Bat flu refers to influenza A viruses found in bats. Bat flu was first discovered in “little yellow-shouldered bats” in Guatemala during a study conducted in 2009 and 2010 by experts from CDC and the Universidad del Valle (University of the Valley) in Guatemala (1). Bat flu viruses have since been detected in some other species of bats in Central and South America (2). Laboratory research conducted at CDC and elsewhere suggests that these viruses would need to undergo significant changes to become capable of infecting and spreading easily among humans. The species of bats currently known to carry bat flu are not native to the continental United States, but are common in Central and South America.

Preliminary laboratory research at CDC suggests that human cells do not support growth of the bat flu viruses in the test tube. This suggests that bat flu viruses may not grow or replicate in humans and would need to undergo significant changes to become capable of infecting and spreading easily among humans. However, testing of the bat flu virus’s genome suggests that its internal genes are compatible with human flu viruses, so CDC scientists cannot rule out the possibility of these viruses eventually becoming capable of infecting humans.

Because the internal genes of bat flu viruses are compatible with human flu viruses, it is possible that these viruses could exchange genetic information with human flu viruses through a process called “reassortment.” Reassortment occurs when two or more flu viruses infect a single host cell, which allows the viruses to swap genetic information. Reassortment can sometimes lead to the emergence of new flu viruses capable of infecting humans.

However, the conditions needed for reassortment to occur between human flu viruses and bat flu viruses remain unknown. A different animal (such as pigs, horses, dogs or seals) would need to serve as a “bridge,” meaning that such an animal would need to be capable of being infected with both this new bat flu virus and human flu viruses for reassortment to occur. Since the discovery of bat flu, at least one study has been conducted to assess the possibility of reassortment events occurring between bat flu and other flu viruses. So far, the results of these studies continue to indicate that bat flu viruses are very unlikely to reassort with other flu viruses to create new and potentially more infectious or dangerous viruses. In their current form bat flu viruses do not appear to pose a threat to human health.

The discovery of bat flu is important for public health because bats represent a new animal species that may act as a source of flu viruses. Flu viruses already are known to spread and cause disease in other animals, including domestic and wild birds, pigs, horses, and dogs, with sporadic outbreaks in seals, whales, ferrets and cats. CDC and disease experts around the world monitor flu viruses that circulate in animals because the previous pandemics of the 20th century as well as the 2009 H1N1 pandemic were caused by flu viruses in animals that gained the ability to infect and spread easily in humans.

The discovery of bat flu has shed light on the evolution of flu A, B and C viruses. It is possible that many of the internal genes of bat influenza viruses are descendants of families of flu viruses that once circulated more widely in previous centuries and that are now extinct – or yet to be discovered. Comparisons between the different bat flu viruses found in Central and South America using a process called phylogenic analysis have shown that there is considerable genetic diversity between these bat flu viruses. This diversity is so great that some flu researchers concluded that in bat populations in Central and South America the bat flu viruses found there may have as much genetic diversity in some gene segments as those found in the flu viruses of all other mammal and bird species combined. This suggests that these viruses have been evolving in bats over a very long time, potentially centuries.

The bat flu viruses discovered in Central and South America are very different from other flu viruses in humans and animals. All flu A viruses have hemagglutinin (HA) surface proteins, and until the discovery of these viruses, there were only 16 different classes (or “subtypes”) of HA proteins known to exist in nature. The new bat flu viruses found in Central and South America are distinct enough from those pre-existing subtypes that CDC scientists have classified them as new subtypes, denoted as “H17” and “H18”. The other surface protein-coding gene of bat flu viruses, neuraminidase (NA), is extraordinarily different from that of known flu viruses, as well. It is possible this gene came from ancient bat flu viruses that are extinct or yet to be discovered. CDC scientists have proposed new designations for the NA subtypes found in bats: “N10” and “N11.”

Flu scientists think the HA and NA surface proteins of bat flu viruses function differently than these proteins do in flu viruses found in humans, other mammals and birds. For example, in humans, HA surface proteins play a role in infection by allowing a flu virus to attach to and gain entry into a human respiratory tract cell. Likewise, NA surface proteins found on flu viruses that infect humans, birds, and other mammals also play a role in infection by allowing a flu virus to escape an infected cell to infect a different, uninfected cell. However, the HA and NA proteins found on the bat flu viruses in Central and South America do not perform these functions in the same way, according to an analysis of their crystal structures. Researchers concluded that these surface proteins must have a different mechanism of action in the bats. Therefore, the means by which these bat flu viruses enter or exit cells to cause infection in the bats remains unknown.

The discovery of the bat flu virus was made possible by field work conducted by CDC’s Global Disease Detection (GDD) Regional Center in Guatemala in collaboration with CDC’s Pathogen Discovery Program, CDC’s Rabies program and the Universidad del Valle in Guatemala.

A total of 316 healthy bats from 21 different species were captured from eight locations in southern Guatemala during two consecutive years, 2009 and 2010. As part of the study, 180 bats were collected in May 2009 and 136 bats were collected in September 2010. With the assistance of the GDD Guatemala Regional Center and the Universidad del Valle, the CDC Rabies program within CDC’s Office of Infectious Diseases and GDD took the lead in swabbing the bats. Rectal swabs and tissues were collected from each of the bats.

Swabs that were negative for rabies were analyzed to detect other pathogenic viruses by the Pathogen Discovery Program, which is located in CDC’s Division of Viral Diseases. Initial viral screening conducted by the Pathogen Discovery Program determined that three of the 316 bats tested positive for flu. All were from a single species known as little yellow-shouldered bats.

CDC’s Pathogen Discovery Program was able to identify and sequence the complete genome of the new virus using high-throughput sequencing instruments in the laboratory (specifically 454 pyro sequencing and Illumina GAIIx) at CDC’s laboratories at its Atlanta headquarters and Emory University’s sequencing core, respectively.