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“Swine Flu” was circulating undetected, scientists say

May 23, 2009
Courtesy Science
and World Science staff

By se­quenc­ing the genomes of more than 50 sam­ples of the new A(H1N1) in­flu­en­za or “Swine Flu” vi­rus, re­search­ers have found that the vi­rus is dis­tantly re­lat­ed to its near­est rel­a­tives. 

That sug­gests its genes have been cir­cu­lat­ing un­de­tected for an ex­tend­ed per­i­od, ac­cord­ing to sci­en­tists, and that in the fu­ture pig popula­t­ions will need to be closely mon­i­tored for emerg­ing in­flu­en­za vi­ruses.

The vi­rus has sickened 11,168 people world­wide and caused 86 deaths, most of them in Mex­ico, ac­cord­ing to the World Health Org­an­iz­ation.

Re­bec­ca Garten at the U.S. Cen­ters for Dis­ease Con­trol and Pre­ven­tion and col­leagues se­quenced the full or par­tial genomes of 2009 A(H1N1) vi­ruses iso­lat­ed in Mex­i­co and the Un­ited States. 

They in­ves­t­i­gated the ori­gins of the vi­rus’ eight gene seg­ments and found that the com­bina­t­ion of these gene seg­ments has not pre­vi­ously been re­ported among swine or hu­man in­flu­en­za vi­ruses. All of the seg­ments orig­i­nat­ed in avi­an hosts and then be­gan cir­cu­lat­ing in pigs at var­i­ous times in his­to­ry, from 1918 through to 1998, ac­cord­ing to the group. 

Six of the eight seg­ments were found to have orig­i­nat­ed from combined ge­net­ic ma­te­ri­al from hu­man, avi­an and swine vi­ruses that have been cir­cu­lat­ing in North Amer­i­ca and Asia since about 1998. The oth­er two seg­ments were found to be de­rived from Eur­a­sian swine vi­ruses. 

The se­quences for the gene seg­ments did not re­veal the sig­na­tures of high trans­mis­si­bil­ity or vir­u­lence that have been found in oth­er in­flu­en­za A vi­ruses, sug­gest­ing that oth­er, yet-unknown ge­net­ic se­quences are re­spon­si­ble for the new vi­rus’ abil­ity to rep­li­cate and spread in hu­mans, the sci­en­tists re­ported.

The find­ings are pub­lished in the May 22 is­sue of the re­search jour­nal Sci­ence.

The investigators al­so took a clos­er look at the new A(H1N1) vi­rus’ he­mag­glu­tin pro­tein, which is con­sid­ered re­spon­si­ble for the vi­rus’ abil­ity to bind to and in­fect its host cell. Test-tube ex­pe­ri­ments that ex­am­ined how fer­ret im­mune sys­tem mo­le­cules re­acted against this pro­tein sug­gested the new strain has prop­er­ties that are si­m­i­lar to those of oth­er swine A(H1N1) vi­ruses but dis­tinct from sea­son­al hu­man flu. Re­search­ers will need to con­tin­ue to look for changes in the he­mag­glu­tin pro­tein in the new vi­rus, which may af­fect the se­lec­tion of vac­cine can­di­dates, the au­thors said.


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By sequencing the genomes of more than 50 samples of the new A(H1N1) influenza or “Swine Flu” virus, researchers have found that the virus is distantly related to its nearest relatives. That suggests its genes have been circulating undetected for an extended period, according to scientists, and that in the future pig populations will need to be closely monitored for emerging influenza viruses. Rebecca Garten at the U.S. Centers for Disease Control and Prevention and colleagues sequenced the full or partial genomes of 2009 A(H1N1) viruses isolated in Mexico and the United States. They investigated the origins of the virus’ eight gene segments and found that the combination of these gene segments has not previously been reported among swine or human influenza viruses. All of the segments originated in avian hosts and then began circulating in pigs at various times in history, from 1918 through to 1998, according to the group. Six of the eight segments were found to have originated from triple “reassortant” swine viruses — which include genetic material from human, avian and swine viruses’ as the result of these virus’ tendency to swap pieces of their genomes with each other — that have been circulating in North America and Asia since about 1998. The other two segments were found to be derived from Eurasian swine viruses. The sequences for the gene segments did not reveal the signatures of high transmissibility or virulence that have been found in other influenza A viruses, suggesting that other, yet-unknown genetic sequences are responsible for the new virus’ ability to replicate and spread in humans, the scientists reported. The findings are published in the May 22 issue of the research journal Science. The researchers also took a closer look at the new A(H1N1) virus’ hemagglutinin protein, which is considered responsible for the virus’ ability to bind to and infect its host cell. Test-tube experiments that examined how ferret immune system molecules reacted against this protein suggest that the new strain has properties that are similar to those of other swine A(H1N1) viruses but distinct from seasonal human flu. Researchers will need to continue to look for changes in the hemagglutinin protein in the new virus, which may affect the selection of vaccine candidates, the authors said.