics in Africa.
Using genomics to improve preparedness and response of future epidemics or pandemics in Africa.
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DOI：
10.1016/s2666-5247(20)30169-5
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发表时间：
2020-11
期刊：
影响因子：
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通讯作者：
Jere KC
中科院分区：
文献类型：
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作者：
Chaguza C;Nyaga MM;Mwenda JM;Esona MD;Jere KC
新出现的传染病，如COVID-191和埃博拉病毒病2，对公共卫生构成重大威胁。尽管埃博拉病毒在非洲中部和西部已经存在多年，但许多非洲国家尚未在公共卫生领域充分利用基因组学。目前由严重急性呼吸系统综合征冠状病毒2型（SARS-CoV-2）引起的COVID-19大流行突出了这种情况。1截至2020年10月5日，即COVID-19大流行9个月后，来自54个非洲国家中的21个国家的2980份SARS-CoV-2患者样本基因组已存入GISAID数据库。大多数非洲SARS-CoV-2基因组来自南非（n= 1409）、冈比亚（360）、刚果民主共和国（346）、肯尼亚（290）、埃及（152）、塞内加尔（136）、尼日利亚（87）、加纳（53）和摩洛哥（48）。虽然从非洲采样的基因组数量略高于南美洲（n= 1988），但亚洲（n= 9874），大洋洲（n= 12313），北美（n= 34670）和欧洲（n= 75670）的采样广度要高得多。大多数非洲国家缺乏基因组数据，这表明这些数据对公共卫生威胁的益处尚未充分实现，以备新出现的传染病之需。正如在COVID-19大流行的早期阶段所看到的那样，对不明原因呼吸道疾病患者的样本进行测序不仅确定了SARS-CoV-2是致病病原体及其人畜共患病来源，而且还促进了诊断分子检测的发展，为治疗和感染控制提供信息。1基因组数据还提供了足够的分辨率，可用于监测当地传播情况，并推断病毒在各国之间的输入途径和时间。3，4这一推论对SARS-CoV-2至关重要，特别是在非洲环境中，检测延迟是值得注意的，但血清调查（例如，在马拉维和肯尼亚）显示病毒的高暴露，5表明输入发生早于预期。此外，对非洲不断演变的病毒（包括SARS-CoV-2）进行基因组监测，可以为合理设计特异和敏感的分子检测提供信息，以指导治疗和预防，并监测有利于致病性和传播性的病毒适应性。6至关重要的是，基因组数据为设计拯救生命的疫苗提供了信息，这是至关重要的，特别是在没有有效治疗方法的情况下。7基因组数据的应用并不局限于调查已知的疫情或流行病。8宏基因组学和转录组学可用于诊断可能在非洲造成未被发现的疫情的不明原因感染，如孟加拉国的神经侵袭性脑膜炎基孔肯雅病毒疫情。9由于病毒库在地理上是多样的10，下一个致命病毒的起源是未知的，基因组学可以导致主动流行病情报-例如，早期识别有可能蔓延到非洲人群中的新型病毒，因此，为未来流行病的循证准备和控制提供信息。在非洲对SARS-CoV-2毒株进行的局部测序取得了一些成功，4世卫组织和非洲疾病控制和预防中心（CDC）在非洲各地扩大对SARS-CoV-2毒株测序的联合举措也证明，有必要将基因组学纳入非洲的公共卫生。然而，非洲各国政府需要对研究基础设施和能力发展进行大量投资，以实现基因组学的好处。如果从事基因组学研究的地方机构在当地得到很好的支持，这些机构可以作为研究的重点。
Emerging infectious diseases, such as COVID-191 and Ebola virus disease, 2 pose a major threat to public health. Despite the presence of Ebola virus disease in central and west Africa for several years, 2 many African countries are yet to fully utilise genomics in public health. This situation is highlighted by the current COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 1 By Oct 5, 2020, 9 months into the COVID-19 pandemic, 2980 SARS-CoV-2 genomes sampled from patients with COVID-19, from 21 of 54 African countries, had been deposited in the GISAID database. Most of the African SARS-CoV-2 genomes are from South Africa (n= 1409), The Gambia (360), Democratic Republic of the Congo (346), Kenya (290), Egypt (152), Senegal (136), Nigeria (87), Ghana (53), and Morocco (48). Although the number of genomes sampled from Africa is slightly higher than that from South America (n= 1988), the breadth of sampling is much higher in Asia (n= 9874), Oceania (n= 12313), North America (n= 34670), and Europe (n= 75670). The absence of genomic data from most African countries shows that the benefits of these data for public health threats are yet to be fully achieved for preparedness and response to emerging infectious diseases. As seen during the early stages of the COVID-19 pandemic, sequencing of samples from patients with respiratory diseases of unknown cause not only identified SARS-CoV-2 as the causative pathogen and its zoonotic origin but also facilitated development of molecular assays for diagnosis to inform treatment and infection control. 1 Genomic data also provide sufficient resolution for monitoring local transmission and for inferring routes and times of importation of viruses between countries. 3, 4 This inference is crucial for SARS-CoV-2, particularly in African settings where delays in testing were notable but serosurveys (eg, in Malawi and Kenya) showed high exposure to the virus, 5 suggesting that importation occurred earlier than expected. Furthermore, genomic surveillance of evolving viruses (including SARS-CoV-2) in Africa could inform rational design of specific and sensitive molecular assays to guide treatment and prevention and to monitor viral adaptations favouring pathogenicity and transmissibility. 6 Crucially, genomic data inform design of life-saving vaccines, which are vital, particularly when no effective treatments are available. 7 Applications for genomic data are not restricted to investigating known outbreaks or epidemics. 8 Metagenomics and transcriptomics could be used to diagnose infections of unknown cause potentially causing undetected outbreaks in Africa, as seen with the neuroinvasive meningitis Chikungunya virus outbreak in Bangladesh. 9 Because the viral repertoire is geographically diverse10 and the origin of the next deadly virus is unknown, genomics could lead to proactive epidemic intelligence—eg, early identification of novel viruses with potential to spill over into the human population in Africa, therefore, informing evidence-based preparedness and control for future epidemics. Some success of local sequencing of SARS-CoV-2 strains in Africa, 4 and the joint initiative by WHO and Africa Centres for Disease Control and Prevention (CDC) to scale-up sequencing of SARS-CoV-2 strains across Africa, supports the need for integration of genomics into public health in Africa. However, substantial investment in research infrastructure and capacity development by African governments will be needed to achieve the benefits of genomics. If local institutions doing genomics research are well supported locally, these institutions could act as focal …