February 23, 2012

What’s New in Swine Flu – Three Novel Viruses

Christine Grillo

Christine Grillo

Contributing Writer

Johns Hopkins Center for a Livable Future

Flu season has arrived, and it’s sure to be a nuisance—but will it be interesting? This year, the CDC is keeping a keen eye on three novel swine flus that have infected humans. This pig-to-human transmission is noteworthy in itself, but there’s more: two of the three swine flu viruses have taken on genetic material from the 2009 H1N1 virus, in a process known as reassortment.

Confirming the onset of flu season is a February 10 Flu Report by the CDC; the arrival of flu season is nothing remarkable. But since August, the CDC has reported three novel influenza A virus variants (H3N2v, H1N1v, H2N2v) that have infected humans in the U.S., for a total of 14 cases. (Twelve of the 14 cases are H3N2v.) All three viruses originated in swine herds, and CDC has labeled the infection of humans with these swine flus as “rare events.” On December 9, the CDC was “taking this situation very seriously.”

A more recent swine flu update by the CDC says that, “Although there is no evidence that sustained human-to-human transmission of H3N2v is occurring, CDC is watching this situation very closely.”

It is unusual for the virus to make the leap from swine to humans. But what particularly piques our interest is the reassortment that has occurred. This is the process by which virus strains swap genetic material. (If you saw last year’s film Contagion, you’ll be familiar with this summary of a reassortment specific to the film: “Somewhere in the world, the wrong bat met up with the wrong pig.”).

In two of these three novel viruses, the matrix [M] gene from the 2009 H1N1 pandemic, which is a human infection, has shown up in the swine viruses. These new swine viruses—with the M gene from the 2009 H1N1—have then infected at least 13 humans.

Michael Jhung, MD, MPH, of the CDC Influenza Division, says in this address: “Although we know that the M gene plays a role in viral assembly and replication, we aren’t certain what the addition of this M gene means in terms of illness severity or transmissibility in humans. Similar H3N2 viruses have circulated in US swine since the 1990s …. August 2011, however, was the first time this virus was found in a person.” (If you have trouble accessing the link directly, try linking from this CDC page.)

David Love, PhD, a microbiologist at the Center, says of this situation: “If a human with the flu meets a pig with a flu, there is a chance for their viruses to swap genes, in a human or animal host, and we have the potential for a situation like what happened in 2009. That is why zoonotic transmission is really scary.”

In half of the 14 cases, the patients have reported exposure to swine, which means that humans probably became infected directly by the infected swine. In the other half of the cases, the mode of transmission is less clear. When I asked the CDC if they had further information on the transmission, Jeffrey Dimond, a public affairs specialist there, wrote, “Limited human to human is thought to have occurred.”

In the cases of direct exposure to swine, some of the exposures have been characterized as “occupational,” while other exposures occurred at an agricultural fair.

Regarding occupational exposures, Love remarked that in industrial pig farms, the animals are crowded together in unhealthy and unsanitary conditions. “How surprised are we that people who work around pigs are being affected?” he said.

As reported in the Seattle Times last month, the hog industry has begun to brace itself against reports of swine flu. The article quotes Liz Wagstrom, chief veterinarian with the National Pork Producers Council: “It’s always something that we need to keep an eye on, that it doesn’t get more severe or spread more quickly. It’s very important the public understand you can’t get flu from eating pork.”

That said, those who work with the live pigs can become infected with their flu viruses. And it seems that, recently, some of those infected workers may have transmitted their infections to other humans. That is a bit worrisome. Thankfully, so far the human-to-human transmission seems limited.

Also, fortunately, all 14 patients have recovered, and the antiviral drugs oseltamivir and zanamivir have “shown activity against swine–origin influenza viruses.”

Here is more information on the three new viruses being reported. The first one listed (H3N2v) is the most widespread, and is the one the CDC seems to be watching most closely.


12 cases (11 children, 1 adult). 6 cases of transmission via exposure to swine. 6 cases of human-to-human transmission. Indiana, Iowa, Maine, Pennsylvania, West Virginia. First detected in August 2011, with infections detected through December 2011.
Reports from September 6, September 9, December 2, December 9, December 23, and January 6 identify H3N2v, a novel virus that has genes from swine, human, and avian lineages, with the M gene from the 2009 H1N1 pandemic. The virus has been detected in 12 people, 11 of them children.  The report also says that these novel H3N2 viruses are “substantially different” from currently circulating seasonal human influenza A H3N2 viruses. The January 6 update states that the 12 cases occurred in five states (Indiana, Iowa, Maine, Pennsylvania, and West Virginia), and 11 were in children. Six of those patients had exposure to swine, while the other six are thought to have been infected via humans. Some of the infected children attend the same day care facility.


1 case (adult). Transmission most likely via occupational exposure to swine. Wisconsin. First detected in December 2011
Despite the familiar name, this is not the same virus from the 2009–10 pandemic. This novel virus, being called H1N1v (the “v” is for “variant”), has borrowed the M gene from the pandemic, and has been circulating among swine. In a December 23 report, the first human case was reported and found in Wisconsin, in an adult who has occupational contact with swine. The virus is a “triple resassortant,” meaning that it has genes from avian, swine, and human influenza viruses. This is the first time this genetic sequence has been detected in a human. The CDC has found no cases of human-to-human transmission with this virus. The patient is fully recovered.


1 case (child). Transmission most likely human-to-human. Minnesota. First detected in December 2011.
A December 9 report identifies a child in Minnesota who was infected with a virus that circulates in swine but does not normally affect humans. The novel virus is H1N2, and CDC has found no evidence of direct or indirect contact with swine. This leaves open the possibility that human-to-human transmission occurred. The patient is fully recovered. The report does not mention reassortment with the M gene from the 2009 pandemic.

One Comment

  1. Posted by Darell Langerman

    In June 2009, the World Health Organization declared the new strain of swine-origin H1N1 as a pandemic. This strain is often called swine flu by the public media. This novel virus spread worldwide and had caused about 17,000 deaths by the start of 2010. On August 10, 2010, the World Health Organization declared the H1N1 influenza pandemic over, saying worldwide flu activity had returned to typical seasonal patterns.`^

    Take a look at the most up-to-date post on our personal online site

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