During the months that we have experienced a pandemic caused by covid-19, we have learned a lot about this new disease caused by a new and tiny coronavirus.

At the Complutense University of Madrid we began on March 14, 2020 to organize ourselves as a network of university laboratories to cooperate with the saturation of the covid-19 PCR diagnostic laboratories. So we did not know how long we would be holding on to the pipette. Now it’s been almost a year.

One of the first things we learned is that rapid and accurate detection of the SARS-CoV-2 virus is crucial to controlling the outbreak.

The accelerated and universal generalized transmission indicated that we were facing a disease that was possibly also transmitted between people who did not present symptoms. It can be visualized as an iceberg, where patients with clear symptoms represent the visible tip and those who do not show them, or are presymptomatic, would be an immense part of the infected that remains hidden in the water.

This myriad of hidden infected are those that maintain transmission to the healthy. This is what happened in the beginning and what continues to happen now. From my experience with malaria, associating the spread of COVID-19 with the existence of countless asymptomatic patients was almost automatic.

Transmission mechanism

Contagion causes the virus to quickly adhere to cells in the respiratory system for which it has an affinity. These cells are known to possess receptors called ACE2 (angiotensin-converting enzyme-2) that occur widely on the surface of the nasopharynx, trachea, bronchi, and lung.

The infection of these cells favors the reproduction of the virus inside them. It is then released to mucosal secretions, including saliva. The multiplied viruses go out through the mouth and the breath, through aerosols, to start a new cycle of contagion in another healthy person.

This infection mechanism early suggested the important role of aerosols that are commonly expelled by breathing and speaking as an essential means of transmission of SARS-CoV-2, although this route of transmission was slow to be accepted.

This was in contrast to the accumulating scientific evidence corroborating the high risk of contracting COVID-19 by sharing the air we breathe with infected people.

Nasopharyngeal samples and PCR

Precisely due to the characteristics of primary infection of the respiratory system, nasopharyngeal and oropharyngeal swabs were, at first, the way to obtain samples from the upper respiratory tract for PCR tests. These detect exactly the genetic material of the virus. There is practically no doubt: when it is detected, it is there.

However, collecting swabs requires close contact between healthcare providers and patients, which poses a risk of virus transmission. In addition, collecting nasopharyngeal or oropharyngeal specimens causes discomfort and may lead to bleeding. Therefore, nasopharyngeal or oropharyngeal swabs add an element of complexity to serial viral load monitoring.

Saliva samples

Unlike swab sampling, saliva samples can be easily obtained. It is simple to ask patients and any healthy person to deposit it – without spitting – in a sterile vial in an environment of privacy and isolation.

Since no invasive procedures are required, saliva collection does not require specialized and highly equipped personnel. Those in charge of collecting the samples only receive a closed airtight container. This absolutely minimizes the possibility of exposing healthcare personnel to SARS-CoV-2. In addition, these hermetic samples facilitate their transport safely and without risk of contagion to the analysis laboratories.

Recently, a systematic review of 5,922 patients confirmed that the detection of SARS-CoV-2 in saliva has a high concordance rate with that of nasopharyngeal samples. Thus, saliva has been used for SARS-CoV screening in asymptomatic populations in Japan and Canada with excellent results. Virus has even been detected in saliva in a percentage of cases where it was not detected in swabs.

We must bear in mind that samples, both saliva and nasopharyngeal, may suffer transient fluctuations in viral load. This is due to individual practices such as blowing the nose or drinking or feeding. And this is the explanation for those minimal cases of discordance between the results of the analysis of both types of samples.

Thus, the advantages of using saliva as the sample of choice to detect SARS-CoV-2 by PCR are evident. Very especially for screening and for periodic control of groups.

Periodic batch screening

The probability of becoming infected with SARS-CoV-2 through contact with asymptomatic patients is still very high. A recent study shows that at least a third of SARS-CoV-2 infections are asymptomatic. And nearly three-quarters of people with a positive PCR test who are asymptomatic will remain asymptomatic. This prevalence analysis includes 365,104 cases from the United Kingdom and 61,075 from Spain.

Therefore, it is appropriate to establish community screening programs and stable groups (such as educational centers or companies). The screens provide immediate information to create barriers to the spread of the virus.

These screenings fall within the desirable COVID ZERO strategy (recently proposed by Devi Sridhar, Professor of Global Public Health at the University of Edinburgh), emphasizing the false dichotomy between “saving the economy” and “saving lives”, to escape from perpetual crisis and avoid endless confinements.

In this context, in addition to using saliva to facilitate sampling, analytical screening, to be efficient in large groups, requires solving two additional limitations.

The first is to speed up the PCR method which remains the most accurate assay for detecting SARS-CoV-2. Until recently, it required a tedious viral RNA extraction step, which has been solved with virus inactivation techniques and exposure of its naked RNA to the PCR method. Likewise, this new procedure has also been perfected to be performed directly in saliva.

The other limitation consists in being able to increase the capacity of doing many PCRs to expand the screening to large populations or groups. The solution has come from a method that is used in the control of infections in veterinary health: this consists of grouping samples from several individuals in the same tube to perform only a single test on the group.

Using this type of batch analysis, if we do groups of 10 people, a single PCR analyzes the status of the 10 individuals. Therefore, 10 times more analyzes can be done with a notable lower economic cost and the need for resources. If the pooled PCR test is negative, all individuals are likely to be negative and no further testing is necessary. If it is positive, each of the 10 samples will be independently analyzed to identify the positive cases and initiate the relevant isolation.

A potential objection to this idea of using lots of saliva is the loss of sensitivity. However, the PCR signal to the presence of the virus is so sensitive that it is even positive at low viral loads, and has shown that in batches of 10, or even 20, the virus is adequately detected.

If this sensitivity is coupled with the periodic analysis of a group, for example weekly, the sensitivity increases considerably with the time factor. By having a kind of continuous sensor of the newly infected, a very powerful tool is introduced for the early detection of covid-19 outbreaks in asymptomatic and presymptomatic patients.

We can do better

It would be a huge failure if we continue in the same lockdown situation next fall. It is not acceptable that there are thousands of people dying every week. Each positive test in an asymptomatic patient serves to isolate the estimated time of contagion. Therefore, each positive test represents an indeterminate number of human lives that can be saved. This is what the COVID ZERO strategy, mentioned above, represents.

The Complutense University of Madrid has chosen to have a safe space for face-to-face academic activities and this periodic batch test procedure in saliva is being implemented for this purpose. The COVID-Lot project prioritizes direct PCR of saliva batches for large-scale deployment in the early control of covid-19 outbreaks.

This project is a proof of concept that it is possible to have high goals in this pandemic with resources as limited as those of a public university. The challenges to get out of the pandemic go through having reliable, powerful and effective tools that provide robust information to adopt control measures.

In this year of a pandemic, we have witnessed that confinements are, precisely and contradictorily, the result of the measures taken against confinement. The high rate of hospitalization produced by having asymptomatic circulating patients is not really fully understood.

We can do better. Covid-19 control strategies should take into account the high prevalence and transmission of asymptomatic SARS-CoV-2 infection. Perhaps it is time to have specific control systems for this hidden form of contagion while the immunity acquired by vaccines unfolds. Periodic batch saliva tests are a simple, fast, and scalable opportunity to do so.

José Manuel Bautista, Professor of Biochemistry and Molecular Biology, Complutense University of Madrid

This article was originally published on The Conversation. Read the original.