The novel coronavirus – SARS-CoV-2 – may have been in Europe for longer than previously thought. Recent studies have suggested that it was circulating in Italy as early as December 2019. More surprisingly, researchers at 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 preprint server, medRxiv. The paper is currently being subject to critical review by outside experts in preparation for publication in a scientific journal. Until this process of peer review has been completed, though, the evidence needs to be treated with caution.
So, how was the experiment conducted and what exactly did the scientists find?
One of the early findings about SARS-CoV-2 is that it is found in the faeces of infected people. As the virus makes its way through the gut – where it can cause gastrointestinal symptoms – it loses its outer protein layer, but bits of genetic material called RNA survive the journey intact and are “shed” in faeces. At this point, it is no longer infectious – as far as current evidence tells us.
But the fact that these bits of coronavirus RNA can be found in untreated wastewater (known as “influent”) is useful for tracking outbreaks. Indeed, they can predict where an outbreak is likely to occur a week to ten days before they show up in official figures – the reason being that people shed coronavirus before symptoms become evident. These “pre-symptomatic” people then have to get sick enough to be tested, get the results, and be admitted to a hospital as an official “case”, hence the week or so lag.
As a result, many countries, including Spain, are now monitoring wastewater for traces of coronavirus. In this particular study, wastewater epidemiologists were examining frozen samples of influent between January 2018 and December 2019 to see when the virus made its debut in the city.
They found evidence of the virus on January 15, 2020, 41 days before the first official case was declared on February 25, 2020. All the samples before this date were negative, except for a sample from March 12, 2019, which gave a positive result in their PCR test for coronavirus. PCR is the standard way of testing to see if someone currently has the disease.
PCR involves getting samples of saliva, mucus, frozen wastewater or whatever else the virus is thought to be lurking in, clearing all the unnecessary stuff out of the sample, then converting the RNA – which is a single strand of genetic material – into DNA (the famous double-stranded helix). The DNA is then “amplified” in successive cycles until key bits of genetic material that are known to only exist in a particular virus are plentiful enough to be detected with a fluorescent probe.
In coronavirus testing, scientists typically screen for 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 screened for two regions of this gene and both were only detected around the 39th cycle of amplification. (PCR tests become less “specific” with increasing rounds of amplification. Scientists generally use 40 to 45 rounds of amplification.)
There are several explanations for this positive result. One is that SARS-CoV-2 is present in the sewage 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 labs as positive samples are regularly being handled, and it can be difficult to prevent very small traces of positive sample contaminating others.
Another explanation is that there is other RNA or DNA in the sample that resembles the test target site enough for it to give a positive result at the 39th cycle of amplification.
Further tests need to be carried out to conclude that the sample contains SARS-CoV-2, and a finding of that magnitude would need to be replicated separately by independent laboratories.
A curious thing about this finding is that it disagrees with epidemiological data about the virus. The authors don’t cite reports of a spike in the number of respiratory disease cases in the local population following the date of the sampling.
Also, we know SARS-CoV-2 to be highly transmissible, at least in its current form. If this result is a true positive it suggests the virus was present in the population at a high enough incidence to be detected in an 800ml sample of sewage, but then not present at a high enough incidence to be detected for nine months, when no control measures were in place.
So, until further studies are carried out, it is best not to draw definitive conclusions.
Estonia, Latvia, Lithuania
Against seemingly all the odds, we have a new Brexit deal. As an apparent vindication of UK prime minister Boris Johnson’s strategy to ramp up the threat of a no-deal departure from the EU and to force concessions from Brussels, one would imagine that Number 10 is rather happy right now. But that happiness will be tempered with caution, because some major issues lie ahead.
Negotiations in Brussels have produced legal texts on arrangements for Northern Ireland and on the political declaration, which outlines the broad outline of what the two sides want from their future relationship. These are the product of months of planning by the British government, so it’s reasonable to ask what has actually changed since former prime minister Theresa May struck her original deal.
Reading the text, the first impression is that there’s much more that hasn’t changed than has.
The protocol on Northern Ireland and Ireland has long been in the firing line. It proposes a backstop arrangement that would keep Northern Ireland in close alignment with the EU unless and until both UK and EU agreed to change that.
On that front, the introduction of a section on “democratic consent” is an important shift on the EU side. This provides a mechanism for the Northern Ireland Assembly to vote on whether to maintain the provisions of the protocol, with a requirement to have cross-community support. That means the UK is now no longer subject to the EU’s approval if it wants to end the backstop arrangement.
That said, a voting requirement to have majorities from both unionist and nationalist groupings makes it very hard to achieve – especially since the Northern Ireland Executive broke down several years ago and is still not in operation. While the Democratic Unionist Party (DUP) might control unionist voting, it can only do the same with nationalists if it creates a much more benign and cooperative environment. And even if that does happen and arrangements are voted down by Stormont, there is still a long phasing-out period, so things cannot move too quickly.
From the EU’s perspective, this arrangement provides a degree of security, mainly because any decision to overturn the system is not solely in the hands of the UK – which has not been the most reliable partner of late.
The other big change is on customs arrangements. Instead of creating a temporary customs area for the whole of the UK, the revised Protocol makes Northern Ireland a part of the UK’s customs territory. Because that would imply border controls, a rather convoluted system of custom duty collection is set out.
In essence, the system collects duties from businesses, dependent upon where goods are coming from and going to, with the possibility of various exemptions that will be agreed down the line.
It’s a much more complex system than before, but it does allow Johnson to argue that the entire UK is leaving the EU’s customs union, allowing it to benefit from any new trade deals that might be concluded.
Meanwhile, the political declaration, the main change is that the UK now suggests it is looking for a much looser future relationship, based on a free trade agreement, rather than anything that might include participation in the EU’s single market or customs union.
While these are all noteworthy, they do represent only a very small part of the totality of the withdrawal agreement, as agreed by May last November. The Protocol still kicks into effect at the end of a transition period and the effect is still that Northern Ireland is kept very close to EU’s regulatory standards for many years. The future relationship remains as aspirational as May’s plans – until such a document is negotiated and ratified, by some future British government, no one can be sure what it will look like.
Nor did this negotiation touch on citizens’ rights, financial liabilities, the power of the EU’s courts to issue definitive rulings on matters of dispute (an important matter for hard Brexit supporters in the Conservative Party) or the institutional arrangements for managing all of this. Even as Number 10 goes into its selling mode, those continuities from last year’s text will be present in many people’s minds.
The plan still seems to be for the government to present this deal to the UK parliament in a special Saturday sitting on October 19. We already know that the DUP has issues with the revised text because it places Northern Ireland in a different legal position to the rest of the UK, so winning that vote looks even harder than it already did. The government will hope that it can present the deal to MPs as the last, best hope for a Brexit settlement – but, with wobbles from the DUP, Johnson will struggle to get close to a majority.
Even if he does, the potential to keep that majority together for the subsequent passage of the Withdrawal Agreement Bill looks even less likely. And remember that, as things stand today, this text isn’t even signed off by the 27 EU member states – there’s now not really enough time for them to digest and approve something that moves them off their previous position.
In short, this might still fall apart for Johnson, just as it did for May.