COVID 刺激了傳染病基因組測序的繁榮

從登革熱到伊泌拉，亞洲和非洲的實驗室正在使用在大流行期間獲得的測序技術和技能來快速追踪地方病。

資料來源：新聞 / 2022 年 12 月 15 日 / 自然 / 財團法人台灣紅絲帶基金會編譯

許多實驗室正在使用在大流行期間獲得的基因組測序設備來追踪其他疾病。

圖片來源：T. Narayan/Bloomberg via Getty

去年，當柬埔寨一名三歲男孩感染禽流感時，位於金邊的柬埔寨巴斯德研究所的研究人員使用在 COVID-19 大流行期間購買的基因組測序技術，在一天內對該男孩的樣本進行了測序。 他們證實他感染了 H9N2，這是一種常見於鳥類的病毒。 後來，他們對男孩家中一隻雞的病毒樣本進行了測序，顯示他就是這樣被感染的，而且病毒不太可能傳播給其他人。 在大流行之前，樣本會被送到國外進行測序，而此類信息通常需要數週或數月才能到達。

該實驗室是亞洲和非洲眾多在大流行期間提高了測序能力的實驗室之一，現在正著眼於 COVID-19 之外的其他疾病研究。「自 2022 年初以來，我們一直在考慮如何將這種能力用於其他病原體」，例如霍亂、瘧疾、脊髓灰質炎和伊波拉病毒，在亞的斯.亞貝巴非洲疾病控制和預防中心病原體基因組學計畫負責人 Sofonias Tessema 說。

新加坡杜克國立大學 (Duke–NUS) 醫學院的病毒免疫學家 Ruklanthi de Alwis 說，在大流行之前，基因組測序主要用於許多地區的研究，但現在它被用於公共衛生。 測序數據與其他臨床信息相結合可用於診斷疾病、識別傳播鏈、追踪突變、追踪爆發、加快公共衛生響應並促進疫苗開發。

許多國家都希望自己進行測序，Paul Pronyk 說，他也是杜克大學國立大學的一名傳染病醫生，該大學支持亞洲病原體基因組學計畫 (PGI)，該計畫旨在加強亞洲的基因組監測。「將標本送往海外進行分析的日子已經屈指可數了」，他補充道。

但一些研究人員擔心，用於 SARS-CoV-2 測序的資金將會枯竭，新機器將閒置。 印度韋洛爾基督教醫學院的病毒學家 Gagandeep Kang 說，許多國家有能力對其他病原體進行測序，但因為沒有錢而沒有這樣做。「我對我們能夠在多大程度上推進這一點持懷疑態度」。

快速發展

基因組測序能力的增長迅速而全面。 該研究所的病毒學家 Erik Karlsson 說，在大流行期間，柬埔寨巴斯德研究所獲得資金購買了一台 Illumina 下一代基因組測序儀和幾台 Oxford Nanopore 第三代測序儀，包括小型便攜式設備。 它還購買了服務器和計算機，並升級了研究所的互聯網連接，以分析由此產生的大量生物信息學數據。

Karlsson 說，此類投資將 SARS-CoV-2 基因組測序的成本從 2020 年初的 1,000 美元降低到 2021 年底的 20 美元。 這種能力還被用於對最近爆發的流感和屈公熱的樣本以及登革熱病毒和一些蝙蝠和囓齒動物病毒的樣本進行快速測序。「它有點膨脹成很多不同的東西」，卡爾森說。 現在，他的團隊正在對環境樣本進行批量「宏基因組」測序，例如來自活體動物市場、豬屠宰場和蝙蝠洞的空氣。

整個非洲也發生了類似的擴張。 2018 年，只有 7 個國家擁有用於公共衛生目的的下一代測序設備，現在約有 38 個國家擁有這些設施，Tessema 在描述非洲 PGI 支持的擴張時說。 Tessema 說，這項工作在大流行之前就開始了，但令人擔憂的 SARS-CoV-2 變異株的出現加速了資金的獲取和各國對基因組技術的採用。 自 2020 年以來，整個非洲大陸的設施已經對超過 140,000 個 SARS-CoV-2 基因組進行了測序。

當今年早些時候在剛果民主共和國 (DRC) 的貝尼發現一例伊波拉病例時，該人的樣本被採集到約 240 公里外的戈馬實驗室進行檢測和測序，避免了將樣本運送到到該國首都金薩沙1,600多公里外非洲的延誤。 實驗室很快確定伊波拉序列與幾年前在該地區傳播的序列有關，並不代表新的溢出事件。 Tessema 說，剛果民主共和國的實驗室能夠快速對伊波拉樣本進行測序，因為他們正在使用可用於 SARS-CoV-2 測序的試劑和設備。

轉向其他疾病

總部位於瑞士日內瓦的全球診斷聯盟 FIND 的基因組學和測序項目負責人 Anita Suresh 說，隨著許多地區對 SARS-CoV-2 的檢測減少，各國開始轉向對地方性病原體進行測序。 一些組織已經宣布資助非洲和亞洲的非 SARS-CoV-2 病原體測序，包括位於華盛頓州西雅圖的比爾和梅琳達.蓋茨基金會，該基金會支持非洲 PGI 和亞洲 PGI。

從立百病毒到結核病，每個國家都有自己的優先事項。 有些是由在大流行期間減少或被忽視的疾病暴發驅動的，位於科倫坡的免疫學家 Neelika Malavige 說，她是被忽視疾病藥物倡議登革熱計畫的負責人。「登革熱今年捲土重來」。

研究人員表示，這種對測序興趣的增加正在產生更多的研究數據，以及合作開發新療法和疫苗的機會。 但是缺乏能夠解讀測序數據的人，比如生物信息學家和流行病學家。 Olivo Miotto 說，這是一個挑戰，他在牛津大學研究瘧疾，並在曼谷 Mahidol Oxford 熱帶醫學研究中心工作。

Karlsson 說，許多人都接受過如何解釋 COVID-19 數據的培訓，但他們不知道如何將其應用於其他疾病。「全球仍然缺乏訓練有素的勞動力」。

成本挑戰

研究人員擔心捐助者和政府對基因組監測的投資將會枯竭。 達卡兒童健康研究基金會的分子微生物學家 Senjuti Saha 說，慈善資助者通常不支持長期監測。

測序儀每年也要花費數萬美元進行維護。 Pronyk 說，所需的試劑很昂貴，而且在沒有成熟供應鏈的地區成本更高，解決分配缺口將是 Asia PGI 的首要任務。

比爾和梅琳達·蓋茨基金會病原體基因組測序工作的負責人戴維·布拉澤斯 (David Blazes) 說，在某些地方，可能需要幾個月的時間才能讓技術人員修理壞掉的機器。 研究人員表示，還需要開展工作來開發對 SARS-CoV-2 以外的病原體進行測序的標準化流程，並降低測序成本。

doi: https://doi.org/10.1038/d41586-022-04453-2

COVID spurs boom in genome sequencing for infectious diseases

From dengue to Ebola, laboratories in Asia and Africa are using sequencing technology and skills acquired during the pandemic to track endemic diseases quickly.

NEWS / 15 December 2022 / Nature

Many labs are using genome-sequencing equipment acquired during the pandemic to track other diseases.Credit: T. Narayan/Bloomberg via Getty

When a three-year old boy in Cambodia came down with avian influenza last year, researchers at the Pasteur Institute of Cambodia in Phnom Penh used genome-sequencing technology bought during the COVID-19 pandemic to sequence samples from the boy in a single day. They confirmed that he had H9N2, a common virus found in birds. Later, they sequenced samples of the virus from a chicken living in the boy’s house, suggesting that that was how he was infected and that the virus was unlikely to spread to other people. Before the pandemic, samples would have been sent abroad for sequencing and such information would typically have taken weeks or months to arrive.

The lab is one of many across Asia and Africa that increased its sequencing capacity during the pandemic and is now looking beyond COVID-19 to study other diseases. “Since early 2022, we’ve been thinking about how to utilize this capacity for other pathogens”, such as cholera, malaria, polio and Ebola, says Sofonias Tessema, who heads the pathogen genomics programme at the Africa Centres for Disease Control and Prevention in Addis Ababa.

Before the pandemic, genomic sequencing was mainly reserved for research in many regions, but now it is being used for public health, says Ruklanthi de Alwis, a viral immunologist at Duke–National University of Singapore (Duke–NUS) Medical School. Sequencing data combined with other clinical information can be used to diagnose diseases, identify chains of transmission, track mutations, trace outbreaks, speed up the public-health response and contribute to vaccine development.

Many countries want to do their own sequencing, says Paul Pronyk, an infectious-diseases physician also at Duke–NUS, which supports the Asia Pathogen Genomics Initiative (PGI) — a programme that aims to enhance genomic surveillance in Asia. “The days of sending your specimens overseas for analysis are numbered,” he adds.

But some researchers worry that the funding that paid for SARS-CoV-2 sequencing will dry up and new machines will sit idle. Many countries have the capacity to sequence other pathogens but aren’t doing so because there is no money, says Gagandeep Kang, a virologist at the Christian Medical College in Vellore, India. “I’m a bit sceptical about how much we will be able to advance this.”

Rapid expansion

The growth in genome-sequencing capacity has been swift and sweeping. During the pandemic, the Pasteur Institute of Cambodia obtained funds to buy an Illumina next-generation genome sequencer and several Oxford Nanopore third-generation sequencers, including small portable devices, says Erik Karlsson, a virologist at the institute. It also bought servers and computers and upgraded the institute’s Internet connection to analyse the resulting reams of bioinformatics data.

Such investments lowered the cost of sequencing a SARS-CoV-2 genome from US$1,000 in early 2020 to $20 by the end of 2021, says Karlsson. And that capacity has also been used to quickly sequence samples from recent outbreaks of influenza and Chikungunya, as well as samples of dengue virus and some bat and rodent viruses. “It kind of ballooned into a lot of different things,” says Karlsson. Now, his team is doing bulk ‘metagenomic’ sequencing of environmental samples, such as air from live-animal markets, swine slaughterhouses and bat caves.

A similar expansion has taken place across Africa. In 2018, just 7 countries had next-generation sequencing equipment for public-health purposes, and now some 38 countries have those facilities, says Tessema, describing an expansion supported by the Africa PGI. That work started before the pandemic, but the emergence of SARS-CoV-2 variants of concern accelerated access to funding and countries’ adoption of genomic technologies, says Tessema. Since 2020, facilities across the continent have sequenced more than 140,000 SARS-CoV-2 genomes.

When a case of Ebola was identified in Beni in the Democratic Republic of the Congo (DRC) earlier this year, samples from the person were taken some 240 kilometres to a lab in Goma for testing and sequencing, avoiding the delay of transporting them across the country to the capital Kinshasa, more than 1,600 kilometres away. The lab quickly identified that the Ebola sequences were linked to those circulating a couple of years earlier in the region, and did not represent a new spillover event. Labs in the DRC are able to sequence Ebola samples rapidly because they are using the reagents and equipment available for SARS-CoV-2 sequencing, says Tessema.

Pivoting to other diseases

As testing for SARS-CoV-2 declines in many regions, countries are starting to pivot to sequencing endemic pathogens, says Anita Suresh, who oversees genomics and sequencing projects at FIND, the global alliance for diagnostics, headquartered in Geneva, Switzerland. Several organizations have announced grants for sequencing non-SARS-CoV-2 pathogens in Africa and Asia, including the Bill and Melinda Gates Foundation in Seattle, Washington, which supports Africa PGI and Asia PGI.

From Nipah virus to tuberculosis, every country has its own priorities. Some are driven by disease outbreaks that had decreased or been neglected during the pandemic, says Neelika Malavige, an immunologist who heads the dengue programme at the Drugs for Neglected Diseases Initiative and is based in Colombo. “Dengue is back with a vengeance this year.”

This increased interest in sequencing is generating more data for research, and opportunities to collaborate on new treatments and vaccines, say researchers. But there is a shortage of people who can interpret sequencing data, such as bioinformaticians and epidemiologists. This poses a challenge, says Olivo Miotto, who studies malaria at the University of Oxford, and is based at the Mahidol Oxford Tropical Medicine Research Unit in Bangkok.

Many people have been trained in how to interpret COVID-19 data, but they don’t know how to apply this to other diseases, says Karlsson. “There’s still a global paucity of trained workforce.”

Cost challenges

Researchers are worried that donor and government investment in genomic surveillance will dry up. Philanthropic funders typically don’t support long-term surveillance, says Senjuti Saha, a molecular microbiologist at the Child Health Research Foundation in Dhaka.

Sequencing machines also cost tens of thousands of dollars each year to maintain. The reagents required are expensive, and they can cost more in regions without established supply chains, says Pronyk, who says solving the distribution gaps will be a priority for Asia PGI.

In some places, it can take months to get a technician to repair a broken machine, says David Blazes, who leads work on pathogen genomic sequencing at the Bill and Melinda Gates Foundation. Work is also needed to develop standardized processes for sequencing pathogens other than SARS-CoV-2 and to bring the costs of sequencing down, say researchers.

doi: https://doi.org/10.1038/d41586-022-04453-2