Reinfections in COVID-19 Patients: Impact of Virus Genetic Variability and Host Immunity

Safety and efficiency of COVID-19 vaccine in North Africa

Background In the absence of a specific treatment for COVID-19, preventive measures have been implemented to control this pandemic and vaccination is one of them. However, it is crucial to verify the safety and efficiency of every vaccine. The aim was to determinate the predictive factors of side effects and reinfection after COVID-19 vaccine. Methods A cross-sectional study was conducted in February 2022 among Tunisians infected with COVID-19 between March 2020 and February 2022, using an online self-administered questionnaire. We conducted univariate and multivariate analyses using binary stepwise logistic regression. Results A total of 1541 was selected from 1911 individuals. Comorbidities affected a quarter of the population (22.3%). Before the initial infection, 39.3% had received full vaccination, and 8.7% had received partial vaccination. By February 2022, the majority (82.9%) had received at least two vaccine doses. The reinfection rate was 30.6%. All vaccines prior to the first infection was identified as a protective factor against reinfection. Inactivated virus vaccinations were less likely to induce adverse effects. Conclusion ach vaccine has its own set of advantages and disadvantages: mRNA-based vaccines had a higher incidence of side effects but all vaccines provided better protection against reinfection.

Network-based uncertainty quantification for mathematical models in epidemiology

After the new Coronavirus disease (COVID-19) emerged in the end of January 2020 in Germany, a large number of individuals suffered from severe symptoms and eventually needed intensive care in hospitals. Due to the rapid spread of the disease, the number of deceased individuals increased as well, which is a motivation to prevent as many new infections as possible. Therefore, the knowledge about the current evolution of the virus spread is crucial to predict its future behavior and to react with suitable interventions. In this paper, the evolution of the COVID-19 pandemic in Germany is forecasted by a network-based inference method, in which the interactions of individuals are taken into account using a contact matrix. Then the results are compared to the predictions without considering a contact matrix as well as to the logistic regression, which shows the advantage of incorporating the contact matrix. Furthermore, the basic reproduction number of the pandemic in Germany using a neural network approach is estimated and used for further predictions of the evolution of COVID-19 in Germany. In order to mathematically model the different compartments of the population in the considered regions, the classical SIR model is employed. In this work, we deploy the LASSO (Least Absolute Shrinkage and Selection Operator) for the unknown parameter estimation. Furthermore, we calculate and illustrate the MAPE (Mean Absolute Percentage Error) of the estimations to show the accuracy of the predictions. The results include model parameter estimation and model validation, as well as the outbreak forecasting using network-informed algorithms. Our findings show that the network-inference based approach outperforms the logistic regression as well as the neural network approach and the SIR model calibration without a contact network. Furthermore according to the results, the network-inference based approach is particularly suitable for short- to mid-term predictions, even when there is not much information about the new disease. Moreover, the predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing the availability of data, but could not outperform the network-inference based algorithm.

SARS-CoV-2 in an immunocompromised host: convalescent plasma therapy and viral evolution elucidated by whole genome sequencing

The evolution of SARS-CoV-2 within immunocompromised hosts who fail to clear the virus over many months has been proposed as a route to the development of Variants of Concern (VoCs). We present a case of an immunocompromised male patient with a prolonged SARS-CoV-2 infection. During hospitalisation, 7 weeks after first diagnosis, his condition worsened to require continuous ventilation support. Resolution of symptoms was observed after convalescent plasma therapy. Whole genome sequencing of the virus showed Pango lineage B.1.221. Between the first sample and the second from bronchoalveolar lavage fluid 7 weeks later, we identified eight mutations, including minor variants, which could be used to estimate the chronology of mutations. This suggests an elevated mutation rate, in-host accumulation of mutations and further evidence for sources of VoCs. Prolonged SARS-CoV-2 infections in immunocompromised hosts increase the likelihood of hospital stays and morbidity, and also pose an increased risk to global public health.

Assessing Stress and Anxiety in Firefighters During the Coronavirus Disease-2019 Pandemic: A Comparative Adaptation of the Stress and Anxiety in the Viral Epidemic-9 Items and Stress and Anxiety in the Viral Epidemics-6 Items Scales

OBJECTIVE

This study assessed the reliability and validity of the Stress and Anxiety to Viral Epidemics-9 items (SAVE-9) and Stress and Anxiety to Viral Epidemics-6 items (SAVE-6) scales for measuring viral anxiety among firefighters during the coronavirus disease-2019 pandemic.

METHODS

An online survey was conducted among 304 firefighters assigned in Gyeonggi-do. The SAVE-9 scale, initially developed for healthcare workers, was adapted for firefighters. We compared it with the SAVE-6 scale designed for the general population among the firefighters sample. The confirmatory factor analysis (CFA) was conducted to explore the factor structure of both scales. Internal consistency reliability was checked using Cronbach's alpha and McDonald's omega. Convergent validity was assessed in accordance with the Patient Health Questionnaire-9 and Generalized Anxiety Disorder-7 scales.

RESULTS

The SAVE-9 scale demonstrated a Cronbach alpha of 0.880, while the SAVE-6 scale yielded an alpha of 0.874. CFA indicated good model fits for both SAVE-9 and SAVE-6 scales among firefighters sample. The SAVE-9 and SAVE-6 comparably measures viral anxiety of firefighters.

CONCLUSION

Both of the SAVE-9 and SAVE-6 scales are reliable and valid instruments for assessing viral anxiety among firefighters during the pandemic.

Evidence of SARS-CoV-2 reinfection: analysis of 35,000 subjects and overview of systematic reviews

BACKGROUND

Reinfection by SARS-CoV-2 is a rare but possible event. We evaluated the prevalence of reinfections in the Province of Modena and performed an overview of systematic reviews to summarize the current knowledge.

METHODS

We applied big data analysis and retrospectively analysed the results of oro- or naso-pharyngeal swab results tested for molecular research of viral RNA of SARS-CoV-2 between 1 January 2021 and 30 June 2021 at a single center. We selected individuals with samples sequence of positive, negative and then positive results. Between first and second positive result we considered a time interval of 90 days to be sure of a reinfection. We also performed a search for and evaluation of systematic reviews reporting SARS-CoV-2 reinfection rates. Main information was collected and the methodological quality of each review was assessed, according to A Measurement Tool to Assess systematic Reviews (AMSTAR).

RESULTS

Initial positive results were revealed in more than 35,000 (20%) subjects; most (28%) were aged 30-49 years old. Reinfection was reported in 1,258 (3.5%); most (33%) were aged 30-49 years old. Reinfection rates according to vaccinated or non-vaccinated subjects were 0.6% vs 1.1% (p < 0.0001). Nine systematic reviews were identified and confirmed that SARS-CoV-2 reinfection rate is a rare event. AMSTAR revealed very low-moderate levels of quality among selected systematic reviews.

CONCLUSIONS

There is a real, albeit rare risk of SARS-CoV-2 reinfection. Big data analysis enabled accurate estimates of the reinfection rates. Nevertheless, a standardized approach to identify and report reinfection cases should be developed.

Effectiveness of Molnupiravir and Nirmatrelvir-Ritonavir in Hospitalized Patients With COVID-19 : A Target Trial Emulation Study

BACKGROUND

Whether hospitalized patients benefit from COVID-19 oral antivirals is uncertain.

OBJECTIVE

To examine the real-world effectiveness of molnupiravir and nirmatrelvir-ritonavir in hospitalized patients with COVID-19 during the Omicron outbreak.

DESIGN

Target trial emulation study.

SETTING

Electronic health databases in Hong Kong.

PARTICIPANTS

The molnupiravir emulated trial included hospitalized patients with COVID-19 aged 18 years or older between 26 February and 18 July 2022 (n = 16 495). The nirmatrelvir-ritonavir emulated trial included hospitalized patients with COVID-19 aged 18 years or older between 16 March and 18 July 2022 (n = 7119).

INTERVENTION

Initiation of molnupiravir or nirmatrelvir-ritonavir within 5 days of hospitalization with COVID-19 versus no initiation of molnupiravir or nirmatrelvir-ritonavir.

MEASUREMENTS

Effectiveness against all-cause mortality, intensive care unit (ICU) admission, or use of ventilatory support within 28 days.

RESULTS

The use of oral antivirals in hospitalized patients with COVID-19 was associated with a lower risk for all-cause mortality (molnupiravir: hazard ratio [HR], 0.87 [95% CI, 0.81 to 0.93]; nirmatrelvir-ritonavir: HR, 0.77 [CI, 0.66 to 0.90]) but no significant risk reduction in terms of ICU admission (molnupiravir: HR, 1.02 [CI, 0.76 to 1.36]; nirmatrelvir-ritonavir: HR, 1.08 [CI, 0.58 to 2.02]) or the need for ventilatory support (molnupiravir: HR, 1.07 [CI, 0.89 to 1.30]; nirmatrelvir-ritonavir: HR, 1.03 [CI, 0.70 to 1.52]). There was no significant interaction between drug treatment and the number of COVID-19 vaccine doses received, thereby supporting the effectiveness of oral antivirals regardless of vaccination status. No significant interaction between nirmatrelvir-ritonavir treatment and age, sex, or Charlson Comorbidity Index was observed, whereas molnupiravir tended to be more effective in older people.

LIMITATION

The outcome of ICU admission or need for ventilatory support may not capture all severe COVID-19 cases; unmeasured confounders, such as obesity and health behaviors, may exist.

CONCLUSION

Molnupiravir and nirmatrelvir-ritonavir reduced all-cause mortality in both vaccinated and unvaccinated hospitalized patients. No significant reduction in ICU admission or the need for ventilatory support was observed.

PRIMARY FUNDING SOURCE

Health and Medical Research Fund Research on COVID-19, Government of the Hong Kong Special Administrative Region; Research Grants Council, Collaborative Research Fund; and Health Bureau, Government of the Hong Kong Special Administrative Region.

Long-term effects of COVID-19 on lungs and the clinical relevance: a 6-month prospective cohort study

Background: We aimed to explore the prevalence of prolonged symptoms, pulmonary impairments and residual disease on chest tomography (CT) in COVID-19 patients at 6 months after acute illness. Methods: In this prospective, single-center study, hospitalized patients with radiologically and laboratory-confirmed COVID-19 were included. Results: A high proportion of the 116 patients reported persistent symptoms (n = 54; 46.6%). On follow-up CT, 33 patients (28.4%) demonstrated residual disease. Multivariate analyses revealed that only neutrophil-to-lymphocyte ratio was an independent predictor for residual disease. Conclusion: Hospitalized patients with mild/moderate COVID-19 still had persistent symptoms and were prone to develop long-term pulmonary sequelae on chest CT. However, it did not have a significant effect on long-term pulmonary functions.

Post-Vaccine SARS-CoV-2 Reinfection and Associated Factors Among Health Care Providers in Addis Ababa Public Hospitals, Addis Ababa, 2022: A Cross-Sectional Study

Background of the study

The protection against Coronavirus variants 2019 by pre-existing antibodies due to the current vaccination or natural infection is a global concern. In Ethiopia, case reports show that a significant number of health professionals are reported to get re-infected after vaccination. There are also more studies that revealed the symptomatic SARS-COV-2 re-infection, in particular, among healthcare providers actively engaged in Addis Ababa public health facilities.

Objective

This study has aimed at assessing the magnitude of post-vaccine reinfection of SARS-COV-2 and associated factors among health care providers in Addis Ababa public hospitals, Addis Ababa, 2022 G.C.

Methods

A facility-based cross-sectional study was conducted from July 11 to July 30, 2022. A total of 422 health professionals were included. A simple random sampling method was employed to select 40% of the total hospitals. Then the total sample size was equally allocated to each selected hospital, and then each individual was selected purposefully. The data was collected using a structured, self-administered questionnaire. The analysis was done using SPSS version 26.0, and for data entry, EPi Info version 7.1 was used. Both bivariable and multivariable logistic regression analyses were used to determine the p-value.

Results

Overall, 418 healthcare providers were enrolled in this study, making the response rate 99.05%. The magnitude of SARS-COV-2 reinfection was 60 (14.4%) (95% CI 10.8-17.9). Healthcare professionals who took infection prevention (IP) training on COVID-19 (AOR = 7.177: CI = 4.761-9.698) were associated with SARS-COV-2 reinfection; those with a history of chronic respiratory diseases (AOR = 3.029: CI = 2.406-9.133) were associated with SARS-COV-2 reinfection; health professionals who took the third dose of SARS-COV-2 vaccine (AOR = 1.75: CI = 1.14-2.68) and being a midwife were statistically significant.

Conclusion and Recommendation

This study showed the prevalence of SARS-COV-2 reinfection among vaccinated healthcare providers with a pre-vaccination infection history was high; IP training on COVID-19 was needed; educational status, profession, type of vaccine taken in the first dose, chronic respiratory diseases, and number of vaccinations were significantly associated with SARS-COV-2 reinfection after vaccination. Giving IP training, encouraging taking the vaccine as protocol, and using proper personal protective equipment are recommended.

Effects of vaccination, new SARS-CoV-2 variants and reinfections on post-COVID-19 complications

Post-COVID-19 complications involve a variety of long-lasting health complications emerging in various body systems. Since the prevalence of post-COVID-19 complications ranges from 8-47% in COVID-19 survivors, it represents a formidable challenge to COVID-19 survivors and the health care system. Post-COVID-19 complications have already been studied in the connection to risk factors linked to their higher probability of occurrence and higher severity, potential mechanisms underlying the pathogenesis of post-COVID-19 complications, and their functional and structural correlates. Vaccination status has been recently revealed to represent efficient prevention from long-term and severe post-COVID-19 complications. However, the exact mechanisms responsible for vaccine-induced protection against severe and long-lasting post-COVID-19 complications remain elusive. Also, to the best of our knowledge, the effects of new SARS-CoV-2 variants and SARS-CoV-2 reinfections on post-COVID-19 complications and their underlying pathogenesis remain to be investigated. This hypothesis article will be dedicated to the potential effects of vaccination status, SARS-CoV-2 reinfections, and new SARS-CoV-2 variants on post-COVID-19 complications and their underlying mechanisms Also, potential prevention strategies against post-COVID complications will be discussed.

Assessment of the Humoral Immune Response Following COVID-19 Vaccination in Healthcare Workers: A One Year Longitudinal Study

The continuous variability of SARS-CoV-2 and the rapid waning of specific antibodies threatens the efficacy of COVID-19 vaccines. We aimed to evaluate antibody kinetics one year after SARS-CoV-2 vaccination with an mRNA vaccine in healthcare workers (HCW), with or without a booster. A marked decline in anti-Spike(S)/Receptor Binding Domain (RBD) antibody levels was registered during the first eight months post-vaccination, followed by a transitory increase after the booster. At three months post-booster an increased antibody level was maintained only in HCW vaccinated after a prior infection, who also developed a higher and long-lasting level of anti-S IgA antibodies. Still, IgG anti-nucleocapsid (NCP) fades five months post-SARS-CoV-2 infection. Despite the decline in antibodies one-year post-vaccination, 68.2% of HCW preserved the neutralization capacity against the ancestral variant, with a decrease of only 17.08% in the neutralizing capacity against the Omicron variant. Nevertheless, breakthrough infections were present in 6.65% of all participants, without any correlation with the previous level of anti-S/RBD IgG. Protection against the ancestral and Omicron variants is maintained at least three months after a booster in HCW, possibly reflecting a continuous antigenic stimulation in the professional setting.

SARS-CoV-2 reinfections: Overview of efficacy and duration of natural and hybrid immunity

Seroprevalence surveys suggest that more than a third and possibly more than half of the global population has been infected with SARS-CoV-2 by early 2022. As large numbers of people continue to be infected, the efficacy and duration of natural immunity in terms of protection against SARS-CoV-2 reinfections and severe disease is of crucial significance for the future. This narrative review provides an overview on epidemiological studies addressing this issue. National surveys covering 2020-2021 documented that a previous SARS-CoV-2 infection is associated with a significantly reduced risk of reinfections with efficacy lasting for at least one year and only relatively moderate waning immunity. Importantly, natural immunity showed roughly similar effect sizes regarding protection against reinfection across different SARS-CoV-2 variants, with the exception of the Omicron variant for which data are just emerging before final conclusions can be drawn. Risk of hospitalizations and deaths was also reduced in SARS-CoV-2 reinfections versus primary infections. Observational studies indicate that natural immunity may offer equal or greater protection against SARS-CoV-2 infections compared to individuals receiving two doses of an mRNA vaccine, but data are not fully consistent. The combination of a previous SARS-CoV-2 infection and a respective vaccination, termed hybrid immunity, seems to confer the greatest protection against SARS-CoV-2 infections, but several knowledge gaps remain regarding this issue. Natural immunity should be considered for public health policy regarding SARS-CoV-2.

Heterologous immunization with inactivated vaccine followed by mRNA-booster elicits strong immunity against SARS-CoV-2 Omicron variant

The recent emergence of the Omicron variant has raised concerns on vaccine efficacy and the urgent need to study more efficient vaccination strategies. Here we observed that an mRNA vaccine booster in individuals vaccinated with two doses of inactivated vaccine significantly increased the plasma level of specific antibodies that bind to the receptor-binding domain (RBD) or the spike (S) ectodomain (S1 + S2) of both the G614 and the Omicron variants, compared to two doses of homologous inactivated vaccine. The level of RBD- and S-specific IgG antibodies and virus neutralization titers against variants of concern in the heterologous vaccination group were similar to that in individuals receiving three doses of homologous mRNA-vaccine or a boost of mRNA vaccine after infection, but markedly higher than that in individuals receiving three doses of a homologous inactivated vaccine. This heterologous vaccination regime furthermore significantly enhanced the RBD-specific memory B cell response and S1-specific T cell response, compared to two or three doses of homologous inactivated vaccine. Our study demonstrates that mRNA vaccine booster in individuals vaccinated with inactivated vaccines can be highly beneficial, as it markedly increases the humoral and cellular immune responses against the virus, including the Omicron variant.

SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19

The review aims to consolidate research findings on the molecular mechanisms and virulence and pathogenicity characteristics of coronavirus disease (COVID-19) causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and their relevance to four typical stages in the development of acute viral infection. These four stages are invasion; primary blockade of antiviral innate immunity; engagement of the virus's protection mechanisms against the factors of adaptive immunity; and acute, long-term complications of COVID-19. The invasion stage entails the recognition of the spike protein (S) of SARS-CoV-2 target cell receptors, namely, the main receptor (angiotensin-converting enzyme 2, ACE2), its coreceptors, and potential alternative receptors. The presence of a diverse repertoire of receptors allows SARS-CoV-2 to infect various types of cells, including those not expressing ACE2. During the second stage, the majority of the polyfunctional structural, non-structural, and extra proteins SARS-CoV-2 synthesizes in infected cells are involved in the primary blockage of antiviral innate immunity. A high degree of redundancy and systemic action characterizing these pathogenic factors allows SARS-CoV-2 to overcome antiviral mechanisms at the initial stages of invasion. The third stage includes passive and active protection of the virus from factors of adaptive immunity, overcoming of the barrier function at the focus of inflammation, and generalization of SARS-CoV-2 in the body. The fourth stage is associated with the deployment of variants of acute and long-term complications of COVID-19. SARS-CoV-2's ability to induce autoimmune and autoinflammatory pathways of tissue invasion and development of both immunosuppressive and hyperergic mechanisms of systemic inflammation is critical at this stage of infection.

SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review

Background: From the start of the COVID-19 pandemic, new SARS-CoV-2 variants have emerged that potentially affect transmissibility, severity, and immune evasion in infected individuals. In the present systematic review, the impact of different SARS-CoV-2 variants on clinical outcomes is analyzed. Methods: A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020. Two databases (PubMed and ScienceDirect) were searched for original articles published from 1 January 2020 to 23 November 2021. The articles that met the selection criteria were appraised according to the Newcastle–Ottawa Quality Assessment Scale. Results: Thirty-three articles were included, involving a total of 253,209 patients and 188,944 partial or complete SARS-CoV-2 sequences. The most reported SARS-CoV-2 variants showed changes in the spike protein, N protein, RdRp and NSP3. In 28 scenarios, SARS-CoV-2 variants were found to be associated with a mild to severe or even fatal clinical outcome, 15 articles reported such association to be statistically significant. Adjustments in eight of them were made for age, sex and other covariates. Conclusions: SARS-CoV-2 variants can potentially have an impact on clinical outcomes; future studies focused on this topic should consider several covariates that influence the clinical course of the disease.

Evaluation of disease severity during SARS-COV-2 reinfection, January 2020 to April 2021, England: an observational study

Objective

We aimed to look at the burden of disease caused by SARS-COV-2 reinfections and identified potential risk factors for disease severity.

Methods

We used national surveillance data to collect information on all SARS-CoV-2 primary infection and suspected reinfection cases between January 2020 until early May 2021. Reinfection cases were positive COVID-19 PCR or antigen test, 90 days after their first COVID-19 positive test. We collected information on case demographics, hospital and ICU admission, immunisation status and if individuals were at risk of complication for COVID-19.

Results

Deaths reported within 28 days of testing positive were 61% (95% confidence interval: 56% to 65%) lower in suspected COVID-19 reinfection than primary infection cases. In the unvaccinated cohort, reinfections were associated with 49% (37% to 58%) lower odds of hospital admission in cases aged 50 to 65 years in the population not identified at risk of complication for COVID-19, and 34% (17% to 48%) in those at risk. ICU admission at reinfection compared to primary infection decreased 76% (55% to 87%). Individuals at risk and those aged below 50 years, who received at least 1 dose of vaccine against COVID-19, were 62% (39% to 74%) and 58% (24% to 77%) less likely to get admitted to hospital at reinfection, respectively.

Conclusion

Prior SARS-CoV-2 infection was associated with lower odds of dying, and both prior infection and immunisation showed a protective effect against severe disease in selected populations. Older age, sex and underlying comorbidities appeared as principal risk factors for illness severity at reinfection.

Funding

PHE/UKHSA