What genomic peculiarities characterized the Spanish flu, which killed between 50 and 100 million people from 1918 onwards? Using tissue samples collected in Germany in 1918, researchers have now reconstructed the genome of the influenza viruses of that time and compared them both with other historical samples from America and with seasonal flu viruses that are circulating today. Thus, the H1N1 virus responsible for the 1918 pandemic exhibited characteristic changes that likely made it more virulent than previous strains. In addition, it showed a clear regional variability – and possibly forms the basis of all seasonal H1N1 strains circulating today.
The 1918 influenza pandemic, known as the Spanish flu, killed an estimated 50 to 100 million people worldwide. It peaked in the fall of 1918, and another wave followed in the spring of 1919. Although there were suspicions at the beginning of the pandemic that it was caused by a virus, it was not until 1930 that its viral origin was proven. In the 1990s, research on pandemic-era tissue samples identified the virus as an influenza A virus of the H1N1 subtype. Two complete genomes of the virus have since been isolated from American samples, as have several other incomplete ones. However, genetic material from that time is rare, so many questions remain unanswered.
Searching for clues in medical history museums
In search of other suitable samples, a team led by Livia Patrono from the Robert Koch Institute (RKI) in Berlin analyzed a total of 13 lung samples from the years 1900 and 1931 that were kept in the Medical History Museum of the Charité Berlin and the Natural History Museum in Vienna. Six of the lungs preserved in formalin were from the time of the pandemic. Patrono and her team analyzed the genome in all of the samples and actually found influenza A virus RNA in three of them. “All are from samples from 1918 and the lungs show that bronchopneumonia was present,” the researchers said.
Two of the samples with proven influenza A viruses were collected in Berlin in June 1918, i.e. in the early phase of the pandemic. The researchers were able to sequence sections of the viral genome from these samples. In the third sample, collected in Munich in 1918, the flu RNA was so well preserved that the researchers were able to sequence the entire genome. Patrono and her team compared the genomic data with the two already known genome sequences from the USA, one from September 1918 from New York, the other from November 1918 from Alaska.
Genetic Variability
The result: While the two Berlin genomes are very similar – as far as can be judged despite the incompleteness – the virus genome isolated from the Munich sample already shows several variations. The two genetic sequences from New York and Alaska show further mutations. “Taken together, these comparisons show that there was measurable genomic variability, and that genomes sampled on the same continents and during the same period of the pandemic showed less overall divergence than genomes sampled on different continents and during different time periods,” write the explorers.
The comparison between the genomes from the early and peak phase of the pandemic also provides information about which mutations could have increased the virulence of the influenza strain at the time. “Our results show variations at two sites in the nucleoprotein gene of the influenza A virus,” the researchers report. “These are related to resistance to the host’s antiviral response.” While the prepandemic virus strains still bore typical structures of the avian influenza viruses at these sites, the 1918 and 1919 influenza viruses replaced them with appendages that are still found in most today find human pathogenic H1N1 strains. As a result of these mutations, the virus could have adapted better to humans.
Further analysis required
In addition, the researchers performed molecular clock modeling to estimate the evolutionary timescales on which the virus evolved. Accordingly, the mutation rate of the virus may have been higher than previously thought, making the pandemic virus the ancestor of almost all H1N1 flu viruses found today. “Our analyzes suggest that the seasonal H1N1 viruses circulating today evolved from the pandemic strain of the time,” the authors write. This contradicts hypotheses that assume that today’s seasonal influenza viruses have evolved primarily through the exchange of genome segments between different strains.
“Due to our very small sample size – three complete and two incomplete genomes – all results are to be regarded as preliminary,” the authors restrict. In order to substantiate the hypotheses, further genome analyzes are required. “We anticipate that the main obstacle to a better understanding of the evolution of the 1918 influenza viruses will be the identification of surviving pathological specimens,” they write. However, pathological collections in museums could be an important source.
Source: Livia Patrono (Robert Koch Institute, Berlin) et al., Nature Communications, doi: 10.1038/s41467-022-29614-9