We now have to conclude that this was mammal to mammal transmission.
Wendy Puryear, a molecular virologist at Tufts University, told me that seals sick with the virus will sometimes convulse so badly that they can barely hold their bodies straight. Every seal she’s seen that tested positive has ended up dead within days.
At least 24,000 sea lions died in Peru, Chile, Argentina, Uruguay, and Brazil between January–October 2023.
In some South American countries, apart from a few carcasses that were buried, the rest have remained on the beaches, rotting and scavenged upon. How do you even scale up to remove 17,000 dead bodies out in the middle of nowhere, places where you can't even bring down machinery, and humongous cliffs? Dr. Uhart said.
Mammal-to-Mammal Transmission
Seals and sea lions live in colonies, often densely packed on small rocks in the ocean or at the coast. They are often in close contact with gulls, terns and other birds carrying the H5N1 virus. Seals and sea lions are carnivores and occasionally eat sick or dead birds. However, the rocks and surrounding waters are contaminated with infectious bird excrement which are likely to cause infections. For some time there was no conclusive evidence of mammal-to-mammal transmission and the primary route of infection was suspected to be bird-to-mammal transmission, occurring over and over again. However, some mammal-to-mammal transmission was nonetheless suspected. Now the widespread and almost total mortality of seal pups in Argentina is highly suggestive of mammal-to-mammal transmission. Seal pups don't predate birds and "little to no interaction" with birds was observed at those beaches. This mades some occurences of mammal-to-mammal transmission highly likely. A recent pre-print finally provides phylogenetic evidence for mammal-to-mammal transmission. Furthermore there is evidence of spillback from seals into the tern population and a distinct clade shared by terns and pinnipeds across South America, in Argentina, Peru, Chile and Brazil.
The most likely source of infection for sea lions in South America is associated with HPAI-infected birds: a spillover from wild birds to mammals seems to be the main cause of infection. In fact, sea lions in Peru were in close contact with infected birds and have even been reported ingesting dead and dying birds. However, it is important to consider and evaluate potential direct transmission among sea lions due to their gregarious behavior, the large number of affected individuals and the clustering of deaths in groups. Most importantly, sea lion mortality seems not always associated with wild or domestic bird mortality (e.g., in Argentina there are no official reports of large bird mortalities on the coasts where sea lions are dying), but this requires further research because it could be due to underreporting of cases by this country.
In 2012, it was shown for the first time that an avian A/H5N1 influenza virus could become transmissible via the air between ferrets after changing three phenotypic viral properties. Only a handful of amino acid substitutions resulted in the following: (a) a shift in receptor-binding specificity of the hemagglutinin (HA) protein from the avian-type α-2,3-linked sialic acid (SA) to the mammalian-type α-2,6-linked SA receptor, (b) an increased acid stability of HA, and (c) an increase in polymerase activity in mammalian cells. Although this airborne-transmissible A/H5N1 virus was generated in the lab, two years later, the same phenotypic changes emerged under natural conditions during the 2014 avian-origin A/H10N7 virus outbreak in seals, which resulted in the death of 10% of the seal population in the North Sea. Not unexpectedly, this A/H10N7 seal virus was also found to be transmissible via the air in the ferret model, confirming the adaptive viral requirements for transmission. Although we understand the biological mechanisms regarding the receptor-binding specificity and polymerase adaptations that favor the transmissibility of influenza viruses, the contribution of HA acid stability to mammalian adaptation and transmission is less well understood.
HPAI H5N1 was confirmed in seals and terns. Moreover, genomic characterization showed viruses from pinnipeds and terns in Argentina form a distinct clade with marine mammal viruses from Peru, Chile and Brazil. These mammal-clade viruses share an identical set of mammalian adaptation mutations which are notably also found in the terns. Our combined ecological and phylogenetic data support mammal-to-mammal transmission and occasional mammal-to-bird spillover. To our knowledge, this is the first multinational transmission of H5N1 viruses in mammals ever observed globally.
Two wild bird-to-marine mammal transmissions in Peru appear to be dead-end spillover events with no secondary cases (A/common dolphin/Peru/PIU-SER002/2022 and A/South American sea lion/Peru/LIM-SER036/2023). In contrast, a third wild bird-to-marine mammal transmission is associated with a multinational clade of 26 viruses, including 20 from marine mammals in Peru (n = 1), Chile (n = 8), Argentina (n = 9), and Brazil (n = 2). The time-scaled MCC tree estimates that the third wild bird-to-marine mammal transmission event occurred between 24-Nov-2022 and 7-Jan-2023, based on the estimated time to the most recent common ancestor. The multinational marine mammal clade also includes a human case from Chile (A/Chile/25945/2023), a wild bird virus from Chile (A/sanderling/Arica y Parinacota/240265/2023), and four viruses obtained from terns in Argentina (one South American tern from Punta Bermeja in August 2023, one royal tern and two South American terns from Punta Delgada in October 2023) that are closely related to the marine mammal viruses from Argentina. Our results showed that the human, sanderling, and four tern viruses positioned in the marine mammal clade appear to be independent spillover events from marine mammals (Figures 2 and 3A). This is further supported by the fact that these viruses share mutations in PB2 that are associated with mammalian adaptation and are present in viruses forming to the marine mammal clade.
Chile
An ongoing mass mortality event including over 13.000 sea lions is associated with H5N1.
"In reviewing the report of dead animals associated with avian influenza during the first half of 2023, we recorded that, from 7 February to 30 June, 15,185 dead marine wildlife have been identified. The breakdown is as follows: 13,025 common sea lions, 2,093 Humboldt penguins, 30 chungungos, 21 spiny porpoises, 15 Chilean dolphins and one huillín," explained the National Director of SERNAPESCA, Soledad Tapia.
The HPAI A(H5N1) virus traveled approximately 5000 kilometers from Peru to Tierra del Fuego (by way of the Pacific Ocean), and approximately 2800 kilometers from Tierra del Fuego to Uruguay and Brazil (by way of the Atlantic Ocean), infecting sea lions along the way. During this time, H5N1 killed approximately 5% and 12% of the Peruvian and Chilean sea lion populations, respectively.
Peru
A mass mortality event including more than 5.000 sea lions is associated with H5N1.
We report a massive mortality of 5,224 sea lions (Otaria flavescens) in Peru that seemed to be associated with highly pathogenic avian influenza A(H5N1) virus infection. The transmission pathway may have been through the close contact of sea lions with infected wild birds. We recommend evaluating potential virus transmission among sea lions.
The synchronized high mortality rate we observed was concerning; up to 100 dead animals were found floating together in the sea, and 1,112 animals died on 1 island that has one of highest populations of sea lions in Peru. Those unprecedented massive mortalities for this region and even the entire world killed ≈5% of Peru’s population of this species in a few months.
We call for more attention to human–infected animal interaction in this geographic region (Figure, panel F) to identify any rise in infections and prevent a new pandemic.
Researchers are not ruling out a terrifying hypothesis: that the virus may have learned to spread from mammal to mammal, as it apparently did on a Spanish mink farm. It would be the first time that this has occurred in nature.
Thijs Kuiken lists another reason for concern: “There is video footage showing people in Peru trying to rescue sea lions potentially infected with the virus. This close contact increases the chances of the virus being transmitted from sea lions to humans.”
We report 40 variable sites previously linked to altered polymerase activity and replication efficiency, increased virus binding to α2-3 and α2-6, enhanced transmission, and increased virulence and pathogenicity, including in mammals. However, we did not find mutations in PB2 (E627K, D701N, K702R) that have been specifically linked to mammalian host adaptation and enhanced transmission. In fact, the viruses sequenced from sea lion and dolphin were genetically similar to each other, but also to viruses from all positive birds, underscoring that it is not possible to discern the direction of transmission among these species from the data available.
We suspect that direct HPAI transmission between sea lions could be occurring, rather than independent spillovers into sea lions from avian sources, but additional sequence data and analysis will be required to further characterise mammal-to-mammal transmission.
There was an epidemiological silence, in which the public institutions stated that everything was under control. And suddenly these reports appeared of people finding dead sea lions all over the Peruvian coast. That is when the institutions began to take some samples.
Argentina
An ongoing mass mortality event including over 17.000 seals, mostly elephant seal pups, and 1367 sea lions is associated with H5N1. Additional adult elephant seal losses are expected, but hard to quantify due to the premature end of the catastrophic 2023 breeding season.
Buenos Aires - The National Agri-Food Health and Quality Service (Senasa) has confirmed the first positive case of Highly Pathogenic Avian Influenza (HPAI) H5 in wild mammals. The finding was made in seven of 21 sea lions found dead in Rio Grande, in the province of Tierra del Fuego, Antarctica and South Atlantic Islands.
The Chubut Department of Flora and Fauna in Southern Argentina confirmed they have registered more than 1,300 bird flu-caused deaths of baby elephant seals on the province’s shores, the largest number of deaths since they started keeping records. (...) Bersano said they were surprised by the data because the initial concern about the effects of bird flu was focused on the population of one and two-haired sea lions, which have a larger number of specimens and about which over 250 deaths have been reported.
The report details that during the elephant seal breeding season, calf mortality historically remained below 1%. However, this year extreme mortality was recorded, ranging from 56 to 74%, depending on the site monitored. This drastic change in the mortality pattern is cause for concern and requires in-depth analysis.
In addition to the high mortality of hatchlings, an unusual number of dead adults and sub-adults was observed, and a significant reduction of between 40% and 70% of adult individuals on the shores, varying according to sector and sex.
A 13-km beach. in a high-
density area at the peak of the 2023 breeding season (October 10), yielded a mortality of 70% of the 1.691 pups
born. Comparatively, in 2022. at the same place and about the same time in the breeding season, mortality was 0.8% for 3,135 pups born. In 2023, mortality reached at least 96% by early November, when reproduction was over. Virtually identical results were found in the two other sampled beaches, including a low-density area of
about five kilometers with a few harems (only 11 pups were alive of the at least 287 born in 2023). (...) It is estimated that more than 17.400 pups may have died in this epidemic context.
According to veterinarian Marcela Uhart at the University of California, Davis, since newborn elephant seal pups suckle their mothers to feed, there is little chance that the pups ate infected birds. “This is all highly suggestive of some sort of transmission between mammals,” Uhart told New Scientist.
At the sites where elephant seals were found dead, they had little to no interaction with infected bird populations, Campagna says. It is also highly unlikely that such a large number of mammals could have been infected in less than a month without the infection being transmitted among them. “We now have to conclude that this was mammal to mammal transmission,” he says.
Specifically, we found Q591K and D701N mutations in polymerase basic 2 associated with increased pathogenicity to mammals. The virus we detected in the tern from South America also has those mutations, but they were absent from previously reported HPAI H5N1 viruses from avian hosts in South America (except for A/sanderling/Arica y Parinacota/240265/2023, which has the D701N mutation). That finding further supports the hypothesis that HPAI H5N1 viruses from sea lions from Peru and Chile acquired mammalian adaptation mutations that improved their ability to infect pinnipeds while possibly retaining the ability to infect avian hosts.
The sight of elephant seals found dead or dying along the breeding beaches can only be described as apocalyptic.
Brazil
An ongoing mass mortality event including over 900 seals and sea lions is associated with H5N1.
At least 522 seals and sea lions have been found dead along the coast of southern Brazil, authorities said Wednesday, blaming the die-off on avian flu.
The southernmost state of Rio Grande do Sul has confirmed an unprecedented 942 sea mammal deaths following infection by the highly pathogenic avian influenza (HPAI), which was reported for the first time ever in the South American country this year.
Uruguay
An ongoing mass mortality event including 400 seals and sea lions is associated with H5N1.
An estimated 400 seals and sea lions have turned up dead on the coast of Uruguay in recent weeks, blamed by authorities on bird flu.
USA, New England, Maine
19 harbor and gray seals tested positive for H5N1.
“To get strong evidence of mammal-to-mammal transmission, you need two things: lots of infected animals and time,” explained Sawatzki. “Time for the virus to mutate, and time for the mutated virus to be transmitted to another seal. As the virus acquires mutations, we can see shared mutations in the sequences that are specific only to mammals and that haven’t been seen in a bird before. We had the numbers, but this outbreak didn't last long enough to provide evidence for seal-to-seal transmission.”
Transmission from wild birds to seals was evident for >2 distinct HPAI H5N1 lineages in this investigation and likely occurred through environmental transmission of shed virus. Viruses were not likely acquired by seals through predation or scavenging of infected animals, because birds are not a typical food source for harbor or gray seals. Data do not support seal-to-seal transmission as a primary route of infection. If individual bird–seal spillover events represent the primary transmission route, the associated seal UME suggests that transmission occurred frequently and had a low seal species barrier. We observed novel amino acid changes throughout the virus genome in seals, including amino acid substitutions associated with mammal adaptation.
On July 1, the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service’s National Veterinary Services Laboratories confirmed that samples from four stranded seals in Maine have tested positive for Highly Pathogenic Avian Influenza H5N1.
Canada, Quebec
At least 11 harbor and at least one gray seal tested positive for H5N1. The number of deceased seals was reported to be around 100.
The QMMERN has identified 93 harbour seal carcasses since the beginning of the year, which is 6 times more than an average year and 3 times more than the record year. (...) The QMMERN recovered and sampled 15 carcasses for analysis by the Centre québécois sur la santé des animaux sauvages (Quebec wildlife health centre). The results show that 11 of the 15 harbour seals sampled were infected with the Eurasian strain of avian influenza H5N1 (HPAI).
He added that a first case was detected last week in a grey seal, another species of this amphibious mammal.
Russia, Caspian Sea
While hundreds or maybe thousands of seals have died in a mass mortality event, the cause has ultimately not been confirmed. While infection with some type of avian influenza was a preliminary result of the Dagestan State University, this has later been denied by Russia's Federal Service for Veterinary and Phytosanitary Surveillance. One case of H5N1 in a seal has been confirmed, but in a different location, just north of Japan.
Preliminary studies of the mass death of Caspian seals have shown that the animals were infected with bird flu. At the same time, it is too early to conclude that it was the virus that caused the deaths, research is still ongoing," said Alimurad Hajiyev, Director of the Institute of Ecology and Sustainable Development of the DGU.
Germany
1 seal tested positive for H5N1.
The avian influenza virus was found in a dead seal in the Friedrichskoog seal station in the Dithmarschen district. On Friday (July 21) , the Friedrich-Loeffler-Institut ( FLI ) confirmed an infection with the highly pathogenic avian influenza virus of the H5N1 subtype after the Schleswig-Holstein state laboratory had detected H5.
United Kingdom, Scotland
4 harbor and gray seals tested positive for H5N1.
“Three out of the four harbour seals and one of the two grey seals from 2021 and early 2022 tested positive for HPAIV H5N1,” said SMASS in a statement. The animals were found in Aberdeenshire, Highlands, Fife and Orkney.
