Tracking viruses in a community can mean testing lots and lots of people. That can be expensive, require a lot of permissions, approvals, a big and capable laboratory capacity and take a lot of time. If you can find a way to screen one sample while still representing a lot of people, life is much easier. An ideal “catch-all” method will let us see what viruses are circulating and identify water contamination, treatment failures and alert public health officials to the potential for infection and illness. A new report from the city of Quito in Ecuador describes such a method and its findings.

Testing sewage using broadly reactive sensitive molecular tools aims to find all that is there, rather than the presence of just one or a few specific viruses, for example, an adenovirus or a norovirus or an enterovirus (including polioviruses, echoviruses and Coxsackieviruses) as has been done before.[2-6]

Using a big molecular net is an approach that has proven useful for virus detection and discovery before,[7-9] yielding all sorts of viral goodies and knowledge in recent years.

Test the river to examine the population

In this new study, urban river water was sampled from three sites downstream from sewage outlets along the city of Quinto. Human adenovirus and Escherichia coli were used to indicate whether human waste was indeed present in the river water.

A lot of virus runs through it

After water samples were concentrated, unbiased high-throughput or “next generation” gene sequencing (HTS or NGS) was used.

The study found signs of 29 different viral families including 26 species of virus that are known to cause human illness as well as others for which the jury is still deciding.

Species included:

• Human Mastadenovierus F (often called adenoviruses)
• Sapporo virus (sapoviruses)
• Norwalk virus (noroviruses)
• Mamastovirus 1, 6, 8, 9 (astroviruses)
• Parechovirus A (human parechoviruses)
• Primate bocaparvovirus 1 and 2  (human bocavirus 1, 2 and 3)
• Salivirus A
• Hepatovirus A (hepatitis A virus)
• Aichivirus A (aichviruses)
• Enterovirus A, B, C (enteroviruses)

The study didn’t describe the complete genome sequence from the viral discoveries but it found a hint that a new papillomavirus genotype may exist in the mix and perhaps some novel enteroviruses as well.

Virology research project boost for Ecuador

Many of these virus groups were identified in Ecuador for the first time. There is a wealth of future research that can now be done, looking at these viruses in humans and such broad methods are ideal to help fill in the gaps of viruses that humans are infected by and shed.

Much more work is required to identify what cells the more rare viruses replicate in and how they bind to them, the nature of our immune response to them, their age, whether they cause disease, persist, are seasonal…and the list goes on. 

A victim of our discovery success

For a while now we’ve been living in an age of virus discovery.

One downside to this success is that we are discovering viruses far faster than we characterise and fully understand them and light-years faster than we are developing drugs or vaccines to protect ourselves from the worst among them. Many challenges lie ahead and there is much research to do.

References

1. Quito’s virome: Metagenomic analysis of viral diversity in urban streams of Ecuador’s capital city
   https://www.sciencedirect.com/science/article/pii/S0048969718327050
2. One-year survey of enteroviruses, adenoviruses, and reoviruses isolated from effluent at an activated-sludge purification plant.
   https://aem.asm.org/content/41/1/51.long
3. Eukaryotic Viruses in Wastewater Samples from the United States
   https://aem.asm.org/content/75/5/1402
4. Viruses and Water Quality
   https://jamanetwork.com/journals/jama/article-abstract/341460
5. Environmental surveillance of wild poliovirus circulation in Egypt—Balancing between detection sensitivity and workload
   https://www.ncbi.nlm.nih.gov/pubmed/15847928
   
6. Presence of Noroviruses and Other Enteric Viruses in Sewage and Surface Waters in The Netherlands
   https://aem.asm.org/content/71/3/1453
7. Frequent detection of highly diverse variants of cardiovirus, cosavirus, bocavirus, and circovirus in sewage samples collected in the United States.
   https://www.ncbi.nlm.nih.gov/pubmed/19794058
8. High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage.
   https://www.ncbi.nlm.nih.gov/pubmed/22933275
9. Metagenomic analysis of DNA viruses in a wastewater treatment plant in tropical climate.
   https://www.ncbi.nlm.nih.gov/pubmed/22040222
10. Detection by Direct Next Generation Sequencing Analysis of Emerging Enterovirus D68 and C109 Strains in an Environmental Sample From Scotland
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110882/