Genomic evidence for reinfection with SARS-CoV-2: a case study

The immunopathogenesis of SARS-CoV-2 infection: Overview of lessons learned in the first 5 years

This review provides a broad overview of lessons learned in the five years since COVID-19 was identified. It is a bimodal disease, starting with an initially virus-driven phase, followed by resolution or ensuing inappropriate immune activation causing severe inflammation that is no longer strictly virus dependent. Humoral immunity is beneficial for preventing or attenuating the early stage, without benefit once the later stage begins. Neutralizing antibodies elicited by natural infection or vaccination are short-lived and highly vulnerable to viral sequence variation. By contrast, cellular immunity, particularly the CD8+ T cell arm, has a role in preventing or attenuating severe disease, is far less susceptible to viral variation, and is longer-lived than antibodies. Finally, an ill-defined phenomenon of prolonged symptoms after acute infection, termed "long COVID," is poorly understood but may involve various immunologic defects that are hyperactivating or immunosuppressive. Remaining issues include needing to better understand the immune dysregulation of severe disease to allow more tailored therapeutic interventions, developing antibody strategies that cope with the viral spike sequence variability, prolonging vaccine efficacy, and unraveling the mechanisms of long COVID to design therapeutic approaches.

Repeated detection of SARS-CoV-2 in pet dogs in Ibadan, Oyo State, Nigeria: a cause for vigilance

BACKGROUND

The COVID-19 pandemic of 2020 was unprecedented in its devastating impact on the global economy, public health, travel and tourism, education, sports, religion, and social lives. Studies conducted thereafter on the disease and its causative agent, SARS-CoV-2, have highlighted the need for effective and sustainable public health interventions.

METHODS

This study investigated the prevalence and endemicity of SARS-CoV-2 infection in pet dogs using immunochromatography assay (IC) and quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) of their blood, rectal swabs, and nasal swabs in Ibadan, Oyo State, Nigeria between 2022 and 2024.

KEY FINDINGS

For the IC, positivity rates of 11.7% (23/197), 85.7% (6/7), and 100% (3/3) were recorded for 2022, 2023 and 2024 while for the RT-qPCR, positivity rates of 37.9% (11/29), 33.3% (2/6) and 100% (3/3) were recorded for 2022, 2023 and 2024. This repeated detection of SARS-CoV-2 in three of the dogs tested over the three-year period suggests continuous shedding of the virus by these animals and indicates endemicity of the virus in the study area. Findings highlight the urgent need for optimized SARS-CoV-2 rapid diagnostic tools tailored for veterinary applications to ensure rapid and reliable detection of the virus, especially in resource-constrained settings.

CONCLUSION

Considering the zoonotic nature of SARS-CoV-2 and its potential for mutation into more virulent strains that can be transmissible to humans, the findings of this study have significant implications for public health and implementation of One Health strategies by policymakers, and highlight the need for robust SARS-CoV-2 surveillance in domestic animals to mitigate potential zoonotic risks.

Antibodies response in symptomatic and asymptomatic SARS-CoV-2 infected persons in Thailand

Antibody assays of IgM, IgG and surrogate isotype independent virus neutralizing antibody (sVNT) targeting receptor binding domain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) were employed in 97 real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR) confirmed Coronavirus Disease 2019 (COVID-19) patients with varying severity admitted to King Chulalongkorn Memorial Hospital. Concordance rate was 100% regardless of severity, onset of symptoms and magnitude of viral load. Per available samples, antibodies appeared on the same day of symptom onset in one patient; one day after in 18 patients and two days after in 19 patients. In two patients, antibodies appeared as early as 4 days after infection (exposure). IgM and IgG were evident in all patients' first assay (within two days of admission). sVNT was also evident within two days of admission in all but 3 patients. IgM usually remained positive during the entire course of hospital stay, where the longest in this study was 32 days. Antibody assays were also applied to samples collected at a State Quarantine premise from 77 asymptomatic Thais returning from Sudan in October. Virus was detected by real-time RT-PCR in 15 cases (day 0 = 6, day 3 = 4, day 5 = 4 and day 9 = 1). Twenty-nine (including 11 RT-PCR positive cases) were antibody positive on day 0, while 4 PCR positive with antibody negative on day 0 became antibody positive on day 14. Evaluation on antibody response at days 7 or 10 is needed to help build a case to shorten length of quarantine among negative cases.

COVID-19 breakthrough infections in vaccinated individuals at BPKIHS, Nepal

BACKGROUND

Although there have been reports of COVID-19 breakthrough infections in vaccinated individuals, the vaccines have demonstrated a high efficacy in preventing severe illness and death. Nepal has reported fewer studies of COVID-19 breakthrough infections. Hence, this study has objective to assess the prevalence, and to describe clinical characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) breakthrough infection.

METHODS

This descriptive study was conducted from January to December 2022. The study enrolled 200 individuals who had received the recommended doses of the COVID-19 vaccine and they were RT-PCR positive diagnosed with vaccine breakthrough infections after 14 days of completing the vaccination course. The patient's demographic and clinical profiles, as well as their outcomes in terms of severity, length of hospital stay, and mortality were recorded.

RESULTS

The prevalence of SARS-CoV2 infection was 6.3% (547/8682). Among fully vaccinated personnel, the prevalence of breakthrough infections was 6.2% (200/3175). This study found the Omicron variants in respondents. The mean age of the patients was 38.28 years, and 41.5% (83/200) of the breakthrough cases were healthcare workers. The mean time gap between the second dose of vaccination and a positive RT-PCR test was 354.68 days. Of the 200 breakthrough cases, 89% (178) had mild symptoms, 9% (17) had moderate symptoms requiring hospitalization, and 2% (4) were severe cases that required intensive care facility. Among the severe cases, 3 out 4 were above 60 years old. Furthermore, the patients greater than 60 years had longer hospital stays (p < 0.0001) however no deaths were recorded.

CONCLUSION

Fully vaccinated individuals can experience COVID-19 breakthrough infections and the majority of cases present with mild symptoms. Elderly patients have a higher likelihood of severe disease and longer hospital stay compared to younger patients. The results of this study emphasize the importance of vaccination in mitigating the severity of the disease.

From intramuscular to nasal: unleashing the potential of nasal spray vaccines against coronavirus disease 2019

Coronavirus disease 2019, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected 700 million people worldwide since its outbreak in 2019. The current pandemic strains, including Omicron and its large subvariant series, exhibit strong transmission and stealth. After entering the human body, the virus first infects nasal epithelial cells and invades host cells through the angiotensin-converting enzyme 2 receptor and transmembrane serine protease 2 on the host cell surface. The nasal cavity is an important body part that protects against the virus. Immunisation of the nasal mucosa produces immunoglobulin A antibodies that effectively neutralise viruses. Saline nasal irrigation, a type of physical therapy, can reduce the viral load in the nasal cavity and prevent viral infections to some extent. As a commonly used means to fight SARS-CoV-2, the intramuscular (IM) vaccine can induce the human body to produce a systemic immune response and immunoglobulin G antibody; however, the antibody is difficult to distribute to the nasal mucosa in time and cannot achieve a good preventive effect. Intranasal (IN) vaccines compensate for the shortcomings of IM vaccines, induce mucosal immune responses, and have a better effect in preventing infection. In this review, we discuss the nasal defence barrier, the harm caused by SARS-CoV-2, the mechanism of its invasion into host cells, nasal cleaning, IM vaccines and IN vaccines, and suggest increasing the development of IN vaccines, and use of IN vaccines as a supplement to IM vaccines.

Investigation of epidemiological and clinical characteristics of people infected with SARS-CoV-2 during the second pandemic of COVID-19 in Chengdu, China

Objective

This study investigated the epidemiological and clinical characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infected patients during the second pandemic of COVID-19 (coronavirus disease of 2019) in Chengdu, China. Furthermore, the differences between first infection and re-infection cases were also compared and analyzed to provide evidence for better prevention and control of SARS-CoV-2 re-infection.

Methods

An anonymous questionnaire survey was conducted using an online platform (wjx.cn) between May 20, 2023 to September 12, 2023.

Results

This investigation included 62.94% females and 32.97% of them were 18-30 years old. Furthermore, 7.19-17.18% of the participants either did not receive vaccination at all or only received full vaccination, respectively. Moreover, 577 (57.64%) participants were exposed to cluster infection. The clinical manifestations of these patients were mainly mild to moderate; 78.18% of participants had a fever for 1-3 days, while 37.84% indicated a full course of disease for 4-6 days. In addition, 40.66% of the participants had re-infection and 72.97% indicated their first infection approximately five months before. The clinical symptoms of the first SARS-CoV-2 infection were moderate to severe, while re-infection indicated mild to moderate symptoms (the severity of symptoms other than diarrhea and conjunctival congestion had statistically significant differences) (p < 0.05). Moreover, 70.53 and 59.21% of first and re-infection cases had fever durations of 3-5 and 0-2 days, respectively. Whereas 47.91 and 46.40% of first and re-infection cases had a disease course of 7-9 and 4-6 days.

Conclusion

The SARS-CoV-2 infected individuals in Chengdu, China, during the second pandemic of COVID-19 had mild clinical symptoms and a short course of disease. Furthermore, compared with the first infection, re-infection cases had mild symptoms, low incidences of complications, short fever duration, and course of disease.

High Post-Infection Protection after COVID-19 among Healthcare Workers: A Population-Level Observational Study

Background

Even though a few years have passed since the coronavirus disease 2019 (COVID-19) outbreak, information regarding certain aspects of the disease, such as post-infection immunity, is still quite limited. This study aimed to evaluate post-infection protection and COVID-19 features among healthcare workers (HCWs), during three successive surges, as well as the rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection, reactivation, re-positivity, and severity.

Methods

This cross-sectional population-level observational study was conducted from 20 April 2020 to 18 February 2021. The study population included all HCWs in public or private hospitals in Fars Province, Southern Iran. The infection rate was computed as the number of individuals with positive polymerase chain reaction (PCR) tests divided by the total number of person-days at risk. The re-infection was evaluated after 90 days.

Results

A total of 30,546 PCR tests were performed among HCWs, of which 13,749 (61.94% of total HCWs) were positive. Considering the applied 90-day threshold, there were 44 (31.2%) cases of reactivation and relapse, and 97 (68.8% of infected and 1.81% of total HCWs) cases of reinfection among 141 (2.64%) diagnosed cases who experienced a second episode of COVID-19. There was no significant difference in symptoms (P=0.65) or the necessity for ICU admission (P=0.25). The estimated protection against repeated infection after a previous SARS-CoV-2 infection was 94.8% (95% CI=93.6-95.7).

Conclusion

SARS-CoV-2 re-positivity, relapse, and reinfection were rare in the HCW population. After the first episode of infection, an estimated 94.8% protection against recurring infections was achieved. A preprint version of this manuscript is available at DOI:10.21203/rs.3.rs-772662/v1 (https://www.researchsquare.com/article/rs-772662/v1).

COVID-19 reinfections in Mexico City: implications for public health

Background

Since its appearance, COVID-19 has immensely impacted our society. Public health measures, from the initial lockdowns to vaccination campaigns, have mitigated the crisis. However, SARS-CoV-2's persistence and evolving variants continue to pose global threats, increasing the risk of reinfections. Despite vaccination progress, understanding reinfections remains crucial for informed public health responses.

Methods

We collected available data on clinical and genomic information for SARS-CoV-2 samples from patients treated in Mexico City from 2020 epidemiological week 10 to 2023 epidemiological week 06 encompassing the whole public health emergency's period. To identify clinical data we utilized the SISVER (Respiratory Disease Epidemiological Surveillance System) database for SARS-CoV-2 patients who received medical attention in Mexico City. For genomic surveillance we analyzed genomic data previously uploaded to GISAID generated by Mexican institutions. We used these data sources to generate descriptors of case number, hospitalization, death and reinfection rates, and viral variant prevalence throughout the pandemic period.

Findings

The fraction of reinfected individuals in the COVID-19 infected population steadily increased as the pandemic progressed in Mexico City. Most reinfections occurred during the fifth wave (40%). This wave was characterized by the coexistence of multiple variants exceeding 80% prevalence; whereas all other waves showed a unique characteristic dominant variant (prevalence >95%). Shifts in symptom patient care type and severity were observed, 2.53% transitioned from hospitalized to ambulatory care type during reinfection and 0.597% showed the opposite behavior; also 7.23% showed a reduction in severity of symptoms and 6.05% displayed an increase in severity. Unvaccinated individuals accounted for the highest percentage of reinfections (41.6%), followed by vaccinated individuals (31.9%). Most reinfections occurred after the fourth wave, dominated by the Omicron variant; and after the vaccination campaign was already underway.

Interpretation

Our analysis suggests reduced infection severity in reinfections, evident through shifts in symptom severity and care patterns. Unvaccinated individuals accounted for most reinfections. While our study centers on Mexico City, its findings may hold implications for broader regions, contributing insights into reinfection dynamics.

Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population

SARS-CoV-2 reinfections increased substantially after Omicron variants emerged. Large-scale community-based comparisons across multiple Omicron waves of reinfection characteristics, risk factors, and protection afforded by previous infection and vaccination, are limited. Here we studied ~45,000 reinfections from the UK's national COVID-19 Infection Survey and quantified the risk of reinfection in multiple waves, including those driven by BA.1, BA.2, BA.4/5, and BQ.1/CH.1.1/XBB.1.5 variants. Reinfections were associated with lower viral load and lower percentages of self-reporting symptoms compared with first infections. Across multiple Omicron waves, estimated protection against reinfection was significantly higher in those previously infected with more recent than earlier variants, even at the same time from previous infection. Estimated protection against Omicron reinfections decreased over time from the most recent infection if this was the previous or penultimate variant (generally within the preceding year). Those 14-180 days after receiving their most recent vaccination had a lower risk of reinfection than those >180 days from their most recent vaccination. Reinfection risk was independently higher in those aged 30-45 years, and with either low or high viral load in their most recent previous infection. Overall, the risk of Omicron reinfection is high, but with lower severity than first infections; both viral evolution and waning immunity are independently associated with reinfection.

Using SARS-CoV-2 Sequencing Data to Identify Reinfection Cases in the Global Emerging Infections Surveillance Program, United States

The Centers for Disease Control and Prevention defines SARS-CoV-2 reinfection as a positive COVID-19 test result >90 days after the collection date for the initial positive test or if sequencing confirms a different lineage is causing the reinfection. Reinfection dynamics have been examined by using PCR or antigen surveillance data. We identified patients in the US Military Health System who had >1 positive SARS-CoV-2 test during March 2020-July 2022 by using whole-genome sequencing data to identify reinfection cases, then compared those data with patient demographics, symptoms, and vaccination status. We identified 267 reinfections, of which 90% were caused by the SARS-CoV-2 Omicron variant. Reinfection symptom severity correlated with initial symptom severity and time since first infection. Furthermore, we found intrahost mutation rates varied greatly in 72 cases of continuing infections with the same variant. Continued investigations of reinfections caused by emerging SARS-CoV-2 variants of concern is needed to maintain US military readiness.

SARS-CoV-2 Reinfection Cases in a Household-Based Prospective Cohort in Rio de Janeiro

This was a household-based prospective cohort study conducted in Rio de Janeiro, in which people with laboratory-confirmed coronavirus disease 2019 (COVID-19) and their household contacts were followed from April 2020 through June 2022. Ninety-eight reinfections were identified, with 71 (72.5%) confirmed by genomic analyses and lineage definition in both infections. During the pre-Omicron period, 1 dose of any COVID-19 vaccine was associated with a reduced risk of reinfection, but during the Omicron period not even booster vaccines had this effect. Most reinfections were asymptomatic or milder in comparison with primary infections, a justification for continuing active surveillance to detect infections in vaccinated individuals. Our findings demonstrated that vaccination may not prevent infection or reinfection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). Therefore we highlight the need to continuously update the antigenic target of SARS CoV-2 vaccines and administer booster doses to the population regularly, a strategy well established in the development of vaccines for influenza immunization programs.

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.

Risk Factors Contributing to Reinfection by SARS-CoV-2: A Systematic Review

This article aims to systematize the evidence regarding risk factors associated with COVID-19 reinfection. We conducted a systematic review of all the scientific publications available until August 2022. To ensure the inclusion of the most recent and relevant information, we searched the PubMed and Scopus databases. Thirty studies were reviewed, with a significant proportion being analytical observational case-control and cohort studies. Upon qualitative analysis of the available evidence, it appears that the probability of reinfection is higher for individuals who are not fully immunized when exposed to a new variant, females, those with pre-existing chronic diseases, individuals aged over 60, and those who have previously experienced severe symptoms of the disease or are immunocompromised. In conclusion, further analytical observational case-control studies are necessary to gain a better understanding of the risk factors associated with SARS-CoV-2 (COVID-19) reinfection.

Risk factors and outcomes for repeat COVID-19 infection among patients with systemic autoimmune rheumatic diseases: A case-control study

OBJECTIVE

To investigate risk factors and outcomes of repeat COVID-19 infections among patients with systemic autoimmune rheumatic diseases (SARDs).

METHODS

We performed a case-control study investigating repeat COVID-19 infection within the Mass General Brigham Health Care System. We systematically identified all SARD patients with confirmed COVID-19 (15/Mar/2020 to 17/Oct/2022). Cases had confirmed repeat COVID-19 infections >60 days apart (index date: repeat COVID-19 date). Controls were matched to cases (up to 3:1) by calendar date of first infection and duration between first COVID-19 infection and index dates. We collected demographics, lifestyle, comorbidities, SARD features, and COVID-19 characteristics at initial infection and index date by medical record review. We used conditional logistic regression to identify associations with repeat COVID-19 infection, adjusting for potential confounders. We described the severity of repeat COVID-19 infection among cases.

RESULTS

Among 2203 SARD patients with COVID-19, we identified 76 cases with repeat COVID-19 infection (80.3 % female) and matched to 207 matched controls (77.8 % female) with no repeat infection. At first infection, cases were younger (mean 49.5 vs. 60.3 years, p < 0.0001), less likely to have hypertension (32.9 % vs. 45.9 %, p = 0.050), and less likely to have been hospitalized for COVID-19 (13.2 % vs. 24.6 %, p = 0.037) than controls. At index date, cases were more likely than controls to be rituximab users (18.4 % vs. 6.3 %, p = 0.0021). In the multivariable model, younger age (OR 0.67 per 10 years, 95 %CI 0.54-0.82), rituximab use vs. non-use (OR 3.38, 95 %CI 1.26-9.08), and methotrexate use vs. non-use (OR 2.24, 95 %CI 1.08-4.61) were each associated with repeat COVID-19 infection. Among those with repeat COVID-19 infection, 5/76 (6.6 %) were hospitalized and there were no deaths.

CONCLUSION

Younger age, rituximab, and methotrexate were each associated with repeat COVID-19 infection risk among patients with SARDs. Reassuringly, there were no deaths, and the hospitalization rate was low among those with repeat COVID-19 infection.

Characterization of Pharmacokinetics, Biotransformation and Elimination of Pomotrelvir Orally Administered in Healthy Male Adults Using Two [14C]-Labeled Microtracers with Separate Labeling Positions

Pomotrelvir is an orally bioavailable, target antiviral inhibitor of the main protease (Mpro) of coronaviruses, including severe acute respiratory syndrome coronavirus 2, the etiological agent of Coronavirus Disease 2019. The pharmacokinetics, metabolism and elimination of two [14C]-labeled microtracers of 5 µCi/700 mg pomotrelvir with separate labeling positions (isotopomers), [lactam carbonyl-14C-pomotelvir] and [benzene ring-U-14C-pomotrelvir], following a single oral dose in healthy adult males was evaluated in two separate cohorts. Pomotrelvir was rapidly absorbed and eliminated primarily through metabolism and subsequently excreted via urine and feces. There were no differences in pomotrelvir pharmacokinetics between the two cohorts. The mean total radioactive dose recovered was 93.8% (n = 8) in the lactam cohort (58% in urine and 36% in feces) and 94.2% (n = 8) in the benzene cohort (75% in urine and 19% in feces), with ≥80% of [14C] recovered within 96 hours after dosing. About 5% and 3% of the intact pomotrelvir was recovered in feces and urine, respectively. Eleven major metabolites were detected and characterized using liquid chromatography-accelerator mass spectrometry and liquid chromatography tandem mass spectrometry methods, with three and six different metabolites elucidated in the samples collected from lactam and benzene cohorts, respectively, and two metabolites observed in both cohorts. The major metabolism pathway of pomotrelvir is through hydrolysis of its peptide bonds followed by phase II conjugations. These results support that the application of two radiolabeled isotopomers provided a comprehensive metabolite profiling analysis and was a successful approach in identifying the major disposition pathways of pomotrelvir that has complex routes of metabolism. SIGNIFICANCE STATEMENT: An unconventional approach using two differentially labeled [14C] microtracers, [lactam carbonyl-14C-pomotrelvir] and [benzene ring-U-14C-pomotrelvir] evaluated the mass balance of orally administered pomotrelvir in healthy adult males in two separate cohorts. The radioactive dose recovered in excreta was about 94% for both cohorts. While the two isotopomers of the radiolabeled-pomotrelvir showed no major differences in pharmacokinetics overall, they allowed for differential detection of their radiolabeled metabolites and appropriate characterization of their plasma exposure and excretion in urine and feces.

Lessons identified for a future pandemic

Pandemics are complex events requiring a coordinated, global response. The response to the pandemic exposed vulnerabilities in system preparedness. Lessons arising from the COVID-19 pandemic are characterized by four broad themes: (i) investment in public health and health infrastructure, (ii) countermeasures (medical and non-medical), (iii) risk communication and public health measures and (iv) investment in people and partnerships. Learning from the COVID-19 pandemic identifies an approach that focusses on capacities and capabilities that are pathogen agnostic, ensuring that we can respond to diverse emerging infectious disease threats will be essential. The lessons learned from previous and ongoing infectious disease outbreaks should be kept under constant review, in line with technological and scientific advances, to improve our ability to detect, mitigate and respond to new and emerging threats.

How immune breakthroughs could slow disease progression and improve prognosis in COVID-19 patients: a retrospective study

BACKGROUND

Previous infections and vaccinations have produced preexisting immunity, which differs from primary infection in the organism immune response and may lead to different disease severities and prognoses when reinfected.

OBJECTIVES

The purpose of this retrospective cohort study was to investigate the impact of immune breakthroughs on disease progression and prognosis in patients with COVID-19.

METHODS

A retrospective cohort study was conducted on 1513 COVID-19 patients in Chengdu Public Health Clinical Medical Center from January 2020 to November 2022. All patients were divided into the no immunity group (primary infection and unvaccinated, n=1102) and the immune breakthrough group (previous infection or vaccination, n=411). The immune breakthrough group was further divided into the natural immunity subgroup (n=73), the acquired immunity subgroup (n=322) and the mixed immunity subgroup (n=16). The differences in clinical and outcome data and T lymphocyte subsets and antibody levels between two groups or between three subgroups were compared by ANOVA, t test and chi-square test, and the relationship between T lymphocyte subsets and antibody levels and the disease progression and prognosis of COVID-19 patients was assessed by univariate analysis and logistic regression analysis.

RESULTS

The total critical rate and the total mortality rate were 2.11% and 0.53%, respectively. The immune breakthrough rate was 27.16%. In the no immunity group, the critical rate and the mortality rate were all higher, and the coronavirus negative conversion time was longer than those in the immune breakthrough group. The differences in the critical rate and the coronavirus negative conversion time between the two groups were all statistically significant (3.72% vs. 0.24%, 14.17 vs. 11.90 days, all p<0.001). In addition, in the no immunity group, although lymphocyte counts and T subsets at admission were higher, all of them decreased consistently and significantly and were significantly lower than those in the immune breakthrough group at the same time from the first week to the fourth week after admission (all p<0.01). The total antibody levels and specific Immunoglobulin G (IgG) levels increased gradually and were always significantly lower than those in the immune breakthrough group at the same time from admission to the fourth week after admission (all p<0.001). Moreover, in the natural immunity subgroup, lymphocyte counts and T subsets at admission were the highest, and total antibody levels and specific IgG levels at admission were the lowest. Then, all of them decreased significantly and were the lowest among the three subgroups at the same time from admission to one month after admission (total antibody: from 546.07 to 158.89, IgG: from 6.00 to 3.95) (all p<0.001). Those in the mixed immunity subgroup were followed by those in the acquired immunity subgroup. While lymphocyte counts and T subsets in these two subgroups and total antibody levels (from 830.84 to 1008.21) and specific IgG levels (from 6.23 to 7.51) in the acquired immunity subgroup increased gradually, total antibody levels (from 1100.82 to 908.58) and specific IgG levels (from 7.14 to 6.58) in the mixed immunity subgroup decreased gradually. Furthermore, T lymphocyte subsets and antibody levels were negatively related to disease severity, prognosis and coronavirus negative conversion time. The total antibody, specific IgM and IgG levels showed good utility for predicting critical COVID-19 patients and dead COVID-19 patients.

CONCLUSION

Among patients with COVID-19 patients, immune breakthroughs resulting from previous infection or vaccination, could decelerate disease progression and enhance prognosis by expediting host cellular and humoral immunity to accelerate virus clearance, especially in individuals who have been vaccinated and previously infected.

CLINICAL TRIAL REGISTRY

Chinese Clinical Trial Register ChiCTR2000034563.

De novo design of a stapled peptide targeting SARS-CoV-2 spike protein receptor-binding domain

Although effective vaccines have been developed against SARS-CoV-2, many regions in the world still have low rates of vaccination and new variants with mutations in the viral spike protein have reduced the effectiveness of most available vaccines and treatments. There is an urgent need for a drug to cure this disease and prevent infection. The SARS-CoV-2 virus enters the host cell through protein-protein interaction between the virus's spike protein and the host's angiotensin converting enzyme (ACE2). Using protein design software and molecular dynamics simulations, we have designed a 17-residue peptide (pep39), that binds to the spike protein receptor-binding domain (RBD) and blocks interaction of spike protein with ACE2. We have confirmed the binding activity of the designed peptide for the original spike protein and the delta variant spike protein using micro-cantilever and bio-layer interferometry (BLI) based methods. We also confirmed that pep39 strongly inhibits SARS-CoV-2 virus replication in Vero E6 cells. Taken together these data suggest that a newly designed spike protein RBD blocking peptide pep39 has a potential as a SARS-CoV-2 virus inhibitor.

Remdesivir administration for SARS-CoV-2 pneumonia in ICU and non-ICU patients: outcome and posttreatment differences - the Italian Military Hospital experience

BACKGROUND

Four-hundred forty-nine patients affected by Covid-19 were hospitalized at the Rome Military Hospital between March 2020 and July 2022. Depending on the severity of the disease, they were assigned either to the Functional Health Emergency Unit - if suffering from interstitial pneumonia with a clinical manifestation of dyspnea associated with peripheral oxygen saturation  < 92%, and oxygen atmospheric pressure therapy - or to the intensive care unit - if the blood gas-lytic index P/F (ratio between partial pressure of arterial O2 and inspired fraction of O2) was below 150. This prospective observation and monocentric study aim to verify the outcome (healing/death) of early use of remdesivir in pneumonia patients.

RESULTS

The results highlight the importance of the adoption of remdesivir in the initial stages of infection to prevent the systemic spread and viral multiplication and, in the subsequent phase, a cytokine storm resulting in acute respiratory failure and multiorgan failure. The use of the drug in the most advanced stages of the disease is not associated with a real impact on patient outcomes. Therefore, there is a statistically significant correspondence between the early use of remdesivir in the treatment of SARS-CoV-2 disease - in addition to guidelines therapies - and a favorable clinical outcome.

CONCLUSIONS

This work shows therapeutic efficacy in the first 5 days of intravenous administration of remdesivir, following the loading dose. It is also necessary to underline the different behaviors of the drug when administered late in patients undergoing mechanical ventilation, compared to those who only needed low-flow oxygen therapy, whose share of recovery - decidedly relevant - reaches statistical significance.

A Mechanical Assay for the Quantification of Anti-RBD IgG Levels in Finger-Prick Whole Blood

A large portion of the global population has been vaccinated with various vaccines or infected with SARS-CoV-2, the virus that causes COVID-19. The resulting IgG antibodies that target the receptor binding domain (RBD) of SARS-CoV-2 play a vital role in reducing infection rates and severe disease outcomes. Different immune histories result in the production of anti-RBD IgG antibodies with different binding affinities to RBDs of different variants, and the levels of these antibodies decrease over time. Therefore, it is important to have a low-cost, rapid method for quantifying the levels of anti-RBD IgG in decentralized testing for large populations. In this study, we describe a 30 min assay that allows for the quantification of anti-RBD IgG levels in a single drop of finger-prick whole blood. This assay uses force-dependent dissociation of nonspecifically absorbed RBD-coated superparamagnetic microbeads to determine the density of specifically linked microbeads to a protein A-coated transparent surface through anti-RBD IgGs, which can be measured using a simple light microscope and a low-magnification lens. The titer of serially diluted anti-RBD IgGs can be determined without any additional sample processing steps. The limit of detection for this assay is 0.7 ± 0.1 ng/mL referenced to the CR3022 anti-RBD IgG. The limits of the technology and its potential to be further developed to meet the need for point-of-care monitoring of immune protection status are discussed.

Evidence of leaky protection following COVID-19 vaccination and SARS-CoV-2 infection in an incarcerated population

Whether SARS-CoV-2 infection and COVID-19 vaccines confer exposure-dependent ("leaky") protection against infection remains unknown. We examined the effect of prior infection, vaccination, and hybrid immunity on infection risk among residents of Connecticut correctional facilities during periods of predominant Omicron and Delta transmission. Residents with cell, cellblock, and no documented exposure to SARS-CoV-2 infected residents were matched by facility and date. During the Omicron period, prior infection, vaccination, and hybrid immunity reduced the infection risk of residents without a documented exposure (HR: 0.36 [0.25-0.54]; 0.57 [0.42-0.78]; 0.24 [0.15-0.39]; respectively) and with cellblock exposures (0.61 [0.49-0.75]; 0.69 [0.58-0.83]; 0.41 [0.31-0.55]; respectively) but not with cell exposures (0.89 [0.58-1.35]; 0.96 [0.64-1.46]; 0.80 [0.46-1.39]; respectively). Associations were similar during the Delta period and when analyses were restricted to tested residents. Although associations may not have been thoroughly adjusted due to dataset limitations, the findings suggest that prior infection and vaccination may be leaky, highlighting the potential benefits of pairing vaccination with non-pharmaceutical interventions in crowded settings.

SIRSi-vaccine dynamical model for the Covid-19 pandemic

Covid-19, caused by severe acute respiratory syndrome coronavirus 2, broke out as a pandemic during the beginning of 2020. The rapid spread of the disease prompted an unprecedented global response involving academic institutions, regulatory agencies, and industries. Vaccination and nonpharmaceutical interventions including social distancing have proven to be the most effective strategies to combat the pandemic. In this context, it is crucial to understand the dynamic behavior of the Covid-19 spread together with possible vaccination strategies. In this study, a susceptible-infected-removed-sick model with vaccination (SIRSi-vaccine) was proposed, accounting for the unreported yet infectious. The model considered the possibility of temporary immunity following infection or vaccination. Both situations contribute toward the spread of diseases. The transcritical bifurcation diagram of alternating and mutually exclusive stabilities for both disease-free and endemic equilibria were determined in the parameter space of vaccination rate and isolation index. The existing equilibrium conditions for both points were determined in terms of the epidemiological parameters of the model. The bifurcation diagram allowed us to estimate the maximum number of confirmed cases expected for each set of parameters. The model was fitted with data from São Paulo, the state capital of SP, Brazil, which describes the number of confirmed infected cases and the isolation index for the considered data window. Furthermore, simulation results demonstrate the possibility of periodic undamped oscillatory behavior of the susceptible population and the number of confirmed cases forced by the periodic small-amplitude oscillations in the isolation index. The main contributions of the proposed model are as follows: A minimum effort was required when vaccination was combined with social isolation, while additionally ensuring the existence of equilibrium points. The model could provide valuable information for policymakers, helping define disease prevention mitigation strategies that combine vaccination and non-pharmaceutical interventions, such as social distancing and the use of masks. In addition, the SIRSi-vaccine model facilitated the qualitative assessment of information regarding the unreported infected yet infectious cases, while considering temporary immunity, vaccination, and social isolation index.

SARS-CoV-2-specific T cell responses wane profoundly in convalescent individuals 10 months after primary infection

A key question in the coronavirus disease 2019 (COVID-19) pandemic is the duration of specific T cell responses against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) post primary infection, which is difficult to address due to the large-scale COVID-19 vaccination and re-exposure to the virus. Here, we conducted an analysis of the long-term SARS-CoV-2-specific T cell responses in a unique cohort of convalescent individuals (CIs) that were among the first to be infected worldwide and without any possible antigen re-exposure since then. The magnitude and breadth of SARS-CoV-2-specific T cell responses correlated inversely with the time that had elapsed from disease onset and the age of those CIs. The mean magnitude of SARS-CoV-2-specific CD4 and CD8 T cell responses decreased about 82% and 76%, respectively, over the time period of ten months after infection. Accordingly, the longitudinal analysis also demonstrated that SARS-CoV-2-specific T cell responses waned significantly in 75% of CIs during the follow-up. Collectively, we provide a comprehensive characterization of the long-term memory T cell response in CIs, suggesting that robust SARS-CoV-2-specific T cell immunity post primary infection may be less durable than previously expected.

Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved

BACKGROUND

SARS-CoV-2 recombinants involving the divergent Delta and Omicron lineages have been described, and one of them, "Kraken" (XBB.1.5), has recently been a matter of concern. Recombination requires the coexistence of two SARS-CoV-2 strains in the same individual. Only a limited number of studies have focused on the identification of co-infections and are restricted to co-infections involving the Delta/Omicron lineages.

METHODS

We performed a systematic identification of SARS-CoV-2 co-infections throughout the pandemic (7609 different patients sequenced), not biassed towards the involvement of highly divergent lineages. Through a comprehensive set of validations based on the distribution of allelic frequencies, phylogenetic consistency, re-sequencing, host genetic analysis and contextual epidemiological analysis, these co-infections were robustly assigned.

RESULTS

Fourteen (0.18%) co-infections with ≥ 8 heterozygous calls (8-85 HZs) were identified. Co-infections were identified throughout the pandemic and involved an equal proportion of strains from different lineages/sublineages (including pre-Alpha variants, Delta and Omicron) or strains from the same lineage. Co-infected cases were mainly unvaccinated, with mild or asymptomatic clinical presentation, and most were at risk of overexposure associated with the healthcare environment. Strain segregation enabled integration of sequences to clarify nosocomial outbreaks where analysis had been impaired due to co-infection.

CONCLUSIONS

Co-infection cases were identified throughout the pandemic, not just in the time periods when highly divergent lineages were co-circulating. Co-infections involving different lineages or strains from the same lineage were occurring in the same proportion. Most cases were mild, did not require medical assistance and were not vaccinated, and a large proportion were associated with the hospital environment.

SARS-CoV-2 Reinfections in Health-Care Workers, 1 March 2020-31 January 2023

Objective: To study SARS-CoV-2 reinfections in health-care workers (HCWs) of the University Health Agency Giuliano-Isontina (ASUGI), covering the provinces of Trieste and Gorizia (northeastern Italy) routinely screened for SARS-CoV-2 via nasopharyngeal swab. Design: Cohort study of HCWs (N = 8205) followed since the start of the pandemic (1 March 2020) through 31 January 2023. The risk of reinfection during the Omicron transmission period (after 30 November 2021) among HCWs previously infected by SARS-CoV-2 was estimated based on days since last dose of COVID-19 vaccine received, adjusting for age, sex, job task, workplace, number of doses of COVID-19 vaccines and number of swab tests performed. In the crude as well as adjusted incidence rate analysis, reinfections occurring 15+ days after a first dose of COVID-19 vaccine or 8+ days following a second or more dose were counted. Results: In a highly vaccinated population, during the entire study period (1 March 2020-31 January 2023) 5253 HCWs incurred at least one SARS-CoV-2 infection, 4262 HCWs were infected only once, and 1091 were reinfected. Reinfections almost entirely (99.1% = 1071/1091) occurred after 30 November 2021, peaking in July 2022 (N = 161). Six hundred eighty-three reinfections followed a pre-Omicron primary event against 408 reinfections following an Omicron event. Reinfections during the Omicron transmission period occurred a mean of 400 ± 220 days after primary SARS-CoV-2 infection; 512 ± 205 days following a pre-Omicron primary event, as opposed to 218 ± 74 days after an Omicron primary infection. Thirty-four hospitalizations were observed, all before the Omicron wave, following 18 (0.4%) primary SARS-CoV-2 infections and 16 (1.5%) reinfections. By excluding events occurring <15 days after a first dose or <8 days after a further dose of COVID-19 vaccine, 605 reinfections followed a pre-Omicron primary event (raw incidence = 1.4 × 1000 person-days) against 404 after a primary Omicron infection (raw incidence = 0.3 × 1000 person-days). Apart from nurse aids (slightly enhanced biological risk) and academic HCWs (remarkably lower risk with pre-Omicron primary events), the effect of occupation in terms of job task and workplace was marginal. Furthermore, whilst the risk of reinfection was lower in males and HCWs < 60 years old following a pre-Omicron primary infection, HCWs aged 30-50 were more likely to be infected after an Omicron primary event. Regardless of timeline of primary SARS-CoV-2 event, the risk of reinfection decreased with higher number of doses of COVID-19 vaccines, being lowest after the second booster. In particular, VE was 16% for one dose, 51% for two doses, 76% for the booster and 92% for the second booster with a pre-Omicron primary SARS-CoV-2 event. The latter figures increased to 72%, 59%, 74% and 93%, respectively, with Omicron primary infections. Conclusions: SARS-CoV-2 reinfections were frequent during the Omicron transmission period, though featured by mild or no symptoms. Whilst the impact of occupation on biological risk was relatively marginal, COVID-19 vaccination had the strongest protective effect against reinfection, with a 93% VE by second booster following an Omicron primary infection.

Longitudinal study of humoral immunity against SARS-CoV-2 of health professionals in Brazil: the impact of booster dose and reinfection on antibody dynamics

Introduction

The pandemic caused by SARS-CoV-2 has had a major impact on health systems. Vaccines have been shown to be effective in improving the clinical outcome of COVID-19, but they are not able to fully prevent infection and reinfection, especially that caused by new variants.

Methods

Here, we tracked for 450 days the humoral immune response and reinfection in 52 healthcare workers from Brazil. Infection and reinfection were confirmed by RT-qPCR, while IgM and IgG antibody levels were monitored by rapid test.

Results

Of the 52 participants, 19 (36%) got reinfected during the follow-up period, all presenting mild symptoms. For all participants, IgM levels dropped sharply, with over 47% of them becoming seronegative by the 60th day. For IgG, 90% of the participants became seropositive within the first 30 days of follow-up. IgG antibodies also dropped after this period reaching the lowest level on day 270 (68.5 ± 72.3, p<0.0001). Booster dose and reinfection increased the levels of both antibodies, with the interaction between them resulting in an increase in IgG levels of 130.3 arbitrary units.

Conclusions

Overall, our data indicate that acquired humoral immunity declines over time and suggests that IgM and IgG antibody levels are not associated with the prevention of reinfection.

Kinetics of specific anti-SARS-CoV-2 IgM, IgA, and IgG responses during the first 12 months after SARS-CoV-2 infection: A prospective longitudinal study

Coronavirus 2019 (COVID-19) is a global health threat. The kinetics of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) need to be assessed, as the long-term duration of these immunoglobulins remains largely controversial. The aim of this study was to assess the longitudinal dynamics of anti-SARS-CoV-2 antibodies against the nucleocapsid (N) protein and the receptor-binding domain (RBD) of the spike protein up to one year in a cohort of 190 COVID-19 patients. Between March and September 2021, we enrolled patients from two regional hospitals in Casablanca, Morocco. Blood samples were collected and analyzed for antibody levels. We used the commercial Euroimmun ELISA for the determination of anti-N IgM, the Abbott Architect™ SARS-CoV-2 IgG test for the detection of anti-RBD IgG, and an in-house kit for the assay of anti-N IgG and anti-N IgA. IgM and IgA antibodies were assessed 2-5, 9-12, 17-20 and 32-37 days after symptom onset. IgG antibodies were also assessed 60, 90, 120 and 360 days after symptom onset. One-third of patients developed IgM (32%), while two-thirds developed IgA (61%). One month of symptom onset, most patients developed IgG, with 97% and 93% positivity for anti-RBD IgG and anti-N IgG, respectively. The anti-RBD IgG positivity rate remained high up to one year of follow-up. However, the anti-N IgG positivity rate decreased over time, with only 41% of patients testing positive after one year's follow-up. IgG levels were significantly higher in older people (over 50 years) than in other study participants. We also found that patients who had received two doses of ChAdOx1 nCoV-19 vaccine prior to infection had a lower IgM response than unvaccinated patients. This difference was statistically significant two weeks after the onset of symptoms. We present the first study in Africa to measure the kinetics of antibody response (IgA, IgM and IgG) to SARS-CoV-2 over one year. Most participants remained seropositive for anti-RBD IgG after one year but showed a significant decline in antibody titers.

An ecological study on reinfection rates using a large dataset of RT-qPCR tests for SARS-CoV-2 in Santiago of Chile

Introduction

As the SARS-CoV-2 continues to evolve, new variants pose a significant threat by potentially overriding the immunity conferred by vaccination and natural infection. This scenario can lead to an upswing in reinfections, amplified baseline epidemic activity, and localized outbreaks. In various global regions, estimates of breakthrough cases associated with the currently circulating viral variants, such as Omicron, have been reported. Nonetheless, specific data on the reinfection rate in Chile still needs to be included.

Methods

Our study has focused on estimating COVID-19 reinfections per wave based on a sample of 578,670 RT-qPCR tests conducted at the University of Santiago of Chile (USACH) from April 2020 to July 2022, encompassing 345,997 individuals.

Results

The analysis reveals that the highest rate of reinfections transpired during the fourth and fifth COVID-19 waves, primarily driven by the Omicron variant. These findings hold despite 80% of the Chilean population receiving complete vaccination under the primary scheme and 60% receiving at least one booster dose. On average, the interval between initial infection and reinfection was found to be 372 days. Interestingly, reinfection incidence was higher in women aged between 30 and 55. Additionally, the viral load during the second infection episode was lower, likely attributed to Chile's high vaccination rate.

Discussion

This study demonstrates that the Omicron variant is behind Chile's highest number of reinfection cases, underscoring its potential for immune evasion. This vital epidemiological information contributes to developing and implementing effective public health policies.

Analysis of SARS-CoV-2 variants from patient specimens in Nevada from October 2020 to August 2021

In early 2020, the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the human population quickly developed into a global pandemic. SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19) which has a broad range of respiratory illnesses. As the virus circulates, it acquires nucleotide changes. These mutations are potentially due to the inherent differences in the selection pressures within the human population compared to the original zoonotic reservoir of SARS-CoV-2 and formerly naïve humans. The acquired mutations will most likely be neutral, but some may have implications for viral transmission, disease severity, and resistance to therapies or vaccines. This is a follow-up study from our early report (Hartley et al. J Genet Genomics. 01202021;48(1):40-51) which detected a rare variant (nsp12, RdRp P323F) circulating within Nevada in mid 2020 at high frequency. The primary goals of the current study were to determine the phylogenetic relationship of the SARS-CoV-2 genomes within Nevada and to determine if there are any unusual variants within Nevada compared to the current database of SARS-CoV-2 sequences. Whole genome sequencing and analysis of SARS-CoV-2 from 425 positively identified nasopharyngeal/nasal swab specimens were performed from October 2020 to August 2021 to determine any variants that could result in potential escape from current therapeutics. Our analysis focused on nucleotide mutations that generated amino acid variations in the viral Spike (S) protein, Receptor binding domain (RBD), and the RNA-dependent RNA-polymerase (RdRp) complex. The data indicate that SARS-CoV-2 sequences from Nevada did not contain any unusual variants that had not been previously reported. Additionally, we did not detect the previously identified the RdRp P323F variant in any of the samples. This suggests that the rare variant we detected before was only able to circulate because of the stay-at-home orders and semi-isolation experience during the early months of the pandemic. IMPORTANCE: SARS-COV-2 continues to circulate in the human population. In this study, SARS-CoV-2 positive nasopharyngeal/nasal swab samples were used for whole genome sequencing to determine the phylogenetic relationship of SARS-CoV-2 sequences within Nevada from October 2020 to August 2021. The resulting data is being added to a continually growing database of SARS-CoV-2 sequences that will be important for understanding the transmission and evolution of the virus as it spreads around the globe.

Within-Host Evolution of SARS-CoV-2 in a B-Cell Depleted Patient With Successful Treatment

Prolonged viral shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in an immunocompromised host is a challenge as the treatment and infection control for chronic coronavirus disease 2019 infection is not well established and there is a potential risk of new variants emerging. A 48-year-old woman who underwent chemotherapy, including rituximab and steroid, had reactivation of SARS-CoV-2 68 days after the virus was first detected. She successfully recovered after receiving convalescent plasma and intravenous immunoglobulin. Genomic analysis demonstrated that viruses collected from the nasopharyngeal specimens at day 0 and day 68 had 18 different nucleotide mutations, implying within-host evolution after in-depth epidemiologic investigation.

Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain

Centers for Disease Control and Prevention guidelines consider SARS-CoV-2 reinfection when sequential COVID-19 episodes occur >90 days apart. However, genomic diversity acquired over recent COVID-19 waves could mean previous infection provides insufficient cross-protection. We used genomic analysis to assess the percentage of early reinfections in a sample of 26 patients with 2 COVID-19 episodes separated by 20-45 days. Among sampled patients, 11 (42%) had reinfections involving different SARS-CoV-2 variants or subvariants. Another 4 cases were probable reinfections; 3 involved different strains from the same lineage or sublineage. Host genomic analysis confirmed the 2 sequential specimens belonged to the same patient. Among all reinfections, 36.4% involved non-Omicron, then Omicron lineages. Early reinfections showed no specific clinical patterns; 45% were among unvaccinated or incompletely vaccinated persons, 27% were among persons <18 years of age, and 64% of patients had no risk factors. Time between sequential positive SARS-CoV-2 PCRs to consider reinfection should be re-evaluated.

4’-fluorouridine as a potential COVID-19 oral drug?: a review

The available antiviral drugs against coronavirus disease 2019 (COVID-19) are limited. Oral drugs that can be prescribed to non-hospitalized patients are required. The 4′-fluoruridine, a nucleoside analog similar to remdesivir, is one of the promising candidates for COVID-19 oral therapy due to its ability to stall viral RdRp. Available data suggested that 4'-fluorouridine has antiviral activity against the respiratory syncytial virus, hepatitis C virus, lymphocytic choriomeningitis virus, and other RNA viruses, including SARS-CoV-2. In vivo study revealed that SARS-CoV-2 is highly susceptible to 4'-fluorouridine and was effective with a single daily dose versus molnupiravir administered twice daily. Although  4'-fluorouridine is considered as strong candidates, further studies are required to determine its efficacy in the patients and  it’s genetic effects on humans. In this review, we the antiviral activity of 4′-fluorouridine is reviewed and compared it to other drugs currently in development. The current literature on 4′-fluorouridine's antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is compiled and discussed.

COVID-19 Reinfection Rate and Related Risk Factors in Fars Province, Iran: A Retrospective Cohort Study

Background

Reinfection with Coronavirus Diseases 2019 (COVID-19) has raised remarkable public health concerns globally. Therefore, the present retrospective cohort study intended to investigate COVID-19 reinfection in registered patients of Fars province in Iran from February 2020 to April 2021.

Methods

The patients' data, including the COVID-19 infection, symptoms, comorbidities, and demographics, were collected using the Health Information Systems (HISs). The patients were divided into three groups in terms of the duration between the initial infection and reinfection, including 28-44, 45-89, and more than 90 days. Following the univariate analysis, logistic regression was used to investigate the factors effective on COVID-19 reinfection.

Results

A total of 213768 patients had a positive Polymerase Chain Reaction (PCR) test. The reinfection rate was 0.97% (2079 patients). Of these re-infected individuals, 14.9%, 18.5%, and 66.6% had their second positive test 28-45, 45-89, and ≥90 days later, respectively. The mean duration between the initial infection and reinfection was 130.56 days (29-370 days). The chance of reinfection was significantly higher in the youths (Odds Ratio (OR)=2.055; P<0.001), men (OR=1.283; P<0.001), urban population (OR=1.313; P<0.001), and healthcare providers (OR=4.453; P<0.001). The patients with chronic pulmonary diseases, chronic kidney diseases, and malignancy were 1.421 (P=0.036), 2.239 (P<0.001), and 3.437 (P<0.001) times, respectively, more likely prone to reinfection.

Conclusion

The results of this study showed that there is a higher risk of reinfection in several vulnerable groups including healthcare providers, young individuals, residents of urban areas, men, and individuals with underlying diseases.

Global prevalence of coronavirus disease 2019 reinfection: a systematic review and meta-analysis

BACKGROUND

In December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged with a high transmissibility rate and resulted in numerous negative impacts on global life. Preventive measures such as face masks, social distancing, and vaccination helped control the pandemic. Nonetheless, the emergence of SARS-CoV-2 variants, such as Omega and Delta, as well as coronavirus disease 2019 (COVID-19) reinfection, raise additional concerns. Therefore, this study aimed to determine the overall prevalence of reinfection on global and regional scales.

METHODS

A systematic search was conducted across three databases, PubMed, Scopus, and ProQuest Central, including all articles pertaining to COVID-19 reinfection without language restriction. After critical appraisal and qualitative synthesis of the identified relevant articles, a meta-analysis considering random effects was used to pool the studies.

RESULTS

We included 52 studies conducted between 2019 and 2022, with a total sample size of 3,623,655 patients. The overall prevalence of COVID-19 reinfection was 4.2% (95% confidence interval [CI]: 3.7-4.8%; n = 52), with high heterogeneity between studies. Africa had the highest prevalence of 4.7% (95% CI: 1.9-7.5%; n = 3), whereas Oceania and America had lower estimates of 0.3% (95% CI: 0.2-0.4%; n = 1) and 1% (95% CI: 0.8-1.3%; n = 7), respectively. The prevalence of reinfection in Europe and Asia was 1.2% (95% CI: 0.8-1.5%; n = 8) and 3.8% (95% CI: 3.4-4.3%; n = 43), respectively. Studies that used a combined type of specimen had the highest prevalence of 7.6% (95% CI: 5.8-9.5%; n = 15) compared with those that used oropharyngeal or nasopharyngeal swabs only that had lower estimates of 6.7% (95% CI: 4.8-8.5%; n = 8), and 3.4% (95% CI: 2.8-4.0%; n = 12) respectively.

CONCLUSION

COVID-19 reinfection occurs with varying prevalence worldwide, with the highest occurring in Africa. Therefore, preventive measures, including vaccination, should be emphasized to ensure control of the pandemic.

Atypical Course of SarsCov-2 Infection in a Patient with Multiple Myeloma Treated with Autologous Stem Cell Transplantation

Covid-19 infection has more relevant consequences in frail and comorbid patients, but little is known about its course in patients with hematologic malignancies. In this report, we would like to present the case of a patient with multiple myeloma treated with recent autologous bone marrow stem cell transplantation and affected by Covid-19 pneumonia, presenting with a possible reinfection or an extremely long viral shedding.

Real-time updating of dynamic social networks for COVID-19 vaccination strategies

Vaccination strategy is crucial in fighting the COVID-19 pandemic. Since the supply is still limited in many countries, contact network-based interventions can be most powerful to set an efficient strategy by identifying high-risk individuals or communities. However, due to the high dimension, only partial and noisy network information can be available in practice, especially for dynamic systems where contact networks are highly time-variant. Furthermore, the numerous mutations of SARS-CoV-2 have a significant impact on the infectious probability, requiring real-time network updating algorithms. In this study, we propose a sequential network updating approach based on data assimilation techniques to combine different sources of temporal information. We then prioritise the individuals with high-degree or high-centrality, obtained from assimilated networks, for vaccination. The assimilation-based approach is compared with the standard method (based on partially observed networks) and a random selection strategy in terms of vaccination effectiveness in a SIR model. The numerical comparison is first carried out using real-world face-to-face dynamic networks collected in a high school, followed by sequential multi-layer networks generated relying on the Barabasi-Albert model emulating large-scale social networks with several communities.

Longitudinal analysis of SARS-CoV-2 reinfection reveals distinct kinetics and emergence of cross-neutralizing antibodies to variants of concern

The ongoing evolution of SARS-CoV-2 continues to raise new questions regarding the duration of immunity to reinfection with emerging variants. To address these knowledge gaps, controlled investigations in established animal models are needed to assess duration of immunity induced by each SARS-CoV-2 lineage and precisely evaluate the extent of cross-reactivity and cross-protection afforded. Using the Syrian hamster model, we specifically investigated duration of infection acquired immunity to SARS-CoV-2 ancestral Wuhan strain over 12 months. Plasma spike- and RBD-specific IgG titers against ancestral SARS-CoV-2 peaked at 4 months post-infection and showed a modest decline by 12 months. Similar kinetics were observed with plasma virus neutralizing antibody titers which peaked at 2 months post-infection and showed a modest decline by 12 months. Reinfection with ancestral SARS-CoV-2 at regular intervals demonstrated that prior infection provides long-lasting immunity as hamsters were protected against severe disease when rechallenged at 2, 4, 6, and 12 months after primary infection, and this coincided with the induction of high virus neutralizing antibody titers. Cross-neutralizing antibody titers against the B.1.617.2 variant (Delta) progressively waned in blood over 12 months, however, re-infection boosted these titers to levels equivalent to ancestral SARS-CoV-2. Conversely, cross-neutralizing antibodies to the BA.1 variant (Omicron) were virtually undetectable at all time-points after primary infection and were only detected following reinfection at 6 and 12 months. Collectively, these data demonstrate that infection with ancestral SARS-CoV-2 strains generates antibody responses that continue to evolve long after resolution of infection with distinct kinetics and emergence of cross-reactive and cross-neutralizing antibodies to Delta and Omicron variants and their specific spike antigens.

Reinfection of COVID-19 among doctors at a tertiary care centre in Northern India: A report from a resource-limited setting

Background and Aims

There is an increasing recognition of reinfection in coronavirus disease 2019 (COVID-19). We studied the reinfection of COVID-19 disease among doctors at a tertiary care centre in Northern India.

Methods

All COVID-19 patients readmitted for COVID-19 disease after any duration with at least a positive Real time- polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus 2 were included. Their clinical profile, vaccination status, outcome and Centre for disease control (CDC), Atlanta, USA reinfection criteria screening were recorded.

Results

A total of 57 (0.53%) doctors were identified and 56 of them satisfied the CDC criteria. It included 13 (20.3%) females and 89.3% of cases were from clinical specialities; 98.2% of individuals had the first infection in 2020 and mean duration between 2 infections was 156.29 ± 76.02 (35-298) days. Duration between two episodes of the disease with more than 90 days apart was in 80.3% cases. One (1.8%) patient developed severe disease and two (3.6%) cases were of moderate severity. Symptoms were similar in both infections except significantly higher number of extra-respiratory complaints (2.2% vs. 9.1%). There were 37.5% cases who had received first dose of vaccination of any duration at the time of second infection. Nine (16.1%) and four (7.1%) patients with more than 4 weeks after the first and second dose of vaccination developed the second infection, respectively.

Conclusion

Majority of reinfection were symptomatic and developed after 90 days and so majority followed CDC criteria. Breakthrough infections among vaccinated healthcare worker are real, and with sustained exposure to the virus, they should continue to use precaution including hand hygiene and mask in order to prevent reinfection.

Epitope Coverage of Anti-SARS-CoV-2 Nucleocapsid IgA and IgG Antibodies Correlates with Protection against Re-Infection by New Variants in Subsequent Waves of the COVID-19 Pandemic

The COVID-19 pandemic continues to affect individuals across the globe, with some individuals experiencing more severe disease than others. The relatively high frequency of re-infections and breakthrough infections observed with SARS-CoV-2 highlights the importance of extending our understanding of immunity to COVID-19. Here, we aim to shed light on the importance of antibody titres and epitope utilization in protection from re-infection. Health care workers are highly exposed to SARS-CoV-2 and are therefore also more likely to become re-infected. We utilized quantitative, multi-antigen, multi-epitope SARS-CoV-2 protein microarrays to measure IgG and IgA titres against various domains of the nucleocapsid and spike proteins. Potential re-infections in a large, diverse health care worker cohort (N = 300) during the second wave of the pandemic were identified by assessing the IgG anti-N titres before and after the second wave. We assessed epitope coverage and antibody titres between the 'single infection' and 're-infection' groups. Clear differences were observed in the breadth of the anti-N response before the second wave, with the epitope coverage for both IgG (p = 0.019) and IgA (p = 0.015) being significantly increased in those who did not become re-infected compared to those who did. Additionally, the IgG anti-N (p = 0.004) and anti-S titres (p = 0.018) were significantly higher in those not re-infected. These results highlight the importance of the breadth of elicited antibody epitope coverage following natural infection in protection from re-infection and disease in the COVID-19 pandemic.

SARS-CoV-2 multi-antigen protein microarray for detailed characterization of antibody responses in COVID-19 patients

Antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target multiple epitopes on different domains of the spike protein, and other SARS-CoV-2 proteins. We developed a SARS-CoV-2 multi-antigen protein microarray with the nucleocapsid, spike and its domains (S1, S2), and variants with single (D614G, E484K, N501Y) or double substitutions (N501Y/Deletion69/70), allowing a more detailed high-throughput analysis of the antibody repertoire following infection. The assay was demonstrated to be reliable and comparable to ELISA. We analyzed antibodies from 18 COVID-19 patients and 12 recovered convalescent donors. The S IgG level was higher than N IgG in most of the COVID-19 patients, and the receptor-binding domain of S1 showed high reactivity, but no antibodies were detected against the heptad repeat domain 2 of S2. Furthermore, antibodies were detected against S variants with single and double substitutions in COVID-19 patients who were infected with SARS-CoV-2 early in the pandemic. Here we demonstrated that the SARS-CoV-2 multi-antigen protein microarray is a powerful tool for detailed characterization of antibody responses, with potential utility in understanding the disease progress and assessing current vaccines and therapies against evolving SARS-CoV-2.

Evaluation of possible COVID-19 reinfection in children: A multicenter clinical study

BACKGROUND

Although it was originally unknown whether there would be cases of reinfection of coronavirus disease 2019 (COVID-19) as seen with other coronaviruses, cases of reinfection were reported from various regions recently. However, there is little information about reinfection in children.

METHODS

In this study, we aimed to investigate the incidence and clinical findings of reinfection in pediatric patients who had recovered from COVID-19. We retrospectively evaluated all patients under 18 years of age with COVID-19 infection from a total of eight healthcare facilities in Turkey, between March 2020 and July 2021. Possible reinfection was defined as a record of confirmed COVID-19 infection based on positive reverse transcription-polymerase chain reaction (RT-PCR) test results at least 3 months apart.

RESULTS

A possible reinfection was detected in 11 out of 8840 children, which yielded an incidence of 0.12%. The median duration between two episodes of COVID-19 was 196 (92-483) days. When initial and second episodes were compared, the rates of symptomatic and asymptomatic disease were similar for both, as was the severity of the disease (p = 1.000). Also, there was no significant difference in duration of symptoms (p = 0.498) or in hospitalization rates (p = 1.000). Only one patient died 15 days after PCR positivity, which resulted in a 9.1% mortality rate for cases of reinfection in pediatric patients.

CONCLUSION

We observed that children with COVID-19 were less likely to be exposed to reinfection when compared with adults. Although the clinical spectrum of reinfection was mostly similar to the first episode, we reported death of a healthy child during the reinfection.

Validation of a SARS-CoV-2 Surrogate Virus Neutralization Test in Recovered and Vaccinated Healthcare Workers

Vaccination against COVID-19 is the main public health approach to fight against the pandemic. The Spike (S) glycoprotein of SARS-CoV-2 is the principal target of the neutralizing humoral response. We evaluated the analytical and clinical performances of a surrogate virus neutralization test (sVNT) compared to conventional neutralization tests (cVNTs) and anti-S eCLIA assays in recovered and/or vaccinated healthcare workers. Our results indicate that sVNTs displayed high specificity and no cross-reactivity. Both eCLIA and sVNT immunoassays were good at identifying cVNT serum dilutions ≥1:16. The optimal thresholds when identifying cVNT titers ≥1:16, were 74.5 U/mL and 49.4 IU/mL for anti-S eCLIA and sVNT, respectively. Our data show that neutralizing antibody titers (Nab) differ from one individual to another and may diminish over time. Specific assays such as sVNTs could offer a reliable complementary tool to routine anti-S serological assays.

Vaccine-elicited B and T cell immunity to SARS-CoV-2 is impaired in chronic lung disease patients

The protection afforded by vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to individuals with chronic lung disease is not well established. To understand how chronic lung disease impacts SARS-CoV-2 vaccine-elicited immunity we performed deep immunophenotyping of the humoral and cell mediated SARS-CoV-2 vaccine response in an investigative cohort of vaccinated patients with diverse pulmonary conditions including asthma, chronic obstructive pulmonary disease (COPD), and interstitial lung disease (ILD). Compared to healthy controls, 48% of vaccinated patients with chronic lung diseases had reduced antibody titers to the SARS-CoV-2 vaccine antigen as early as 3-4 months after vaccination, correlating with decreased vaccine-specific memory B cells. Vaccine-specific CD4 and CD8 T cells were also significantly reduced in patients with asthma, COPD, and a subset of ILD patients compared to healthy controls. These findings reveal the complex nature of vaccine-elicited immunity in high-risk patients with chronic lung disease.

Rapid System to Detect Variants of SARS-CoV-2 in Nasopharyngeal Swabs

Currently, the reference method for identifying the presence of variants of SARS-CoV-2 is whole genome sequencing. Although it is less expensive than in the past, it is still time-consuming, and interpreting the results is difficult, requiring staff with specific skills who are not always available in diagnostic laboratories. The test presented in this study aimed to detect, using traditional real-time PCR, the presence of the main variants described for the spike protein of the SARS-CoV-2 genome. The primers and probes were designed to detect the main deletions that characterize the different variants. The amplification targets were deletions in the S gene: 25-27, 69-70, 241-243, and 157-158. In the ORF1a gene, the deletion 3675-3677 was chosen. Some of these mutations can be considered specific variants, while others can be identified by the simultaneous presence of one or more deletions. We avoided using point mutations in order to improve the speed of the test. Our test can help clinical and medical microbiologists quickly recognize the presence of variants in biological samples (particularly nasopharyngeal swabs). The test can also be used to identify variants of the virus that could potentially be more diffusive as well as not responsive to the vaccine.

Time to death and its predictors among adult patients with COVID-19: A retrospective cohort study in Ethiopia

Background

Coronavirus (COVID-19) disease affected people throughout the globe and has become a severe threat to the health and wellbeing of the global community. Time to death and predictors of mortality vary across settings. So far, no or few related studies have been undertaken in Ethiopia. Studying the time to death from COVID-19 and its predictors is essential to understand the characteristics of the disease and thereby contribute to the identification of indicators for early detection and initiation of treatment. Therefore, this study aimed to estimate time to death and its predictors among adults with COVID-19 in Ethiopia.

Methods

A retrospective follow-up study was conducted among 602 adults with COVID-19 attending Eka Kotebe General Hospital, COVID-19 Treatment Center, between 13 March 2020 and 13 November 2020. The data were entered by Epi-data version 4.2 while the analysis was carried out using STATA version 16. A Kaplan-Meier survivor curve was computed to estimate the survival probabilities. A log-rank test was used to compare the difference in survival curves. Cox proportional hazard models were fitted to identify the predictors of time to death.

Results

The overall median time to death was 21 days. Older adults (aged ≥65 years) [adjusted hazard ratio (AHR) 2.22, 95% confidence interval (CI) 1.02-4.86], being men (AHR 3.04, 95% CI 1.61-5.74), shortness of breathing at admission (AHR 2.29, 95% CI 1.16-4.54), comorbidity (AHR 2.23, 95% CI 1.04-4.80), diabetes mellitus (AHR 2.31, 95% CI 1.30-4.08), altered cardiac function (AHR 2.07, 95% CI 1.21-3.43), and baseline white blood cell count of greater than 10 (103/µl) (AHR 2.62, 95% CI 1.55-4.44) were independent predictors of COVID-19 mortality.

Conclusion

Male sex, older adults, shortness of breathing at admission, patients with comorbidities, and higher blood cell count were significant predictors of time to death from COVID-19. Therefore, concerned stakeholders should focus on those predictors of mortality and design interventions accordingly to enhance the survival of patients with COVID-19.

Genomic evidence of SARS-CoV-2 reinfection cases in southern Brazil

Cases of reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported worldwide. We investigated reinfection cases in a set of more than 30,000 samples, and the SARS-CoV-2 genomes from selected samples from four patients with at least two positive diagnoses with an interval ≥ 45 days between tests were sequenced and analyzed. Comparative genomic and phylogenetic analysis confirmed three reinfection cases and suggested that the fourth one was caused by a virus of the same lineage. Viral sequencing is crucial for understanding the natural course of reinfections and for planning public health strategies for management of COVID-19.

Kinetics of SARS-CoV-2 IgM and IgG Antibodies 3 Months after COVID-19 Onset in Moroccan Patients

Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses serious global public health problems. Characterization of the immune response, particularly antibodies to SARS-CoV-2, is important for establishing vaccine strategies. The purpose of this study was to evaluate longitudinally the kinetics of anti-SARS-CoV-2 antibodies against spike protein (S1) for up to 3 months in a cohort of 169 COVID-19 patients. We enrolled COVID-19 patients at two regional hospitals in Casablanca, Morocco, between March and September 2021. Blood samples were collected and N-specific IgM and S-specific IgG levels were measured by a commercial Euroimmun ELISA. IgM antibodies were assessed 2-5 (D00), 9-12 (D07), 17-20 (D15), and 32-37 (D30) days after symptom onset; IgG antibodies were assessed at these time points plus 60 (D60) and 90 (D90) days after symptom onset. We found that at 3 months after symptom onset, 79% of patients had detectable SARS-CoV-2-specific IgG antibodies, whereas their IgM seropositivity was 19% by 1 month after symptom onset. The IgM level decreased to 0.34 (interquartile range [IQR] 0.19-0.92) at 1 month after symptom onset, whereas the IgG level peaked at D30 (3.10; IQR 1.83-5.64) and remained almost stable at D90 (2.95; IQR 1.52-5.19). IgG levels were significantly higher in patients older than 50 years than in those younger than 50 at all follow-up time points (P < 0.05). Statistical analysis showed no significant difference in median anti-S1 antibody levels among infected patients based on gender or comorbidities. This study provides information on the longevity of anti-SARS-CoV-2 IgM and IgG antibodies in COVID-19 patients.

Mutational Patterns Observed in SARS-CoV-2 Genomes Sampled From Successive Epochs Delimited by Major Public Health Events in Ontario, Canada: Genomic Surveillance Study

BACKGROUND

The emergence of SARS-CoV-2 variants with mutations associated with increased transmissibility and virulence is a public health concern in Ontario, Canada. Characterizing how the mutational patterns of the SARS-CoV-2 genome have changed over time can shed light on the driving factors, including selection for increased fitness and host immune response, that may contribute to the emergence of novel variants. Moreover, the study of SARS-CoV-2 in the microcosm of Ontario, Canada can reveal how different province-specific public health policies over time may be associated with observed mutational patterns as a model system.

OBJECTIVE

This study aimed to perform a comprehensive analysis of single base substitution (SBS) types, counts, and genomic locations observed in SARS-CoV-2 genomic sequences sampled in Ontario, Canada. Comparisons of mutational patterns were conducted between sequences sampled during 4 different epochs delimited by major public health events to track the evolution of the SARS-CoV-2 mutational landscape over 2 years.

METHODS

In total, 24,244 SARS-CoV-2 genomic sequences and associated metadata sampled in Ontario, Canada from January 1, 2020, to December 31, 2021, were retrieved from the Global Initiative on Sharing All Influenza Data database. Sequences were assigned to 4 epochs delimited by major public health events based on the sampling date. SBSs from each SARS-CoV-2 sequence were identified relative to the MN996528.1 reference genome. Catalogues of SBS types and counts were generated to estimate the impact of selection in each open reading frame, and identify mutation clusters. The estimation of mutational fitness over time was performed using the Augur pipeline.

RESULTS

The biases in SBS types and proportions observed support previous reports of host antiviral defense activity involving the SARS-CoV-2 genome. There was an increase in U>C substitutions associated with adenosine deaminase acting on RNA (ADAR) activity uniquely observed during Epoch 4. The burden of novel SBSs observed in SARS-CoV-2 genomic sequences was the greatest in Epoch 2 (median 5), followed by Epoch 3 (median 4). Clusters of SBSs were observed in the spike protein open reading frame, ORF1a, and ORF3a. The high proportion of nonsynonymous SBSs and increasing dN/dS metric (ratio of nonsynonymous to synonymous mutations in a given open reading frame) to above 1 in Epoch 4 indicate positive selection of the spike protein open reading frame.

CONCLUSIONS

Quantitative analysis of the mutational patterns of the SARS-CoV-2 genome in the microcosm of Ontario, Canada within early consecutive epochs of the pandemic tracked the mutational dynamics in the context of public health events that instigate significant shifts in selection and mutagenesis. Continued genomic surveillance of emergent variants will be useful for the design of public health policies in response to the evolving COVID-19 pandemic.

Reinfection with SARS-CoV-2 and Waning Humoral Immunity: A Case Report

Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it is uncertain whether these confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify patients with recurrent shedding. We sequenced viruses from two distinct episodes of symptomatic COVID-19 separated by 144 days in a single patient, to conclusively describe reinfection with a different strain harboring the spike variant D614G. This case of reinfection was one of the first cases of reinfection reported in 2020. With antibody, B cell and T cell analytics, we show correlates of adaptive immunity at reinfection, including a differential response in neutralizing antibodies to a D614G pseudovirus. Finally, we discuss implications for vaccine programs and begin to define benchmarks for protection against reinfection from SARS-CoV-2.

Identification of Genomic Variants of SARS-CoV-2 Using Nanopore Sequencing

Background and Objectives: SARS-CoV-2 is the first global threat and life-changing event of the twenty-first century. Although efficient treatments and vaccines have been developed, due to the virus's ability to mutate in key regions of the genome, whole viral genome sequencing is needed for efficient monitoring, evaluation of the spread, and even the adjustment of the molecular diagnostic assays. Materials and Methods: In this study, Nanopore and Ion Torrent sequencing technologies were used to detect the main SARS-CoV-2 circulating strains in Timis County, Romania, between February 2021 and May 2022. Results: We identified 22 virus lineages belonging to seven clades: 20A, 20I (Alpha, V1), 21B (Kappa), 21I (Delta), 21J (Delta), 21K (Omicron), and 21L (Omicron). Conclusions: Results obtained with both methods are comparable, and we confirm the utility of Nanopore sequencing in large-scale epidemiological surveillance due to the lower cost and reduced time for library preparation.