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Russian-South African scientific mission to study the clinical and epidemiological characteristics of the new coronavirus infection caused by the genetic variant omicron (hereinafter referred to as the Mission) was organized in accordance with the agreement between the presidents of Russia and the Republic of South Africa and took place in South Africa from 13 to 22 December 2021.
From the Russian side, 20 leading scientists and experts of Rospotrebnadzor and the Ministry of Health of Russia took part in the Mission, including representatives of the Central Research Institute of Epidemiology of Rospotrebnadzor, the Russian Research Institute "Microbe" of Rospotrebnadzor, the State Scientific Center of Virology and Biotechnology "Vector" of Rospotrebnadzor, the Volgograd Research Institute of Rospotrebnadzor, etc.
From the Republic of South Africa, leading scientists and experts from the Department of Health, South African Medical Research Council, National Institute of Communicable Diseases, National Health Laboratory Network, Stellenbosch University, Durban University, Chris Hani Baragwanath Hospital, Charlotte Maxeke Johannesburg Academic Hospital, and Jubilee District Hospital of Gauteng Province took part in the mission.
During the mission the parties organized three working groups (epidemiological, virological and clinical) and consulted on the full spectrum of issues related to fighting the new coronavirus infection, including features related to the omicron variant in the areas of epidemiology, laboratory diagnosis, virological monitoring, immunology, clinical features, and therapy of infection.
The consultations were held in a spirit of openness, scientific interest and with a focus on the development of both bilateral and multilateral cooperation in the fight against infectious diseases within BRICS.
Scientists from the RSA provided information on the epidemiological situation, organization of laboratory diagnosis of COVID-19, genetic monitoring, assessment of features of the "omicron" strain of the SARS-CoV-2. There was an opportunity to learn the structure of the country’s healthcare system, the algorithm of patients triage and national protocol of medical care for patients with COVID-19, level I-III
hospitals in the province of Gauteng.
There were organized visits to central and district medical institutions, and diagnostic laboratories in Johannesburg and Pretoria. South African scientists shared information on the features of the identification and differentiation of the new variant "omicron" from other variants circulating in the population, including on the basis of clinical data.
Russian scientists shared their experience in fighting new coronavirus infection, organizing epidemiological monitoring, studying the genetic features of the infectious agent of coronavirus infection, assessing the immune status of those infected and vaccinated in the context of protection against new genetic variants of the coronavirus.
The participants of the joint mission discussed the features of a new coronavirus infection caused by the omicron strain and its impact on the spread of infection, the severity of the clinical course, medical care and vaccination. In the course of the mission data were obtained on the epidemiological characteristics of the new genetic variant and the features of its distribution in the RSA. The increased transmissibility of the omicron variant from person to person has been shown, resulting in increased incidence (the baseline reproductive rate increased to 2.5 in December, doubling time of 3.18-3.61 days) and an increase in the positive sample rate to 35.5% with no indication of a more severe clinical course.
It is noted that considering the significant number of South African residents who have had COVID-19 and demographic differences, the data on clinical severity can be adjusted in the conditions of the spread of the omicron variant in the Russian Federation.
It was noted that young age groups played a significant role at the initial stage of the spread of infection. It was also shown that the densely populated Tshwane district, which includes the capital city of Pretoria and which is near to the economic hub of Johannesburg, was the location of the initial clusters of transmission of the genetic variant "omicron".
A phylogenetic lineage independent of the "delta" and "beta" variants and the possibility to use genotyping PCR assay for rapid identification of a new SARSCoV-2 virus gene variant have been convincingly demonstrated. There is a high incidence of SARS-CoV2 infection in younger patients, especially in children in the initial stages (up to 50% of all patients seeking medical care for various reasons are infected), clinical characteristics of influenza, large number of asymptomatic cases and population seropositivity of up to 70% in the RSA.
The course of the disease is more severe among unvaccinated people with risk factors, especially in older age groups, high frequency (15-20% overall) of reinfection and infection in vaccinated people is characterized by a milder course. During the mission, Russian specialists made a presentation of the Rospotrebnadzor mobile laboratory which is mounted on an automobile chassis. The possibilities of its joint use for epizootological monitoring of dangerous infections in remote areas of South Africa were discussed.
Based on the results of the joint Mission, the participants agreed on:
- Taking into account the need to develop bilateral scientific cooperation in the field of fighting epidemics;
- Noting the contribution that scientists from Russia and the RSA are making to global efforts to combat the pandemic of a new coronavirus infection;
- Expressing commitment to the protection of public health as the primary goal of the fight against the pandemic;
- Emphasizing that anti-epidemic measures should be scientifically justified, noted that:
The level of monitoring for a new coronavirus infection in South Africa made it possible to promptly identify a new genetic variant of concern, called omicron, and to inform the international community of the risks associated with its spread; The study of epidemiological features, clinical characteristics, molecular and genetic properties of circulating pathogens, and cooperation of existing national and regional sequencing networks underlie the identification of new virus variants with high epidemic potential;
Studies of the efficiency of immunological protection both after vaccination and after a previous disease or their combination show that compared to the initial variant, the degree of neutralization of the omicron variant is reduced from 3 to 41 times, depending on immunological status. Thus, the disease, followed by vaccination or re-vaccination, is likely to increase the effectiveness of neutralization
and provide protection from the severe course of the disease when infected with the "omicron" variant;
Scientific cooperation and data exchange serve as the basis for making sciencebased decisions, including restrictions on cross-border movement. Taking into account the global spread of the omicron variant, which has already been identified in 94 countries of the world and the newly obtained data on the danger of a new genetic variant of the SARS-CoV-2 virus, the further ban on air traffic between
states has lost its relevance;
Openness, commitment to a common task to fight coronavirus infection pandemic and close cooperation between scientists of the Russian Federation and the Republic of South Africa give confidence in the soonest victory of world science over the pandemic;
Scientists of the Russian Federation and the Republic of South Africa are intensifying the exchange of data and research results in the field of epidemiology, virology, immunology, pathogenesis and therapy of new coronavirus infection. As a result of the joint mission, other areas of scientific cooperation in the field of epidemic prevention and response were identified and a draft road map for scientific cooperation between Russia and the RSA in this area for 2022-2024 was developed.
Distributed by APO Group on behalf of South African Government.
