Ministry of Health launches blanket screening of positive samples for the presence of coronavirus mutations

The monitoring and accelerated rapid screening of positive samples for the presence of coronavirus mutations is a basic prerequisite for keeping the pandemic under control. The Ministry considers it an absolute priority in the current period, and has therefore introduced compensation for discriminative PCR tests and created a network of sequencing centres across the Czech republic.

In order to detect coronavirus mutations in the Czech Republic, the Ministry of Health has issued a National strategy for the molecular-biological surveillance of SARS-CoV-2 and defined a system of screening positive samples.

To ensure the targeted and universal screening of positive samples for the presence of known mutations, it is necessary to involve the greatest possible number of laboratories which participate in testing for SARS-CoV-2 in discriminative PCR. “Our objective is the timely detection of mutations, their identification and tracking. It is our absolute priority, not least because over summer people will be travelling a lot, thus increasing the risk of bringing mutations back to the Czech Republic. Therefore, we are introducing the blanket testing of all positive samples using a discriminative PCR, which will detect known mutations. Thanks to compensation, this will take full effect from July. At present, a sequencing centre is in operation in every region which tests selected samples and searches for new mutations,” said Minister of Health Adam Vojtěch, noting that it is still important for people not to forget about coronavirus, as it hasn’t disappeared. “Citizens should keep in mind that the boundary between the current good situation and its worsening is very thin indeed. Just look at Great Britain. Let us enjoy the reopening of services, let us travel, but let us continue to protect ourselves and remain vigilant.”

From July, all laboratories will receive compensation for this activity paid from public health insurance, equal  to 614 crowns. This will ensure the examination of every positive sample diagnosed using the PCR method, which laboratories are also compensated for (CZK 614 + CZK 47 for sampling). In total, laboratories will receive CZK 1,275 for standard and discriminative PCR from the health insurance company.

“In a year and a half of the pandemic, we have developed a dense network of laboratories that detect coronavirus. These laboratories must now focus on screening positive samples. Discriminative PCR testing does not require new equipment, but only the securing of material. Should any of the laboratories not perform this blanket screening, they can make arrangements with another laboratory and pass on the samples. Laboratories are and will be informed regularly about which mutations must currently be monitored through our National Reference Laboratory for flu and non-flu respiratory viral diseases,” explained Barbora Macková, Director of the National Institute of Public Health.

The Ministry of Health has developed a network of sequencing centres in order to detect entirely new mutations of coronavirus. It is composed of laboratories within the framework of state allowance organisations. Most of them are directly controlled by the Ministry, while others are part of the Biological Centre of the Czech Academy of Sciences and the State Veterinary Institute belonging under the Ministry of Agriculture. The Ministry of Health has reserved 80 million crowns for sequencing for its organisations. The total capacity of this network is 4,500 samples per month, which is sufficient given the current epidemic situation. “We are continuously evaluating the current capacity and should the epidemic situation worsen and the number of cases begin to rise, we are prepared to react immediately and increase the sequencing capacity across the country,” added the Minister. The list of sequencing centres is published on the Ministry’s website.

If the laboratory detects a mutation, it is obliged to report this finding to the Information System of Infectious Diseases (ISIN), where the data can then be accessed by the respective Regional Public Health Authorities (KHS). The results of sequencing are also reported to the international databases. “The hygienists will use this information for priority tracking of the infected person’s contacts. The aim is to restrict the spread, especially of dangerous virus variants” The regional public health authority will control the collection of samples from patients based on the given parameters, so as to sequence samples with an important clinical or epidemiological context. These include the selection of samples for instance from patients who have been vaccinated, samples from patients with proven reinfection, from children and patients under 50 years of age with a severe course of illness, or patients where there is a risk of import from high-risk areas,” explains Chief Hygienist of the Czech Republic Pavla Svrčinová. 

Each sequencing centre will sequence 70 to 100 samples per week. In the course of June, the sequencing centres examined 800 samples and their number increases every month. An overview of detected mutations is published regularly by the National Institute of Public Health (only in the Czech language).

“We welcome that the Ministry of Health prioritizes the screening of positive samples and sequencing, and has defined a strategy and network of sequencing centres. In particular the compensated discriminative PCR testing, which is the step before sequencing and will be performed universally, will certainly help detect mutations. MeSES sees sequencing as a way to keep the pandemic under control. Naturally, it will also depend on citizens’ self-discipline and the observance of measures, especially when returning from holiday,” concluded epidemiologist and member of MeSES, Rastislav Maďar.