Swine influenza A/Mexico/2009 (H1N1) update

phases5-6Here is an update on the global swine flu situation as of 29 April 2009.

Not surprisingly, laboratory confirmed case counts continue to rise globally. There are 91 cases in the US in 10 states (Arizona, California, Indiana, Kansas, Massachusetts, Michigan, Nevada, New York, Ohio, Texas). There has been a laboratory confirmed fatal case in Texas, in a Mexican toddler visiting the US with his family. Eight other countries report a total of 57 laboratory confirmed cases, with no changes in the numbers in Mexico. Other countries reporting cases are Austria (1), Canada (13), Germany (3), Israel (2), New Zealand (3), Spain (4) and the United Kingdom (5). Globally nine countries have confirmed 148 cases with 2 deaths.

These numbers might not appear to justify the enormous reactions of health agencies such as CDC and WHO. Remember that there are probably many more infections with this virus, not only in the countries that report isolation of the virus but in other areas as well. It will likely take several weeks before we have a good appreciation for how extensively the virus has spread.

On Tuesday WHO raised the level of influenza pandemic alert from phase 4 to phase 5. According to WHO, “Phase 5 is characterized by human-to-human spread of the virus into at least two countries in one WHO region. While most countries will not be affected at this stage, the declaration of Phase 5 is a strong signal that a pandemic is imminent and that the time to finalize the organization, communication, and implementation of the planned mitigation measures is short.” WHO regions include African, European, Eastern Mediterranean, Americas, Southeast Asia, and Western Pacific. The cases in 4 European countries fulfilled the requirement for moving to phase 5.

Incredibly, Egypt began slaughtering 300,000 pigs as a ‘precautionary measure’ against the spread of swine flu. Farmers will not be compensated because the meat will be sold for consumption. This is a somewhat controversial move, because it is highly unlikely that pigs anywhere will play a role in further spread of the virus, which is now adapted to humans.

Sequences of viral RNAs from 20 swine flu isolates have now been posted on the NCBI website. Included are isolates from California, Texas, New York, Ohio, Kansas, and Germany (taken from a tourist who returned from Mexico). It is difficult to understand why RNA sequences of none of the Mexican isolates have  been posted, which would enable us to determine if the viruses in that country are different from the others. However, examination of the sequences of the New York and German isolates, which presumably originated in Mexico, reveal no significant differences with sequences from other isolates. From this information I conclude that the apparent higher virulence of swine flu in Mexico is not a consequence of a genetically diverged virus.

Other interesting information that can be gleaned from sequence information is contained in a statement from CDC: “…the HA, PB2, PB1, PA, NP, NS genes
contain gene segments from influenza viruses isolated from swine in North America [such as, A/swine/Indiana/P12439/00], while the NA and M genes are most closely related to corresponding genes from influenza viruses isolated in swine population in Eurasia.
However, the NA and M genes from 2 swine virus isolates from America are also closely related to the novel H1N1 virus (A/swine/Virginia/670/1987, A/swine/Virginia/67a/1987), if a reasonable nucleotide substitution rate is accepted. Thus, H1N1 from Mexico may be a swine flu virus strain of entirely American origin, possibly even of relatively ancient origin.” In the coming days I will attempt to construct a history of the evolution of swine influenza. In the meantime it may well be that this new human strain emerged from the US, as did the 1918-19 pandemic virus.

It is curious that CDC originally asserted that the new swine influenza virus inherited genes from human, pig, and bird viruses. Dr Anne Schuchat made this statement during a press conference on 23 Apr 2009, noting that  “Preliminary testing of viruses from the 1st 2 patients shows that they are very similar. We know so far that the viruses contain genetic pieces from 4 different virus sources. This is unusual. The 1st is our North American swine influenza viruses. North American avian influenza viruses, human influenza viruses, and swine influenza viruses found in Asia and Europe. That particular genetic combination of swine influenza virus segments has not been recognized before in the US or elsewhere.”

I am not sure why the sequence information now available indicates a very different origin for these viruses.

Although many still describe this virus as swine flu, it is technically no longer a pig virus – having acquired the ability to be transmitted among humans and cause disease, it is now a human virus. I realize that the official strain names are cumbersome (A/Mexico/4482/2009 [H1N1]), and therefore it is likely that we will be using ‘swine flu H1N1’ at least until the next pandemic.

Swine influenza daily update

influenza-virion1Here is an update on the global swine flu situation as of 28 April 2009.

There are now 64 laboratory confirmed cases of infection with the H1N1 swine influenza strain, up from 40 the day before. States reporting cases are California (10), Kansas, (2), New York City (45), Ohio (1) and Texas (6). These are the same states that reported isolations on the previous day. There are new laboratory confirmed isolations of the virus in Australia (3), Israel (1, a traveler returning from Mexico), and New Zealand (3). The number of laboratory confirmed cases in Mexico remains the same as the previous day: 26 cases, 7 deaths. This brings the total number of countries reporting laboratory confirmed cases to seven.

Swine influenza virus isolates from the US and Mexico have been given names according to the proper nomenclature, which takes the following form:
Influenza type/Country/isolate number/year (subtype).

Accordingly, the following swine influenza virus strains have been isolated:

A/California/04/2009 (H1N1)
A/California/06/2009
(H1N1)
A/California/07/2009 (H1N1)
A/California/08/2009 (H1N1)
A/California/10/2009 (H1N1)
A/Texas/04/2009 (H1N1)
A/Texas/05/2009 (H1N1)
A/Kansas/03/2009 (H1N1)
A/Ohio/07/2009 (H1N1)
A/New York/19/2009 (H1N1)
A/New York/20/2009 (H1N1)
A/Mexico/4482/2009 (H1N1)
A/Mexico/4486/2009 (H1N1)
A/Mexico/4108/2009 (H1N1)
A/Mexico/4115/2009 (H1N1)
A/Mexico/4603/2009 (H1N1)
A/Mexico/4604/2009 (H1N1)

I expect to see many more isolates from different countries in the coming weeks.

Today the CDC released genome sequences of the viral RNAs of six swine flu isolates from California and Texas (Addendum: sequences of New York, Ohio, and Kansas isolates were added late yesterday). The influenza virus genome consists of eight segments of RNA, each coding for one or more proteins (illustrated). Each RNA segment has a name – PB2, PB1, PA, HA, NP, NA, MP, and NS. Mystery Rays has done a quick analysis of the sequences. The isolates are all the same strain, but they are not identical. Unfortunately we don’t yet have genome sequence from any Mexican isolate – otherwise we could determine if they are significantly different. Such information might provide clues about why the disease in Mexico seems to be more severe than elsewhere.

A comparison with RNA sequences of other influenza virus isolates shows that most of the viral RNAs are from swine influenza viruses, with the possible exception of the PB1 RNA, which may be derived from a human H1N1 virus. This observation is somewhat surprising, because last week we were told that the new swine virus had RNA segments from pig, human, and avian influenza viruses. According to ProMED-mail, the NA and MP genes are related to those of influenza viruses from Asian-European swine, and the other genes appear to originate from swine flu viruses from pigs in North America. The data are in accord with the original assertion of the CDC that all genes of the new isolate were derived from swine viruses.

The fact that A/California/04/2009 and related isolates are pig viruses, with little or no genetic material from human influenza virus strains, is fascinating. Clearly these strains are different from viruses that circulate in pigs because they can be transmitted among humans and cause respiratory disease. It will be very important to compare the sequences of these isolates with viruses obtained from pigs in an attempt to determine what changes enabled the virus to adapt to humans.

New swine influenza viruses in humans

swineA new strain of swine influenza virus has been recently isolated from seven persons in the US. Is it time to break out the swine flu vaccine of 1976?

Last week the CDC reported that swine influenza virus had been isolated from two children with respiratory illness in California. The cases were not linked and the children recovered from the illness. The virus was identified as a swine influenza H1N1 strain, similar to viruses that have circulated in American pigs for the past ten years. However some of the viral genes are derived from Eurasian swine influenza viruses. The isolates are new because this particular combination of swine influenza virus RNAs has not been observed before among swine or human viruses.

A similar virus was subsequently identified in five additional individuals in Texas. It’s curious that one of the California children had traveled to Texas before becoming ill, but whether or not the cases are related has not been revealed.

What is the origin of these new swine viruses? None of the people who were infected had known contact with pigs. Others must have acquired the virus from pigs, who then passed it on – demonstrating that the virus can be transmitted among humans.

At the moment these infections don’t seem to be cause for alarm. Because influenza virus surveillance is more intense than ever before, it is likely that new viruses will always be detected. Furthermore, respiratory disease caused by these new viruses has not been very severe. Another mitigating factor is that the influenza season is nearly over – viral transmission wanes when the weather becomes warmer and more humid.

It is believed that swine influenza originated in 1918-19, when pigs became infected with the pandemic influenza virus strain. Since that time, the H1N1 swine virus has been transmitted back to humans. The hypothesis for the origin of swine influenza is supported by the finding that pigs can be experimentally infected with the human 1918 pandemic influenza virus strain. Furthermore, other human influenza virus strains are known to infect pigs. For example, in the early 1970s, a human H3N2 subtype entered the European swine population.

Pigs can be infected with both human and avian influenza virus strains because the cells of their respiratory tract bear receptors for both kinds of viruses. Based on this observation, it has been suggested that influenza viruses pass from birds through pigs on their way to infecting people. For example, if a pig is infected with avian and human influenza A viruses, reassortment of the viral RNAs occurs, leading to new virus strains to which humans are not immune. The 1957 and 1968 human pandemic viruses were reassortants of human and bird strains, although there is no evidence that these viruses arose in pigs. The role of pigs as a ‘mixing vessel’ for influenza virus has been questioned in view of the recent transmission of avian influenza viruses directly to humans.

Swine influenza viruses probably routinely pass among humans and swine; in this case they were detected as a consequence of heightened surveillance. Gerald Ford won’t be rolling over in his grave over this incident.

Weingartl, H., Albrecht, R., Lager, K., Babiuk, S., Marszal, P., Neufeld, J., Embury-Hyatt, C., Lekcharoensuk, P., Tumpey, T., Garcia-Sastre, A., & Richt, J. (2009). Experimental Infection of Pigs with the Human 1918 Pandemic Influenza Virus Journal of Virology, 83 (9), 4287-4296 DOI: 10.1128/JVI.02399-08

de Jong, J., Smith, D., Lapedes, A., Donatelli, I., Campitelli, L., Barigazzi, G., Van Reeth, K., Jones, T., Rimmelzwaan, G., Osterhaus, A., & Fouchier, R. (2007). Antigenic and Genetic Evolution of Swine Influenza A (H3N2) Viruses in Europe Journal of Virology, 81 (8), 4315-4322 DOI: 10.1128/JVI.02458-06

Van Reeth, K. (2007). Avian and swine influenza viruses: our current understanding of the zoonotic risk Veterinary Research, 38 (2), 243-260 DOI: 10.1051/vetres:2006062

Reverse zoonoses: Human viruses that infect other animals

bonoboThe many human viral diseases that have crossed from other animal species  – such as AIDS, Ebola, SARS, encephalitis and respiratory diesease caused by henipaviruses – demonstrate the pathogenic potential of the zoonotic pool. Are there also reverse zoonoses – diseases of humans that are transferred to other animal species?

An example of a reverse zoonosis occurred just last week at Lincoln Park Zoo in Chicago, where a 9 year old chimpanzee died of respiratory disease caused by human metapneumovirus. This member of the paramyxovirus family is responsible for approximately 10% of all respiratory tract infections. All seven members of a group of chimpanzees were infected with the virus, but only one became ill. The virus was likely transmitted to the chimps by humans, but precisely how and when is not known. Outbreaks of fatal respiratory disease in wild chimpanzees have been reported previously, and human metapneumovirus has been one of several human viruses isolated from these primates. Such infections are expected to occur more frequently in zoological parks, and ando also in game preserves as human encroachment of these facilities increases.

Influenza virus may also be frequently transmitted from humans to other animal species. An outbreak of influenza recently lead to the death of 6 bonobos (a species of chimpanzee) in a Congo wildlife sanctuary. Although the influenza subtype responsible for the outbreak has not been identified, it has been suggested that the source was one or more visitors during the February epidemic of influenza in Kinshasha.

Human influenza viruses are frequently isolated from pigs. Since its emergence in 1968, the H3N2 subtype has infected pigs many times throughout the world, and has often caused serious outbreaks. More recently the influenza H1N1 subtype has been shown to infect pigs. Influenza viruses remain in the pig population for long periods of time, and may serve as reservoirs for the recycling of older influenza virus strains back into the human population.

Just as increasing human population, travel, and the global food business increase the likelhood that viruses will jump from animals into humans, the same factors ensure the reverse spread as well – often with dire consequences for zoological parks and wild and domestic animals. And the viruses we pass on may come back to haunt us another day.

Kaur, T., Singh, J., Tong, S., Humphrey, C., Clevenger, D., Tan, W., Szekely, B., Wang, Y., Li, Y., Alex Muse, E., Kiyono, M., Hanamura, S., Inoue, E., Nakamura, M., Huffman, M., Jiang, B., & Nishida, T. (2008). Descriptive epidemiology of fatal respiratory outbreaks and detection of a human‐related metapneumovirus in wild chimpanzees at Mahale Mountains National Park, Western Tanzania. American Journal of Primatology, 70 (8), 755-765 DOI: 10.1002/ajp.20565

Yu, H., Zhou, Y., Li, G., Zhang, G., Liu, H., Yan, L., Liao, M., & Tong, G. (2009). Further evidence for infection of pigs with human-like H1N1 influenza viruses in China Virus Research, 140 (1-2), 85-90 DOI: 10.1016/j.virusres.2008.11.008

de Jong, J., Smith, D., Lapedes, A., Donatelli, I., Campitelli, L., Barigazzi, G., Van Reeth, K., Jones, T., Rimmelzwaan, G., Osterhaus, A., & Fouchier, R. (2007). Antigenic and Genetic Evolution of Swine Influenza A (H3N2) Viruses in Europe Journal of Virology, 81 (8), 4315-4322 DOI: 10.1128/JVI.02458-06

Swine flu at Fort Dix

swineThe death of a dozen pigs from swine influenza last week in the Philippines reminded me of an incident at Fort Dix, NJ in 1976. The infection of humans with a strain of swine influenza lead to a nationwide immunization campaign to curb a pandemic that never occurred.

An explosive outbreak of febrile respiratory disease raced through the 19,000 personnel at Fort Dix in January 1976. Virological laboratory studies revealed the presence of a new swine influenza strain which was named A/New Jersey/76 (Hsw1N1). The virus infected 230 soldiers and caused severe respiratory disease in 13, including one death.

At the time it was believed that a swine virus had caused the 1918-19 influenza pandemic. Therefore scientists were concerned that the virus had returned to Fort Dix and would soon cause another catastrophic outbreak. Dr. Edwin Kilbourne, a noted influenza researcher, and others convinced the US Public Health Service to contract for the production of 150 million doses of vaccine. In March of 1976 President Gerald Ford announced a program to inoculate every man, woman and child in the United States against swine flu. Immunizations began in October, but only 45 million doses had been distributed when the program was halted in December. By then it was clear that A/New Jersey/76 was going nowhere. An unfortunate consequence was that many individuals developed Guillain-Barré syndrome, a neurological disease involving muscle weakness, paralysis, and sometimes death.

Why didn’t A/New Jersey/76 spread to the general population? One factor was the limited contact between basic trainees and others who more frequently travel outside the facility. Older personnel may have been immune, because military influenza vaccine formulations from 1955 through 1969 contained a swine influenza component. Competition with concurrent circulating influenza virus strain, A/Victoria, might have  limited the impact of A/New Jersey virus which is believed to transmit poorly among humans.

In retrospect, the swine flu program had many flaws. The vaccine should have been stockpiled until it was clear that an epidemic was taking place. Today we realize that the 1918 influenza virus is derived from an avian strain, not a swine strain – had this information been available in 1976, the immunization campaign would not have taken place. Presumably these and many other errors will not be repeated when the time comes to immunize against the next pandemic strain.

To this day the origin of A/New Jersey/76 virus is an enigma. One theory is that a swine virus was brought to Fort Dix early in 1976 as recruits returned after the holidays. However, none of the personnel who were interviewed admitted to having contact with pigs. The virus seems to have circulated at Fort Dix for about a month, then disappeared.