在美國疫情的嚴峻情況下，大家對COVID-19病毒也越發關注，那麼COVID-19基因組序列的研究能否幫助我們徹底解決新型冠狀病毒呢?一起看看霍普金斯大學教授的論文。
美國疫情下，基因組測序在對抗COVID-19中的作用分子生物學家Peter Thielen和Thomas Mehoke正在對導致COVID-19的SARS-CoV-2病毒的基因組進行快速測序。他們的工作將有助於闡明病毒在傳播過程中是如何進化的，以及遏制措施的效果如何。4月3日，約翰霍普金斯應用物理實驗室(Johns Hopkins Applied Physics Laboratory)的分子生物學家彼得·蒂倫(Peter Thielen)和託馬斯·梅霍克(Thomas Mehoke)發表了一份工作報告，他們正在對SARS-CoV-2的不同變異進行基因組測序，引起疾病的COVID-19病毒，以便在病毒傳播時追蹤其突變。他們與約翰霍普金斯大學護理學院的博士生莎拉·拉法夫(Sarah LaFave)一起，討論他們如何開展工作，以及如何為應對這一流行病的不斷變化提供信息。為了篇幅和清晰度，這段對話已被編輯過。
什麼是基因組測序?為什麼了解COVID-19基因組序列很重要?
蒂倫：基因組測序是一種技術，使我們能夠閱讀和解釋在DNA或RNA中發現的遺傳信息。當我們從檢測出COVID-19陽性的患者樣本中觀察病毒基因組序列時，我們對了解他們的病毒版本起源很感興趣。例如，病毒看起來和華盛頓州的情況相似嗎?還是在紐約?還是在歐洲?現在，我們正在分析許多SARS-CoV-2病毒的基因組序列，這種病毒導致COVID-19病毒，在巴爾的摩地區和馬裡蘭州傳播。我們的目標是了解病毒在傳播過程中是如何進化的。到目前為止，全世界已經發表了1000多個COVID-19基因組。
約翰霍普金斯大學回應COVID-19
報導COVID-19大流行如何影響JHU的運作，以及霍普金斯大學的專家和科學家如何應對outbreakMehoke：隨著疫情的進展，這項工作將有助於我們了解該病毒在馬裡蘭州的控制情況。
因此，通過觀察特定人樣本中導致COVID-19的病毒的基因組序列，你可以開始了解病毒是如何傳播的，因為隨著病毒在不同地理區域的變異和傳播，基因組序列看起來有點不同?
蒂倫：對。我們分析的最初兩個COVID-19序列表明，在局部傳播的病毒有著與在華盛頓州傳播的病毒不同的微小遺傳變化。這表明馬裡蘭州的病毒可能是從中國以外的地理位置輸入的，因為我們預計華盛頓州的病例最初是從中國傳入的。從邏輯上講，由於旅行方式的原因，我們預計會有更多的病毒從歐洲國家進口。但是當我們生成更多的序列時，我們會知道更多關於這是否是真的。
你的數據還有其他潛在的公共衛生用途嗎?
梅霍克：是的，你可以用基因組序列來估計實際感染人群的數量。因此，我們不僅可以從我們所看到的基因組中確定檢測出陽性的人數，還可以估計該州的陽性病例總數，這可以讓我們更好地了解問題的範圍。鑑於某些地區的測試規模有限，這一點尤其重要。
看來速度是這項工作的一個非常重要的部分。你的實驗室怎麼能這麼快開始這項研究?
蒂倫：在過去的幾年裡，我們的中心和合作夥伴一直在發展分析流感的能力，為下一次流感爆發做準備。我們已經注意到了可能導致大流行病的不同病原體，我們可以迅速調整我們的所有資源。
圖片說明：APL生物學家湯姆·梅霍克在約翰·霍普金斯醫院的分子診斷實驗室回顧了對引起COVID-19病毒的SARS-CoV-2的DNA測序分析。
圖片來源：約翰霍普金斯大學APL/ED惠特曼
邁霍克：我們不想在一年後寫關於這個的論文，說「病毒可能是這樣傳播的。」我們想把數據交到那些現在可以做點什麼的人手中。我們正試圖使它儘可能快速和自動化，從擦拭某人的鼻子到獲得基因組序列。
你如何獲得遺傳物質然後運行基因組序列?
梅霍克：首先，醫院裡有人擦拭病人的鼻子，我們從樣本中提取基因組物質。我們在一個小的手持式DNA測序儀上做這項工作，這個測序儀比手機小，可以通過USB連接到筆記本電腦。
蒂倫：我們使用筆記本電腦上的數據分析軟體對基因組進行測序，然後直接上傳到國際資料庫。病毒基因組學社區的人們可以訪問這些資料庫，以便世界各地的科學家能夠獲得儘可能廣泛的數據。
各國科學家之間的基因組測序合作是如何進行的?
蒂倫：國際合作的規模之大令人難以置信。我們正與美國國立衛生研究院福格蒂國際中心合作，與中低收入國家的研究人員合作，在這些環境下開展這類工作。低收入和中等收入國家在疫情爆發期間通常是「數據黑點」。現在，這些新技術已經問世，中低收入國家可以很容易地建立測序能力，只需要一臺筆記本電腦和一臺手持測序儀，而不需要大型研究實驗室。我們目前正在努力讓我們的國際合作夥伴與我們在約翰霍普金斯大學的能力相同。
我們還與國際藝術網密切合作。他們的理念是，科學家應該儘可能多地共享數據，並迅速獲取信息。我們非常支持這種理念。我們在霍普金斯大學內外進行對話，儘可能多地分享知識。
發表在健康，科學+技術，聲音+意見
標記基因組學，q+a，冠狀病毒
附上原文，以供參考，拒絕轉載，侵權必刪：
THE ROLE OF GENOMIC SEQUENCING IN COMBATING COVID-19Molecular biologists Peter Thielen and Thomas Mehoke are rapidly sequencing the genome of SARS-CoV-2, the virus that causes COVID-19. Their work will help shed light on how the virus evolves as it spreads and how well containment efforts are working.ByHub staff report / Published April 3Peter Thielen and Thomas Mehoke, molecular biologists at the Johns Hopkins Applied Physics Laboratory, are working to sequence the genomes of different variations of SARS-CoV-2, the virus that causes the illness COVID-19, in order to track its mutations as it spreads. They joined Sarah LaFave, a PhD student at the Johns Hopkins School of Nursing, to discuss how they are carrying out their work and how it can inform the evolving response to the pandemic. The conversation has been edited for length and clarity.
What is genomic sequencing and why is it important to understand the genomic sequence of COVID-19?
Thielen: Genomic sequencing is a technique that allows us to read and interpret genetic information found within DNA or RNA. When we look at virus genome sequences from patient samples that test positive for COVID-19, we're interested in understanding where their version of the virus originated. For example, does the virus look similar to how it looks in Washington State? Or in New York? Or in Europe? Right now, we're working to analyze many genome sequences from SARS-CoV-2, the virus that causes COVID-19, that are circulating in the Baltimore area and in Maryland. Our goal is to understand how the virus is evolving as it spreads. So far, there are over 1,000 COVID-19 genomes that have been published worldwide.
Johns Hopkins responds to COVID-19
Coverage of how the COVID-19 pandemic is affecting operations at JHU and how Hopkins experts and scientists are responding to the outbreakMehoke: As the outbreak progresses, this work will help us understand how well the virus is contained in Maryland.
So by looking at the genomic sequence of the virus causing COVID-19 in a particular person's sample, you can begin to understand how the virus is spreading because the genomic sequence looks a little different as the virus mutates and spreads in different geographic areas?
Thielen: Right. The initial two COVID-19 sequences that we've analyzed suggest that the viruses circulating locally have small genetic changes that are different from the ones circulating in, for example, Washington State. This suggests that the virus here in Maryland may have been imported from geographic locations other than China, because we expect that cases in Washington State were originally introduced from China. Logically, we're expecting that we would see more virus imported from European countries because of travel patterns. But we'll know more about whether or not that is true as we generate more sequences.
Are there other potential public health uses of your data?
Mehoke: Yes, you could use the genomic sequence to estimate the actual infected population size. So rather than just determining the number of people who have tested positive, from the genomes that we are seeing, we can estimate the total number of positive cases in the state, and that can give us a better understanding up-front of the scope of the problem. This is especially important given the limited scale of testing in some locations.
It seems like speed must be a really important part of this work. How was your lab able to start this research so quickly?
Thielen: For the last several years, our center and our partners have been developing capacity to analyze flu in preparation for whatever the next outbreak might be. We've had an eye on different pathogens that could lead to pandemics, and we can quickly modify all our resources.
Image caption:APL biologist Tom Mehoke reviews the DNA sequencing analysis of SARS-CoV-2, the virus causing COVID-19, at the molecular diagnostics laboratory at Johns Hopkins Hospital.
IMAGE CREDIT: JOHNS HOPKINS APL / ED WHITMAN
Mehoke: We don't want to be writing papers about this a year from now saying, "This is how the virus might be spreading." We want to get data into the hands of people who can do something with it right now. We're trying to make it as quick and as automated as possible to go from swabbing someone's nose to getting a genomic sequence.
How do you acquire the genetic material and then run the genomic sequence?
Mehoke: First, someone at the hospital swabs a patient's nose, and we pull genomic material out of that sample. We do this work on a little handheld DNA sequencer, which is smaller than a phone, that connects over USB to a laptop.
Thielen: We use data analysis software on our laptops to sequence the genome, and then upload the sequences directly into international databases. The databases can be accessed by people in the viral genomics community so that scientists around the world can have access to the widest array of data as possible.
How do the genomic sequencing collaborations between scientists across countries work?
Thielen: There is an incredible amount of international collaboration. We're working with the NIH's Fogarty International Center to collaborate with researchers in low- and middle-income countries to perform this type of work in those settings. Low- and middle-income countries are usually "data dark spots" during an outbreak. Now that these new technologies are available, low- and middle-income countries can pretty easily set up sequencing capacity using just a laptop computer and a handheld sequencer, without the need for large research laboratories. We are currently working to get our international collaborators up and running with the same capacity that we have at Johns Hopkins.
Mehoke: We're also working closely with the international ARTIC network. Their philosophy is that scientists should share data as much as possible and get information out quickly. We're very supportive of that philosophy. We're having conversations within and outside of Hopkins to share knowledge as much as we can.
Posted in Health, Science+Technology, Voices+Opinion
Tagged genomics, q+a, coronavirus
Source of articles：https://hub.jhu.edu/
在美國疫情下，大家都希望儘快找到消滅COVID-19病毒的方法，如果能夠靠COVID-19基因組序列找到疫苗就非常值得關注，希望大家能夠平安健康的度過疫情期。