Polymerase Chain Reaction Positivity Rate for Covid-19 in General Medicine in Toledo (Spain) from May 19 to September 30, 2020. Is it Re-Outbreak, Second Wave of Virus or Lack of Testing?

Epidemic Waves

There is no exact technical definition of what an epidemic wave is or is not. A wave implies a rise in the number of sick individuals, a definite peak, and a decline. The question of whether there are first and second waves, or whether they are ups and downs of the same wave, is difficult to decide. For the WHO, the COVID-19 pandemic behaves like a single great wave that rises and falls [22]. However, if after a peak the number of infections there are an almost total decrease, it is possible to speak of a wave [23, 24].

In our study, in the context of Toledo (Spain) a second wave can be clearly observed during the months of July- September, after a large decrease in cases of the first wave (March-June 2020), and the lifting of social confinement measures. In reality, this was the expectation during the summer months, with more people travelling and creating new chains of transmission [25, 26]. As Europe reopens, COVID-19 cases have accelerated almost everywhere, leaving countries in a battle to control outbreaks before undoing months of hard-earned progress [11, 27, 28]. On the other hand, the transmission pattern in Latin America is different from that in Europe. In Latin America they seem to have given rise to waves whose evolution is slower and more extended over time, which gradually grow without reaching a defined maximum height, at least when the cases are counted at the national level. This is most likely due to the fact that the control measures have been sufficient to prevent exponential growth, but insufficient to reduce the basic reproductive number below 1 [23].

Spain is reporting 10,000 cases a day, more than it had at the height of the outbreak in the spring. France has once again reported thousands of cases a day. In Germany, the numbers are still low, but are constantly increasing. The pandemic is affecting countries that saw few cases in the spring, such as Greece and Malta, but it is also rebounding in places that suffered terribly, including the cities of Madrid and Barcelona. In short, the number of weekly infections in Europe is higher now than in the first peak of March [11, 29, 30]. It has been speculated that in many countries, the resurgence is driven by “young people who are living their lives in a normal way”, because new cases are younger [26]. This situation also seems to be shown in our study, with a mean age of the positive cases of 36 years, and with only 5% of patients>65 years.

Although, at first glance, the numbers of second wave infections could be higher than in the first wave, this is a confusion of terms; one factor of course is increased testing: many countries did not have the capacity to conduct such high-volume testing at the beginning of the year. But, also, in Spain, where PCR was not performed, but rather seriously ill patients in hospitals, the official figures were only a “minimal morbidity”, since they did not include light infections, nor asymptomatic who did not have a PCR test. In this way, it was considered that the official data of the “first wave” should be multiplied by at least 3 or 5 or even by 10 to get closer to the real ones [31, 32, 33, 34], so the size of the waves is reversed [35].

Regarding Spain, specialists point to a precipitous de- escalation as the cause of the outbreaks and insist that the solution lies in tracing and improving data management [36]. Seroprevalence surveys that measure antibodies have shown that at most only about a fifth of people have antibodies to SARS-CoV-2. So, the pandemic will not end until we reach a level of herd immunity, either through naturally- occurring immunity and/or vaccination. Until then, testing and contact tracing remain essential public health strategies [37, 38, 39, 40, 41]. However, the “second wave” once the blockade is removed it is not happening in all places. The question is why [38]. On the contrary, other places are already facing their “third wave” [42]. In our study, if a second wave can be clearly described, beginning approximately four weeks after removing the blockage.

Re-Shoots or Second Waves. The Importance of the Total Number of PCR Performed

When cases are observed to be increasing, the word “outbreak” or “re-outbreak” or “epidemic wave” could be used. The problem can arise when only the “infection rate” (cases per 100,000 people) of one place is known compared to others, so that only this data can give rise to unnecessary worries or a false peace of mind, if it is not known, in addition to the positive results, the total number of tests performed for each location. The evidence for the increase in the outbreak may be limited, in part, by the artificial fact of the increase in the availability of test. It should be noted that high levels of test may not explain the increase in cases. When the ratio of positive PCR tests to all tests performed is increasing, this suggests a genuine increase in the number of new infections [13].

This dynamic is verified in our study, where the percentage of positives over the total tests (positivity rate), went from zero in May and June (the lifting of the quarantine at the national level occurred on June 21, 2020), to 22% at the end of July, and 47% in the middle of August (the peak of the second wave; it can be estimated in 8-10 weeks for the peak of the outbreak since the lifting of the blockade), maintaining and subsequently decreasing slightly to 41%, 38%, and 21% at the end of September, this is probably due to the fact that the control measures have been sufficient to prevent exponential growth, but insufficient to reduce the basic reproductive number by below 1 [23].

Test System, Trace. Is it Being Detected Eell? Is the Outbreak Out of Control?

The test is our window to the pandemic and how it is spreading. Without evidence we have no way of understanding the pandemic. The tests allow us to identify infected people, guiding the medical treatment they receive. It allows the isolation of the infected and the tracking and quarantine of their contacts. And it can help allocate medical and staff resources more efficiently [43]. For some places, after the first wave of COVID-19, an elimination strategy has been advocated, or of “COVID zero” (that it requires strict quarantine measures and border closures) and a tracing and isolation system to “suppress” localized outbreaks [25].

While the virus spread largely undetected in February, widespread testing now reveals its movements. Less than 3% of tests have been reported to be positive in most European countries, a sign of healthy testability. The WHO suggests that a country cannot bring the coronavirus under control until less than 5% of tests are positive. It has been reported that by September 11, 2020, in Spain, the rate of positive PCR tests is around 11% [44]. But our study, for Toledo (Spain) shows 30% positivity for the entire period studied.

One of the keys to slowing the spread of the virus is to perform PCR testing on as many people as possible who have been in contact with infected people. But the average number of potential cases that Spain manages to track is, for example, lower than that of Zambia (9.7 for each confirmed case of COVID-19), a quarter than that of Italy (37.5 for each confirmed case of COVID-19) and a twentieth that of Finland (185 for each confirmed case of COVID-19) [45].

In this context, the GP will play a key role in controlling outbreaks of the COVID-19 pandemic: detecting suspected cases as early as possible and conducting tests to confirm new infections so that transmission chains can be shortened [46]. In any case, a pure test, trace and isolation strategy is probably not feasible, nor totally useful in isolation from other measures in most countries, and a degree of social distancing, would be a tool for public health needed to mitigate the COVID-19 pandemic [47, 48].

Positivity Rate

As more and more people are being tested, the focus is shifting to the positivity rate: how many of the people tested are actually infected?. The positivity rate is the percentage of tests that are positive (number of tests per confirmed case) and aims to answer the question: How many tests does it take to find a case?. In our study, it is evident that by August 2020 transmission was not decreasing due to the increase in cases produced. The same pattern could be observed in Spain at that time, where there were more cases than in other comparable European countries.

A key question is: Are enough tests being done to monitor the outbreak? In order to adequately control the spread of the virus, countries with more widespread outbreaks need more testing. So an important way to understand whether countries are testing enough is to look at the proportion of tests that return a positive result, known as the positive rate. There are huge differences between countries. Some countries, such as Australia, South Korea, and Uruguay have a positive rate of less than 1%: hundreds or even thousands of tests are needed to find a case in these countries. Others, like Mexico and Nigeria, have positive rates of 20% to 50% or even more. In these countries, one case is found for every few tests performed. Countries with a very high positive rate are unlikely to test extensively enough to find all cases [43]. In other places such as Italy, a drop in the number of daily cases of coronavirus has been reported despite increased testing [30].

In our study, there are very high positivity rates at the peak of the second wave, and a high number of tests, which should be interpreted as confirmation of a re-outbreak, although certainly not all cases were found, as the number of tests was not sufficiently increased. One might think that “a large part” of the increase in cases is due to the increase in diagnostic capacity (the number of tests), but the data do not support this statement. Few tests are done in May and June because there are few patients; since the end of July there are more patients, and more tests have to be done. In addition, the increase in the positivity rate is a bad sign because it suggests that fewer tests are done to rule out infections and more to confirm them. The same dynamic has been described for the whole of Spain [49].

A positivity rate below 7.2% has been reported to be a good number; if the positivity test rate is greater than 10%, it is one of those red flags (the “warning flag” level). The increase in the positivity rate means a higher percentage of the infected population. Rates depend really on how many people are being tested and who is being tested. If tests are done only on people who are fairly certain they have the disease, there will be a high positive rate. If 10 times more than suspect people are tested and many of them are not infected, then the positivity rate will decrease. For other experts, high data for the positivity rate may also indicate that insufficient testing is being done. Some scientists have suggested that this 10% mark is really relevant as an indicator that the tests are not sufficiently widespread and that there is really not a good handling of the situation. While a 0% positivity rate would be ideal, the goal may be to get it below 10% [50, 51, 52].

Another way of looking at the scope of testing relative to the scale of the outbreak is to ask: How many tests are done to find a COVID-19 case? It is simply the inverse of data on the positive rate. It is unlikely that where very few tests are done per confirmed case, they will do so broadly enough to find all cases [43]. The WHO has suggested around 10 to 30 tests per confirmed case as a general benchmark of adequate testing. In general, when the tests are carried out quite extensively, it has been found that between 3 and 12% of the tests are positive. Thus, the level of ten negative tests by one positive is proposed as a general benchmark of a system that is doing enough tests to collect all cases [53]. Thus, the WHO percentage of positive PCR should be less than 5% to consider that the epidemic is being controlled [54]. At the end of March, during the worst of the pandemic, the positivity rate in Spain was 28.2%, which indicated that only those people with a high probability of having the infection were being tested [31, 32]. In our study, the positivity rates during the rise, peak, and subsequent plateau suggest that not enough tests are being done to find all cases, as the number of tests is not sufficiently increased.

The use of pre-test probability among the evaluated subjects has been proposed to know the sufficiency of the test availability instead of the number of tests. Pre- test probability means the “level of suspicion”, of having coronavirus among the tested subject [55]. In our study, all patients who consulted the GP with suspicious symptoms of COVID-19 were included. While a wide range of symptoms can accompany the coronavirus, the majority of patients exhibited one of three symptoms: fever, cough, and shortness of breath [56, 57].

Thus, in our study, PCR was performed on all suspected cases at the general medical level, which greatly increased the pre-test probability. Thus, the conclusion of having missed cases for not performing the necessary number of tests would be nuanced. In the United States, some lawmakers have focused on the positive coronavirus test rate among the general population, with some saying it must be below 3 percent to safely reopen schools. But most places have much higher positive rates: 7 percent for the entire United States, 8 percent for Spain, and more than 40 percent for some Latin American countries [12, 58].

Testing Accuracy: the Main Problem is False Negatives

There is broad consensus that widespread testing for SARS-CoV-2 is essential to safely reopen a country. A

major concern has been the availability of the tests, but the precision of the tests can be a major problem in the long term [59].

PCR diagnostic tests involving a nasopharyngeal swab can be inaccurate in two ways. A false positive result mislabels an infected person, with consequences including unnecessary quarantine and contact tracing. False negative results are more problematic because infected people, who may be asymptomatic, may not be isolated and can infect others. If the SARS-CoV-2 diagnostic tests were perfect, a positive test would mean someone carries the virus and a negative test would not. With imperfect tests, a negative result just means that a person is less likely to become infected. In our study, the PCR tests were the standard of the Regional Health System of Castilla-La Mancha, but the Health Authorities do not routinely report their sensitivity and specificity. In any case, to calculate the probability, you can use Bayes’ theorem, which incorporates information about the person and the precision of the test. Any result of a diagnostic test should be interpreted in the context of the probability of disease prior to the test. The pre-test probability may depend on the local prevalence of Covid-19, history of exposure to SARS-CoV-2, and symptoms. While the exact sensitivity and specificity of RT-PCR tests for COVID-19 is unknown, it appears that a positive test is highly suggestive of true COVID-19 [60, 61].

But, if the pre-test probability is too high (above 50%, for example), the test loses its value because negative results cannot reduce the probability of infection enough to reach the threshold. Negative results, even on a highly sensitive test, cannot rule out infection if the pre-test probability is high. It is possible that multiple simultaneous or repeated tests may exceed the limited sensitivity of a single test; however, these strategies need validation [60, 62]. In summary, a positive RT-PCR test for the covid-19 test carries more weight than a negative test due to the high specificity of the test but moderate sensitivity [10, 63]. However, it must be remembered that since the sensitivity of molecular detection depends on the severity of the disease, the type of sample and the time of sampling during the course of infection [17, 19].

Due to the sensitivity of the test, a single strand of viral RNA can be detected, but this does not necessarily mean that someone is infected or contagious. This can be a problem in general population screenings, where many of these people may have had an active infection a few weeks ago and still carry the RNA in their nasal swabs, but less in the context of clinically suspicious cases in GM, as in our study [61]. On the other hand, false positive results from the COVID-19 swab test could be increasingly likely in a future context of the low prevalence of the virus in the population. When there is a low pre-test probability, positive results should be interpreted with caution and a second sample should be tested for confirmation [61].