Even after the end of the COVID pandemic, new SARS-CoV-2 variants are constantly emerging and are responsible for COVID-19 waves worldwide. Dr. Markus Hoffmann's team has shown that new variants are characterized by mutations in the spike protein, which can alter cell entry and canreduce the virus’s inhibition by antibodies. Additionally, the team has discovered that new SARS-CoV-2 variants can regain characteristics previously seen only in early pandemic variants, which may increase pathogenic potential. Our goal is to identify the biological properties of new SARS-CoV-2 variants to understand, in the long term, how the virus adapts to spreading in humans.

Coronaviruses infect mammals (including hedgehogs, bats, pigs, camels, and cattle) and birds, in which they sometimes cause severe diseases of the digestive and nervous systems. The coronaviruses NL63, OC43, 229E, and HKU1 are widespread and infect humans year-round. Infection with these viruses typically causes mild respiratory illnesses. It is estimated that about 30 percent of patients with colds who visit a doctor have a coronavirus infection. Severe cases are rare and are primarily observed in young children, elderly individuals, and immunocompromised patients. NL63, OC43, 229E, and HKU1 were likely transmitted from animals to humans many years ago and have been circulating continuously in the population since then (Figure 1).

In the winter season of 2002, a previously unknown, severe respiratory illness emerged in southern China, known as severe acute respiratory syndrome (SARS). SARS initially spread within China, with massive outbreaks, particularly in hospitals. Travelers then carried the disease to numerous other countries, and although the center of the SARS epidemic was in Asia, many SARS cases were also observed in countries like Canada. Despite its global spread, the transmissibility of SARS was significantly lower than that of influenza. Therefore, the SARS pandemic was halted in the summer of 2003 through rigorous traveler monitoring and quarantine measures, even though no vaccine or medication was available. By that time, nearly 800 people had died from the disease, and in Asia alone, the economic damage was estimated at around 30 to 50 billion US dollars. Following the major SARS outbreak of 2002/2003, a few mild cases were observed in the winter of 2004, but no new cases have been reported since 2004.

At the beginning of the SARS epidemic, it was still unclear which pathogen was causing the illness. However, using polymerase chain reaction (PCR) and electron microscopy, a new coronavirus was soon detected in SARS patients. It was subsequently shown that the virus met the so-called Koch’s postulates: it was always detectable in SARS patients, could be replicated in cell cultures, and induced a SARS-like disease in infected animals. Furthermore, the virus could be isolated from infected animals. This confirmed that the new coronavirus was responsible for SARS. Accordingly, this virus was then named SARS coronavirus (SARS-CoV or SARS-CoV-1).

In the course of investigating the SARS outbreak and searching for its origin, viruses very similar to the SARS coronavirus were detected in bats. It was concluded that bats represent the so-called natural reservoir of the SARS coronavirus. However, these bats do not appear to have transmitted the virus directly to humans. Instead, intermediate hosts—the civet cat and raccoon dog (Figure 1)—were responsible. These animals are offered for consumption in restaurants and traded in markets in certain regions of China. It is now considered certain that the first SARS coronavirus infections were linked to visits to a market where (wild) animals were sold, known as “wet markets.”

Coronaviruses use one of their envelope proteins, the spike (S) protein, to enter host cells. For this, the S protein must bind to a suitable receptor on the cell surface. The SARS coronavirus utilizes the cellular protein angiotensin-converting enzyme 2 (ACE2) for this purpose (Figure 2). The interaction between the S protein and ACE2 appears to play a crucial role in determining the virus's transmissibility and its ability to cause SARS. Only those variants of the SARS coronavirus that could bind to ACE2 with high efficiency were transmitted between humans or detected in patients. Remarkably, ACE2 is not only important for viral entry into cells but may also play a role in the development of SARS disease. The ACE2 protein normally functions to protect the lungs from damage, and this vital function of ACE2 is impaired by SARS coronavirus infection. Research from the Department of Infection Biology shows that the new coronavirus SARS-CoV-2, which causes the COVID-19 pandemic, also uses ACE2 and TMPRSS2 for cell entry.

The first COVID-19 cases were observed during the winter season of 2019 in Wuhan, the capital of Hubei Province in China. The virus then spread globally within a few months. In just the first two years, 2020 and 2021, the COVID-19 pandemic was associated with an excess mortality of 18 million deaths worldwide and caused severe economic disruptions. The rapid availability of vaccines significantly contributed to containing the pandemic. The vaccines provide reliable, long-term protection against severe illness, but they only offer transient protection against infection. Additionally, the emergence of virus variants that evade antibody inhibition necessitates the adaptation of the vaccines. In 2023, the WHO declared the COVID-19 pandemic over, but new SARS-CoV-2 variants continue to emerge, leading to waves of COVID-19 cases worldwide.

The Department of Infection Biology made significant contributions to COVID-19 research. Infection biologists demonstrated that SARS-CoV-2, like SARS-CoV, uses the cellular protein ACE2 as a receptor for cell entry and that the interaction between the virus's spike protein and ACE2 is inhibited by antibodies produced after a SARS-CoV-2 infection. They also showed that the cellular protease TMPRSS2 activates the spike protein through cleavage (Hoffmann et al., Cell, 2020). These findings indicated that SARS-CoV and SARS-CoV-2 likely infect a similar range of cells and organs and may cause disease through related mechanisms. They also identified ACE2 and TMPRSS2 as targets for antiviral therapy, which were intensively researched in the following years.

Further studies by the Infection Biology group revealed that a cleavage sequence for the cellular protease furin, present in the spike protein of SARS-CoV-2 but absent in the spike proteins of most closely related viruses, is crucial for entry into lung cells (Hoffmann et al., Molecular Cell, 2020). Based on these results, a two-step activation process for the SARS-CoV-2 spike protein was established: first, the spike protein is cleaved by furin at the so-called S1/S2 site within infected cells. Then, the “pre-cleaved” spike protein is cleaved by TMPRSS2 at the S2' site. This cleavage occurs during cell entry and is essential for lung cell penetration (Figure 3). In cell lines, the cellular protease cathepsin L can substitute for TMPRSS2, but this is likely not possible in an infected host. These findings suggest that the furin cleavage site is probably a virulence factor, a hypothesis confirmed by subsequent studies in animal model , and explain why the drug hydroxychloroquine, which inhibits cathepsin L but not TMPRSS2, is not suitable for COVID-19 therapy (Hoffmann et al., Nature, 2020).

In the early months of the pandemic, the SARS-CoV-2 genome showed few changes. However, as the proportion of recovered and vaccinated individuals in the population steadily increased, virus variants emerged that adapted to spread in a population with a high proportion of people with pre-existing immune responses against the virus. The Department of Infection Biology was able to show that these virus variants carry mutations in the spike protein that allow the virus to evade antibody responses without significantly reducing receptor binding and activation by a protease (Hoffmann et al., Cell, 2021). The Alpha, Beta, Gamma, and Delta variants emerged initially, with marked antibody escape observed particularly for the Beta, Gamma, and Delta variants. The Delta variant had the highest potential to cause disease, likely due to a mutation in the furin cleavage site that enhanced furin's cleavage of the site. By late 2021, the Delta variant was replaced by the Omicron variant, and the Department of Infection Biology demonstrated that this represented a quantum leap in SARS-CoV-2 evolution: the Omicron variant had more than 30 mutations in the spike protein, roughly three times more than previous variants, allowing it to evade antibody responses with unprecedented efficiency. However, the mutations in the spike protein not only affected antibody inhibition but also led to a change in protease preference—for cell line entry, Omicron exhibited a preference for cathepsin L over TMPRSS2, unlike the Alpha, Beta, Gamma, and Delta variants. This shift in protease usage was associated with reduced entry into lung cells, likely responsible for the partial attenuation of the Omicron variant.

The Omicron variant BA.1, which established the global dominance of Omicron viruses, was followed by numerous Omicron subvariants, including BA.2, BA.3, BA.4, BA.5, BA.2.12.1, BA.2.75, BQ.1, XBB.1, CHH.1, XBB1.5, XBB1.16, and EG.5. These variants showed increased antibody escape compared to their predecessors and exhibited the aforementioned preference for cathepsin L. This progression culminated in the emergence of the highly mutated, BA.2-derived Omicron subvariant BA.2.86 in the fall of 2023. The Department of Infection Biology demonstrated that, unlike all other Omicron subvariants, this variant uses TMPRSS2 for entry into lung cells (Figure 5) and enters these cells very efficiently (Zhang et al., Cell, 2024). Thus, the variant regained a property seen only in the early Alpha to Delta variants, which is believed to increase the virus's pathogenic potential. Therefore, it is doubtful that the spread of SARS-CoV-2 in a population with high baseline immunity will lead to continuous attenuation.

The BA.2.86 variant did not become globally dominant because it was relatively effectively inhibited by antibodies. Only after acquiring an additional mutation in the spike protein did the virus efficiently evade the antibody response, and the resulting JN.1 variant led to global COVID-19 waves. Currently, the JN.1 subvariants KP.3.1.1 and XEC are dominant. The Department of Infection Biology has shown that both variants are effectively inhibited by the new JN.1-derived vaccine and is currently studying the biological properties of these variants.