Periodic Reporting for period 1 - CoVICIS (EU-Africa Concerted Action on SAR-CoV-2 Virus Variant and Immunological Surveillance)
Okres sprawozdawczy: 2021-11-01 do 2023-04-30
CoVICIS is a multidisciplinary project addressing key questions associated with the evolution of the SARS-CoV-2 panndemic with the ultimate goal of generating scientific data that will contribute to the control of the pandemic. The specific objectives are as follows:
1. Identification of emerging VOC through genomic surveillance in different cohorts of unvaccinated individuals in South Africa, Italy and Switzerland through the respective national surveillance program (coordinated in Geneva);
2. Characterization of the virologic and immunologic properties of emerging VOC
3. Identification of differences in clinical (asymptomatic versus severe Covid-19) and immune responses in different population cohorts (adults vs children, healthy vs immuno-compromised) in different geographic regions infected with different VOC;
4. Delineation of the impact of VOC on the effectiveness of vaccine-induced immune response;
5. Identification of immune correlates of protection against VOC through the development of algorithms predicting the impact of emerging VOC on the efficacy of vaccines
1. Identification of emerging VOC through genomic surveillance in different cohorts of unvaccinated individuals in South Africa, Italy and Switzerland through the respective national surveillance program (coordinated in Geneva);
2. Characterization of the virologic and immunologic properties of emerging VOC
3. Identification of differences in clinical (asymptomatic versus severe Covid-19) and immune responses in different population cohorts (adults vs children, healthy vs immuno-compromised) in different geographic regions infected with different VOC;
4. Delineation of the impact of VOC on the effectiveness of vaccine-induced immune response;
5. Identification of immune correlates of protection against VOC through the development of algorithms predicting the impact of emerging VOC on the efficacy of vaccines
In this reporting period, significant progress has been made towards these objectives:
Objective 1 Identification of emerging VOC through genomic surveillance: Access to the three large genomic surveillance programs in Europe and South Africa, makes it possible for CoVICIS to achieve this objective. Collectively more than 100,000 sequences have been produced since the start of CoVICIS program. CoVICIS partners identified the arrival of Omicron and its significant sublineages in different geographic regions in the world, and have observed the end of substantial regional variation.
Objective 2 Characterization of the virologic and immunologic properties of emerging VOC: For the virological characterization, we found that defect in infectivity due to single mutations involved in immune escape are compensated by the combination of mutations found on Spikes. For the immunological properties, our findings indicates that the virus has made a big step toward being resistant to the vaccine induce humoral immune response. In contrast, studies confirm that cross-reactive CD4 and CD8 T cell immunity between the ancestral SARS-CoV-2 strain and the Omicron BA.1 BA4/5 and XBB.1.5 variants tested is preserved, with no indication of significant T cell escape.
Objective 3 Identification of differences in clinical and immune responses in unvaccinated children cohorts: The Swiss Ciao Corona cohort have shown that the Omicron wave and the rollout of vaccines led to almost 100% seropositivity as well as better neutralising capacity in children and adolescents. From the Italian SALISARV1 Hospitalized children cohort, 37% reported at least one symptom referable to Long COVID, with 22% required hospitalization. From the South African hospitalised unvaccinated children’s cohort showed that SARS-CoV-2 is an important primary cause of disease in childhood with a significant burden of care.
Objective 4 Delineation of the impact of VOC on the effectiveness of vaccine-induced immune response: A large number of cohorts of different risk, gender and age groups in different geographic regions contributed to this objective. The major finding includes: 1) Combination of vaccination and infection confers higher anti-RBD IgG levels and higher neutralizing capacity than vaccination alone, likely providing better protection against COVID-19; 2) two vaccine doses are not protective against the Omicron BA.1 variant in patients with hematological malignancies, autoimmune disease, solid organ transplant and may have minimal benefits in solid cancer patients. Protection was marginally improved by a 3rd vaccination.
Objective 5 Identification of immune correlates of protection against VOC: Data relevant to the analysis of immune correlates of protections from Lausanne, Zurich and Milan have been transferred to the CoVICIS data repository. Initial results from the CHUV ImmunoVax cohort indicated that a combination of vaccination and natural infection creates a longer lasting immunological response than vaccination alone.
Objective 1 Identification of emerging VOC through genomic surveillance: Access to the three large genomic surveillance programs in Europe and South Africa, makes it possible for CoVICIS to achieve this objective. Collectively more than 100,000 sequences have been produced since the start of CoVICIS program. CoVICIS partners identified the arrival of Omicron and its significant sublineages in different geographic regions in the world, and have observed the end of substantial regional variation.
Objective 2 Characterization of the virologic and immunologic properties of emerging VOC: For the virological characterization, we found that defect in infectivity due to single mutations involved in immune escape are compensated by the combination of mutations found on Spikes. For the immunological properties, our findings indicates that the virus has made a big step toward being resistant to the vaccine induce humoral immune response. In contrast, studies confirm that cross-reactive CD4 and CD8 T cell immunity between the ancestral SARS-CoV-2 strain and the Omicron BA.1 BA4/5 and XBB.1.5 variants tested is preserved, with no indication of significant T cell escape.
Objective 3 Identification of differences in clinical and immune responses in unvaccinated children cohorts: The Swiss Ciao Corona cohort have shown that the Omicron wave and the rollout of vaccines led to almost 100% seropositivity as well as better neutralising capacity in children and adolescents. From the Italian SALISARV1 Hospitalized children cohort, 37% reported at least one symptom referable to Long COVID, with 22% required hospitalization. From the South African hospitalised unvaccinated children’s cohort showed that SARS-CoV-2 is an important primary cause of disease in childhood with a significant burden of care.
Objective 4 Delineation of the impact of VOC on the effectiveness of vaccine-induced immune response: A large number of cohorts of different risk, gender and age groups in different geographic regions contributed to this objective. The major finding includes: 1) Combination of vaccination and infection confers higher anti-RBD IgG levels and higher neutralizing capacity than vaccination alone, likely providing better protection against COVID-19; 2) two vaccine doses are not protective against the Omicron BA.1 variant in patients with hematological malignancies, autoimmune disease, solid organ transplant and may have minimal benefits in solid cancer patients. Protection was marginally improved by a 3rd vaccination.
Objective 5 Identification of immune correlates of protection against VOC: Data relevant to the analysis of immune correlates of protections from Lausanne, Zurich and Milan have been transferred to the CoVICIS data repository. Initial results from the CHUV ImmunoVax cohort indicated that a combination of vaccination and natural infection creates a longer lasting immunological response than vaccination alone.
Progress made in this reporting period has made the following scientific and social impact:
• Genomic surveillance programs provided timely information to the national and international governing bodies on the emergence and evolution of SARS-CoV-2, confirmed the end of substantial regional variation: a variant would emerge in one part of the world and would quickly become the dominant variant in every part of the world, mostly following a similar pattern of Delta>Omicron BA.1> BA.2> BA.5> BQ.1 > XBB
• Cohort studies have resulted in several findings with impact on public health policies on vaccination and disease management:
o Combination of vaccination and infection lead to higher antibody responses than vaccination alone and therefore likely providing better protection
o Fourth booster vaccine is of value in maintaining humoral immunity to SARS-CoV-2
o Vaccination with 2 doses has limited benefit for immunocompromised individuals; however a 3rd dose significantly increases humoral immune response in autoimmune and solid cancer patients
• Genomic surveillance programs provided timely information to the national and international governing bodies on the emergence and evolution of SARS-CoV-2, confirmed the end of substantial regional variation: a variant would emerge in one part of the world and would quickly become the dominant variant in every part of the world, mostly following a similar pattern of Delta>Omicron BA.1> BA.2> BA.5> BQ.1 > XBB
• Cohort studies have resulted in several findings with impact on public health policies on vaccination and disease management:
o Combination of vaccination and infection lead to higher antibody responses than vaccination alone and therefore likely providing better protection
o Fourth booster vaccine is of value in maintaining humoral immunity to SARS-CoV-2
o Vaccination with 2 doses has limited benefit for immunocompromised individuals; however a 3rd dose significantly increases humoral immune response in autoimmune and solid cancer patients