COVID-19 vaccine-induced adaptive immunity against SARS-CoV-2 variants

The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has necessitated the rapid development and deployment of vaccines worldwide. mRNA-based vaccines against COVID-19 have demonstrated a high degree of efficacy against the original SARSCoV- 2 strain. However, the emergence of several genetic variants of the virus presents significant challenges to worldwide efforts in controlling the pandemic. To date, five dominant variants, namely Alpha, Beta, Gamma, Delta, and Omicron, have caused major epidemic waves of SARS-CoV-2 infections. Understanding the adaptive immune responses induced by COVID-19 vaccines against these variants is crucial for evaluating vaccine effectiveness and informing public health strategies. COVID-19 mRNA vaccines stimulate robust adaptive immune responses characterized by the production of antibodies targeting the spike (S) protein of SARS-CoV-2 and the generation of memory T cells. In this study, we developed an immunoassay based on SARS-CoV-2 proteins and a live virus microneutralization test (MNT) to measure the production and persistence of vaccine-induced and naturally acquired neutralizing antibodies. Additionally, we employed an activationinduced marker (AIM) assay to analyse the activation of memory T cells against SARS-CoV-2 variants. Immune responses were studied in Finnish healthcare workers. The results of this study demonstrate that the completion of a two-dose mRNA vaccine regimen leads to consistent and high production of S-specific antibodies across all studied age groups. Vaccinated individuals exhibit the ability to neutralize the SARS-CoV-2 Alpha variant, while neutralization against the Beta and Delta variants is reduced. Furthermore, a majority of vaccinated participants display the presence of SARS-CoV-2 S-specific memory CD4+ and CD8+ T cells, which exhibit cross-recognition of the different SARS-CoV-2 variants. S-specific antibody levels were found to decline within months following vaccination, while T cell responses remained stable for at least six months. These results highlight the durability of memory T cell responses and their role in providing sustained protection against SARS-CoV-2 variants. KEYWORDS: SARS-CoV-2, COVID-19, vaccine response, adaptive immune response, genetic variant, pandemicHengitystieinfektioita aiheuttavan uuden SARS-CoV-2-koronaviruksen ilmaantuminen johti maailmanlaajuisen COVID-19-pandemiaan, jonka hillitseminen on vaatinut nopeaa rokotteiden kehittämistä ja käyttöönottoa. COVID-19 mRNArokotteet ovat osoittautuneet tehokkaiksi alkuperäistä SARS-CoV-2-virusta vastaan, mutta uusien geneettisten varianttien ilmaantuminen on asettanut haasteita pandemian hallinnalle. Tähän mennessä viisi dominoivaa varianttia – Alpha-, Beta-, Gamma-, Delta- ja Omikron-variantit - ovat aiheuttaneet merkittäviä SARS-CoV-2-virusinfektioiden aaltoja. COVID-19-rokotuksessa syntyvän hankitun immuniteetin ymmärtäminen on ratkaisevan tärkeää rokotteen tehokkuuden sekä tulevien rokotusstrategioiden ja uusintarokotustarpeen arvioinnissa. COVID-19 mRNA-rokotteet saavat aikaan voimakkaan immuunivasteen, mukaan lukien SARS-CoV-2-viruksen piikkiproteiini-spesifisten vasta-aineiden tuotannon ja muisti-T-solujen kehittymisen. Tässä väitöskirjassa pystytettiin virusproteiineja tunnistava vasta-ainetesti ja elävää SARS-CoV-2-virusta hyödyntävä mikroneutralisaatiotesti mittaamaan rokotteen ja luonnollisen infektion synnyttämien vasta-aineiden määrää sekä niiden kykyä neutraloida SARS-CoV-2-variantteja. Lisäksi työssä hyödynnettiin T-solujen aktivaatiomääritystä, jolla analysoitiin muisti-T-solujen kykyä tunnistaa muuntuneita SARS-CoV-2-variantteja. Rokotevasteita tutkittiin suomalaisissa terveydenhuollon työntekijöissä. Tämän väitöskirjan tulokset osoittivat, että kahden rokoteannoksen jälkeen kaikki tutkittavat tuottivat vasta-aineita S-proteiinia kohtaan iästä ja sukupuolesta riippumatta. Vasta-ainevaste oli yhtä voimakas Alpha-varianttia kohtaan kuin alkuperäistä SARS-CoV-2-virusta kohtaan, kun taas Beta- ja Delta-varianttien neutralisaatio oli heikentynyt sekä rokotetuilla että luonnollisen taudin sairastaneilla. Suurimmalla osalla rokotetuista henkilöistä voitiin todeta SARS-CoV-2-viruksen Sproteiinin tunnistavia auttaja- ja sytotoksisia-T-soluja. Lisäksi T-solut tunnistivat virusvariantteja yhtä hyvin kuin alkuperäistä virusta. Vasta-ainetasot laskivat muutamien kuukausien kuluessa rokotuksesta, kun taas muisti-T-soluaktivaation havaittiin säilyvän samalla tasolla vielä kuuden kuukauden kuluttua rokotuksesta. Nämä tulokset osoittavat, että mRNA-rokotteet tarjoavat kestävän suojan SARSCoV-2-virusvarianttien aiheuttamaa tautia vastaan muisti-T-solujen välityksellä. AVAINSANAT: COVID-19, SARS-CoV-2-virus, rokotevaste, virusmuunno

Patterns of Aggregated Commuting Times in the Helsinki Capital Region

Suuret joukkoliikenne- ja väylähankkeet vaikuttavat päivittäiseen liikkuvuuteemme muuttaessaan meille arjessamme tärkeimpien paikkojen, kuten kotiemme ja työpaikkojemme maantieteellistä saavutettavuutta. Siksi on olemassa selvä tarve arvioida etukäteen näiden hankkeiden vaikutuksia ihmisten liikkuvuuteen. Perinteisesti käytettävissä olevat menetelmät ovat kuitenkin asettaneet suuria rajoitteita saavutettavuuden ja liikkuvuuden mittaamiselle ja tutkimiselle, ja huolimatta kaikkialle levinneiden matkapuhelinten mahdollistamista moderneista datankeruumenetelmistä liikkuvuuden tutkiminen on edelleen haasteellista datan saatavuusongelmien vuoksi. Puhdas liikkuvuustutkimus ei myöskään mahdollista muutosten vaikutusten arviointia ennakkoon. Modernin saavutettavuusdatan käyttäminen liikkuvuusdatan asemasta on kuitenkin yksi mahdollinen ratkaisu. Tutkimuksessani selvitin kyseisen ratkaisun hyödynnettävyyttä. Yhdistin modernin, multimodaalisen ja monivuotisen saavutettavuusaineiston, Pääkaupunkiseudun matka-aikamatriisin, sen kanssa spatiaalisesti yhteensopivaan yhdyskuntarakennetilaston työmatka-aineistoon arvioidakseni pääkaupunkiseudun matka-aikakertymiä. Eri matkustustapojen osuuksia arvioin aiemmin julkaistun kyselytutkimuksen perusteella. Näin yhdistetyn aineiston avulla tutkin pääkaupunkiseudun työmatkojen matka-aikakertymien muutoksia tilastoalueittain matka-aikamatriisin kolmen eri aineistovuoden – 2013, 2015 ja 2018 – välillä, selvittääkseni tämänkaltaisten ennakkoarvioiden käyttökelpoisuutta hankkeiden aiheuttamia liikkuvuusmuutoksia arvioitaessa. Koska pieni osuus työmatka-aineistosta oli toimialaluokiteltua, tutkin myös toimialojen alueellisia eroja. Tutkimukseni tulokset osoittavat, että joukkoliikenteellä tehtyjen matkojen osalta liikennehankkeiden vaikutukset ovat uskottavasti nähtävissä matka-aikakertymien alueellisista muutoksista, useiden suurien joukkoliikennehankkeiden luomien uusien yhteyksien – Kehäradan, runkolinja 560:n ja Länsimetron – palvelemien alueiden erottuessa muusta aineistosta selvästi. Yksityisautoilla tehtyjen matkojen ja toimialakohtaisten erojen osalta tulokset eivät kuitenkaan ole näin selkeitä, mahdollisesti suurten tiehankkeiden puutteen, lähdedatan epätarkkuuksien ja toimialaluokitellun työmatka-aineiston osan rajoitusten vuoksi. Johtopäätökseni on, että modernia, matka-aikamatriisin tapaista saavutettavuusaineistoa voidaan uskottavasti käyttää suurten joukkoliikennehankkeiden liikkuvuusvaikutusten ennakkoarviointiin, vaikka tulosten lopullinen tarkkuus vaikuttaakin riippuvan voimakkaasti lähdeaineistojen tarkkuudesta, mikä tulisi ottaa huomioon tämänkaltaisia ennakkoarvioita laadittaessa. Matka-aikojen vuorokaudenaikaisen vaihtelun sekä itselläni käytössä ollutta aineistoa alueellisesti tarkempien matkustustapamieltymyksiä koskevien tietojen vaikutusten selvittämiselle on kuitenkin selkeä jatkotutkimuksen tarve.Large-scale transport infrastructure projects change our daily mobility patterns, as they change the geographical accessibility of the places where we spend most of our time, such as our homes and workplaces. Thus, there is a clear need for advance evaluation of the effects of those projects. Traditionally, however, the available methods have imposed severe limitations for both measuring accessibility and surveying mobility, and despite modern data collection methods enabled by the ever-present mobile phones, surveying mobility remains challenging due to data accessibility restrictions. Furthermore it would not enable any advance evaluation of mobility changes. However, using a modern accessibility dataset instead of a mobility one does offer a possible answer. In my study, I set out to investigate this possibility. I combined a modern, multimodal and longitudinal accessibility dataset, the Helsinki Region Travel Time Matrix (TTM), with a spatially compatible, census-based longitudinal commuting dataset to evaluate the aggregated journey times in the Helsinki Capital Region (HCR), the area covered by the TTM, and estimated the shares of different transport modes based on a previously published travel survey. Armed with this combined dataset, I assessed the changes in aggregated journey times between the three years that were included in the TTM dataset – 2013, 2015 and 2018 – by statistical district to estimate its usability for these kind of advance mobility evaluations. As a small subset of the commuting dataset was classified by industry, I also assessed regional differences between industries. My results demonstrate that for travel by public transport, the effects of new transport projects are plausibly identifiable in these aggregated patterns, with a number of areas served by several new, large-scale public transport infrastructure projects – the Ring Rail, the trunk bus lane 560 and the Western extension of the metro line – being outliers in the results. For travel by private car and for the industry-level changes, the results are more inconclusive, possibly due to absence of massive projects affecting the road network throughout the dataset timeframe, potential inaccuracies in the source data and limitations of the industry-classified part of the dataset. In conclusion, a modern accessibility dataset such as the TTM can be plausibly used to estimate the mobility effects of large-scale public transport infrastructure projects, although the final accuracy of the results is likely to be heavily dependent of the precision of the original datasets, which should be taken into account when such assessments are made. Further research is clearly needed to assess the effects of diurnal variations in travel times and the effects of more precise transport mode preference data

No evidence of autoimmunity to human OX1 or OX2 orexin receptors in Pandemrix-vaccinated narcoleptic children

Narcolepsy type 1, likely an immune-mediated disease, is characterized by excessive daytime sleepiness and cataplexy. The disease is strongly associated with human leukocyte antigen (HLA) DQB1∗06:02. A significant increase in the incidence of childhood and adolescent narcolepsy was observed after a vaccination campaign with AS03-adjuvanted Pandemrix influenza vaccine in Nordic and several other countries in 2010 and 2011. Previously, it has been suggested that a surface-exposed region of influenza A nucleoprotein, a structural component of the Pandemrix vaccine, shares amino acid residues with the first extracellular domain of the human OX2 orexin/hypocretin receptor eliciting the development of autoantibodies. Here, we analyzed, whether H1N1pdm09 infection or Pandemrix vaccination contributed to the development of autoantibodies to the orexin precursor protein or the OX1 or OX2 receptors. The analysis was based on the presence or absence of autoantibody responses against analyzed proteins. Entire OX1 and OX2 receptors or just their extracellular N-termini were transiently expressed in HuH7 cells to determine specific antibody responses in human sera. Based on our immunofluorescence analysis, none of the 56 Pandemrix-vaccinated narcoleptic patients, 28 patients who suffered from a laboratory-confirmed H1N1pdm09 infection or 19 Pandemrix-vaccinated controls showed specific autoantibody responses to prepro-orexin, orexin receptors or the isolated extracellular N-termini of orexin receptors. We also did not find any evidence for cell-mediated immunity against the N-terminal epitopes of OX2. Our findings do not support the hypothesis that the surface-exposed region of the influenza nucleoprotein A would elicit the development of an immune response against orexin receptors. © 2020 The AuthorsPeer reviewe

A Highly Sensitive and Specific SARS-CoV-2 Spike- and Nucleoprotein-Based Fluorescent Multiplex Immunoassay (FMIA) to Measure IgG, IgA, and IgM Class Antibodies

Validation and standardization of accurate serological assays are crucial for the surveillance of the coronavirus disease 2019 (COVID-19) pandemic and population immunity. We describe the analytical and clinical performance of an in-house fluorescent multiplex immunoassay (FMIA) for simultaneous quantification of antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleoprotein and spike glycoprotein. Furthermore, we calibrated IgG-FMIA against World Health Organization (WHO) International Standard and compared FMIA results to an in-house enzyme immunoassay (EIA) and a microneutralization test (MNT). We also compared the MNT results of two laboratories. IgG-FMIA displayed 100% specificity and sensitivity for samples collected 13 to 150 days post-onset of symptoms (DPO). For IgA- and IgM-FMIA, 100% specificity and sensitivity were obtained for a shorter time window (13 to 36 and 13 to 28 DPO for IgA- and IgM-FMIA, respectively). FMIA and EIA results displayed moderate to strong correlation, but FMIA was overall more specific and sensitive. IgG-FMIA identified 100% of samples with neutralizing antibodies (NAbs). Anti-spike IgG concentrations correlated strongly (r = 0.77 to 0.84, P < 2.2 x 10(-16)) with NAb titers, and the two laboratories' NAb titers displayed a very strong correlation (r = 0.95, P< 2.2 x 10(-16)). Our results indicate good correlation and concordance of antibody concentrations measured with different types of in-house SARS-CoV-2 antibody assays. Calibration against the WHO international standard did not, however, improve the comparability of FMIA and EIA results. IMPORTANCE SARS-CoV-2 serological assays with excellent clinical performance are essential for reliable estimation of the persistence of immunity after infection or vaccination. In this paper we present a thoroughly validated SARS-CoV-2 serological assay with excellent clinical performance and good comparability to neutralizing antibody titers. Neutralization tests are still considered the gold standard for SARS-CoV-2 serological assays, but our assay can identify samples with neutralizing antibodies with 100% sensitivity and 96% specificity without the need for laborious and slow biosafety level 3 (BSL-3) facility-requiring analyses.Peer reviewe

Serological Follow-Up Study Indicates High Seasonal Coronavirus Infection and Reinfection Rates in Early Childhood

Seasonal human coronaviruses (HCoVs) cause respiratory infections, especially in children. Currently, the knowledge on early childhood seasonal coronavirus infections and the duration of antibody levels following the first infections is limited. Here we analyzed serological follow-up samples to estimate the rate of primary infection and reinfection(s) caused by seasonal coronaviruses in early childhood. Serum specimens were collected from 140 children at ages of 13, 24, and 36 months (1, 2, and 3 years), and IgG antibody levels against recombinant HCoV nucleoproteins (N) were measured by enzyme immunoassay (EIA). Altogether, 84% (118/140) of the children were seropositive for at least one seasonal coronavirus N by the age of 3 years. Cumulative seroprevalences for HCoVs 229E, HKU1, NL63, and OC43 increased by age, and they were 45%, 27%, 70%, and 44%, respectively, at the age of 3 years. Increased antibody levels between yearly samples indicated reinfections by 229E, NL63, and OC43 viruses in 20-48% of previously seropositive children by the age of 3 years. Antibody levels declined 54-73% or 31-77% during the year after seropositivity in children initially seropositive at 1 or 2 years of age, respectively, in case there was no reinfection. The correlation of 229E and NL63, and OC43 and HKU1 EIA results, suggested potential cross-reactivity between the N specific antibodies inside the coronavirus genera. The data shows that seasonal coronavirus infections and reinfections are common in early childhood and the antibody levels decline relatively rapidly. IMPORTANCE The rapid spread of COVID-19 requires better knowledge on the rate of coronavirus infections and coronavirus specific antibody responses in different population groups. In this work we analyzed changes in seasonal human coronavirus specific antibodies in young children participating in a prospective 3-year serological follow-up study. We show that based on seropositivity and changes in serum coronavirus antibody levels, coronavirus infections and reinfections are common in early childhood and the antibodies elicited by the infection decline relatively rapidly. These observations provide further information on the characteristics of humoral immune responses of coronavirus infections in children. The rapid spread of COVID-19 requires better knowledge on the rate of coronavirus infections and coronavirus specific antibody responses in different population groups. In this work we analyzed changes in seasonal human coronavirus specific antibodies in young children participating in a prospective 3-year serological follow-up study.Peer reviewe

No evidence of autoimmunity to human OX1 or OX2 orexin receptors in Pandemrix-vaccinated narcoleptic children

 Narcolepsy type 1, likely an immune-mediated disease, is characterized by excessive daytime sleepiness and cataplexy. The disease is strongly associated with human leukocyte antigen (HLA) DQB1∗06:02. A significant increase in the incidence of childhood and adolescent narcolepsy was observed after a vaccination campaign with AS03-adjuvanted Pandemrix influenza vaccine in Nordic and several other countries in 2010 and 2011. Previously, it has been suggested that a surface-exposed region of influenza A nucleoprotein, a structural component of the Pandemrix vaccine, shares amino acid residues with the first extracellular domain of the human OX2 orexin/hypocretin receptor eliciting the development of autoantibodies. Here, we analyzed, whether H1N1pdm09 infection or Pandemrix vaccination contributed to the development of autoantibodies to the orexin precursor protein or the OX1 or OX2 receptors. The analysis was based on the presence or absence of autoantibody responses against analyzed proteins. Entire OX1 and OX2 receptors or just their extracellular N-termini were transiently expressed in HuH7 cells to determine specific antibody responses in human sera. Based on our immunofluorescence analysis, none of the 56 Pandemrix-vaccinated narcoleptic patients, 28 patients who suffered from a laboratory-confirmed H1N1pdm09 infection or 19 Pandemrix-vaccinated controls showed specific autoantibody responses to prepro-orexin, orexin receptors or the isolated extracellular N-termini of orexin receptors. We also did not find any evidence for cell-mediated immunity against the N-terminal epitopes of OX2. Our findings do not support the hypothesis that the surface-exposed region of the influenza nucleoprotein A would elicit the development of an immune response against orexin receptors.</p

Long-Lasting T Cell Responses in BNT162b2 COVID-19 mRNA Vaccinees and COVID-19 Convalescent Patients

Peer reviewe

Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has raised concern about increased transmissibility, infectivity, and immune evasion from a vaccine and infection-induced immune responses. Although COVID-19 mRNA vaccines have proven to be highly effective against severe COVID-19 disease, the decrease in vaccine efficacy against emerged Beta and Delta variants emphasizes the need for constant monitoring of new virus lineages and studies on the persistence of vaccine-induced neutralizing antibodies. To analyze the dynamics of COVID-19 mRNA vaccine-induced antibody responses, we followed 52 health care workers in Finland for 6 months after receiving two doses of BNT162b2 vaccine with a 3-week interval. We demonstrate that, although anti-S1 antibody levels decrease 2.3-fold compared to peak antibody levels, anti-SARS-CoV-2 antibodies persist for months after BNT162b2 vaccination. Variants D614G, Alpha, and Eta are neutralized by sera of 100% of vaccinees, whereas neutralization of Delta is 3.8-fold reduced and neutralization of Beta is 5.8-fold reduced compared to D614G. Despite this reduction, 85% of sera collected 6 months postvaccination neutralizes Delta variant. IMPORTANCE A decrease in vaccine efficacy against emerging SARS-CoV-2 variants has increased the importance of assessing the persistence of SARS-CoV-2 spike proteinspecific antibodies and neutralizing antibodies. Our data show that after 6 months post two doses of BNT162b2 vaccine, antibody levels decrease yet remain detectable and capable of neutralizing emerging variants. By monitoring the vaccine-induced antibody responses, vaccination strategies and administration of booster doses can be optimized.Peer reviewe

Low pre-vaccination SARS-CoV-2 seroprevalence in Finnish health care workers: a prospective cohort study

Background: Health care workers are at risk of acquiring SARS-CoV-2 infection. Our aim was to study the prevalence of SARS-CoV-2 nucleoprotein and spike protein specific antibodies in health care workers with occupational exposure to COVID-19 in Turku, Finland, from May to December 2020.Methods: Health care workers of Turku University Hospital units caring for COVID-19 patients or handling clinical SARS-CoV-2 samples were invited to participate in the study. The presence of SARS-CoV-2 nucleoprotein and spike protein specific IgG antibodies were analysed with in-house enzyme immunoassay.Results: At study enrolment, only one of the 222 (0.5%) study participants was seropositive for SARS-CoV-2 protein specific antibodies. Two additional study participants (2/222, 0.9%) seroconverted during the follow-up. All these participants were diagnosed with a RT-PCR-positive COVID-19 infection before turning seropositive.Conclusion: In our study population, the prevalence of SARS-CoV-2 seropositivity remained low. The absence of seropositive cases without previous RT-PCR confirmed infections demonstrate good access to diagnostics. In addition to high vaccine coverage, high standards of infection prevention practices and use of standard personal protective equipment seem sufficient in preventing occupational SARS-CoV-2 infection in a setting with low number of circulating virus. However, it remains unclear whether similar protective practices would also be effective against more transmissible SARS-CoV-2 variants.</p

Serological Follow-Up Study Indicates High Seasonal Coronavirus Infection and Reinfection Rates in Early Childhood

Seasonal human coronaviruses (HCoVs) cause respiratory infections, especially in children. Currently, the knowledge on early childhood seasonal coronavirus infections and the duration of antibody levels following the first infections is limited. Here we analyzed serological follow-up samples to estimate the rate of primary infection and reinfection(s) caused by seasonal coronaviruses in early childhood. Serum specimens were collected from 140 children at ages of 13, 24, and 36 months (1, 2, and 3 years), and IgG antibody levels against recombinant HCoV nucleoproteins (N) were measured by enzyme immunoassay (EIA). Altogether, 84% (118/140) of the children were seropositive for at least one seasonal coronavirus N by the age of 3 years. Cumulative seroprevalences for HCoVs 229E, HKU1, NL63, and OC43 increased by age, and they were 45%, 27%, 70%, and 44%, respectively, at the age of 3 years. Increased antibody levels between yearly samples indicated reinfections by 229E, NL63, and OC43 viruses in 20-48% of previously seropositive children by the age of 3 years. Antibody levels declined 54-73% or 31-77% during the year after seropositivity in children initially seropositive at 1 or 2 years of age, respectively, in case there was no reinfection. The correlation of 229E and NL63, and OC43 and HKU1 EIA results, suggested potential cross-reactivity between the N specific antibodies inside the coronavirus genera. The data shows that seasonal coronavirus infections and reinfections are common in early childhood and the antibody levels decline relatively rapidly. IMPORTANCE The rapid spread of COVID-19 requires better knowledge on the rate of coronavirus infections and coronavirus specific antibody responses in different population groups. In this work we analyzed changes in seasonal human coronavirus specific antibodies in young children participating in a prospective 3-year serological follow-up study. We show that based on seropositivity and changes in serum coronavirus antibody levels, coronavirus infections and reinfections are common in early childhood and the antibodies elicited by the infection decline relatively rapidly. These observations provide further information on the characteristics of humoral immune responses of coronavirus infections in children.The rapid spread of COVID-19 requires better knowledge on the rate of coronavirus infections and coronavirus specific antibody responses in different population groups. In this work we analyzed changes in seasonal human coronavirus specific antibodies in young children participating in a prospective 3-year serological follow-up study.</p