The data on viruses that Prof. Richard Neher at the Biozentrum, University of Basel, receives every day, gives him a precise overview of the development of the SARS-CoV-2 virus and the variant Omicron. Indeed, it is a huge amount of data, more than he and his team has ever had about any virus before. With the online platform Nextstrain, he and his team follow in real-time how the pathogen is spreading worldwide.
To which extent is Nextstrain currently being used for research into the SARS-CoV-2 virus?
We have more data on SARS-CoV-2 than ever before for a single virus. There are now six million fully sequenced virus genomes worldwide. Between 10,000 and 50,000 are added every day. We have around 95,000 sequences from Switzerland alone. All of this data flows into Nextstrain. This gives us an incredibly good basis for our analyses. We already have 1,200 sequences for Omicron, although we have only known this variant for two weeks.
What exactly does Nextstrain do with all these sequences?
With this data, we can analyze how the genome and the molecular details of the viral proteins have changed over time, when a variant emerged, how a variant has replaced other variants over time or make inferences on how immune-evasive a certain variant could be, that is how good it can escape a preexisting immune response.
What does it take for a variant to become dominant or does it always become dominant in all parts of the world?
No, Beta and Gamma one year ago, for example, did not become dominant globally, but dominated in Africa and South America, respectively. The different degrees of preexisting immunity probably played a major role here. Because the first wave was relatively strong in these regions and many people had already been infected, the new beta and gamma variants were more successful. These two variants evaded immunity more strongly than Alpha or the original variant and thus might have had an advantage over them.
Does Nextstrain also provide evidence for the origins of a mutant like Omicron?
Yes, if you are lucky, the sequences also provide clues about the place of origin. For this, however, data has to have been collected in that particular region. In regard to Omicron, we actually don't know of any close relatives, so this question has still not been answered.
How did you find out about Omicron?
In this case, a colleague, Tom Peacock, who works as a virologist at Imperial College London, brought Omicron to our attention. It was also immediately clear to colleagues in South Africa that this variant was important. We knew about Omicron around two days before the WHO classified it as a variant of concern.
The news about Omicron is rolling in thick and fast. What is the current situation?
Currently, Omicron is still rare in Europe. But if it continues developing like this, Omicron will be dominant in Europe in about two to four weeks. At the moment, data from Denmark and the UK shows us that the number of infections double about every three to four days.
How infectious is Omicron compared to the Delta variant?
It is almost three times more transmissible. However, this is not due to the virus itself but to the fact that both vaccinated and unvaccinated people become infected, while vaccinated are protected from infection by Delta to a large degree.
Does that mean the vaccination no longer provides protection?
There is increasing evidence that the vaccination continues to protect at least against a severe disease. However, according to our current knowledge, full vaccination protection is no longer given. A 3rd dose, or booster, can raise antibody levels and this rise can to some extend can compensate for the loss of recognition of Omicron.
What can be said about the Omicron mortality rate?
Not much at the moment. Even though there are several reports that infections lead less frequently to severe disease, this does not tell us much about the Omicron variant itself. Many people who are infected with Omicron have already had a Covid infection or have been vaccinated. This is probably the main reason for the fewer severe cases, not changes in the virus itself.
With the current corona measures, the politicians are once again relying on the factor of time in order to delay the spread. Does that make sense from an epidemiological point of view?
In 2020, this was definitely the case. We were able to vaccinate most people before they came into contact with the virus, thus preventing countless severe cases. The mortality rate has decreased multifold. And by reducing the number of contacts, the first waves were flattened and the pressure on our health system was relieved. In addition, we were able to gain time to develop therapies against the disease. For these reasons, I believe that this strategy was right. Also, regarding Omicron, where we still don’t know the opponent we are dealing with well, it is appropriate to slow its spreads for as long as possible.
Is there an end of the pandemic in sight?
The pandemic will end at some point, but the virus will remain.
What does that mean for the future?
I believe it is important to realize that we need to reduce inequality in the global health system. Immunosuppressed people, such as sub-optimally treated HIV-positive people can develop chronic infections in which the virus persists for months. This might be an important factor in the evolution of variants because the virus changes rapidly in such chronic infections. This pandemic has shown time and again that we are all in this together. We have to address global health inequality with respect to COVID-19, vaccines, and infectious disease more generally.
Richard Neher developed Nextstrain together with his colleague Trevor Bedford from the Fred Hutchinson Cancer Research Center in 2015. The idea of Nextstrain goes back to research on the flu viruses. The two researchers wanted to find out to what extent evolution can be predicted. This is an important question, especially for the flu, because the seasonal influenza vaccine has to be updated every year. Forecasting can make the vaccine formulation more effective.
With Nextstrain, a wide variety of virus outbreaks can be analyzed, be it SARS-CoV-2, influenza virus, or dengue, Zika or Ebola virus. Epidemiologists, virologists and health experts around the world use this tool to see in almost real-time how the pathogens change and spread.