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1.
J Travel Med ; 2022.
Article in English | Web of Science | ID: covidwho-2161106

ABSTRACT

BACKGROUND: In view of limited evidence that specifically addresses vaccine effectiveness (VE) in the older population, this study aims to evaluate the real-world effectiveness of BNT162b2 and CoronaVac in older adults during the Omicron BA.2 outbreak. METHODS: This case-control study analysed data available between January and March 2022 from the electronic health databases in Hong Kong and enrolled individuals aged 60 or above. Each case was matched with up to 10 controls by age, sex, index date and Charlson Comorbidity Index for the four outcomes (COVID-19 infection, COVID-19-related hospitalisation, severe complications, and all-cause mortality) independently. Conditional logistic regression was conducted to evaluate VE of BNT162b2 and CoronaVac against COVID-19-related outcomes within 28 days after COVID-19 infection among participants stratified by age groups (60-79, >/= 80 years old). RESULTS: A dose-response relationship between the number of vaccine doses received and protection against severe or fatal disease was observed. Highest VE (95% CI) against COVID-19 infection was observed in individuals aged >/=80 who received three doses of BNT162b2 [75.5% (73.1%-77.7%)] or three doses of CoronaVac [53.9% (51.0%-56.5%)] compared to those in the younger age group who received three doses of BNT162b2 [51.1% (49.9%-52.4%)] or three doses of CoronaVac [2.0% (-0.1%-4.1%)]. VE (95% CI) was higher for other outcomes, reaching 91.9% (89.4%-93.8%) and 86.7% (84.3%-88.8%) against COVID-19-related hospitalisation;85.8% (61.2%-94.8%) and 89.8% (72.4%-96.3%) against COVID-19-related severe complications;and 96.4% (92.9%-98.2%) and 95.0% (92.1%-96.8%) against COVID-19-related mortality after three doses of BNT162b2 and CoronaVac in older vaccine recipients, respectively. A similar dose-response relationship was established in younger vaccine recipients and after stratification by sex and Charlson Comorbidity Index. CONCLUSION: Both BNT162b2 and CoronaVac vaccination were effective in protecting older adults against COVID-19 infection and COVID-19-related severe outcomes amidst the Omicron BA.2 pandemic, and VE increased further with the third dose.

2.
Virol J ; 19(1): 197, 2022 11 25.
Article in English | MEDLINE | ID: covidwho-2139346

ABSTRACT

Currently, the majority of the global population has been vaccinated with the COVID-19 vaccine, and characterization studies of antibodies in vivo from Omicron breakthrough infection and naive infection populations are urgently needed to provide pivotal clues about accurate diagnosis, treatment, and next-generation vaccine design against SARS-CoV-2 infection. We showed that after infection with Omicron-BA.2, the antibody levels of specific IgM against the Wuhan strain and specific IgG against Omicron were not significantly elevated within 27 days of onset. Interestingly, in this study, the levels of humoral immunity against Omicron-specific IgM were significantly increased after breakthrough infection, suggesting that the detection of Omicron-specific IgM antibodies can be used as a test criterion of Omicron breakthrough infection. In addition, we observed that serums from unvaccinated individuals and the majority of vaccinated infections possessed only low or no neutralizing activity against Omicron at the onset of Omicron breakthrough infections, and at the later stage of Omicron-BA.2 breakthrough infection, levels of neutralization antibody against the Wuhan and Omicron strains were elevated in infected individuals. The findings of this study provide important clues for the diagnosis of Omicron breakthrough infections, antibody characterization studies and vaccine design against COVID-19.


Subject(s)
Antibody Formation , COVID-19 , Humans , SARS-CoV-2 , Antibodies, Viral , COVID-19 Vaccines , Immunoglobulin M
3.
Front Immunol ; 13: 1065345, 2022.
Article in English | MEDLINE | ID: covidwho-2123419

ABSTRACT

Background: Several systemic inflammatory biomarkers have been associated with poor overall survival (OS) and disease severity in patients with coronavirus disease 2019 (COVID-19). However, it remains unclear which markers are better for predicting prognosis, especially for COVID-19 Omicron BA.2 infected patients. The present study aimed to identify reliable predictors of prognosis of COVID-19 Omicron BA.2 from inflammatory indicators. Methods: A cohort of 2645 COVID-19 Omicron BA.2 infected patients were retrospectively analyzed during the Omicron BA.2 surge in Shanghai between April 12, 2022, and June 17, 2022. The patients were admitted to the Shanghai Fourth People's Hospital, School of Medicine, Tongji University. Six systemic inflammatory indicators were included, and their cut-off points were calculated using maximally selected rank statistics. The analysis involved Kaplan-Meier curves, univariate and multivariate Cox proportional hazard models, and time-dependent receiver operating characteristic curves (time-ROC) for OS-associated inflammatory indicators. Results: A total of 2347 COVID-19 Omicron BA.2 infected patients were included. All selected indicators proved to be independent predictors of OS in the multivariate analysis (all P < 0.01). A high derived neutrophil to lymphocyte ratio (dNLR) was associated with a higher mortality risk of COVID-19 [hazard ratio, 4.272; 95% confidence interval (CI), 2.417-7.552]. The analyses of time-AUC and C-index showed that the dNLR (C-index: 0.844, 0.824, and 0.718 for the 5th, 10th, and 15th day, respectively) had the best predictive power for OS in COVID-19 Omicron BA.2 infected patients. Among different sub-groups, the dNLR was the best predictor for OS regardless of age (0.811 for patients aged ≥70 years), gender (C-index, 0.880 for men and 0.793 for women) and disease severity (C-index, 0.932 for non-severe patients and 0.658 for severe patients). However, the platelet to lymphocyte ratio was superior to the other indicators in patients aged <70 years. Conclusions: The prognostic ability of the dNLR was higher than the other evaluated inflammatory indicators for all COVID-19 Omicron BA.2 infected patients.


Subject(s)
COVID-19 , Neutrophils , Humans , Male , Female , Retrospective Studies , China/epidemiology , Lymphocytes , Prognosis
4.
Vaccines (Basel) ; 10(11)2022 Nov 21.
Article in English | MEDLINE | ID: covidwho-2116257

ABSTRACT

The recurrence of the COVID-19 pandemic in 2022 has had a great impact on people's mentality, although the government has controlled it through a series of effective measures. What is noteworthy is that the public opinion on vaccines has changed significantly, and at present, the level of public's trust in the COVID-19 vaccine is what we are concentrating on. For the current situation, new measures should be explored. Vaccines have been proven to be effective in reducing the rate of serious cases and death among infected people. However, vaccination rates still need to be improved, especially among the elderly. For people with low antibody levels, the fourth injection is recommended. Studying vaccines effective against virus mutation is the focus of future research.

5.
J Pediatric Infect Dis Soc ; 2022 Nov 12.
Article in English | MEDLINE | ID: covidwho-2115732

ABSTRACT

Acute fulminant cerebral edema in children following SARS-CoV-2 infection has been rarely reported. Such patients frequently demonstrate rapid progression rapid progression and are usually fatal. In this retrospective study, we describe the detailed clinical, laboratory, and neuroimaging features of six fatal cases in Taiwan. All patients had shock initially, five showed rapid progression to multi-organ failure and disseminated intravascular coagulation, and three developed acute respiratory distress syndromes. The inflammatory biomarkers in the first 3 days, including interleukin 6, ferritin, lactate dehydrogenase and D-dimer, showed significant elevation in all cases. Hyper-inflammatory response may play a role in the pathophysiology.

6.
Vaccines (Basel) ; 10(10)2022 Oct 19.
Article in English | MEDLINE | ID: covidwho-2082011

ABSTRACT

BACKGROUND: Real-world evidence on the effectiveness of inactivated vaccines against the Delta and Omicron (BA.2.38) variants remains scarce. METHODS: A retrospective cohort study was conducted to estimate the adjusted vaccine effectiveness (aVE) of one, two, and three doses of inactivated vaccines in attenuating pneumonia, severe COVID-19, and the duration of viral shedding in Delta and Omicron cases using modified Poisson and linear regression as appropriate. RESULTS: A total of 561 COVID-19 cases were included (59.2% Delta and 40.8% Omicron). In total, 56.4% (184) of Delta and 12.0% (27) of Omicron cases had COVID-19 pneumonia. In the two-dose vaccinated population, 1.4% of Delta and 89.1% of Omicron cases were vaccinated for more than 6 months. In Delta cases, the two-dose aVE was 52% (95% confidence interval, 39-63%) against pneumonia and 61% (15%, 82%) against severe disease. Two-dose vaccination reduced the duration of viral shedding in Delta cases, but not in booster-vaccinated Omicron cases. In Omicron cases, three-dose aVE was 68% (18%, 88%) effective against pneumonia, while two-dose vaccination was insufficient for Omicron. E-values were calculated, and the E-values confirmed the robustness of our findings. CONCLUSIONS: In Delta cases, two-dose vaccination within 6 months reduced pneumonia, disease severity, and the duration of viral shedding. Booster vaccination provided a high level of protection against pneumonia with Omicron and should be prioritized.

7.
Hum Vaccin Immunother ; : 2129196, 2022 Oct 21.
Article in English | MEDLINE | ID: covidwho-2081918

ABSTRACT

The rapid replacement of Omicron BA.1 by BA.2 sublineage is very alarming, raising the question of whether BA.2 can escape the immunity acquired after BA.1 infection. We compared the neutralizing activity toward the Omicron BA.1 and BA.2 sub-lineages in five groups: COVID-19 patients; subjects who had received two doses of mRNA vaccine; subjects naturally infected with SARS-CoV-2 who had received two doses of mRNA; and subjects who had received three doses of homologous or heterologous vaccine. The results obtained highlight the importance of vaccine boosters in eliciting neutralizing antibody responses against Omicron sub-lineages, and suggest that the adenovirus vectored vaccine elicits a lower response against BA.1 than against BA.2 sub-lineage.

8.
J Travel Med ; 2022 Oct 17.
Article in English | MEDLINE | ID: covidwho-2077808

ABSTRACT

BACKGROUND: In view of limited evidence that specifically addresses vaccine effectiveness (VE) in the older population, this study aims to evaluate the real-world effectiveness of BNT162b2 and CoronaVac in older adults during the Omicron BA.2 outbreak. METHODS: This case-control study analysed data available between January and March 2022 from the electronic health databases in Hong Kong and enrolled individuals aged 60 or above. Each case was matched with up to 10 controls by age, sex, index date and Charlson Comorbidity Index for the four outcomes (COVID-19 infection, COVID-19-related hospitalisation, severe complications, and all-cause mortality) independently. Conditional logistic regression was conducted to evaluate VE of BNT162b2 and CoronaVac against COVID-19-related outcomes within 28 days after COVID-19 infection among participants stratified by age groups (60-79, ≥ 80 years old). RESULTS: A dose-response relationship between the number of vaccine doses received and protection against severe or fatal disease was observed. Highest VE (95% CI) against COVID-19 infection was observed in individuals aged ≥80 who received three doses of BNT162b2 [75.5% (73.1%-77.7%)] or three doses of CoronaVac [53.9% (51.0%-56.5%)] compared to those in the younger age group who received three doses of BNT162b2 [51.1% (49.9%-52.4%)] or three doses of CoronaVac [2.0% (-0.1%-4.1%)]. VE (95% CI) was higher for other outcomes, reaching 91.9% (89.4%-93.8%) and 86.7% (84.3%-88.8%) against COVID-19-related hospitalisation; 85.8% (61.2%-94.8%) and 89.8% (72.4%-96.3%) against COVID-19-related severe complications; and 96.4% (92.9%-98.2%) and 95.0% (92.1%-96.8%) against COVID-19-related mortality after three doses of BNT162b2 and CoronaVac in older vaccine recipients, respectively. A similar dose-response relationship was established in younger vaccine recipients and after stratification by sex and Charlson Comorbidity Index. CONCLUSION: Both BNT162b2 and CoronaVac vaccination were effective in protecting older adults against COVID-19 infection and COVID-19-related severe outcomes amidst the Omicron BA.2 pandemic, and VE increased further with the third dose.

9.
Med (N Y) ; 3(10): 705-721.e11, 2022 10 14.
Article in English | MEDLINE | ID: covidwho-2076532

ABSTRACT

BACKGROUND: The continual emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern, in particular the newly emerged Omicron (B.1.1.529) variant and its BA.X lineages, has rendered ineffective a number of previously FDA emergency use authorized SARS-CoV-2 neutralizing antibody therapies. Furthermore, those approved antibodies with neutralizing activity against Omicron BA.1 are reportedly ineffective against the subset of Omicron subvariants that contain a R346K substitution, BA.1.1, and the more recently emergent BA.2, demonstrating the continued need for discovery and characterization of candidate therapeutic antibodies with the breadth and potency of neutralizing activity required to treat newly diagnosed COVID-19 linked to recently emerged variants of concern. METHODS: Following a campaign of antibody discovery based on the vaccination of Harbor H2L2 mice with defined SARS-CoV-2 spike domains, we have characterized the activity of a large collection of spike-binding antibodies and identified a lead neutralizing human IgG1 LALA antibody, STI-9167. FINDINGS: STI-9167 has potent, broad-spectrum neutralizing activity against the current SARS-COV-2 variants of concern and retained activity against each of the tested Omicron subvariants in both pseudotype and live virus neutralization assays. Furthermore, STI-9167 nAb administered intranasally or intravenously provided protection against weight loss and reduced virus lung titers to levels below the limit of quantitation in Omicron-infected K18-hACE2 transgenic mice. CONCLUSIONS: With this established activity profile, a cGMP cell line has been developed and used to produce cGMP drug product intended for intravenous or intranasal use in human clinical trials. FUNDING: Funded by CRIPT (no. 75N93021R00014), DARPA (HR0011-19-2-0020), and NCI Seronet (U54CA260560).


Subject(s)
Antibodies, Neutralizing , COVID-19 , Administration, Intranasal , Animals , Antibodies, Neutralizing/therapeutic use , Antibodies, Viral/therapeutic use , COVID-19/drug therapy , Humans , Immunoglobulin G , Membrane Glycoproteins , Mice , Neutralization Tests , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Viral Envelope Proteins
10.
Front Public Health ; 10: 1018399, 2022.
Article in English | MEDLINE | ID: covidwho-2065652

ABSTRACT

The rapid spread of SARS-CoV-2 variants in the global population is indicative of the development of selective advantages in emerging virus strains. Here, we performed a case-control investigation of the clinical and demographic characteristics, clinical history, and virological markers to predict disease progression in hospitalized adults for COVID-19 between December 2021 and January 2022 in Chennai, India. COVID-19 diagnosis was made by a commercial TaqPath COVID-19 RT-PCR, and WGS was performed with the Ion Torrent Next Generation Sequencing System. High-quality (<5% of N) complete sequences of 73 Omicron B.1.1.529 variants were randomly selected for phylogenetic analysis. SARS-CoV-2 viral load, number of comorbidities, and severe disease presentation were independently associated with a shorter time-to-death. Strikingly, this was observed among individuals infected with Omicron BA.2 but not among those with the BA.1.1.529, BA.1.1, or the Delta B.1.617.2 variants. Phylogenetic analysis revealed severe cases predominantly clustering under the BA.2 lineage. Sequence analyses showed 30 mutation sites in BA.1.1.529 and 33 in BA.1.1. The mutations unique to BA.2 were T19I, L24S, P25del, P26del, A27S, V213G, T376A, D405N and R408S. Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and the Omicron BA.1.1.529 variant but not with Omicron BA.1.1 or BA.2 suggests that the newer strains are largely immune escape variants. The number of vaccine doses received was independently associated with increased odds of developing asymptomatic disease or recovery. We propose that the novel mutations reported herein could likely bear a significant impact on the clinical characteristics, disease progression, and epidemiological aspects of COVID-19. Surging rates of mutations and the emergence of eclectic variants of SARS-CoV-2 appear to impact disease dynamics.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , COVID-19 Testing , Disease Progression , Humans , India/epidemiology , Phylogeny , SARS-CoV-2/genetics , Viral Load
11.
3rd International Conference on Information Science, Parallel and Distributed Systems, ISPDS 2022 ; : 116-121, 2022.
Article in English | Scopus | ID: covidwho-2063273

ABSTRACT

Omicron BA.2, a new variant of severe acute respiratory syndrome coronavirus (SARS-CoV-2), has attracted worldwide attention due to its high infectivity and vaccine escape mutation. Based on the SEIR model being susceptible to changes in external factors and having specific errors, the ARIMA model is data-dependent and can only capture linear relationships. In this paper, based on the traditional infectious disease dynamic model SEIR and the differential integrated mean autoregressive model ARIMA, an SEIR-ARIMA mixed model is proposed to predict and evaluate the virus outbreak in March in Jilin Province, China. The data from SEIR and ARIMA models were processed using SPSS to obtain the predicted values f and e, respectively. Linear regression modeling was performed on the predicted values f and e to establish the SEIR-ARIMA model. MATLAB is used to complete the best linear fitting line. Furthermore, The results show that the model's predicted value is in good agreement with the actual value. It shows that the SEIR-ARIMA mixed model based on the SEIR-ARIMA model has a good prediction effect, which is beneficial for the country to make the right decision when facing the epidemic. It is of great value for preventing other types of infectious diseases in China in the future. © 2022 IEEE.

12.
Emerg Microbes Infect ; 11(1): 2800-2807, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2062777

ABSTRACT

An outbreak of COVID-19 caused by the SARS-CoV-2 Omicron BA.2 sublineage occurred in Shanghai, China from February 26 to June 30, 2022. We use official reported data retrieved from Shanghai municipal Health Commissions to estimate the incidence of infections, severe/critical infections, and deaths to assess the disease burden. By adjusting for right censoring and RT-PCR sensitivity, we provide estimates of clinical severity, including the infection fatality ratio, symptomatic case fatality ratio, and risk of developing severe/critical disease upon infection. The overall infection rate, severe/critical infection rate, and mortality rate were 2.74 (95% CI: 2.73-2.74) per 100 individuals, 6.34 (95% CI: 6.02-6.66) per 100,000 individuals and 2.42 (95% CI: 2.23-2.62) per 100,000 individuals, respectively. The severe/critical infection rate and mortality rate increased with age, noted in individuals aged 80 years or older. The overall fatality ratio and risk of developing severe/critical disease upon infection were 0.09% (95% CI: 0.09-0.10%) and 0.27% (95% CI: 0.24-0.29%), respectively. Having received at least one vaccine dose led to a 10-fold reduction in the risk of death for infected individuals aged 80 years or older. Under the repeated population-based screenings and strict intervention policies implemented in Shanghai, our results found a lower disease burden and mortality of the outbreak compared to other settings and countries, showing the impact of the successful outbreak containment in Shanghai. The estimated low clinical severity of this Omicron BA.2 epidemic in Shanghai highlight the key contribution of vaccination and availability of hospital beds to reduce the risk of death.


Subject(s)
COVID-19 , Humans , Aged, 80 and over , SARS-CoV-2 , China/epidemiology , Cost of Illness , Disease Outbreaks
13.
J Clin Virol ; 157: 105299, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2041915

ABSTRACT

BACKGROUND: SARS-CoV-2 has evolved, leading to the emergence of new Variants Of Concern (VOCs) with significant impact on transmissibility. Although the transmission process is complex, higher nasopharyngeal viral load (NP-VL) can be considered as a proxy for greater transmissibility. OBJECTIVES: The aim of this analysis was to compare NP-VL across a set of representative VOCs observed in mildly symptomatic patients. STUDY DESIGN: Observational single-center comparative analysis of patients with early mild-to-moderate COVID-19, enrolled within the early treatment access program of Lazzaro Spallanzani Institute (March 2021-March 2022). NP-VL before drug administration was estimated through RT-PCR, based on cycle threshold values (CTs); VOCs were identified by Sanger sequencing. VOCs' average treatment effect (ATE) was estimated on the CTs fitted in the log2 scale, controlling for potential confounders. RESULTS: A total of 707 patients were included. VOCs were: 10% Alpha, 3% Gamma, 34% Delta, 34% BA.1, 19% BA.2. Mean CTs for BA.1 and BA.2 were lower than Delta and BA.1, respectively. After adjusting for calendar time, age, immunodeficiency and vaccination, CTs for Gamma were lower than those seen for Alpha and higher than Delta, for Delta were similar to BA.1, for BA.2 were lower than Delta and BA.1. CONCLUSIONS: Our analysis shows higher NP-VL of BA.2 compared to previously circulating VOCs, even after controlling for factors potentially contributing to the amount of nasopharyngeal viral RNA, included vaccination, supporting the increased transmissibility of BA.2. Further studies are necessary to clarify this mechanism and to provide guidance for public health measures.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Viral Load , Nasopharynx , RNA, Viral/genetics , RNA, Viral/analysis
15.
J Infect Dis ; 226(10): 1688-1698, 2022 Nov 11.
Article in English | MEDLINE | ID: covidwho-2034602

ABSTRACT

BACKGROUND: As of early 2022, the Omicron variants are the predominant circulating lineages globally. Understanding neutralizing antibody responses against Omicron BA.1 and BA.2 after vaccine breakthrough infections will provide insights into BA.2 infectivity and susceptibility to subsequent reinfection. METHODS: Live virus neutralization assays were used to study immunity against Delta and Omicron BA.1 and BA.2 variants in samples from 86 individuals, 24 unvaccinated (27.9%) and 62 vaccinated (72.1%), who were infected with Delta (n = 42, 48.8%) or BA.1 (n = 44, 51.2%). Among the 62 vaccinated individuals, 39 were unboosted (62.9%), whereas 23 were boosted (37.1%). RESULTS: In unvaccinated infections, neutralizing antibodies (nAbs) against the three variants were weak or undetectable, except against Delta for Delta-infected individuals. Both Delta and BA.1 breakthrough infections resulted in strong nAb responses against ancestral wild-type and Delta lineages, but moderate nAb responses against BA.1 and BA.2, with similar titers between unboosted and boosted individuals. Antibody titers against BA.2 were generally higher than those against BA.1 in breakthrough infections. CONCLUSIONS: These results underscore the decreased immunogenicity of BA.1 compared to BA.2, insufficient neutralizing immunity against BA.2 in unvaccinated individuals, and moderate to strong neutralizing immunity induced against BA.2 in Delta and BA.1 breakthrough infections.


Subject(s)
Antibodies, Neutralizing , Vaccines , Humans , Antibodies, Viral
16.
Front Med (Lausanne) ; 9: 921135, 2022.
Article in English | MEDLINE | ID: covidwho-2032798

ABSTRACT

Background: The severe coronavirus disease 2019 (COVID-19) pandemic is still raging worldwide, and the Omicron BA.2 variant has become the new circulating epidemic strain. However, our understanding of the Omicron BA.2 variant is still scarce. This report aims to present a case of a moderate acute respiratory distress syndrome (ARDS) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron BA.2 variant and to discuss some management strategies that may benefit this type of case. Case Presentation: A 78-year-old man, who had four negative nucleic acid tests and a fifth positive, was admitted to our hospital. This patient was generally good upon admission and tested negative for anti-SARS-CoV-2 antibodies even after receiving two doses of the COVID-19 vaccine. On the 7th day of hospitalization, he developed a moderate ARDS. Improved inflammatory index and decreased oxygen index were primarily found in this patient, and a series of treatments, including anti-inflammation and oxygen therapies, were used. Then this patient's condition improved soon and reached two negative results of nucleic acid tests on the 18th day of hospitalization. Conclusion: At-home COVID-19 rapid antigen test could be complementary to existing detection methods, and the third booster dose of COVID-19 vaccine may be advocated in the face of the omicron BA.2 variant. Anti-inflammatory and oxygen therapies are still essential treatments for ARDS patients infected with SARS-CoV-2 Omicron BA.2 variant.

17.
Cell Rep Med ; 3(10): 100764, 2022 10 18.
Article in English | MEDLINE | ID: covidwho-2031747

ABSTRACT

Omicron has become the globally dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, creating additional challenges due to its ability to evade neutralization. Here, we report that neutralizing antibodies against Omicron variants are undetected following COVID-19 infection with ancestral or past SARS-CoV-2 variant viruses or after two-dose mRNA vaccination. Compared with two-dose vaccination, a three-dose vaccination course induces broad neutralizing antibody responses with improved durability against different SARS-CoV-2 variants, although neutralizing antibody titers against Omicron remain low. Intriguingly, among individuals with three-dose vaccination, Omicron breakthrough infection substantially augments serum neutralizing activity against a broad spectrum of SARS-CoV-2 variants, including Omicron variants BA.1, BA.2, and BA.5. Additionally, after Omicron breakthrough infection, memory T cells respond to the spike proteins of both ancestral and Omicron SARS-CoV-2 by producing cytokines with polyfunctionality. These results suggest that Omicron breakthrough infection following three-dose mRNA vaccination induces pan-SARS-CoV-2 immunity that may protect against emerging SARS-CoV-2 variants of concern.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Antibody Formation , Spike Glycoprotein, Coronavirus/genetics , Viral Envelope Proteins/genetics , Antibodies, Viral , Broadly Neutralizing Antibodies , COVID-19/prevention & control , Cytokines , RNA, Messenger
18.
Microorganisms ; 10(8)2022 Aug 20.
Article in English | MEDLINE | ID: covidwho-1997712

ABSTRACT

Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze the dissemination dynamics of Omicron strains in Saint Petersburg, Russia's second largest city. The first case of Omicron lineage BA.1 was registered in St. Petersburg on 10 December 2021. Rapid expansion of the variant and increased incidence followed. The peak incidence was reached in February 2022, followed by an observed decline coinciding with the beginning of spread of the BA.2 variant. SARS-CoV-2 lineage change dynamics were shown in three categories: airport arrivals; clinical outpatients; and clinical inpatients. It is shown that the distribution of lineage BA.1 occurred as a result of multiple imports. Variability within the BA.1 and BA.2 lineages in St. Petersburg was also revealed. On the basis of phylogenetic analysis, an attempt was made to trace the origin of the first imported strain, and an assessment was made of the quarantine measures used to prevent the spread of this kind of infection.

19.
EBioMedicine ; 83: 104232, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1996121

ABSTRACT

BACKGROUND: The Omicron BA.2 sublineage has replaced BA.1 worldwide and has comparable levels of immune evasion to BA.1. These observations suggest that the increased transmissibility of BA.2 cannot be explained by the antibody evasion. METHODS: Here, we characterized the replication competence and respiratory tissue tropism of three Omicron variants (BA.1, BA.1.1, BA.2), and compared these with the wild-type virus and Delta variant, in human nasal, bronchial and lung tissues cultured ex vivo. FINDINGS: BA.2 replicated more efficiently in nasal and bronchial tissues at 33°C than wild-type, Delta and BA.1. Both BA.2 and BA.1 had higher replication competence than wild-type and Delta viruses in bronchial tissues at 37°C. BA.1, BA.1.1 and BA.2 replicated at a lower level in lung parenchymal tissues compared to wild-type and Delta viruses. INTERPRETATION: Higher replication competence of Omicron BA.2 in the human upper airway at 33°C than BA.1 may be one of the reasons to explain the current advantage of BA.2 over BA.1. A lower replication level of the tested Omicron variants in human lung tissues is in line with the clinical manifestations of decreased disease severity of patients infected with the Omicron strains compared with other ancestral strains. FUNDING: This work was supported by US National Institute of Allergy and Infectious Diseases and the Theme-Based Research Scheme under University Grants Committee of Hong Kong Special Administrative Region, China.


Subject(s)
COVID-19 , SARS-CoV-2 , Bronchi , Humans , SARS-CoV-2/genetics , Viral Tropism , Virus Replication
20.
Emerg Microbes Infect ; 11(1): 2304-2314, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1991970

ABSTRACT

Data regarding protection against mortality and severe complications after Omicron BA.2 infection with CoronaVac and BNT162b2 vaccines remains limited. We conducted a case-control study to evaluate the risk of severe complications and mortality following 1-3 doses of CoronaVac and BNT162b2 using electronic health records database. Cases were adults with their first COVID-19-related mortality or severe complications between 1 January and 31 March 2022, matched with up-to 10 controls by age, sex, index date, and Charlson Comorbidity Index. Vaccine effectiveness against COVID-19-related mortality and severe complications by type and number of doses was estimated using conditional logistic regression adjusted for comorbidities and medications. Vaccine effectiveness (95% CI) against COVID-19-related mortality after two doses of BNT162b2 and CoronaVac were 90.7% (88.6-92.3) and 74.8% (72.5-76.9) in those aged ≥65, 87.6% (81.4-91.8) and 80.7% (72.8-86.3) in those aged 50-64, 86.6% (71.0-93.8) and 82.7% (56.5-93.1) in those aged 18-50. Vaccine effectiveness against severe complications after two doses of BNT162b2 and CoronaVac were 82.1% (74.6-87.3) and 58.9% (50.3-66.1) in those aged ≥65, 83.0% (69.6-90.5) and 67.1% (47.1-79.6) in those aged 50-64, 78.3% (60.8-88.0) and 77.8% (49.6-90.2) in those aged 18-50. Further risk reduction with the third dose was observed especially in those aged ≥65 years, with vaccine effectiveness of 98.0% (96.5-98.9) for BNT162b2 and 95.5% (93.7-96.8) for CoronaVac against mortality, 90.8% (83.4-94.9) and 88.0% (80.8-92.5) against severe complications. Both CoronaVac and BNT162b2 vaccination were effective against COVID-19-related mortality and severe complications amidst the Omicron BA.2 pandemic, and risks decreased further with the third dose.


Subject(s)
BNT162 Vaccine , COVID-19 , Adult , COVID-19/prevention & control , Case-Control Studies , Humans , SARS-CoV-2 , Vaccination
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