新冠病毒在世界各地肆虐，尤其是美國華盛頓地區，近日約翰霍普金斯大學研究人員追溯了病毒對華盛頓地區的影響。
約翰霍普金斯大學的研究人員追溯了covid -19的引入對美國華盛頓地區的影響
研究表明，新冠病毒多次進入該區域，但臨床表現相似，表明沒有多種病毒毒株導致不同嚴重程度的疾病
作者Amanda Zrebiec /出版於18小時前
約翰霍普金斯大學(Johns Hopkins University)和衛生系統的科學家們對導致COVID-19的SARS-CoV-2病毒的基因組進行了排序，從而產生了一項研究，該研究描述了這種病毒早期傳入華盛頓特區的情況。
在多項發現中，該研究指出，該病毒進入該區域的次數很多，但臨床表現相似，這表明，儘管存在微小的遺傳差異，但傳播的病毒很可能導致相同的疾病。該研究還提供了有關實施檢疫程序時病例進展情況的信息，以及研究最終疫苗效力的方法。
該研究由約翰霍普金斯應用物理實驗室的分子生物學家發起，使用部分由APL開發的軟體和方法，該團隊的早期成果被收錄在該研究中，目前正在等待同行評議。該研究由JHU COVID-19研究應對項目資助，該項目為快速應對團隊提供種子基金，以在COVID-19大流行中尋找解決方案並增加知識。
「儘管從該地區的樣本中觀察到遺傳多樣性，但從臨床上看似乎是同一種冠狀病毒。我們的數據並沒有顯示病人預後和病毒基因型之間的聯繫。」
彼得帝倫
約翰霍普金斯大學的分子生物學家約翰霍普金斯衛生系統診斷出馬裡蘭州超過37%的早期COVID-19病例來自巴爾的摩-華盛頓大都市地區的患者。對114個診斷陽性樣本進行基因組測序，並對這些患者的疾病表現和預後進行分析。
通過分析，該小組觀察到多個可能的SARS-CoV-2病毒傳入該地區，以及在許多沒有旅行或患病史的患者中，這表明社區傳播在該地區已在3月初確立。他們沒有發現病毒基因變異和病人預後(如住院或ICU)之間的明顯聯繫，這意味著他們沒有發現病毒譜系和病人感染的嚴重程度之間的可能聯繫。
「儘管在樣本地區觀察遺傳多樣性,它似乎是臨床相同的冠狀病毒,」彼得說帝倫,分子生物學家在APL的研究和勘探開發部門的一位聯席作者在研究Shirlee沃爾,博士後的約翰霍普金斯大學彭博公共衛生學院的流行病學。「我們的數據並沒有顯示病人預後和病毒基因型之間的聯繫。」
這種由臨床和基因組序列數據組成的聯繫，讓霍普金斯團隊進一步消除了新冠病毒存在多種「毒株」的觀點，其中一些毒株比其他毒株更致命。
最終的測序樣本包括40名住院患者和22名ICU住院患者。簡而言之,作者寫道,「病毒基因的多樣性,臨床症狀,病人結果表明病毒突變不是臨床表現的主要驅動力,「他們」觀察到嚴重的情況下,定義為進入ICU(包括病人需要呼吸機支持),病毒基因組屬於所有五大系統(分組)。」
這組作者寫道:「控制病毒局部傳播的努力很可能被在疫情早期傳入該地區的數量以及該地區作為一個整體的相互聯繫所混淆。」
該小組還觀察到，針對最初SARS-CoV-2基因組的對策可能適用於所有COVID-19病例。
蒂倫解釋說:「為單一毒株設計疫苗和治療方法，即使是我們在這裡觀察到的具有遺傳多樣性的毒株，也要比像流感這樣變化迅速的病毒簡單得多。」「我們在當地和全球數據中觀察到的情況，讓我們確信這些領域的研究正走在正確的軌道上。」
在這篇論文中，研究小組追蹤了病毒最初進入該地區的路徑，揭示了有近期旅行史的患者的臨床數據，這些患者去過英格蘭和北美其他地區(包括加利福尼亞、科羅拉多、紐約和愛達荷)。研究人員還將該地區的基因多樣性與美國和世界其他地區進行了比較。紐約市所描述的病毒種群的多樣性似乎與華盛頓特區的相似，因為在這兩個地區爆發的病毒都被播種了多次。
病毒病原體的遺傳特徵需要從分子診斷到DNA測序技術以及計算生物學和流行病學的專業知識。這篇論文的作者包括APL研究人員蒂倫、湯姆·梅胡克、賈裡德·埃文斯、克雷格·豪瑟、布萊恩·梅裡特、蒂娜·祖多克、基安娜·布朗特和阿曼達·恩隆德。來自約翰霍普金斯醫學院、懷廷工程學院和彭博公共衛生學院的研究人員由溫斯頓·蒂姆普、赫巴·穆斯塔法和斯圖爾特·雷領導。
他說:「這個跨學科的團隊代表了約翰霍普金斯大學的許多具體優勢，對我們了解美國COVID-19大流行的早期階段做出了重要貢獻」,帝倫說。「隨著大流行的持續和應對措施的出現，跟蹤這些基因變化並確定病毒遺傳、臨床表現和對疫苗效力的潛在影響之間的相關性將是很重要的。」
該小組將繼續使用病毒測序技術對該地區COVID-19進行監測，並將馬裡蘭州暫停營業期間收集的樣本與該州逐步恢復營業期間收集的樣本進行比較。該分析將使研究人員更好地了解該區域內病毒傳播的封鎖和主要模式的有效性。
標記應用物理實驗室，分子生物學，冠狀病毒，covid-19
附上原文，以供參考，拒絕轉載，侵權必刪：
JOHNS HOPKINS RESEARCHERS RETRACE COVID-19'S INTRODUCTION, IMPACT IN D.C. REGION
Study suggests multiple entries of the virus into the region but similar clinical presentation, an indication that there are not multiple strains of the virus causing disease of varying severity
By Amanda Zrebiec / Published 18 hours ago
An effort by scientists from across Johns Hopkins University and Health System to sequence the genome of SARS-CoV-2, the virus causing COVID-19, has produced a study characterizing the early introduction of the virus into the Washington, D.C., metropolitan area.
Among several findings, the study points to multiple entries of the virus into the region but similar clinical presentation, an indication that, despite small genetic differences, circulating viruses are likely causing identical disease. The research also provides information about the progression of cases as quarantine procedures were implemented, and ways to study the efficacy of an eventual vaccine.
Initiated by the work of molecular biologists at the Johns Hopkins Applied Physics Laboratory and using software and approaches developed, in part, at APL, the team's early takeaways are featured in the study, which is awaiting peer review. The study was funded by the JHU COVID-19 Research Response Program, which provided seed grants to rapid response teams to find solutions and increase knowledge amid the COVID-19 pandemic.
"DESPITE OBSERVING GENETIC DIVERSITY IN SAMPLES FROM THE REGION, IT APPEARS TO BE CLINICALLY THE SAME CORONAVIRUS. OUR DATA DOES NOT SHOW A LINKAGE BETWEEN PATIENT OUTCOME AND VIRUS GENOTYPE."
Peter Thielen
Molecular biologist, Johns Hopkins APLThe Johns Hopkins Health System diagnosed more than 37% of early COVID-19 cases in the state of Maryland, from patients living across the Baltimore-Washington metro area. Genomes for 114 of those diagnosed positive samples were sequenced, and those patients' disease presentation and outcomes were analyzed.
Through that analysis, the team observed multiple likely introductions of the SARS-CoV-2 virus into the region, as well as in many patients with no travel or sick contact history, an indication that community transmission was well established in the area in early March. What they did not detect was a distinct link between viral genetic variations and patient outcomes, such as hospital or ICU admission—meaning they found no likely connection between the virus' genealogy and the severity of infection in patients.
"Despite observing genetic diversity in samples from the region, it appears to be clinically the same coronavirus," said Peter Thielen, a molecular biologist in APL's Research and Exploratory Development Department and one of the co-lead authors on the study with Shirlee Wohl, a postdoctoral fellow in the Department of Epidemiology at the Johns Hopkins Bloomberg School of Public Health. "Our data does not show a linkage between patient outcome and virus genotype."
That connection, consisting of the clinical and genome sequence data, allows the Hopkins team to further disabuse the notion that there are multiple "strains" of the novel coronavirus, some of which are deadlier than others.
The final total of sequenced samples included 40 from hospitalized patients and 22 from patients admitted to the ICU. In short, the authors write, "The diversity of virus genetics, clinical symptoms, and patient outcomes suggests that viral mutations are not the main driver of clinical presentation," and they "observed that severe cases, defined as admission to the ICU (including patients requiring ventilator support), had viral genomes belonging to all five major phylogenetic [groupings]."
"Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole," the authors write.
The team also observed that countermeasures for the initial SARS-CoV-2 genome likely apply to all COVID-19 cases.
"Designing vaccines and therapeutics to a single strain, even one with the type of genetic diversity we've observed here, is much more straightforward than a virus that is changing quickly, such as influenza," Thielen explained. "What we observe in the local and global data provides excellent reassurance that research in those areas is on the right track."
In its paper, the team traces the path of the virus' initial introduction into the region, revealing clinical data from patients with recent travel history to England and elsewhere in North America (including California, Colorado, New York, and Idaho). The researchers also compared the region's genetic diversity to that of others in the U.S. and around the world. The diversity of the viral population described in New York City appears to be similar to that of the Washington, D.C., area, as outbreaks in both regions were seeded multiple times.
Genetic characterization of viral pathogens requires expertise ranging from molecular diagnostics to DNA sequencing technologies, as well as computational biology and epidemiology. The paper's authors include APL researchers Thielen, Tom Mehoke, Jared Evans, Craig Howser, Brian Merritt, Tina Zudock, Kianna Blount, and Amanda Ernlund. Researchers from the Johns Hopkins School of Medicine, Whiting School of Engineering, and Bloomberg School of Public Health were led by Winston Timp, Heba Mostafa, and Stuart Ray.
"This interdisciplinary team represents many specific strengths of Johns Hopkins and is an important contribution to our understanding of the early stage of the COVID-19 pandemic in the U.S.," Thielen said. "As the pandemic continues and countermeasures become available, it will be important to track these genetic changes and identify correlations between virus genetics, clinical presentation, and the potential impact on vaccine efficacy."
The team will continue using viral sequencing for COVID-19 surveillance in the region, comparing samples collected during Maryland's stay-at-home order to those gathered during the state's gradual reopening. That analysis will allow the researchers to better understand the effectiveness of the lockdown and primary modes of viral transmission within the region.
Tagged applied physics laboratory, molecular biology, coronavirus, covid-19
Source of articles：https://hub.jhu.edu/
Author：Amanda Zrebiec
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