The new coronavirus – SARS-CoV-2 – may have been in Europe for longer than previously thought. Recent studies have suggested that it circulated in Italy as early as December 2019. More surprisingly, researchers from the University of Barcelona found traces of the virus when testing untreated wastewater samples dated March 12, 2019.
The study was recently published on a prepress server, medRxiv. The document is currently under critical review by external experts in preparation for publication in a scientific journal. Until this peer review process has been completed, however, tests should be treated with caution.
So how was the experiment conducted and what exactly did the scientists find out?
One of the first findings on SARS-CoV-2 is that it is found in the feces of infected people. While the virus makes its way through the intestine ̵
At this point, it is no longer contagious – as far as current evidence tells us.
But the fact that these coronavirus RNA fragments can be found in untreated wastewater (known as “influential”) is useful for tracing outbreaks. In fact, they can predict where an outbreak is likely to occur from a week to ten days before they show up in official figures – the reason is that people release coronaviruses before symptoms become evident.
These “pre-symptomatic” people must therefore get sick enough to be tested, get the results and be hospitalized as an official “case”, hence the week or so.
As a result, many countries, including Spain, are monitoring wastewater for traces of coronavirus. In this particular study, wastewater epidemiologists examined frozen samples of influential people between January 2018 and December 2019 to see when the virus made its city debut.
They found evidence of the virus on January 15, 2020, 41 days before the first official case was declared on February 25, 2020. All samples before this date were negative, except for one sample on March 12, 2019, which gave a result. positive result in their PCR test for coronavirus. PCR is the standard way of testing to see if anyone currently has the disease.
PCR involves taking samples of saliva, mucus, frozen wastewater or whatever you think is hiding the virus, removing all unnecessary things from the sample, then converting RNA – which is a single strand of genetic material – into DNA (the famous double-stranded helix).
DNA is then “amplified” in successive cycles until key fragments of genetic material that are known to exist only in a particular virus are abundant enough to be detected with a fluorescent probe.
Not very specific
In coronavirus tests, scientists typically select more than one gene. In this case, the researchers tested for three. They had a positive result for the March 2019 sample in one of the three genes tested: the RdRp gene. They examined two regions of this gene and both were detected only around the 39th amplification cycle. (PCR tests become less “specific” as the amplification rounds increase. Scientists generally use 40 to 45 amplification rounds.)
There are several explanations for this positive result. One is that SARS-CoV-2 is present in wastewater at a very low level. Another is that the test reaction was accidentally contaminated with SARS-CoV-2 in the laboratory. This sometimes happens in laboratories as positive samples are regularly handled and it can be difficult to prevent very small traces of positive samples from contaminating others.
Another explanation is that there is other RNA or DNA in the sample that remembers enough of the target site of the test to allow a positive result at the 39th amplification cycle.
Further tests must be performed to conclude that the sample contains SARS-CoV-2 and a discovery of this magnitude should be replicated separately by independent laboratories.
Reasons to be careful
A curious thing about this discovery is that it does not agree with the epidemiological data on the virus. The authors do not cite reports of a spike in the number of respiratory disease cases in the local population after the sampling date.
Furthermore, we know that SARS-CoV-2 is highly transmissible, at least in its current form. If this result is a true positive, it suggests that the virus was present in the population with an incidence high enough to be detected in a sample of 800 ml of waste water, but therefore not present with an incidence high enough to be detected for nine months, when no checks were in place.
Therefore, until further studies are conducted, it is best not to draw firm conclusions.
Claire Crossan, Research Fellow, Virology, Glasgow Caledonian University.
This article was republished by The Conversation with a Creative Commons license. Read the original article