Impact of Viruses on Dairy Products and Health

Viruses are among the most overlooked yet consequential microorganisms in the dairy industry. Unlike bacteria or fungi, they cannot grow or reproduce independently – they need a living host cell to survive. In a dairy plant, this dependency becomes a serious operational and public health concern. From derailing cheese and yogurt fermentations to posing direct risks to human health through contaminated raw milk, viruses touch nearly every stage of milk production and processing. Understanding their structure, behavior, and impact is essential for anyone working in dairy science or food safety.

What is a virus? Structure and key characteristics 🔗

A virus is a submicroscopic infectious agent made up of a core of genetic material – either DNA or RNA – enclosed within a protective protein coat called a capsid. Some viruses also have an outer lipid membrane called an envelope. Unlike bacteria, viruses have no cell wall, no cytoplasm, and no metabolic machinery of their own. They are not considered fully living organisms because, on their own, they cannot carry out any biological functions.

The most critical feature of any virus is its absolute dependence on a host cell. As Biology LibreTexts explains, viruses do not encode for all of the enzymes necessary for replication, so they must commandeer a host cell’s machinery to produce more viral particles. Once inside a suitable host, they hijack the cell’s resources – ribosomes, energy systems, and raw materials – to replicate themselves.

How viruses reproduce: the lytic and lysogenic cycles 🔗

Viruses that infect bacteria – called bacteriophages (or simply “phages”) – reproduce through two primary pathways: the lytic cycle and the lysogenic cycle. Both are critical to understanding how viruses behave in a dairy environment.

The lytic cycle 🔗

In the lytic cycle, the phage attaches to specific receptors on the bacterial cell surface, injects its genetic material into the cell, and takes over the host’s metabolic machinery. The cell then produces hundreds of new viral copies, which are assembled and ultimately released when the host cell bursts – a process called lysis. According to ScienceDirect, this cycle can be completed in as little as 16 minutes, with up to 200 new phage particles released per host cell. These newly released phages immediately go on to infect more bacterial cells, setting off a rapid chain reaction of infection.

The lysogenic cycle 🔗

In the lysogenic cycle, the phage takes a different approach. Instead of immediately destroying the host, the viral DNA integrates into the bacterial chromosome and enters a dormant state called a prophage. Biology LibreTexts notes that as the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is reproduced in all of the cell’s offspring. The prophage can remain dormant for many bacterial generations until triggered by environmental stressors – such as UV radiation or exposure to certain chemicals – at which point it switches to the lytic cycle and begins actively destroying cells.

Bacteriophages in dairy fermentation: the core industrial threat 🔗

In the dairy industry, fermented products like cheese, yogurt, sour cream, and buttermilk depend entirely on lactic acid bacteria (LAB) – starter cultures that convert lactose into lactic acid, acidifying the milk and developing texture and flavor. Bacteriophages that target these LAB are, without question, one of the most serious threats to dairy processing worldwide.

Research published in Microbial Cell Factories confirms that phages are the primary cause of fermentation failure in the milk transformation industry. The most commonly affected LAB species include Lactococcus lactis, Streptococcus thermophilus, and species of Lactobacillus, all of which are widely used as starter cultures in commercial cheese and yogurt production.

What happens when phages attack a fermentation vat 🔗

When a virulent phage enters a fermentation vat and finds susceptible LAB cells, lysis begins. As described by QualiTru, a phage infection causes acid production to slow down and eventually stop – and it may impact multiple vats unevenly. In the case of fermented milk products, the acid production stops altogether, causing a lack of coagulation, or the milk may drop to the correct pH but produce a grainy texture with excessive whey separation. Once phage is present in the starter culture, it is usually too late to salvage the fermentation. The cultured dairy products must be discarded or downgraded, which directly translates into profit losses.

A review published in ScienceDirect estimates that between 0.1-10% of milk fermentations fail due to phage activity, resulting in considerable economic losses to the industry. In a factory producing thousands of liters of cheese daily, even the lower end of that range represents significant waste.

Where do phages come from in a dairy plant? 🔗

Phages are ubiquitous in the environment – they are found in water, air, surfaces, and particularly in raw milk. Researchers at CONICET explain that the main path through which phages enter a plant is through the raw material itself – large volumes of raw milk carrying wild lactic bacteria and their specific phages. Beyond raw milk, phages can also persist in cheese whey, and when whey is recycled as a processing ingredient, it can seed new fermentation batches directly with active phage populations.

Of the many phage species found in dairy plants, only three – c2, 936, and P335 – are commonly responsible for most fermentation failures involving Lactococcus lactis, according to research in Applied and Environmental Microbiology. Their prevalence, combined with their varying resistance to heat treatments, makes them particularly difficult to eliminate.

Phage resistance to heat and sanitation 🔗

One of the complications in controlling dairy phages is their resilience. Standard pasteurization – typically heating milk to 72°C for 15 seconds (HTST) – is effective against most bacteria and many pathogens. However, not all phages are equally vulnerable. A study in PMC on inactivation of dairy bacteriophages reports that some Leuconostoc phages can survive pasteurization conditions, and certain phage strains may even withstand temperatures of 90°C for 45 minutes when suspended in milk. This thermal resistance varies widely between phage populations and depends on the initial level of infection.

The International Dairy Federation recommends heating to 90°C for 15 minutes as a more reliable phage-inactivation benchmark, though even this does not guarantee complete elimination of all phage strains present in raw milk.

Control strategies used in the dairy industry 🔗

Because phages cannot be completely eradicated from the dairy environment, the industry relies on a combination of strategies to manage their impact. A review in PMC on bacteriophages and dairy fermentations highlights that rotation of starter cultures is one of the most effective practical tools – by regularly switching the bacterial strains used in fermentation, a plant prevents any single phage population from building up to damaging levels. Other key approaches include proper factory design that limits air circulation of phages between vats, rigorous sanitation of surfaces and equipment, careful handling of raw milk and whey by-products, and the development and use of phage-resistant bacterial strains through methods including CRISPR-Cas-based resistance mechanisms.

Viruses and public health: the risk in raw milk 🔗

While bacteriophages threaten the production process, a separate category of viruses poses a direct risk to the people who consume dairy products – particularly raw, unpasteurized milk. Raw milk can contain a range of pathogens that pasteurization is specifically designed to eliminate.

The U.S. Centers for Disease Control and Prevention (CDC) warns that consuming raw milk can expose people to germs that cause serious foodborne illness, including bacteria and viruses linked to diarrhea, stomach cramping, vomiting, and in severe cases, hemolytic uremic syndrome, kidney failure, and paralysis. Vulnerable groups – including children, pregnant women, older adults, and people with weakened immune systems – face the greatest risk.

Avian influenza (H5N1) in raw milk: an emerging concern 🔗

A more recent and urgent viral threat involves highly pathogenic avian influenza (HPAI) A(H5N1), which has been detected in dairy cattle and raw milk in the United States. The CDC’s guidance for healthcare providers on this issue states that if a person consumed unpasteurized milk with live HPAI A(H5N1) virus, they could theoretically become infected through viral binding in the respiratory tract. Pasteurization effectively kills H5N1 in milk, and based on current evidence, the commercial pasteurized milk supply is considered safe.

Beyond bird flu, Stanford Medicine research has shown that Rift Valley fever virus can remain infectious in refrigerated raw milk for roughly as long as someone would want to drink it – a finding that highlights the broader risk posed by zoonotic viruses present in livestock. The research confirms that pasteurization effectively kills this virus as well, reinforcing the critical role of heat treatment in food safety.

Why pasteurization remains the most important defense 🔗

The U.S. Food and Drug Administration (FDA) notes that pasteurization, first developed by Louis Pasteur in 1864, kills pathogens responsible for diseases including listeriosis, typhoid fever, tuberculosis, diphtheria, Q fever, and brucellosis. The process does not reduce milk’s nutritional value – it simply makes milk safe by eliminating the harmful organisms that raw milk can carry. For viruses specifically, the heat treatment disrupts their protein structures and inactivates their genetic material, rendering them non-infectious.

Raw milk dairy products remain a recurring source of outbreaks. A study published in PMC analyzing U.S. outbreak data from 1998 to 2018 found that consumption of unpasteurized milk can result in transmission of pathogens including Campylobacter, Shiga toxin-producing E. coli, Listeria monocytogenes, and Salmonella enterica, with serious long-term consequences for some individuals including kidney failure and Guillain-Barré syndrome.

Monitoring and detection of viruses in dairy 🔗

Given the scale of potential losses – both economic and health-related – effective monitoring for viral contamination is essential in modern dairy operations. Detection methods range from classical microbiological techniques like plaque assays (which measure how much acid production is reduced in a phage-infected culture) to more advanced molecular tools such as PCR and quantitative PCR (qPCR), which detect and quantify phage DNA rapidly. Electron microscopy can directly visualize phage morphology but requires expensive equipment and is less suitable for routine monitoring.

For public health surveillance, regulatory agencies in many countries require that commercial milk be pasteurized before sale. In the United States, the FDA and CDC recommend that consumers always choose pasteurized milk and dairy products, and MMWR reporting on recent Salmonella outbreaks linked to raw milk continues to reinforce this recommendation, noting that commercially distributed raw dairy products have the potential to cause large and widespread infectious disease outbreaks.

What do you think? With bacteriophage resistance to heat treatment varying so widely between phage strains, should dairy regulations require specific phage-testing standards for fermented products – beyond just bacterial pathogen testing? And given the growing evidence of zoonotic viruses like H5N1 and Rift Valley fever virus surviving in raw milk, how should public health messaging be updated to better communicate viral – not just bacterial – risks to consumers?

References

1. https://bio.libretexts.org/Courses/Mansfield_University_of_Pennsylvania/BSC_3271:_Microbiology_for_Health_Sciences_Sp21_(Kagle)/03:_Viruses/3.01:_Viral_Replication/3.1.02:_The_Viral_Life_Cycle
2. https://www.sciencedirect.com/topics/immunology-and-microbiology/lysogenic-cycle
3. https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/General_Biology_(Boundless)/21:_Viruses/21.02:_Virus_Infections_and_Hosts/21.2B:_The_Lytic_and_Lysogenic_Cycles_of_Bacteriophages
4. https://pmc.ncbi.nlm.nih.gov/articles/PMC3231927/
5. https://qualitru.com/impact-of-bacteriophages-in-dairy-processing-part-1/
6. https://www.sciencedirect.com/science/article/abs/pii/S1043452621000206
7. https://www.conicet.gov.ar/bacteriophage-the-invisible-enemies-of-the-dairy-industry/
8. https://pmc.ncbi.nlm.nih.gov/articles/PMC535134/
9. https://pmc.ncbi.nlm.nih.gov/articles/PMC6563197/
10. https://pmc.ncbi.nlm.nih.gov/articles/PMC3530524/
11. https://www.cdc.gov/food-safety/foods/raw-milk.html
12. https://www.cdc.gov/bird-flu/hcp/unpasteurized-raw-milk/index.html
13. https://med.stanford.edu/news/insights/2025/02/milk-disease-risk-bird-flu-pasteurization.html
14. https://www.fda.gov/food/buy-store-serve-safe-food/dangers-raw-milk-unpasteurized-milk-can-pose-serious-health-risk
15. https://pmc.ncbi.nlm.nih.gov/articles/PMC9987020/
16. https://www.cdc.gov/mmwr/volumes/74/wr/mm7427a1.htm