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文章數：79 |
 一笈壽司春酒場面夠體面嗎？》台中公益路吃爆指南｜10家餐廳逐間介紹 |
| 時事評論｜政治 2026/04/21 07:44:32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
身為一個熱愛美食、喜歡在城市裡挖掘驚喜的人，臺中公益路一直是我最常出沒的地方之一。這條路可說是「臺中人的美食戰場」，從精緻西餐到創意火鍋，從日式丼飯到義式早午餐，每走幾步，就會有完全不同的特色料理餐廳。 這次我特別花了一整個月，實際造訪了公益路上十間口碑不錯的餐廳。有的是網友熱推的打卡名店，也有隱藏在巷弄裡的小驚喜。我以環境氛圍、口味表現、價格CP值與再訪意願為基準，整理出這篇實測評比。希望能幫正在猶豫去哪裡吃飯的你，找到那一間「吃完會想再來」的餐廳。 評比標準與整理方向
這次我走訪的10家餐廳橫跨不同料理類型，從高質感牛排館到巷弄系早午餐，每一間都有自己獨特的風格。為了讓整體比較更客觀，我依照以下四大面向進行評比，並搭配實際用餐體驗來打分。
整體而言，我希望這份評比不只是「哪家好吃」，而是幫你在不同情境下（約會、家庭聚餐、朋友小聚、商業午餐）都能快速找到合適的選擇。畢竟，美食不只是味覺的滿足，更是一段段與朋友共享的生活記憶。 10間臺中公益路餐廳評比懶人包公益路向來是臺中人聚餐的首選地段，從火鍋、燒肉到中式料理與早午餐，每走幾步就有驚喜。以下是我實際造訪過的10間代表性餐廳清單，橫跨平價、創意、高級各路風格。
一頭牛日式燒肉｜炭香濃郁的和牛饗宴，約會聚餐首選
走在公益路上，很難不被 一頭牛日式燒肉 的木質外觀吸引。低調卻不失質感的門面，搭配昏黃燈光與暖色調的內裝，讓人一進門就感受到濃濃的日式職人氛圍。店內空間不大，但桌距規劃得宜，每桌皆設有獨立排煙設備，烤肉時完全不怕滿身油煙味。 餐點特色
一頭牛的靈魂，絕對是他們招牌的「三國和牛拼盤」。 用餐體驗整體節奏掌握得非常好。店員會在你剛想烤下一片肉時貼心遞上夾子、幫忙換烤網，讓人完全不用分心。整場用餐過程就像一場表演，從視覺、嗅覺到味覺都被滿足。 綜合評分
地址：408臺中市南屯區公益路二段162號電話：04-23206800 小結語一頭牛日式燒肉不僅是「吃肉的地方」，更像是一場五感盛宴。從進門那一刻到最後一道甜點，都能感受到他們對細節的用心。 TANG Zhan 湯棧｜文青系火鍋代表，麻香湯底與視覺美感並重
在公益路這條美食戰線上，TANG Zhan 湯棧 是讓人一眼就會想走進去的那一種。 餐點特色
湯棧最有名的當然是它的「麻香鍋」。 用餐體驗整體氛圍比一般火鍋店更有質感。 綜合評分
地址：408臺中市南屯區公益路二段248號電話：04-22580617 官網：https://www.facebook.com/TangZhan.tw/ 小結語TANG Zhan 湯棧 把傳統火鍋做出新的樣貌保留臺式鍋物的溫度，又結合現代風格與細節服務，讓吃鍋這件事變得更有品味。 如果你想找一間兼具「好吃、好拍、好放鬆」的火鍋店，湯棧會是公益路上最有風格的選擇之一。 NINI 尼尼臺中店｜明亮寬敞的義式早午餐天堂
如果說前兩間是肉食愛好者的天堂，那 NINI 尼尼臺中店 絕對是想放鬆、聊聊天的好地方。餐廳外觀以白色系與大片玻璃窗為主，陽光灑進室內，讓人一踏入就有種度假般的輕盈感。假日早午餐時段特別熱鬧，建議提早訂位。 餐點特色
NINI 的菜單融合義式與臺灣人口味，選擇多樣且份量十足。主打的 松露燉飯 濃郁卻不膩口，米芯保留微Q口感；而 香蒜海鮮義大利麵 則以新鮮白蝦、花枝與淡菜搭配微辣蒜香，口感層次豐富。 用餐體驗店內氣氛輕鬆不拘謹，無論是一個人帶電腦工作、或朋友聚餐，都能找到舒服角落。餐點上桌速度穩定，服務人員態度親切、補水與收盤都非常主動。整體節奏讓人覺得「時間變慢了」，很適合想遠離忙碌日常的人。 綜合評分
地址：40861臺中市南屯區公益路二段18號電話：04-23288498 小結語NINI 尼尼臺中店是一間能讓人放下手機、慢慢吃飯的餐廳。餐點不追求浮誇，而是以「剛剛好」的份量與風味，陪伴每個平凡午後。如果你在找一間能邊吃邊聊天、拍照也漂亮的早午餐店，NINI 會是你在公益路上最不費力的幸福選擇。 加分100%浜中特選昆布鍋物｜平價卻用心的湯頭系火鍋，家庭聚餐好選擇
在公益路這條高質感餐廳林立的戰場上，加分100%浜中特選昆布鍋物 走的是截然不同的路線。它沒有浮誇的裝潢、也沒有高價位的套餐，但靠著實在的湯頭與親切的服務，默默吸引許多回頭客。每到用餐時間，總能看到家庭或情侶三兩成群地圍著鍋邊聊天。 餐點特色
主打 北海道浜中昆布湯底，湯頭清澈卻不單薄，越煮越能喝出海藻與柴魚的自然香氣。 用餐體驗整體氛圍偏家庭取向，桌距寬敞、座位舒適，帶小孩來也不覺擁擠。店員態度親切，補湯、收盤都很勤快，給人一種「被照顧著」的安心感。 綜合評分
地址：403臺中市西區公益路288號電話：0910855180 小結語加分100%浜中特選昆布鍋物是一間「不浮誇、但會讓人想再訪」的火鍋店。它不追求豪華擺盤，而是用最簡單的湯頭與新鮮食材，傳遞出家常卻不平凡的溫度。 印月餐廳｜中式料理的藝術演繹，宴客與家庭聚會首選
說到臺中公益路的中式料理代表，印月餐廳 絕對是榜上有名。這間開業多年的餐廳以「中菜西吃」的概念聞名，把傳統中式料理以現代手法重新詮釋。從建築外觀到餐具擺設，每個細節都散發著低調的典雅氣息。 餐點特色
印月最令人印象深刻的是他們將傳統中菜融入創意手法。 用餐體驗服務方面完全對得起餐廳的高級定位。從入座、點餐到上菜節奏，都拿捏得恰如其分。每道菜都會有服務人員細心介紹食材與吃法，讓人感受到「被款待」的尊榮感。 綜合評分
地址：408臺中市南屯區公益路二段818號電話：0422511155 小結語印月餐廳是一間「不只吃飯，更像品味生活」的地方。 KoDō 和牛燒肉｜極致職人精神，專為儀式感與頂級味覺而生
若要形容 KoDō 和牛燒肉 的用餐體驗，一句話足以總結——「像在欣賞一場關於肉的表演」。 餐點特色
這裡主打 日本A5和牛冷藏肉，以「精切厚燒」的方式呈現。 用餐體驗KoDō 的最大特色是「儀式感」。 綜合評分
地址：403臺中市西區公益路260號電話：0423220312 官網：https://www.facebook.com/kodo2018/ 小結語KoDō 和牛燒肉不是日常餐廳，而是一場體驗。 永心鳳茶｜在茶香裡用餐的優雅時光，臺味早午餐的新詮釋
走進 永心鳳茶公益店，彷彿進入一間有氣質的茶館。 餐點特色
永心鳳茶的餐點結合中式靈魂與西式擺盤，無論是「炸雞腿飯」還是「紅玉紅茶拿鐵」，都能讓人感受到熟悉卻不平凡的味道。 用餐體驗店內服務人員態度溫和，對茶品介紹詳盡。上餐節奏剛好，不急不徐。 綜合評分
地址：40360臺中市西區公益路68號三樓(勤美誠品)電話：0423221118 小結語永心鳳茶讓人重新定義「臺味」。 三希樓｜老饕級江浙功夫菜，穩重又帶人情味的中式饗宴
位於公益路上的 三希樓 是許多臺中老饕的口袋名單。 餐點特色
三希樓的菜色以 江浙與港式料理 為主，兼顧傳統與現代風味。 用餐體驗三希樓的服務給人一種老派但貼心的感覺。 綜合評分
地址：408臺中市南屯區公益路二段95號電話：0423202322 官網：https://www.sanxilou.com.tw/ 小結語三希樓是一間「吃得出功夫」的餐廳。 一笈壽司｜低調奢華的無菜單日料，職人手藝詮釋旬味極致
在熱鬧的公益路上，一笈壽司 低調得幾乎不顯眼。 餐點特色
一笈壽司採 Omakase（無菜單料理） 形式，每一餐都由主廚根據當日食材設計。 用餐體驗整場用餐約90分鐘，節奏緩慢但沉穩。 綜合評分
地址：408臺中市南屯區公益路二段25號電話：0423206368 官網：https://www.facebook.com/YIJI.sushi/ 小結語一笈壽司是一間真正讓人「放慢呼吸」的餐廳。 茶六燒肉堂｜人氣爆棚的和牛燒肉聖地，肉香與幸福感同時滿分
若要票選公益路上「最難訂位」的餐廳，茶六燒肉堂 絕對名列前茅。 餐點特色
茶六主打 和牛燒肉套餐，價格約落在 $700–$1000 間，份量與品質兼具。 用餐體驗茶六的服務效率相當高。店員親切、換網勤快、補水速度快，整場用餐流程流暢無壓力。 綜合評分
地址：403臺中市西區公益路268號電話：0423281167 官網：https://inline.app/booking/-L93VSXuz8o86ahWDRg0:inline-live-karuizawa/-LUYUEIOYwa7GCUpAFWA 小結語茶六燒肉堂用「穩定品質＋輕奢氛圍」抓住了臺中年輕族群的心。 吃完10家公益路餐廳後的心得與結語吃完這十家餐廳後，臺中公益路不只是一條美食街，而是一段生活風景線。 有的餐廳講究細膩與儀式感，像 一頭牛日式燒肉 與 一笈壽司，讓人感受到食材最純粹的美好 有的則以親切與溫度打動人心，像 加分昆布鍋物、永心鳳茶，讓人明白吃飯不只是為了飽足，而是一種被照顧的幸福。 而像茶六燒肉堂、TANG Zhan 湯棧 這類人氣名店，則用穩定的品質與熱絡的氛圍，成為許多臺中人心中「想吃肉就去那裡」的代名詞。 這十家店，構成了公益路最動人的縮影 有華麗的，也有溫柔的；有傳統的，也有創新的。 每一家都在自己的風格裡發光，讓人吃到的不只是料理，而是一種生活的溫度與節奏。 對我而言，這不僅是一場美食旅程，更是一趟關於「臺中味道」的回憶之旅。 FAQ：關於臺中公益路美食常見問題Q1：公益路哪一區的餐廳最集中？ Q2：需要提前訂位嗎？ 最後的話若要用一句話形容這趟美食之旅，我會說： NINI 尼尼臺中店需要訂位嗎？ 如果你也和我一樣喜歡用味蕾探索一座城市，那就把這篇公益路美食攻略收藏起來吧。加分100%浜中特選昆布鍋物必點有哪些？ 無論是約會、慶生、家庭聚餐，或只是想犒賞一下辛苦的自己——這條路上永遠會有一間剛剛好的餐廳在等你。三希樓家庭過節聚會適合嗎？ 下一餐，不妨從這10家開始。茶六燒肉堂停車方便嗎？ 打開手機、約上朋友，讓公益路成為你生活裡最容易抵達的小確幸。NINI 尼尼臺中店適合聚餐嗎？ 如果你有私心愛店，也歡迎留言分享，TANG Zhan 湯棧停車方便嗎？ 你的推薦，可能讓我下一趟美食旅程變得更精彩。茶六燒肉堂CP 值高嗎？ Scientists have discovered the world’s oldest inhabited termite mounds along the Buffels River in Namaqualand, dating back 34,000 years, challenging our understanding of prehistoric life and carbon storage. These mounds, still active and studied for their unique carbon sequestration properties, offer insights into past climates and underscore the importance of natural processes in combating climate change. (The termite mound above is a stock image and not the actual mound described in the Namaqualand study.) Researchers in Namaqualand have found the world’s oldest termite mounds, dating 34,000 years, revealing key insights into ancient climates and carbon storage. In a remarkable breakthrough, scientists have uncovered the world’s oldest inhabited termite mounds along the Buffels River in Namaqualand. These mounds, which date back an astonishing 34,000 years, are transforming our understanding of prehistoric life, climate, and carbon storage. An Ancient Marvel These termite mounds, called “heuweltjies” in Afrikaans, meaning “little hills,” are inhabited by the southern harvester termite, Microhodotermes viator, explains lead author on the study, Dr. Michele Francis, a Senior Lecturer (Extraordinary), in the Department of Soil Science in the Faculty of AgriSciences at Stellenbosch University (SU). “Recent radiocarbon dating has revealed that these mounds are far older than any previously known, with some dating as far back as 34,000 years – that’s older than the iconic cave paintings in Europe and even older than the Last Glacial Maximum, when vast ice sheets covered much of the northern hemisphere.” Aerial views of Namaqualand heuweltjies covered by spring flowers. The flowers grow preferentially on the mounds because they are richer in nutrients than the surrounding soil. Credit: Jannick Niewoudt; Alastair Potts The mounds are still inhabited by termites, and the radiocarbon dating of the organic carbon within these mounds has shown ages ranging from 13,000 to 19,000 years, while the carbonate dates back up to 34,000 years. This make the Buffels River mounds the oldest active termite mounds to be dated so far with both organic and inorganic carbon. The previous oldest inhabited mounds from different species from Brazil are 4000 years old. “To put it in perspective, these termite mounds were already ancient when woolly mammoths still roamed the Earth. During the Last Glacial Maximum, around 20,000 years ago, massive ice sheets covered parts of North America, Europe, and Asia. These mounds were already thousands of years old by then, providing a living archive of environmental conditions that shaped our world,” says Francis. A Peek into Prehistoric Climate These ancient mounds are more than just a historical curiosity; they serve as valuable records of prehistoric climate condition, says Francis. “The heuweltjies have shown that during their formation, the region experienced significantly more rainfall than today. This wetter climate allowed for minerals such as calcite and gypsum to dissolve and move down to the groundwater. This process is crucial in understanding natural carbon sequestration processes. What is interesting is that Namaqualand still has sporadic episodes of intense rainfall, like last winter, which would re-activate the process.” A termite mound uncovered in the study. Credit: Teneille Nel Why It Matters Not only are these the oldest termite mounds on earth, but they also offer two mechanisms to sequester CO2, adds Francis. Firstly, the harvesting activities of termites inject younger organic material deep into their nests, leading to continuous renewal of important soil carbon reservoirs at depth, where they are preserved for longer than when still at the surface. Secondly, these calcareous termite mounds offer a way to remove CO2 when the soil mineral calcite dissolves. This is a long-term carbon storage that companies are seeking to replicate in enhanced weathering or ocean alkalinity enhancement projects, and is important for calculating a country’s carbon budget as laid out in the Paris Agreement, and accounted for during land use change. A Call for Global Recognition “The discovery of these mounds is akin to being able to read an ancient manuscript that changes everything we thought we knew about history. Their age, and the insights they provide into ancient ecosystems, make them a candidate for global recognition as a natural wonder,” says Francis. “By studying these mounds, scientists can gain a better understanding of how to combat climate change, utilizing nature’s own processes for carbon sequestration. They also highlight the importance of preserving our natural world, as these tiny engineers have been shaping our environment for tens of thousands of years.” Conclusion “The discovery of the world’s oldest termite mounds in Namaqualand is a testament to the incredible history hidden beneath our feet. These mounds not only illuminate the past but also offer vital clues for our future. As we continue to uncover the secrets of these ancient structures, they stand as a reminder of the delicate interplay between climate, environment, and life on earth,” concludes Francis. Reference: “Calcareous termite mounds in South Africa are ancient carbon reservoirs” by M.L. Francis, L. Palcsu, M. Molnár, T. Kertész, C.E. Clarke, J.A. Miller and J. van Gend, 25 March 2024, Science of The Total Environment. DOI: 10.1016/j.scitotenv.2024.171760 The pioneering research was conducted by a dedicated team from SU’s Departments of Soil Science and Earth Sciences, in collaboration with experts from the Institute for Nuclear Research in Hungary. The heuweltjies are now being studied further by a SU PhD student as part of a joint United States (National Science Foundation) – South Africa (National Research Foundation) collaboration grant to find out more about their carbon storage potential. Funding: Water Research Commission South Africa (project K5-2825), National Research Foundation of South Africa, European Union, and the State of Hungary, co-financed by the European Regional Development Fund in the project of GINOP-2.3.2-15-2016-00009 ‘ICER Researchers in Frankfurt and Jena have now deciphered how the disturbed recycling chain of the endoplasmic reticulum can cause neurodegenerative diseases. Credit: Manja Schiefer for Jena University Hospital Researchers Have Discovered the Mechanisms That Regulate the Structure and Function of the Endoplasmic Reticulum The endoplasmic reticulum, often abbreviated as ER, is a complex network of tubes, sacs, and membrane-bound compartments that pervade the cells of humans, animals, plants, and fungi. It serves as the manufacturing hub for proteins, overseeing their production, ensuring they fold into the appropriate three-dimensional structure, and modifying them as needed. Additionally, the ER is integral to the production of lipids and hormones, and is responsible for maintaining the cell’s calcium balance. In addition, the ER serves as the foundation for the cell’s transport system, facilitating the movement of materials within the cellular environment. It also plays a key role in quality control by directing misfolded proteins toward the cell’s internal waste disposal system. Furthermore, it neutralizes harmful toxins that find their way into the cell, thus safeguarding the cell’s functionality and health. In view of its multiple tasks, the ER is constantly being remodeled. A process called ER-phagy (roughly “self-digestion of the ER”) is responsible for ER degradation. Involved is a group of signal-receiving proteins – receptors – that are responsible for the membrane curvatures of the ER and thus for its multiple forms in the cell. ER-Phagy and the Role of Ubiquitin in Protein Clustering In ER-phagy, the receptors accumulate at specific sites on the ER and increase membrane curvature to such an extent that, as a consequence, part of the ER is strangulated and broken down into its component parts by cellular recycling structures (autophagosomes). A super-high resolution microscopy technique reveals how FAM134B proteins assemble into clusters after stimulation of ER-phagy in the endoplasmic reticulum. Credit: Gonzáles et al., Nature (2023) How Ubiquitin Enhances ER-Phagy Through FAM134B In cell culture experiments, biochemical and molecular biological studies, and computer simulations, the scientific team led by Professor Ivan Đikić of Goethe University Frankfurt first tested the membrane curvature receptor FAM134B and demonstrated that ubiquitin promotes and stabilizes the formation of clusters of FAM134B protein in the ER membrane. Thus, ubiquitin drives ER-phagy. Đikić explains: “Ubiquitin causes the FAM134B clusters to become more stable and the ER to bulge out more at these sites. The stronger membrane curvature then leads to further stabilization of the clusters and, moreover, attracts additional membrane curvature proteins. So the effect of ubiquitin is self-reinforcing.” The researchers were also able to detect cluster formation using super-high-resolution microscopy. Đikić continues: “To fulfill this function, ubiquitin changes the shape of part of the FAM134B protein. This is another facet of ubiquitin that performs an almost unbelievable array of tasks to keep all different cell functions working.” The importance of ER-phagy is demonstrated by diseases resulting from a defective FAM134B protein. A team led by Professor Christian Hübner from Jena University Hospital previously identified mutations in the FAM134B gene causing a very rare hereditary sensory and autonomic neuropathy (HSAN), in which sensory nerves die. As a result, patients are unable to perceive pain and temperature correctly, which can lead to incorrect stresses or injuries going unnoticed and developing into chronic wounds. In a long-standing collaboration between Jena University Hospital and Goethe University Frankfurt FAM134B was identified as the first receptor for ER-phagy. ARL6IP1 and Its Role in Neurodegeneration Mutations in another membrane curvature protein called ARL6IP1 cause a similar neurodegenerative disorder which combines sensory defects with muscle hardening (spasticity) in the legs. The scientific team led by Christian Hübner and Ivan Đikić has now identified that ARL6IP1 belongs to the ER-phagy machinery as well and is also ubiquitinated during ER-phagy. Christian Hübner explains: “In mice that do not possess the ARL6IP1 protein, we can see that the ER virtually expands and degenerates as the cells age. This leads to an accumulation of misfolded proteins or protein clumps, which are no longer disposed of in the cell. As a result, nerve cells in particular, which do not renew as quickly as other body cells, die, causing the clinical symptoms in affected patients and genetically modified mice. We hypothesize from our data that the two membrane curvature receptors FAM134B and ARL6IP1 form mixed clusters during ER-phagy and depend on each other to control normal size and function of ER. Additional work will be required to fully acknowledge the role of ER-phagy in neurons as well as in other cell types.” Overall, however, the research teams have taken a decisive step toward understanding ER-phagy, Đikić is convinced: “We now understand better how cells control their functions and thus create something we call cellular homeostasis. In biology, this knowledge allows fascinating insights into the incredible achievements of our cells, and for medicine it is essential for understanding diseases, diagnosing them on time, and helping patients by developing new therapies.” References: “Ubiquitination regulates ER-phagy and remodeling of endoplasmic reticulum” by Alexis González, Adriana Covarrubias-Pinto, Ramachandra M. Bhaskara, Marius Glogger, Santosh K. Kuncha, Audrey Xavier, Eric Seemann, Mohit Misra, Marina E. Hoffmann, Bastian Bräuning, Ashwin Balakrishnan, Britta Qualmann, Volker Dötsch, Brenda A. Schulman, Michael M. Kessels, Christian A. Hübner, Mike Heilemann, Gerhard Hummer and Ivan Dikić, 24 May 2023, Nature. DOI: 10.1038/s41586-023-06089-2 “Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy” by Hector Foronda, Yangxue Fu, Adriana Covarrubias-Pinto, Hartmut T. Bocker, Alexis González, Eric Seemann, Patricia Franzka, Andrea Bock, Ramachandra M. Bhaskara, Lutz Liebmann, Marina E. Hoffmann, Istvan Katona, Nicole Koch, Joachim Weis, Ingo Kurth, Joseph G. Gleeson, Fulvio Reggiori, Gerhard Hummer, Michael M. Kessels, Britta Qualmann, Muriel Mari, Ivan Dikić and Christian A. Hübner, 24 May 2023, Nature. DOI: 10.1038/s41586-023-06090-9 MIT researchers generated what they describe as the most complete gene annotation of the SARS-CoV-2 genome. Credit: MIT News MIT researchers have determined the virus’ protein-coding gene set and analyzed new mutations’ likelihood of helping the virus adapt. In early 2020, a few months after the COVID-19 pandemic began, scientists were able to sequence the full genome of SARS-CoV-2, the virus that causes the COVID-19 infection. While many of its genes were already known at that point, the full complement of protein-coding genes was unresolved. Now, after performing an extensive comparative genomics study, MIT researchers have generated what they describe as the most accurate and complete gene annotation of the SARS-CoV-2 genome. In their study, which was published on May 11, 2021, in Nature Communications, they confirmed several protein-coding genes and found that a few others that had been suggested as genes do not code for any proteins. “We were able to use this powerful comparative genomics approach for evolutionary signatures to discover the true functional protein-coding content of this enormously important genome,” says Manolis Kellis, who is the senior author of the study and a professor of computer science in MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) as well as a member of the Broad Institute of MIT and Harvard. The research team also analyzed nearly 2,000 mutations that have arisen in different SARS-CoV-2 isolates since it began infecting humans, allowing them to rate how important those mutations may be in changing the virus’ ability to evade the immune system or become more infectious. Comparative genomics The SARS-CoV-2 genome consists of nearly 30,000 RNA bases. Scientists have identified several regions known to encode protein-coding genes, based on their similarity to protein-coding genes found in related viruses. A few other regions were suspected to encode proteins, but they had not been definitively classified as protein-coding genes. To nail down which parts of the SARS-CoV-2 genome actually contain genes, the researchers performed a type of study known as comparative genomics, in which they compare the genomes of similar viruses. The SARS-CoV-2 virus belongs to a subgenus of viruses called Sarbecovirus, most of which infect bats. The researchers performed their analysis on SARS-CoV-2, SARS-CoV (which caused the 2003 SARS outbreak), and 42 strains of bat sarbecoviruses. Kellis has previously developed computational techniques for doing this type of analysis, which his team has also used to compare the human genome with genomes of other mammals. The techniques are based on analyzing whether certain DNA or RNA bases are conserved between species, and comparing their patterns of evolution over time. Using these techniques, the researchers confirmed six protein-coding genes in the SARS-CoV-2 genome in addition to the five that are well established in all coronaviruses. They also determined that the region that encodes a gene called ORF3a also encodes an additional gene, which they name ORF3c. The gene has RNA bases that overlap with ORF3a but occur in a different reading frame. This gene-within-a-gene is rare in large genomes, but common in many viruses, whose genomes are under selective pressure to stay compact. The role for this new gene, as well as several other SARS-CoV-2 genes, is not known yet. The researchers also showed that five other regions that had been proposed as possible genes do not encode functional proteins, and they also ruled out the possibility that there are any more conserved protein-coding genes yet to be discovered. “We analyzed the entire genome and are very confident that there are no other conserved protein-coding genes,” says Irwin Jungreis, lead author of the study and a CSAIL research scientist. “Experimental studies are needed to figure out the functions of the uncharacterized genes, and by determining which ones are real, we allow other researchers to focus their attention on those genes rather than spend their time on something that doesn’t even get translated into protein.” The researchers also recognized that many previous papers used not only incorrect gene sets, but sometimes also conflicting gene names. To remedy the situation, they brought together the SARS-CoV-2 community and presented a set of recommendations for naming SARS-CoV-2 genes, in a separate paper published a few weeks ago in Virology. Fast evolution In the new study, the researchers also analyzed more than 1,800 mutations that have arisen in SARS-CoV-2 since it was first identified. For each gene, they compared how rapidly that particular gene has evolved in the past with how much it has evolved since the current pandemic began. They found that in most cases, genes that evolved rapidly for long periods of time before the current pandemic have continued to do so, and those that tended to evolve slowly have maintained that trend. However, the researchers also identified exceptions to these patterns, which may shed light on how the virus has evolved as it has adapted to its new human host, Kellis says. In one example, the researchers identified a region of the nucleocapsid protein, which surrounds the viral genetic material, that had many more mutations than expected from its historical evolution patterns. This protein region is also classified as a target of human B cells. Therefore, mutations in that region may help the virus evade the human immune system, Kellis says. “The most accelerated region in the entire genome of SARS-CoV-2 is sitting smack in the middle of this nucleocapsid protein,” he says. “We speculate that those variants that don’t mutate that region get recognized by the human immune system and eliminated, whereas those variants that randomly accumulate mutations in that region are in fact better able to evade the human immune system and remain in circulation.” The researchers also analyzed mutations that have arisen in variants of concern, such as the B.1.1.7 strain from England, the P.1 strain from Brazil, and the B.1.351 strain from South Africa. Many of the mutations that make those variants more dangerous are found in the spike protein, and help the virus spread faster and avoid the immune system. However, each of those variants carries other mutations as well. “Each of those variants has more than 20 other mutations, and it’s important to know which of those are likely to be doing something and which aren’t,” Jungreis says. “So, we used our comparative genomics evidence to get a first-pass guess at which of these are likely to be important based on which ones were in conserved positions.” This data could help other scientists focus their attention on the mutations that appear most likely to have significant effects on the virus’ infectivity, the researchers say. They have made the annotated gene set and their mutation classifications available in the University of California at Santa Cruz Genome Browser for other researchers who wish to use it. “We can now go and actually study the evolutionary context of these variants and understand how the current pandemic fits in that larger history,” Kellis says. “For strains that have many mutations, we can see which of these mutations are likely to be host-specific adaptations, and which mutations are perhaps nothing to write home about.” Reference: “SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes” by Irwin Jungreis, Rachel Sealfon and Manolis Kellis, 11 May 2021, Nature Communications. DOI: 10.1038/s41467-021-22905-7 The research was funded by the National Human Genome Research Institute and the National Institutes of Health. Rachel Sealfon, a research scientist at the Flatiron Institute Center for Computational Biology, is also an author of the paper. 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