A genomic analysis of monkeypox viruses from patients in the ongoing outbreak reveals that it most likely has a single origin. This 2022 monkeypox virus diverges from those of 2018-2019 in many more genetic variations than expected for Orthopoxviruses, which may represent ongoing accelerated evolution, according to the authors. The study is published in Nature Medicine.
Professor of Genetics at the University of Valencia and researcher at FISABIO, specialist in epidemiology and evolution of viruses and bacteria
This is the first peer-reviewed paper to analyse the monkey virus (MPXV) genome from patients involved in the recently detected outbreak.
The study employs most of the techniques and methodologies that have been used in the genomic study of the SARS-CoV-2 coronavirus, adapting them to the specific characteristics of MPXV, such as its larger size (almost 10 times that of SARS-CoV-2) and the nature of the hereditary material (DNA instead of RNA). This implies a lower mutation rate but, because it is a larger genome, it allows transmission chains to be analysed with high reliability.
The most remarkable result is to demonstrate that the outbreak, detected in several countries almost simultaneously, has a single origin and, moreover, that this origin involves a virus that has undergone a significant number of changes with respect to the closest viruses of the same species identified so far (related to viruses endemic in central and eastern African countries). These genetic changes appear to be linked to adaptations to the new host (humans, as the natural host of the virus is various rodents and other small mammals).
Although the spread of the MPXV outbreak is nowhere near as rapid and widespread as that of SARS-CoV-2, this is a new example of an emerging infection that can spread rapidly around the world and needs to be addressed as soon as possible to prevent more serious consequences. Genomic surveillance of these and other pathogens is one of the most powerful tools we have at our disposal to achieve this goal.
Research director at the Laboratory of Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC) of the French National Center for Scientific Research (CNRS).
The authors of the study belong to several Portuguese teams from the Portuguese national health institute. They have sequenced the available genomes of the monkeypox virus isolated during the 2022 outbreak and analysed them together with all available sequences. The virus from the 2022 outbreak is very close to a virus that appeared in 2018 and 2019 in Nigeria, and was then exported to the UK, Israel and Singapore.
The researchers propose that the most likely hypothesis is that the virus would have continued to circulate and evolve endemically in Nigeria, and from there would have been exported again.
The results show that the first confirmed case in the UK is probably not the first case of the virus being exported out of Nigeria in this outbreak. The most likely scenario is that the virus has been circulating since 2017 in Nigeria (prior to this outbreak, WHO had identified more than 500 suspected cases in Nigeria in the past five years), and that this outbreak we are now seeing is the result of one or more events of export of the virus from Nigeria, very close in time, with a superdiseminating event (e.g. in saunas or through sexual contact), associated with rapid geographical spread.
This outbreak is particular because of the number of mutations that the sequenced genomes have accumulated. The simian pox virus is an orthopoxvirus. Orthopoxviruses are viruses with a genome with two DNA strands, like our cells. They are viruses with large genomes (more than six times longer than the SARS-CoV-2 genome), very stable, and code for about 200 proteins. They evolve slowly because when the genome is copied, the molecular machinery does not make many mistakes and does not introduce many mutations. However, the sequenced genomes of the current outbreak show many changes, about ten times more than expected given the type of virus we are talking about.
Moreover, these changes preferentially go in one direction, that of converting C to T (using the letters commonly used in genetics). This type of directional change is common in the evolution of many viruses, but the most important thing is that it is not the viruses that cause them, but human proteins that cause the virus to accumulate mutations.
These are enzymes called APOBEC3, produced by host cells, which in principle have an antiviral function (introducing mutations into viruses to inactivate them), but which can have the effect of accelerating the rate of virus mutation. In fact, the action of APOBEC3 enzymes is responsible for the accumulation of many C to T mutations in other viruses, such as HIV, SARS-CoV-2 or human papillomaviruses.
It is very important to say that the repertoire of APOBEC3 enzymes in the human genome is very varied, that it depends on the ancestry and genetic background of each person, and that each cell type in our body can express different types of APOBEC3. This greatly complicates the study and fragments the evolution of viruses, because by infecting different people of different ancestry, a viral lineage may evolve differently; and because by infecting different tissues (skin, muscle, liver) it will also evolve differently.
This is probably what may have happened in the case of this outbreak, and is what the Portuguese researchers propose: this virus jumped into humans in 2019 in Nigeria and has been in uninterrupted human-to-human transmission ever since, has undergone very significant directional mutational pressures from C to T, and has also undergone very strong selection pressures to adapt to human-to-human transmission.
This would have resulted in the accumulation of mutations that may have facilitated effective human-to-human transmission of the virus and led to this outbreak, which has now generated more than 1,700 WHO-confirmed cases across Europe, according to the European Centre for Disease Prevention and Control (ECDC).
- Research article
- Peer reviewed