War in Iran and Afghanistan Threatens Central Asia’s Gateway to Global Markets

By James Durso - Mar 11, 2026

• Fighting between the Taliban government and Pakistan threatens major infrastructure projects such as the Trans-Afghan Railway, TAPI pipeline, and CASA-1000 electricity corridor.
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• U.S.–Israel attacks on Iran are disrupting shipping, airspace, and logistics networks that underpin Central Asia’s southern trade routes through the Persian Gulf.
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• As instability spreads, Central Asian states may shift trade toward the Caspian “Middle Corridor” or China-linked routes instead of corridors through Afghanistan, Pakistan, or Iran.
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The U.S.–Israel attacks on Iran and the Afghanistan–Pakistan conflict threaten Central Asia’s plans to establish southbound trade routes to markets in Asia and Africa.

Military escalation between Afghanistan’s Taliban-led government and Pakistan threatens several emerging trade, transport, and energy corridors linking Central Asia to South Asia, the Persian Gulf, and global markets. Risks are both direct (insecurity along routes) and indirect (border closures, investor withdrawal, and partner-state reluctance).

Pakistan previously moved goods through Afghanistan to Central Asian markets, accounting for significant export volumes (bilateral trade was USD2.4 billion in 2025). That corridor is effectively closed, with border crossings, supply chains, and customs operations stalled. The loss of reliable land access undermines Afghanistan’s (food, fuel, industrial inputs) and Central Asian access southward toward Pakistan’s seaports.

Several high-profile connectivity initiatives depend on peace and stable transit through Afghanistan; heightened conflict raises the risk of delay or failure.

The 760-kilometer Uzbekistan–Afghanistan–Pakistan Railway is intended to link Central Asia directly to the Arabian Sea via Afghanistan and Pakistan. The USD6 billion project will cut transit time by five days and reduce transport costs by 40%, but the current conflict makes construction and future operations insecure. International financiers, including the Asian Development Bank and Persian Gulf investors, are likely to hesitate if Pakistan–Afghan relations remain adversarial. Uzbekistan cannot guarantee safe transit if Pakistan views Taliban-linked militant groups as a threat.

CASA-1000, a $1.2 billion cross-border electricity transmission project exporting surplus hydropower from Kyrgyzstan and Tajikistan to Afghanistan and Pakistan, also becomes vulnerable if conflict escalates.

Construction of the long-delayed Turkmenistan-Afghanistan-Pakistan-India (TAPI) natural gas pipeline is underway, but has made limited progress. TAPI is a 1,814-km pipeline running from Turkmenistan through Afghanistan and Pakistan to India, with a capacity of 33 billion cubic meters (bcm)/year. Construction started in 2015, and the Turkmenistan portion was completed by the end of 2024; the Afghanistan section to Herat is projected for completion by the end of 2026.

Taliban–Pakistan hostility undermines Taliban security guarantees, Pakistan may freeze cooperation on construction segments, and India will not commit to off-take agreements in a conflict zone.

Existing road corridors within Pakistan and Afghanistan are at risk. In Pakistan, the Khyber Pass Road corridor, the Peshawar–Torkham Expressway, and trucking routes carrying Central Asian exports to Karachi and Gwadar are high-risk, raising insurance and transport costs, making Pakistani ports less competitive for Central Asian exporters.

In Afghanistan, the Kabul–Jalalabad highway, the Kabul–Kandahar highway, and routes linking Mazar-i-Sharif to Pakistan are vulnerable, and traffic will slow during security operations.

Pakistan may suspend provisions of the Afghanistan–Pakistan Transit Trade Agreement (APTTA) to pressure the Taliban, leading to retaliation by the Afghan side. Goods from Central Asia transiting Afghanistan will be vulnerable to sudden policy reversals that may strand the cargo, vehicles, and drivers.

The Central Asia–South Asia Economic Corridor (CASAEC) is a regional framework that includes road, rail, and energy integration between Kazakhstan, Uzbekistan, Kyrgyzstan, Tajikistan, Afghanistan, and Pakistan. The fighting could stall corridor planning as Afghanistan–Pakistan coordination collapses, Persian Gulf and Chinese investors pause financing, and Central Asian states may shift focus to westward or eastward routes.

The conflict will increase instability along transit corridors, border closures and freight disruption, higher shipping and insurance costs, reduced investor confidence, and a shift away from Pakistan routes toward Iran or the Caspian Sea. The Trans-Afghan Railway, the TAPI natural gas pipeline and the CASA-1000 electricity project can only succeed if there is peace between Kabul and Islamabad.

Politically, Uzbekistan and Kazakhstan lose strategic depth as southward access to the Arabian Sea becomes blocked. Iran becomes more critical as Central Asian states may reroute trade through Iran, but this is risky amid the U.S./Israel–Iran conflict. China’s Belt and Road Initiative (BRI) planning is disrupted, and China’s efforts to develop north–south corridors through Afghanistan and Pakistan face setbacks if neither side can guarantee stability. Uzbekistan, Turkmenistan, and Tajikistan border Afghanistan and will be concerned about spillover violence and refugee flows from adjacent areas of Afghanistan.

In summary, Central Asia loses a key Southward trade gateway through which goods and transit benefits were expected to expand.

U.S.–Israel attacks on Iran are disrupting regional routes and supply chains. The conflict - particularly around the Strait of Hormuz and Persian Gulf airspace - has significant implications for Central Asia.

The crisis has disrupted tanker traffic through the Strait of Hormuz, an energy corridor that hosts the movement of more than 20 percent of global oil and liquefied natural gas exports. Oil price volatility and rerouting add cost and uncertainty for Central Asian energy imports and transit.

Air and freight logistics have also been affected. Thousands of flights have been canceled or rerouted due to airspace closures, making Asia–Europe routes longer and more expensive. The spill-over includes concerns about airspace over South and Central Asia if instability spreads.

Projects that rely on stable Iran, such as the International North-South Transport Corridor, a 7,200-km multimodal network of sea, rail, and road routes for moving freight between India, Iran, Central Asia, Azerbaijan, Europe, and Russia., will face elevated risk if Iran’s logistics infrastructure (the seaports of Chabahar and Bandar Abbas) is targeted or trade sanctions tighten.

Central Asia depends on Iran for access to sea links and alternative routes outside of Russia and China; the current conflict weakens that option. Although partly complete in sections such as the Azerbaijan–Iran Western Route, Russia–Azerbaijan links, and the Mumbai–Bandar Abbas maritime leg, full efficiency depends on stable operations through Iranian territory.

The Five Nations Railway Corridor is a rail link to connect China, through Afghanistan, Tajikistan, and Kyrgyzstan, to Iran and ultimately to Persian Gulf ports. The corridor is meant to deepen Central Asia’s link to global markets via Iran and help the participants avoid maritime chokepoints. A major escalation in or around Iran threatens construction, cross-border coordination, and raises security costs and deters financing and investment, particularly in sections involving Iranian infrastructure. The corridor is making slow progress with limited freight operations between Iran and Afghanistan.

The Southern Corridor through Iran is a broader set of Iranian rail expansions intended to bolster East-West connectivity between Central Asia, the Middle East, and Europe. Iran has been upgrading tracks and electrifying main corridors that link Central Asian freight to the Persian Gulf and European markets. Projects include the Marand–Cheshmeh-Soraya railway and expansion of the Turkmenistan–Iran rail link toward Turkey and beyond.

Nargiza Umarova of the Institute for Advanced International Studies in Tashkent, Uzbekistan, notes the Southern Corridor is “critical for Central Asia,” but active conflict could cause delays, rerouting of freight, and suspension of services as neighboring countries close borders or airspace. Shuttle services that rely on Iranian rail infrastructure may find it difficult to operate safely under US and Israeli attacks.

The Central Asia–Persian Gulf Multimodal Corridor, under the Ashgabat Agreement, links Uzbekistan, Turkmenistan, Iran, and Oman, and is designed for combined rail, road, and maritime transport. Iran represents a critical section of this corridor, enabling overland freight to reach the Persian Gulf, and conflict-related disruption could curtail services that depend on Iranian logistics capacity, customs cooperation, and security guarantees. The corridor is not yet fully operational, and attacks on Iran will slow work.

The Dauletabad–Sarakhs–Khangiran natural gas pipeline links Central Asian energy exports to Iranian networks. Its continued operation supports regional energy trade and complements transport infrastructure by enhancing the incentives for broader integration. Escalation around Iran could threaten energy infrastructure, encourage sanctions, or lower regional investment in pipeline expansions. The pipeline is operational and moves 12 bcm of gas annually.

South-North land corridors through Afghanistan and Pakistan were emerging as strategic links for Central Asia to South Asia and Indian Ocean transits. These include Trans-Afghan rail and road routes and the partly operational Lapis Lazuli Corridor linking Afghanistan with Turkmenistan and beyond, and Central Asian plans to diversify away from Russia–China routes toward Pakistan and Iran. These land routes are now under severe strain as conflict blocks key junctions and raises security costs, discourages investment, and delays infrastructure completion.

Iran or neighboring states (e.g., Pakistan, Turkey) may close borders or airspace, effectively severing key overland corridors that run through or around Iran. This has already happened in parts of the region during heightened conflict.

Possible alternatives are the Middle Corridor that links Central Asia through the Caspian Sea to Azerbaijan, Georgia, Turkey, and onward to Europe — seen as a safer alternative; and the China–Kyrgyzstan–Uzbekistan Railway, another BRI overland route that increases Central Asian connectivity to China and Europe without relying on Iran links.

With Iran unstable and Pakistan embroiled in conflict, Central Asia’s access to ports becomes more constrained. Alternative maritime access—especially via Iranian ports—becomes riskier and more expensive. Central Asian exporters may increasingly rely on northern or east–west corridors (Russia, China) instead of struggling North-South options. And Iran may move to assert more control over Chabahar Port in light of India’s USD 10 billion in defense deals with Israel.

Rail corridors tied to Iran are optimized to complement maritime freight through Persian Gulf ports. Disruptions in the Strait of Hormuz and shipping routes can cascade back into overland connectivity planning and usage.

Displaced trade flows risk increasing transport costs, delivery times, and logistical uncertainty for Central Asian exporters and importers. Some countries could see trade patterns shift further east toward Chinese markets or Caspian routes. Investment flows into connectivity infrastructure are likely to slow unless security stabilizes, as investors avoid conflict zones.

Heightened geopolitical risk reduces or slows foreign investment and financing for infrastructure projects, and may prompt Central Asian states to pivot toward alternatives such as the Trans-Caspian International Transport Route (Middle Corridor) bypassing Iran.

Despite the disruptions, Central Asian states may pursue diversification by pushing more trade via rail and the Trans-Caspian corridor (bypassing conflict zones), deepening ties with China’s BRI and the Middle Corridor through the Caucasus, and strengthening overland routes to Europe that bypass Afghanistan, Pakistan, and Iran.

The U.S. and Israeli attacks on Iran do not just threaten Iranian territory and infrastructure - they endanger key pieces of the regional connectivity architecture that Central Asia seeks to build for diversifying trade routes, reducing dependence on Russia or maritime chokepoints, and integrating into global markets. Despite Trump’s friendly approach toward Uzbekistan and Kazakhstan, he is likely to prioritize cooperation with Israel in the conflict with Iran, leaving regional economic repercussions to be addressed later. Among the effects may be reduced interest by Persian Gulf investors if they turn their attentions to repairing infrastructure damaged by Iranian attacks or increasing military spending.

These combined geopolitical crises are undermining Central Asia’s planned integration into South Asian and Middle Eastern trade networks, prompting nations to pivot toward more secure connectivity options to sustain economic growth and avoid being cut off from global value chains.

By James Durso

How US-Israel War On Iran Exposes Weaknesses In Gulf Missile Defense Systems – Analysis

March 12, 2026 
Arab News
By Dr. Turki Faisal Al-Rasheed

As US President Barack Obama left his country’s embassy in Dublin in his fully armored limousine, his convoy hit an unexpected snag. The vehicle’s underside scraped on a simple ramp and became stuck at the gate — a multimillion dollar machine defeated by an ordinary piece of pavement. The image is hard to forget — enormous investment, but poor design for real world conditions. Our region risks making the same mistake if we pour money into “exquisite” defenses that fail at the critical moment.

The US Defense Innovation Unit, created in 2015 by then Defense Secretary Ash Carter, was meant to prevent exactly that kind of failure in the military domain. It was designed to break through Pentagon bureaucracy and connect the armed forces with fast-moving technologies from Silicon Valley, shifting from slow, traditional contractors to agile private firms. In reality, this has meant experimenting with autonomous systems, microsatellites, and artificial intelligence, while fighting the inertia, over-centralization, and rent-seeking that often plague big defense programs. The core lesson is simple: if you do not reform how you buy and use technology, you end up with very expensive systems that are not fit for the next war.

That next war is now unfolding over our heads. The ongoing US–Israel war on Iran has exposed a dangerous vulnerability in the US-led missile-defense architecture in the Middle East. Iran has executed a sequenced, systems-level campaign that, in a matter of days, blinded and degraded core elements of the US missile-defense network in our region. By destroying the Qatar-based AN/FPS 132 early-warning radar and at least three AN/TPY 2 X band radars linked to THAAD batteries in Saudi Arabia, the UAE and Jordan, Tehran has turned what was designed as a layered, redundant sensor web into a patchwork with serious gaps.

This tactical success has strategic consequences. It accelerates the depletion of high-end interceptors, exposes critical bases and energy infrastructure, and destabilizes key partners such as Jordan. It also erodes US deterrence credibility in the Indo Pacific, because the same finite interceptor stockpile is supposed to help defend Taiwan and Japan. In other words, the Middle East is consuming systems that Washington also counts on for other theaters — a risk Gulf policymakers must factor into any calculation about escalation.

Iran’s approach follows a three-step logic familiar from suppression of enemy air defenses, but applied to missile defense. First, “kill the eyes” by striking early warning radars. Second, “kill the aim” by targeting fire control radars that guide interceptors. Third, “destroy the batteries” by hitting the launchers themselves. Each step attacks a different dependency in an integrated system. Once enough eyes and aim points are removed, the remaining batteries operate in a fog, with compressed and uneven timelines for detection, classification, and engagement. There is no safe “rear area” if long range missiles and drones can reach radars in places like Jordan, which many once assumed were relatively secure.

For years, the US doctrinal concept in the Gulf has been layered missile defense: early warning from the AN/FPS 132 in Qatar and space-based sensors; upper tier defense by THAAD guided by AN/TPY 2 radars; lower tier coverage by Patriot PAC 3; and a maritime layer from Aegis equipped destroyers. On paper, this looked robust. In reality, Iran has shown how quickly a determined adversary can degrade it, especially when it can attack multiple layers at once.

Worse, Tehran is exploiting a cost exchange crisis. Cheap drones and relatively low-cost ballistic missiles are being mixed in large salvos, forcing defenders to fire interceptors that cost millions of dollars per shot at any track that might be lethal. The political and moral cost of a single “leaker” — a missile that gets through and causes mass casualties — pushes commanders to “engage everything.” Over time, that is a losing game, especially for states that rely heavily on imported interceptors and have limited local production capacity.

For Saudi Arabia, this is not an abstract debate. Vision 2030 rests on three interlinked pillars: diversifying the economy, transforming the Kingdom into a global investment hub, and building an “ambitious nation” with secure, resilient infrastructure. At the same time, Saudi Arabia is pursuing an ambitious energy transition, aiming to source around half of its power from renewables by 2030 and to build more than 100 GW of new solar and wind capacity while maintaining its role in oil and gas. All of this depends on the basic condition: physical security for legacy oil facilities, new gas and petrochemical projects, and a rapidly expanding network of renewable plants, industrial zones, and transmission corridors.

The 2019 Abqaiq–Khurais attacks were an early warning. Iran and its proxies temporarily knocked out roughly half of Saudi crude production and about 5 percent of global daily supply, despite existing air defenses. Today, the Kingdom’s new “air defense shield” — a mix of Patriot, THAAD, and AN/TPY 2 radars to protect Riyadh, Eastern Province oil facilities, and key military sites — is partly dependent on the same regional sensor and interceptor web that Iran is now degrading. As US high-end interceptors are consumed to defend bases across the Gulf, there is growing pressure on the availability and prioritization of defensive assets for Saudi energy and power infrastructure, especially if the conflict widens.

This creates a dangerous trap for the Gulf Cooperation Council. A scheme appears to be unfolding in which the US and Israel, driven by their confrontation with Iran, risk pulling the Gulf deeper into a direct clash with Tehran without fully accounting for our long-term security and development priorities. External actors know that their war with Iran will, one way or another, eventually end. They also know that a prolonged Gulf–Iran confrontation would drain our resources, destabilize our societies, and open the door to deeper foreign intervention under the pretext of “assistance.”

We have seen this movie before. During the Iran–Iraq war, “disaster capitalism” thrived on chaos, arms sales and reconstruction contracts, while regional states paid the human and economic cost. The most dangerous outcome of escalation today is not necessarily regime change in Tehran, but the possible disintegration of the Iranian state into prolonged anarchy. That would unleash refugee flows, militia spillover and sustained disruption in energy markets, directly threatening Saudi stability, Vision 2030, and the security of the entire Gulf.

In this context, the GCC has no choice but to close ranks. The recent GCC positions on the Iran–Israel war has emphasized de-escalation and diplomacy, reflecting a growing recognition that war on Iran’s territory would pose an existential risk to regional stability. Saudi Arabia’s clear declaration of support for Kuwait against potential Iraqi threats has shown what principled solidarity can look like; that spirit must extend to every GCC member and every emerging crisis. Unity is not a slogan. It is our first line of defense against being pressured, divided and targeted one by one.


What should a Saudi-centered response look like? First, we need more autonomous sensor coverage and command and control networks that do not collapse if a handful of US owned radars are destroyed. Second, we must protect and, where possible, localize stocks of critical interceptors, while investing in layered defenses that combine high-end systems with cheaper interceptors and passive protection (hardening, dispersal, deception). Third, we must deliberately shield key Vision 2030 assets — oil, gas and power infrastructure, as well as strategic industrial zones — as priority targets for defense planning, not afterthoughts.

At the same time, the GCC must resist being dragged into a direct US–Israel war on Iran. This does not mean accepting aggression or remaining silent in the face of violations of our sovereignty. It means insisting that any response serves our security, our economies, and our long-term vision for regional stability, rather than the short-term agendas of others. It means rejecting blackmail, hidden agendas and opaque “coalitions” that treat Gulf states as logistics hubs and targets rather than partners.

We stand at a fork in the road. One path leads to escalation, exhaustion and dependence — a future where our defense budgets balloon while our development goals shrink, and where Vision 2030 becomes a casualty of someone else’s war. The other path demands courage, discipline and regional unity: saying “no” to being used, “yes” to self-reliant defense innovation, and “always” to protecting our people and our development first.

In the end, the choice before the GCC is stark: either we become the ramp that wrecks someone else’s armored car, or we build the road that safely carries our own future forward.

• Dr. Turki Faisal Al-Rasheed is an adjunct professor at the University of Arizona’s College of Agriculture, Life & Environmental Sciences, in the Department of Biosystems Engineering. He is the author of “Agricultural Development Strategies: The Saudi Experience.” X: @TurkiFRasheed

Arab News

Arab News is Saudi Arabia's first English-language newspaper. It was founded in 1975 by Hisham and Mohammed Ali Hafiz. Today, it is one of 29 publications produced by Saudi Research & Publishing Company (SRPC), a subsidiary of Saudi Research & Marketing Group (SRMG).

  

Global Virus Network opens international headquarters at University of South Florida

Global Virus Network

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Tampa, FL (March 9, 2026) — The Global Virus Network (GVN) marked the opening of its International Headquarters on March 5 at the University of South Florida (USF) Institute for Translational Virology and Innovation (ITVI), a GVN Center of Excellence. The Global Virus Network represents eminent human and animal virologists from more than 90 Centers of Excellence and Affiliates across over 40 countries working to advance research, collaboration and pandemic preparedness.

The ribbon-cutting formalizes a strategic partnership that positions USF Health as the permanent home of GVN’s global scientific network and expands its capacity to coordinate research, surveillance and response to emerging viral threats. GVN selected USF in 2024 to host its International Headquarters.

“We are proud that the Global Virus Network has chosen to establish its International Headquarters at USF, connecting our students, researchers and clinicians with leading virologists and institutions around the world,” said Moez Limayem, PhD, president of the University of South Florida. “USF is deeply committed to supporting GVN’s global mission, and we are excited to host this international hub for virology and pandemic preparedness. This partnership reflects USF Health’s leadership in global health and advances our mission to drive high-impact research and scientific collaboration.”

Founded fifteen years ago following lessons learned from the HIV/AIDS pandemic, the GVN was created to unite the world’s foremost virologists in a permanent, independent scientific network focused on understanding and confronting viral diseases. The network now includes Centers of Excellence and Affiliates across six continents, working collaboratively to improve how the world detects, studies and responds to viral outbreaks.

“The establishment of the Global Virus Network’s International Headquarters at USF Health reflects the strength of the scientific and clinical ecosystem we are building here in Tampa,” said Charles J. Lockwood, MD, MHCM, executive vice president of USF Health and dean of the USF Health Morsani College of Medicine. “By bringing together world-leading virologists with clinicians, this partnership accelerates the path from discovery to real-world impact, improving how we detect, understand and respond to viral diseases that threaten global health.”

The headquarters is housed within the USF Health Institute for Translational Virology and Innovation, founded and directed by Robert C. Gallo, MD, who is also co-founder and international scientific director of GVN and best known for his pioneering discovery of human retroviruses, including HIV as the cause of AIDS.

“This is a very important and meaningful day for the Global Virus Network and for me personally,” Dr. Gallo said. “When we founded GVN fifteen years ago, our goal was simple but ambitious: to unite the world’s leading virologists into a consequential scientific network dedicated to confronting viral threats. We could not have found a better home for GVN than USF Health. The partnership ensures that the network has the stability and environment needed to expand its global mission in pandemic preparedness and translational virology.”

Mathew Evins, chief executive officer and managing executive of the Global Virus Network, said the headquarters represents a focal point for global scientific collaboration.

“The COVID-19 pandemic underscored the need for independent, globally connected scientific infrastructure that exists between outbreaks, not just during crises,” Evins said. “As we cut this ribbon, we are establishing a permanent hub for collaboration, a place where scientists strengthen surveillance, accelerate research and improve the world’s ability to respond to viral threats. Pandemic preparedness requires sustained international cooperation, and this partnership provides the foundation for that work.”

The establishment of GVN’s International Headquarters at USF reinforces a shared commitment to scientific rigor, long-term preparedness and global collaboration in confronting current and future viral threats.

“What we open today is more than a headquarters,” Dr. Gallo said. “It is a foundation for the future, for scientific discovery, global partnership and protecting public health worldwide.”

To view this story on the GVN website, click here.

Click here for images of event and International HQ

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About the Global Virus Network

The Global Virus Network (GVN) is a worldwide coalition comprising 90+ Virology Centers of Excellence and Affiliates across 40+ countries, whose mission is to facilitate pandemic preparedness against viral pathogens and diseases that threaten public health globally. GVN advances knowledge of viruses through (i) data-driven research and solutions, (ii) fostering the next generation of virology leaders, and (iii) enhancing global resources for readiness and response to emerging viral threats. GVN provides the essential expertise required to discover and diagnose viruses that threaten public health, understand how such viruses spread illnesses, and facilitate the development of diagnostics, therapies, and treatments to combat them. GVN coordinates and collaborates with local, national, and international scientific institutions and government agencies to provide real-time virus informatics, surveillance, and response resources and strategies. GVN's pandemic preparedness mission is achieved by focusing on Education & Training, Qualitative & Quantitative Research, and Global Health Strategies & Solutions. The GVN is a non-profit 501(c)(3) organization. For more information, please visit www.gvn.org.

About USF Health

USF Health is dedicated to making life better through research, education and patient care. It is the partnership of the USF Health Morsani College of Medicine, the College of Nursing, the College of Public Health, the Taneja College of Pharmacy, the School of Physical Therapy and Rehabilitation Sciences, the Biomedical Sciences Graduate and Postdoctoral Programs and USF Health’s multispecialty physicians’ group, the largest on Florida’s west coast. In 2025, U.S. News & World Report ranked the USF Health Morsani College of Medicine as the No. 1 medical school in Florida and in the highest tier nationwide for research. U.S. News also ranked the USF College of Public Health and the USF College of Nursing’s Master of Science program No. 1 in the state. Together with Tampa General Hospital, USF Health forms one of the nation’s premier academic health systems, with more than 1,000 physicians and providers caring for more than one million patients each year. USF Health is part of the University of South Florida, a top-ranked research university and member of the Association of American Universities (AAU). USF serves approximately 50,000 students and generates nearly $10 billion in annual economic impact for Florida. For more information, visit health.usf.edu.

Recent pandemic viruses jumped to humans without prior adaptation, UC San Diego study finds

Large-scale evolutionary analysis shows most zoonotic viruses emerge without prior adaptation, while passing through a laboratory leaves detectable genetic signatures, offering a new tool to interpret outbreak origins

University of California - San Diego

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A new University of California San Diego study published in Cell challenges a long-standing assumption about how animal viruses become capable of sparking human epidemics and pandemics. Using a phylogenetic, genome-wide analysis across multiple viral families, researchers report that most zoonotic viruses — infectious pathogens that spread from animals to humans, including the cause of COVID-19 — do not show evidence of special evolutionary adaptation before spilling over into humans.

“This work has direct relevance to the ongoing controversy around COVID-19 origins,” said Joel Wertheim, PhD, senior author and professor of medicine in the Division of Infectious Diseases and Global Public Health at UC San Diego School of Medicine. “From an evolutionary perspective, we find no evidence that SARS-CoV-2 was shaped by selection in a laboratory or prolonged evolution in an intermediate host prior to its emergence. That absence of evidence is exactly what we would expect from a natural zoonotic event — and it represents another nail in the coffin for theories invoking laboratory manipulation.”

The prevailing model of zoonotic emergence has often assumed that viruses must first acquire adaptive mutations before they can sustain human-to-human spread. To test that assumption, the research team analyzed viral genomes from outbreaks caused by influenza A virus, Ebola virus, Marburg virus, mpox virus, SARS-CoV and SARS-CoV-2. They focused on the evolutionary period  immediately preceding human outbreaks, where any substantial pre-spillover adaptation should leave a detectable imprint.

Across these diverse viruses, the investigators found a strikingly consistent pattern: selection pressures before zoonotic emergence were indistinguishable from those acting during routine circulation in animal reservoirs. In other words, there was no evolutionary signal suggesting that these viruses were being “pre-adapted” for humans prior to their outbreaks. Instead, measurable changes in selection typically appeared only after sustained transmission began in people.

“From a broad epidemiological standpoint, our findings challenge the idea that pandemic viruses are evolutionarily special before they reach humans,” Wertheim said. “Rather than requiring rare, finely tuned adaptations in animals, many viruses may already possess the basic capacity to infect and transmit between humans. What matters most is human exposure to a diverse array of animal viruses.”

The study relies on a sophisticated phylogenetic framework that measures changes in the intensity of natural selection across entire viral genomes. By comparing rates of different types of mutations, the researchers were able to detect whether natural selection was intensified, relaxed or unchanged across key evolutionary transitions. Importantly, the team validated their approach using known examples of and artificially selected viruses propagated in cell culture or in laboratory animals, which produced clear and reproducible evolutionary signatures distinct from natural transmission.

Those controls proved critical when examining one historical outlier: the reemergence of H1N1 influenza A virus in 1977. Unlike other zoonotic events analyzed, the 1977 H1N1 strain showed both unusually limited genetic divergence from 1950s viruses and a clear shift in selection consistent with viruses that propagated in cell culture or in laboratory animals.

“The 1977 influenza story is, in many ways, even more compelling than what we found for COVID-19,” Wertheim said. “Our results provide new molecular evidence supporting the long-suspected idea that the H1N1 pandemic was sparked by a laboratory strain — possibly in the context of a failed vaccine trial.”

Historical records and prior genetic analyses have suggested that the 1977 H1N1 virus appeared almost unchanged after a 20-year absence, a pattern difficult to reconcile with natural evolution. The new findings add another layer, showing that the virus also experienced selection similar to that seen in laboratory-adapted influenza strains and live-attenuated vaccines.

Beyond settling historical debates, the authors argue that their work has important implications for how scientists interpret future outbreaks. By establishing what “normal” zoonotic emergence looks like at the genomic level, the framework provides a benchmark for distinguishing natural spillovers from scenarios involving laboratory handling or prolonged artificial selection.

“This doesn’t mean lab accidents don’t happen,” Wertheim emphasized. “But it does mean that if a virus had been extensively passaged in a lab before an outbreak, we would expect to see it in the evolutionary record. In nearly all pandemics we’ve studied, that signal simply isn’t there.”

Looking ahead, the researchers see potential applications in outbreak forensics, viral surveillance and pandemic preparedness.

“Our goal is not just to understand the past, but to be better prepared for the future,” Wertheim said. “By clarifying how pandemics actually begin, we can focus attention where it belongs — on surveillance, prevention and reducing the opportunities for the constant barrage of viral spillover.”

Link to full study: https://authors.elsevier.com/sd/article/S0092-8674(26)00171-6

Additional co-authors on the study include: Jennifer L. Havens and Jonathan E. Pekar from UC San Diego; Sergei L. Kosakovsky Pond and Jordan D. Zehr from Temple University; Edyth Parker and Kristian G. Andersen from Scripps Research Institute; and, Michael Worobey from the University of Arizona.

The study was funded, in part, with federal funds from the National Institute of Allergy and Infectious Diseases National Institutes of Health, National Institutes of Health (NIH-NIAID) and National Science Foundation (NSF). Jennifer L. Havens acknowledges support from NIH (grant R01AI153044). Sergei L. Kosakovsky Pond and Jordan D. Zehr acknowledge support from NIH (AI183870, GM151683, GM144468) and the NSF (grant DBI/2419522). Jonathan E. Pekar acknowledges support from NIH-NIAID (T15LM011271) and the UC San Diego Merkin Fellowship. Michael Worobey acknowledges support from NIH-NIAID (contract no. 75N93021C00015). Edyth Parker and Kristian G. Andersen acknowledge support from the NIH (grant U01AI151812). Kristian G. Andersen also acknowledges support from the NIH (grant U19AI135995). Joel O. Wertheim acknowledges support from NIH-NIAID (R01AI135992).

Jonathan E. Pekar, Michael Worobey, Kristian G. Anderson, and Joel O. Wertheim have received consulting fees and/or provided compensated expert testimony on SARS-CoV-2 and the COVID-19 pandemic.

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Journal

Cell

 

Scientists trace crop viruses back to the last Ice Age

American Phytopathological Society

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Long before humans cultivated crops or sailed between continents, a group of plant viruses was already evolving among wild plants in Eurasia. According to a new international study published in Plant Disease, the ancestors of modern tymoviruses likely emerged before the last Ice Age, reshaping scientists’ understanding of the vast evolutionary history of plant disease.

Tymoviruses infect dicot plants and are typically spread by leaf-eating beetles, although they can also be transmitted through seeds or direct plant contact. In parts of Eurasia and the Americas, these viruses infect both wild and crop plants, causing serious diseases in economically important crop plants, including several cultivated oilseed and vegetable brassica species and solanaceous crops such as potato, tomato, tobacco, and eggplant. They also infect legumes in Africa, Southeast Asia, and Australia. Because these viruses affect both cultivated plants and wild species, their spread has implications for both agriculture and natural ecosystems.

Led by Adrian J. Gibbs, Emeritus Faculty at the Australian National University, an international team of researchers conducted phylogenetic analysis and genomic sequencing of 109 tymoviruses and reconstructed their evolutionary relationships to estimate when and where this group of viruses first emerged. The newly sequenced tymovirus isolates mostly came from historical virus culture collections. The results suggest that the most recent common ancestor of all known tymoviruses existed before the last Ice Age, with some viral lineages likely reaching the Americas approximately 15,000 years ago. In contrast, the few tymoviruses that are now found on more than one continent appear to have spread globally much more recently—primarily during the past two centuries, coinciding with the expansion of international trade and agricultural exchange.

The analysis also revealed important clues about how these viruses adapt over time. Genes responsible for viral replication and protective structure showed strong evidence of stabilizing evolutionary pressure, while the genes responsible for movement between plant cells appear to evolve more rapidly. This flexibility may help the viruses adapt to new plant hosts, including economically significant crops.

Beyond the scientific findings, the study represents an important collaboration across both geography and generations. The research team includes scientists from South America, Europe, the Middle East, and Australasia, combining expertise in modern genomic sequencing and virus population genetics with decades of historical research on plant viruses. The study’s lead author, Adrian J. Gibbs, published one of the earliest studies describing an Andean tymovirus in 1966, while other contributors have worked on Andean potato viruses since the 1970s.

Understanding how these viruses originated and spread helps researchers anticipate future risks in a world in which plants, seeds, and agricultural products move between continents faster than ever before. The study shows that while the evolutionary roots of some crop viruses stretch back to a world shaped by glaciers and prehistoric ecosystems, human activity in recent centuries has played a major role in shaping their modern distribution. This broader perspective provides valuable information for scientists studying virus evolution and for plant health and biosecurity authorities responsible for protecting crops and ecosystems from emerging diseases.

Read “A Phylogeny of the Tymoviruses, Sensu Stricto, and Its Global Interpretation in Space and Time” to learn more—published in Plant Disease.

Plant Disease, published by The American Phytopathological Society, is the leading international journal for rapid reporting of research on new, emerging, and established plant diseases. The journal publishes papers that describe translational and applied research focusing on practical aspects of disease diagnosis, development, and management in agricultural and horticultural crops.

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Journal

Plant Disease

DOI

10.1094/PDIS-01-25-0061-RE 

Article Title

A Phylogeny of the Tymoviruses, Sensu Stricto, and Its Global Interpretation in Space and Time

How viruses mess with our brains

A team from the UNIGE and the HUG reviewed 900 scientific articles to better understand the impact of viruses on memory, attention, and concentration.

Université de Genève

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What impact does a viral infection have on our memory, attention, and concentration? The COVID-19 pandemic has reignited interest in this question, which has now been extended to other infections such as HIV, herpes, and hepatitis. A team from the University of Geneva (UNIGE) and Geneva University Hospital (HUG) reviewed over 900 scientific articles exploring the links between the immune system and cognitive functions. This analysis, published in Neuroscience & Biobehavioral Reviews, has identified several biological markers associated with cognitive decline in the context of infection. It also provides a solid foundation for future research.

Despite decades of research, the effects of viral infections on cognitive functions—such as memory, concentration, and attention—remain poorly understood. Most studies rely on comprehensive screening tools, applied individually to each disease. However, the emergence of the SARS-CoV-2 virus, along with the frequency and persistence of post-infectious cognitive sequelae, has reignited interest in this area of research.

In a new study, a team from UNIGE and HUG compiled and analysed the results of 931 scientific articles examining the links between the immune system and cognitive functions across various viral infections, including SARS-CoV-2, HIV, herpes, and hepatitis. ''Our goal was to take a cross-disciplinary approach to move beyond the fragmented perspective that prevails in this field,'' explains Julie Péron, associate professor at the Laboratory of Clinical and Experimental Neuropsychology, Faculty of Psychology and Educational Sciences, and at the Interfaculty Center for Affective Sciences, UNIGE, as well as a consulting neuropsychologist in the Neurology Service, Department of Clinical Neurosciences, HUG."

Several Biological ''Signatures'' Identified
This analysis confirms that persistent inflammation—initially a natural response by the body to an attack—could be linked to memory and concentration problems. More importantly, it highlights certain biological markers of the immune system associated with variations in cognitive performance. ''High levels of white blood cells called 'activated monocytes' and pro-inflammatory cytokines—proteins that enable the immune system to communicate—are correlated with a decline in episodic memory and information processing speed, '' says Anthony Nuber-Champier, a PhD student at the Laboratory of Clinical and Experimental Neuropsychology, Faculty of Psychology and Educational Sciences, and at the Interfaculty Center for Affective Sciences, UNIGE, as well as the lead author of the study."

Conversely, certain markers, such as activated CD4+ T cells—also white blood cells—or anti-inflammatory cytokines, seem to be associated with better preservation of cognitive abilities. ''However, immune responses vary from person to person. What appears to be decisive is the balance between these different inflammatory signals in maintaining long-term cognitive stability,'' the researcher points out.

A Solid Foundation for Future Research
These findings contribute to a better understanding of the cognitive disorders observed after certain infections and lay the groundwork for further investigation. They also confirm the conclusions of several clinical studies conducted in the context of long COVID, including the COVID Cog and Trajectory projects, in which UNIGE and HUG are actively involved. Funded by the Swiss National Science Foundation (SNSF), these projects aim to identify neuropsychological and neuropsychiatric deficits in post-COVID-19 patients.

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Journal

Neuroscience & Biobehavioral Reviews

DOI

10.1016/j.neubiorev.2026.106588 

Method of Research

News article

Subject of Research

Not applicable

Article Title

Immune-cognitive relationships across viral infections: A transnosological systematic review