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Genetic Surveillance Study Finds Flu Viruses at Two US Swine Markets

NEW YORK (GenomeWeb) – A team from the US Centers for Disease Control and Prevention, the Minnesota Department of Health, and the University of Minnesota has garnered evidence suggesting influenza A strains circulating at live swine markets in the US could potentially cross over to infect humans.

As they reported online this week in the journal Clinical Infectious Diseases, the researchers used a combination of real-time reverse transcription PCR (rRT-PCR), genome sequencing, viral culturing, and serological testing to not only track influenza A viruses at two mixed species swine markets in Minnesota over three months, but also to look at the possible risk of transmission to people working there.

The team found that influenza A viruses — including some seemingly reassorted viruses — turned up on surfaces at the markets and in more than half the swine lung or oral fluid samples. Meanwhile, some 65 percent of employees had influenza A virus DNA in their nasal swabs.

"At markets where swine and persons are in close contact, swine-origin [influenza A viruses] are prevalent and potentially provide conditions for novel [influenza A virus] emergence," senior author Ruth Lynfield, with the Minnesota Department of Health, and her co-authors wrote.

Past research on animal reservoirs of influenza A viruses have highlighted the potential for human outbreaks stemming from sites such as Asian poultry markets, the team noted, due to the diversity of strains present, types of host animals present, and proximity to humans.

But less is known about the flu viruses present in mammalian and/or domestic live animal markets. To explore this relationship, Lynfield and colleagues collected samples at two live animal markets in Minnesota over 12 weeks in late 2012 and early 2013, focusing on sites suspected of contributing to past swine flu infections in the regions.

Using rRT-PCR, they tested air samples and swab samples taken at each market weekly, as well as nasal swab samples from 17 employees, and around 200 swine oral fluid or lung tissue samples, uncovering influenza A virus DNA in 11 individuals, 117 of 199 swine samples, and several environmental samples.

To look at the viruses in more detail, the researchers did whole-genome sequencing on 122 isolates from the markets: 78 H3N2 viruses, 32 H1N2 viruses, three H1N1 viruses, and nine isolates containing multiple subtypes.

Among other things, the sequence data pointed to diversity in influenza A viruses found there, while highlighting the presence of genetically related isolates at each market.

The researchers also saw close genetic ties between market isolates and an H3N2 strain identified in a 12-year-old boy who visited one of the markets not long before coming down with the flu.

In a related commentary, St. Jude Children's Research Hospital infectious disease researcher Richard Webby noted that such studies are complex to interpret but critical in teasing apart zoonotic flu virus risk and transmission patterns, and he argued that the current study "brings into question the wisdom of live animal markets."

"There is ample evidence to support a human health threat from live birds in these markets, and now mammalian hosts as well," he wrote. "[C]hanges must be made to how they operate. Whether it is manipulations to air flow, animal husbandry, sanitary practices, or other novel solutions, studies to assess the impact of intervention strategies in real world settings are needed.

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