Disappearance of antibodies to SARS-associated coronavirus after recovery

Serological evidence of sarbecovirus exposure along Sunda pangolin trafficking pathways

BACKGROUND

Early in the coronavirus disease 2019 (COVID-19) pandemic, Sunda pangolins (Manis javanica) involved in the illegal wildlife trade in mainland China were identified as hosts of severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs). Although it is unconfirmed whether pangolins or other traded wildlife served as intermediate hosts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the trafficking of pangolins presents a clear risk for transmission of viruses with zoonotic and epizootic potential regardless. We have investigated the origins of pangolin carcasses seized in Hong Kong and have evaluated their potential exposure to SARSr-CoVs, other coronaviruses, and paramyxoviruses, aiming to address a gap in our knowledge with regard to the role of wildlife trade in the maintenance and emergence of pathogens with zoonotic and epizootic potential.

RESULTS

Using a combination of virological and wildlife forensics tools, we investigated 89 Sunda pangolin carcasses seized by Hong Kong authorities during anti-smuggling operations in the territory conducted in 2013 (n = 1) and 2018 (n = 88). Swabs, organ tissues, blood, and other body fluids were collected during post-mortem examination. Two enzyme-linked immunosorbent assays (ELISAs), which employ a double-antigen sandwich format, were used to detect antibodies reactive against SARSr-CoVs. One individual was found to be seropositive with support from both methods, while five individuals exhibited a putatively seropositive result from one ELISA method. Polymerase chain reaction (PCR) screening for coronavirus and paramyxovirus ribonucleic acid (RNA) did not yield any positives. Based on genomic data, the seropositive individual was determined to have likely originated from Java, while the putatively seropositive individuals were determined to have originated from populations in Borneo, Java, and Singapore/Sumatra.

CONCLUSIONS

While the role of pangolins in the evolution and ecology of SARS-CoV-2 is uncertain, our results suggest susceptibility and potential exposure of pangolins to SARSr-CoVs, occurring naturally or associated with the illegal trafficking of these animals. Complex dynamics between natural populations, traded individuals, and pathogen susceptibility complicate conclusions about the role of pangolins, as well as other host species, in the ecology of SARSr-CoVs and potentially zoonotic viruses with risk of future emergence.

T-cell responses in COVID-19 survivors 6-8 months after infection: A longitudinal cohort study in Pune

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune response is crucial for disease management, although diminishing immunity raises the possibility of reinfection.

METHODS

We examined the immunological response to SARS-CoV-2 in a cohort of convalescent COVID-19 patients in matched samples collected at 1 and 6-8 months after infection. The peripheral blood mononuclear cells were isolated from enrolled study participants and flow cytometry analysis was done to assess the lymphocyte subsets of naive, effector, central memory, and effector memory CD4+ or CD8+ T cells in COVID-19 patients at 1 and 6-8 months after infection. Immunophenotypic characterization of immune cell subsets was performed on individuals who were followed longitudinally for 1 month (n = 44) and 6-8 months (n = 25) after recovery from COVID infection.

RESULTS

We observed that CD4 +T cells in hospitalized SARS-CoV-2 patients tended to decrease, whereas CD8+ T cells steadily recovered after 1 month, while there was a sustained increase in the population of effector T cells and effector memory T cells. Furthermore, COVID-19 patients showed persistently low B cells and a small increase in the NK cell population.

CONCLUSION

Our findings show that T cell responses were maintained at 6-8 months after infection. This opens new pathways for further research into the long-term effects in COVID-19 immunopathogenesis.

The Key to Increase Immunogenicity of Next-Generation COVID-19 Vaccines Lies in the Inclusion of the SARS-CoV-2 Nucleocapsid Protein

Vaccination is one of the most effective prophylactic public health interventions for the prevention of infectious diseases such as coronavirus disease (COVID-19). Considering the ongoing need for new COVID-19 vaccines, it is crucial to modify our approach and incorporate more conserved regions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to effectively address emerging viral variants. The nucleocapsid protein is a structural protein of SARS-CoV-2 that is involved in replication and immune responses. Furthermore, this protein offers significant advantages owing to the minimal accumulation of mutations over time and the inclusion of key T-cell epitopes critical for SARS-CoV-2 immunity. A novel strategy that may be suitable for the new generation of vaccines against COVID-19 is to use a combination of antigens, including the spike and nucleocapsid proteins, to elicit robust humoral and potent cellular immune responses, along with long-lasting immunity. The strategic use of multiple antigens aims to enhance vaccine efficacy and broaden protection against viruses, including their variants. The immune response against the nucleocapsid protein from other coronavirus is long-lasting, and it can persist up to 11 years post-infection. Thus, the incorporation of nucleocapsids (N) into vaccine design adds an important dimension to vaccination efforts and holds promise for bolstering the ability to combat COVID-19 effectively. In this review, we summarize the preclinical studies that evaluated the use of the nucleocapsid protein as antigen. This study discusses the use of nucleocapsid alone and its combination with spike protein or other proteins of SARS-CoV-2.

Seasonal human coronavirus humoral responses in AZD1222 (ChaAdOx1 nCoV-19) COVID-19 vaccinated adults reveal limited cross-immunity

Background

Immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is now widespread; however, the degree of cross-immunity between SARS-CoV-2 and endemic, seasonal human coronaviruses (HCoVs) remains unclear.

Methods

SARS-CoV-2 and HCoV cross-immunity was evaluated in adult participants enrolled in a US sub-study in the phase III, randomized controlled trial (NCT04516746) of AZD1222 (ChAdOx1 nCoV-19) primary-series vaccination for one-year. Anti-HCoV spike-binding antibodies against HCoV-229E, HCoV-HKU1, HCoV-OC43, and HCoV-NL63 were evaluated in participants following study dosing and, in the AZD1222 group, after a non-study third-dose booster. Timing of SARS-CoV-2 seroconversion (assessed via anti-nucleocapsid antibody levels) and incidence of COVID-19 were evaluated in those who received AZD1222 primary-series by baseline anti-HCoV titers.

Results

We evaluated 2,020/21,634 participants in the AZD1222 group and 1,007/10,816 in the placebo group. At the one-year data cutoff (March 11, 2022) mean duration of follow up was 230.9 (SD: 106.36, range: 1-325) and 94.3 (74.12, 1-321) days for participants in the AZD1222 (n = 1,940) and placebo (n = 962) groups, respectively. We observed little elevation in anti-HCoV humoral titers post study-dosing or post-boosting, nor evidence of waning over time. The occurrence and timing of SARS-CoV-2 seroconversion and incidence of COVID-19 were not largely impacted by baseline anti-HCoV titers.

Conclusion

We found limited evidence for cross-immunity between SARS-CoV-2 and HCoVs following AZD1222 primary series and booster vaccination. Susceptibility to future emergence of novel coronaviruses will likely persist despite a high prevalence of SARS-CoV-2 immunity in global populations.

An adenovirus-vectored vaccine based on the N protein of feline coronavirus elicit robust protective immune responses

Feline coronavirus (FCoV) is an unsegmented, single-stranded RNA virus belonging to the Alphacoronavirus genus. It can cause fatal feline infectious peritonitis (FIP) in cats of any ages. Currently, there are no effective prevention and control measures to against FCoV. In this study, we developed a recombinant adenovirus vaccine, AD5-N, based on the nucleocapsid(N) protein of FCoV. The immunogenicity of AD5-N was evaluated through intramuscular immunization in 6-week-old Balb/c mice and 9-12 months old cats. Compared to the control group, AD5-N specifically induced a significant increase in IgG and SIgA levels in the vaccinated mice. Furthermore, AD5-N not only effectively promoted strong cellular immune responses in cats but also induced high levels of specific SIgA, effectively helping cats resist FCoV infection. Our findings suggest that adenovirus vector vaccines based on the N gene have the potential to become candidate vaccines for the prevention and control of FCoV infection.

Overview of the SARS-CoV-2 nucleocapsid protein

Since the emergence of SARS-CoV in 2003, researchers worldwide have been toiling away at deciphering this virus's biological intricacies. In line with other known coronaviruses, the nucleocapsid (N) protein is an important structural component of SARS-CoV. As a result, much emphasis has been placed on characterizing this protein. Independent research conducted by a variety of laboratories has clearly demonstrated the primary function of this protein, which is to encapsidate the viral genome. Furthermore, various accounts indicate that this particular protein disrupts diverse intracellular pathways. Such observations imply its vital role in regulating the virus as well. The opening segment of this review will expound upon these distinct characteristics succinctly exhibited by the N protein. Additionally, it has been suggested that the N protein possesses diagnostic and vaccine capabilities when dealing with SARS-CoV. In light of this fact, we will be reviewing some recent headway in the use cases for N protein toward clinical purposes within this article's concluding segments. This forward movement pertains to both developments of COVID-19-oriented therapeutic targets as well as diagnostic measures. The strides made by medical researchers offer encouragement, knowing they are heading toward a brighter future combating global pandemic situations such as these.

Silent battles: immune responses in asymptomatic SARS-CoV-2 infection

SARS-CoV-2 infections manifest with a broad spectrum of presentations, ranging from asymptomatic infections to severe pneumonia and fatal outcomes. This review centers on asymptomatic infections, a widely reported phenomenon that has substantially contributed to the rapid spread of the pandemic. In such asymptomatic infections, we focus on the role of innate, humoral, and cellular immunity. Notably, asymptomatic infections are characterized by an early and robust innate immune response, particularly a swift type 1 IFN reaction, alongside a rapid and broad induction of SARS-CoV-2-specific T cells. Often, antibody levels tend to be lower or undetectable after asymptomatic infections, suggesting that the rapid control of viral replication by innate and cellular responses might impede the full triggering of humoral immunity. Even if antibody levels are present in the early convalescent phase, they wane rapidly below serological detection limits, particularly following asymptomatic infection. Consequently, prevalence studies reliant solely on serological assays likely underestimate the extent of community exposure to the virus.

Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies

Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays. Thus, mAb assessment assays that utilize a more genetically diverse, biologically relevant, virus stock may yield data that are relevant for prediction of mAb efficacy and for enhancing biosurveillance.

COVID-19 Antibody Levels among Various Vaccination Groups, One-Year Antibody Follow-Up in Two University Hospitals from Western and Central Turkey

Various clinical outcomes, reinfections, vaccination programs, and antibody responses resulted from the COVID-19 pandemic. This study investigated the time-dependent changes in SARS-CoV-2 antibody responses in infected and/or vaccinated and unvaccinated individuals and to provide insights into spike and nucleocapsid antibodies, which fluctuate during infectious and non-infectious states. This cohort study was carried out at the Ege University Faculty of Medicine hospital in İzmir (western Turkey) and the Erciyes University Faculty of Medicine hospital in Kayseri (central Turkey) between December 2021 and January 2023, which coincided with the second half of COVID-19 pandemic. The study included 100 COVID-19 PCR-positive patients and 190 healthcare workers (HCWs). Antibody levels were followed up via quantitative anti-SARS-CoV-2 spike and qualitative anti-nucleocapsid immunoassays (Elecsys™). Antibody levels declined after infection but persisted for at least 6-8 months. Individuals who had received only CoronaVac had higher anti-nucleocapsid antibody levels in the early months than those who received mixed vaccination. However, anti-spike antibodies persisted longer and at higher levels in individuals who had received mixed vaccinations. This suggests that combining two different vaccine platforms may provide a synergistic effect, resulting in more durable and broad-spectrum immunity against SARS-CoV-2. The study provides information about the vaccination and antibody status of healthcare workers in the second half of the pandemic and provides valuable insights into the dynamics of antibody responses to COVID-19 infection and vaccination.

Local protection bubbles: an interpretation of the slowdown in the spread of coronavirus in the city of São Paulo, Brazil, in July 2020

After four months of fighting the pandemic, the city of São Paulo, Brazil, entered a phase of relaxed social distancing measures in July 2020. Simultaneously, there was a decline in the social distancing rate and a reduction in the number of cases, fatalities, and hospital bed occupancy. To understand the pandemic dynamics in the city of São Paulo, we developed a multi-agent simulation model. Surprisingly, the counter-intuitive results of the model followed the city's reality. We argue that this phenomenon could be attributed to local bubbles of protection that emerged in the absence of contagion networks. These bubbles reduced the transmission rate of the virus, causing short and temporary reductions in the epidemic curve - but manifested as an unstable equilibrium. Our hypothesis aligns with the virus spread dynamics observed thus far, without the need for ad hoc assumptions regarding the natural thresholds of collective immunity or the heterogeneity of the population's transmission rate, which may lead to erroneous predictions. Our model was designed to be user-friendly and does not require any scientific or programming expertise to generate outcomes on virus transmission in a given location. Furthermore, as an input to start our simulation model, we developed the COVID-19 Protection Index as an alternative to the Human Development Index, which measures a given territory vulnerability to the coronavirus and includes characteristics of the health system and socioeconomic development, as well as the infrastructure of the city of São Paulo.

Antibody response and soluble mediator profile in the first six months following acute SARS-CoV-2 infection

The COVID-19 pandemic has caused a severe global health and economic crisis, with significant consequences for human mortality and morbidity. Therefore, there is an urgent need for more studies on the immune response to SARS-CoV-2 infection, both to enhance its effectiveness and prevent its deleterious effects. This study presents the chronology of antibodies during six months after infection in hospitalized patients and the kinetics of serum soluble mediators of the cellular response triggered by SARS-CoV-2. Samples and clinical data from 330 patients hospitalized at the Hospital da Baleia in Belo Horizonte, Brazil, who were suspected of having COVID-19, were collected at the time of hospitalization and during 6 months after infection. The immune response was analyzed by enzyme-linked immunosorbent assay (ELISA) and flow cytometry. There was a significant difference in IgM specific antibody titers from the 7th to 60th days after infection between COVID-19 negative and positive patients. Soon after 60 days after infection, antibody levels started to reduce, becoming similar to the antibody levels of the COVID-19 negative patients. IgG specific antibodies started to be detectable after 9 days of infection and antibody levels were comparatively higher in positive patients as soon as after 7 days. Furthermore, IgG levels remained higher in these patients during the complete period of 180 days after infection. The study observed similar antibody profiles between different patient groups. The soluble systemic biomarkers evaluated showed a decrease during the six months after hospitalization, except for CCL11, CXCL8, CCL3, CCL4, CCL5, IL-6, IFN-g, IL-17, IL-5, FGF-basic, PDGF, VEGF, G-CSF, and GM-CSF. The results indicate that IgM antibodies are more prominent in the early stages of infection, while IgG antibodies persist for a longer period. Additionally, the study identified that patients with COVID-19 have elevated levels of biomarkers after symptom onset, which decrease over time.

SARS-CoV-2 spike-specific TFH cells exhibit unique responses in infected and vaccinated individuals

Long-term humoral immunity to SARS-CoV-2 is essential for preventing reinfection. The production of neutralizing antibody (nAb) and B cell differentiation are tightly regulated by T follicular help (TFH) cells. However, the longevity and functional role of TFH cell subsets in COVID-19 convalescents and vaccine recipients remain poorly defined. Here, we show that SARS-CoV-2 infection and inactivated vaccine elicited both spike-specific CXCR3+ TFH cell and CXCR3- TFH cell responses, which showed distinct response patterns. Spike-specific CXCR3+ TFH cells exhibit a dominant and more durable response than CXCR3- TFH cells that positively correlated with antibody responses. A third booster dose preferentially expands the spike-specific CXCR3+ TFH cell subset induced by two doses of inactivated vaccine, contributing to antibody maturation and potency. Functionally, spike-specific CXCR3+ TFH cells have a greater ability to induce spike-specific antibody secreting cells (ASCs) differentiation compared to spike-specific CXCR3- TFH cells. In conclusion, the persistent and functional role of spike-specific CXCR3+ TFH cells following SARS-CoV-2 infection and vaccination may play an important role in antibody maintenance and recall response, thereby conferring long-term protection. The findings from this study will inform the development of SARS-CoV-2 vaccines aiming to induce long-term protective immune memory.

Seroprevalence of COVID-19 in Oran: Cross-Sectional Study

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was introduced in Algeria in March 2020. This study aimed to estimate the seroprevalence of SARS-CoV-2 infection in Oran, Algeria, and to identify factors associated with seropositivity. This was a cross-sectional seroprevalence study conducted between 7 and 20 January 2021 across all 26 municipalities in the province of Oran. The study employed a random cluster sampling technique stratified by age and sex to select participants from households, who were then administered a rapid serological test. The overall seroprevalence and specific seroprevalences by municipality were calculated, and the number of COVID-19 cases in Oran was estimated. The correlation between population density and seroprevalence was also examined. Among the participants, 422 (35.6%; 95% confidence interval [CI], 32.9 to 38.4) had a positive serological test for SARS-CoV-2, and eight municipalities had seroprevalence rates above 73%. We found a strong positive correlation between population density and seroprevalence (r = 0.795, P < 0.001), indicating that areas with higher population density had higher numbers of positive COVID-19 cases. Our study provides evidence of a high seroprevalence of SARS-CoV-2 infection in Oran, Algeria. The estimated number of cases based on seroprevalence is much higher than the number of cases confirmed by PCR. Our findings suggest that a large proportion of the population has been infected with SARS-CoV-2, highlighting the need for continued surveillance and control measures to prevent further spread of the virus. IMPORTANCE This is the first and only seroprevalence study of COVID-19 conducted in the general population in Algeria prior to the national vaccination campaign against COVID-19. The significance of this study lies in its contribution to our understanding of the spread of the virus in the population before the implementation of the vaccination program.

Rational design of a booster vaccine against COVID-19 based on antigenic distance

Current COVID-19 vaccines are highly effective against symptomatic disease, but repeated booster doses using vaccines based on the ancestral strain offer limited additional protection against SARS-CoV-2 variants of concern (VOCs). To address this, we used antigenic distance to in silico select optimized booster vaccine seed strains effective against both current and future VOCs. Our model suggests that a SARS-CoV-1-based booster vaccine has the potential to cover a broader range of VOCs. Candidate vaccines including the spike protein from ancestral SARS-CoV-2, Delta, Omicron (BA.1), SARS-CoV-1, or MERS-CoV were experimentally evaluated in mice following two doses of the BNT162b2 vaccine. The SARS-CoV-1-based booster vaccine outperformed other candidates in terms of neutralizing antibody breadth and duration, as well as protective activity against Omicron (BA.2) challenge. This study suggests a unique strategy for selecting booster vaccines based on antigenic distance, which may be useful in designing future booster vaccines as new SARS-CoV-2 variants emerge.

Evaluation of humoral immune response in relation to COVID-19 severity over 1 year post-infection: critical cases higher humoral immune response than mild cases

Introduction

Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2. We investigated the antibody response against SARS-CoV-2 until 1 year after symptom onset.

Methods

We collected 314 serum samples from 97 patients with COVID-19. Antibody responses were tested using an indirect immunofluorescence assay (IFA), enzyme-linked immunosorbent assay (ELISA), and plaque reduction neutralization test (PRNT) to detect specific neutralizing antibodies.

Results

The positivity rates for neutralizing antibodies at a 1:10 titer cutoff were 58.1% at 1 week, 97.8% at 4 weeks, and 78% at 1 year after symptom onset (53.8% in asymptomatic patients and 89.3% in symptomatic patients). The IFA and anti-S1 ELISA IgG results significantly correlated with neutralizing antibody titers. Critical/fatal cases showed significantly higher antibody titers than the asymptomatic or mild-to-moderate illness groups. Nonetheless, the median number of days to the seroconversion of neutralizing antibodies was 10 and 15 in asymptomatic and symptomatic patients, respectively. The asymptomatic group had a significantly higher neutralizing potency index than the mild-to-severe illness groups.

Conclusions

Neutralizing antibodies corresponded to earlier seroconversion but had a shorter presence in the asymptomatic group than in the symptomatic group and were still present 1 year after symptom onset in critical/fatal cases.

Kinetics of Covid-19 antibodies in terms of titre and duration among healthcare workers: A longitudinal study

Background Most individuals with Covid-19 infection develop antibodies specific to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the dynamics of these antibodies is variable and not well-studied. We aimed to determine the titres of naturally acquired antibodies over a 12-week follow-up. Methods We recruited healthcare workers who had tested positive on a specific quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for SARS-CoV-2, and then tested for the presence of immunoglobulin G (IgG) antibody against the same virus at baseline and again at 6 and 12 weeks. The antibody titre was determined by a semi-quantitative assay based on signal/cut-off ratio. Healthcare workers with antibody positivity were divided into those with high titre (ratio ≥12) and low titre (<12). Their demographic details and risk factors were surveyed through a Google form and analysed in relation to the antibody titres at three time-points. Results Of the 286 healthcare workers, 10.48% had high antibody titres. Healthcare workers who had tested positive by qRT-PCR and those who had received the Bacille Calmette-Guérin (BCG) vaccination or other immune-boosters had a higher frequency of high antibody titres. While there was a significant decline in antibody titres at 6 and 12 weeks, 87.46% of individuals positive for IgG antibody persisted to have the antibody even at 12 weeks. Conclusion Healthcare workers who tested positive for SARS-CoV-2 on qRT-PCR had a high positivity for the specific antibody, which continued to express in them even at 12 weeks. Further follow-up is likely to enhance our understanding of antibody kinetics following SARS-CoV-2 infection.

Seroepidemiology of the Seasonal Human Coronaviruses NL63, 229E, OC43 and HKU1 in France

Background

The seasonal human coronaviruses (HCoV) NL63, 229E, OC43, and HKU1 are globally endemic, yet the majority of HCoV infections remain undiagnosed.

Methods

In a cross-sectional study, 2389 serum samples were collected from children and adults in France in 2020. In a longitudinal cohort study, 2520 samples were collected from 898 French individuals followed up between 2020 and 2021. Antibodies to HCoVs were measured using a bead-based multiplex assay.

Results

The rate of waning of anti-HCoV spike immunoglobulin G antibodies was estimated as 0.22-0.47 year^-1 for children, and 0.13-0.27 year^-1 for adults. Seroreversion was estimated as 0.31-1.37 year^-1 in children and 0.19-0.72 year^-1 in adults. The estimated seroconversion rate in children was consistent with 20%-39% of children being infected every year with each HCoV.

Conclusions

The high force of infection in children indicates that HCoVs may be responsible for a substantial proportion of fever episodes experienced by children.

Therapeutic Interventions for COVID-19

SARS-CoV-2, a novel coronavirus, is currently represented a major public health concern. The high transmission rate of this virus increases the mortality rate worldwide. To date, significant efforts and restricted regulations were performed around the world to control this crisis effectively, but unfortunately, there is no specific and successful therapy for COVID-19. Many approaches have been repurposed for SARS-CoV-2 treatment such as antivirals and anti-inflammatories. Furthermore, antibody therapies are one of the main and important approaches of SARS-CoV-2 infection treatment. In recent trials, various immunotherapeutic interventions such as convalescent plasma therapy and monoclonal antibodies, as well as immunomodulatory agents are being proposed. However, the development of a vaccine that provides durable protective immunity will be the most effective therapy for controlling possible epidemics of this virus. The current review summarized all the proposed therapeutic approaches together with information on their safety and efficacy in treating COVID-19, as well as the vaccine candidates. The provided comprehensive information regarding the applied therapeutic strategies against COVID-19 might help the scientific community in any progress toward the treatment of COVID-19 infection.

Transplacental Transfer of SARS-CoV-2 Receptor-Binding Domain IgG Antibodies from Mothers to Neonates in a Cohort of Pakistani Unvaccinated Mothers

The presence of COVID-19 antibodies in the maternal circulation is assumed to be protective for newborns against SARS-CoV-2 infection. We investigated whether maternal COVID-19 antibodies crossed the transplacental barrier and whether there was any difference in the hematological parameters of neonates born to mothers who recovered from COVID-19 during pregnancy. The cross-sectional study was conducted at the Saidu Group of Teaching Hospitals, located in Swat, Khyber Pakhtunkhwa. After obtaining written informed consent, 115 healthy, unvaccinated mother-neonate dyads were included. A clinical history of COVID-19-like illness, laboratory-confirmed diagnosis, and contact history were obtained. Serum samples from mothers and neonates were tested for SARS-CoV-2 anti-receptor-binding domain (anti-RBD) IgG antibodies. Hematological parameters were assessed with complete blood counts (CBC) and peripheral blood smear examinations. The study population consisted of 115 mothers, with a mean age of 29.44 ± 5.75 years, and most women (68/115 (59.1%)) were between 26 and 35 years of age. Of these mothers, 88/115 (76.5 percent) tested positive for SARS-CoV-2 anti-RBD IgG antibodies, as did 83/115 (72.2 percent) neonatal cord blood samples. The mean levels of SARS-CoV-2 IgG antibodies in maternal and neonatal blood were 19.86 ± 13.82 (IU/mL) and 16.16 ± 12.90 (IU/mL), respectively, indicating that maternal antibodies efficiently crossed the transplacental barrier with an antibody transfer ratio of 0.83. The study found no significant difference in complete blood count (CBC) parameters between seropositive and seronegative mothers, nor between neonates born to seropositive and seronegative mothers.

Combination of Recombinant Proteins S1/N and RBD/N as Potential Vaccine Candidates

Despite all successful efforts to develop a COVID-19 vaccine, the need to evaluate alternative antigens to produce next-generation vaccines is imperative to target emerging variants. Thus, the second generation of COVID-19 vaccines employ more than one antigen from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to induce an effective and lasting immune response. Here, we analyzed the combination of two SARS-CoV-2 viral antigens that could elicit a more durable immune response in both T- and B-cells. The nucleocapsid (N) protein, Spike protein S1 domain, and receptor binding domain (RBD) of the SARS-CoV-2 spike surface glycoproteins were expressed and purified in a mammalian expression system, taking into consideration the posttranscriptional modifications and structural characteristics. The immunogenicity of these combined proteins was evaluated in a murine model. Immunization combining S1 or RBD with the N protein induced higher levels of IgG antibodies, increased the percentage of neutralization, and elevated the production of cytokines TNF-α, IFN-γ, and IL-2 compared to the administration of a single antigen. Furthermore, sera from immunized mice recognized alpha and beta variants of SARS-CoV-2, which supports ongoing clinical results on partial protection in vaccinated populations, despite mutations. This study identifies potential antigens for second-generation COVID-19 vaccines.

How Protective are Antibodies to SARS-CoV-2, the Main Weapon of the B-Cell Response?

Since the beginning of the Coronavirus disease (COVID)-19 pandemic in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for more than 600 million infections and 6.5 million deaths worldwide. Given the persistence of SARS-CoV-2 and its ability to develop new variants, the implementation of an effective and long-term herd immunity appears to be crucial to overcome the pandemic. While a vast field of research has focused on the role of humoral immunity against SARS-CoV-2, a growing body of evidence suggest that antibodies alone only confer a partial protection against infection of reinfection which could be of high importance regarding the strategic development goals (SDG) of the United Nations (UN) and in particular UN SDG3 that aims towards the realization of good health and well being on a global scale in the context of the COVID-19 pandemic.In this review, we highlight the role of humoral immunity in the host defense against SARS-CoV-2, with a focus on highly neutralizing antibodies. We summarize the results of the main clinical trials leading to an overall disappointing efficacy of convalescent plasma therapy, variable results of monoclonal neutralizing antibodies in patients with COVID-19 but outstanding results for the mRNA based vaccines against SARS-CoV-2. Finally, we advocate that beyond antibody responses, the development of a robust cellular immunity against SARS-CoV-2 after infection or vaccination is of utmost importance for promoting immune memory and limiting disease severity, especially in case of (re)-infection by variant viruses.

Viral T-cell epitopes - Identification, characterization and clinical application

T-cell immunity, mediated by CD4⁺ and CD8⁺ T cells, represents a cornerstone in the control of viral infections. Virus-derived T-cell epitopes are represented by human leukocyte antigen (HLA)-presented viral peptides on the surface of virus-infected cells. They are the prerequisite for the recognition of infected cells by T cells. Knowledge of viral T-cell epitopes provides on the one hand a diagnostic tool to decipher protective T-cell immune responses in the human population and on the other hand various prophylactic and therapeutic options including vaccination approaches and the transfer of virus-specific T cells. Such approaches have already been proven to be effective against various viral infections, particularly in immunocompromised patients lacking sufficient humoral, antibody-based immune response. This review provides an overview on the state of the art as well as current studies regarding the identification and characterization of viral T-cell epitopes and approaches of clinical application. In the first chapter in silico prediction tools and direct, mass spectrometry-based identification of viral T-cell epitopes is compared. The second chapter provides an overview of commonly used assays for further characterization of T-cell responses and phenotypes. The final chapter presents an overview of clinical application of viral T-cell epitopes with a focus on human immunodeficiency virus (HIV), human cytomegalovirus (HCMV) and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), being representatives of relevant viruses.

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.

Duration of immune protection of SARS-CoV-2 natural infection against reinfection

BACKGROUND

The future of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic hinges on virus evolution and duration of immune protection of natural infection against reinfection. We investigated the duration of protection afforded by natural infection, the effect of viral immune evasion on duration of protection and protection against severe reinfection, in Qatar, between 28 February 2020 and 5 June 2022.

METHODS

Three national, matched, retrospective cohort studies were conducted to compare the incidence of SARS-CoV-2 infection and coronavirus disease 2019 (COVID-19) severity among unvaccinated persons with a documented SARS-CoV-2 primary infection, to incidence among those infection-naïve and unvaccinated. Associations were estimated using Cox proportional hazard regression models.

RESULTS

Effectiveness of pre-Omicron primary infection against pre-Omicron reinfection was 85.5% [95% confidence interval (CI): 84.8-86.2%]. Effectiveness peaked at 90.5% (95% CI: 88.4-92.3%) in the 7th month after the primary infection, but waned to ~ 70% by the 16th month. Extrapolating this waning trend using a Gompertz curve suggested an effectiveness of 50% in the 22nd month and < 10% by the 32nd month. Effectiveness of pre-Omicron primary infection against Omicron reinfection was 38.1% (95% CI: 36.3-39.8%) and declined with time since primary infection. A Gompertz curve suggested an effectiveness of < 10% by the 15th month. Effectiveness of primary infection against severe, critical or fatal COVID-19 reinfection was 97.3% (95% CI: 94.9-98.6%), irrespective of the variant of primary infection or reinfection, and with no evidence for waning. Similar results were found in sub-group analyses for those ≥50 years of age.

CONCLUSIONS

Protection of natural infection against reinfection wanes and may diminish within a few years. Viral immune evasion accelerates this waning. Protection against severe reinfection remains very strong, with no evidence for waning, irrespective of variant, for over 14 months after primary infection.

High Seroprevalence of Anti-SARS-CoV-2 IgM/IgG among Inhabitants of Sakaka City, Aljouf, Saudi Arabia

(1) Backgrounds and Objectives: The global battle to contain the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is still ongoing. This cross-sectional study aimed to detect the seroprevalence of anti-SARS-CoV-2 IgM/IgG among previously symptomatic/asymptomatic and vaccinated/unvaccinated inhabitants of Sakaka City, Aljouf, Saudi Arabia. (2) Methods: Blood samples of 400 participants were tested for the presence of anti-SARS-CoV-2 IgM/IgG using colloidal gold immuno-chromatography lateral flow immunoassay cards. (3) Results: The prevalence of anti-SARS-CoV-2 IgM and IgG positivity was 45.8% and 42.3%, respectively. Statistically significant correlations (p < 0.05) were found between the previous RT-PCR testing for SARS-CoV-2-RNA and positivity for IgM and/or IgG. The highest seroprevalence of IgM and IgG were detected among smokers, participants aged ≥40 years, and patients with chronic diseases. Although most of the participants (58.5%) did not previously experience COVID-19 like symptoms, the anti-SARS-CoV-2 IgM and IgG seropositivity amongst them was 49.1% and 25.6%, respectively, with higher seroprevalence among males than females. At the time of the study, the SARS-CoV-2 vaccination rate at our locality in Saudi Arabia was 43.8% with statistically significant correlation (p < 0.001) between being vaccinated and anti-SARS-CoV-2 IgM and/or IgG positivity, with more positivity after receiving the second vaccine dose. (4) Conclusions: Public assessment reflects the real scale of the disease exposure among the community and helps in identifying the asymptomatic carriers that constitute a major problem for controlling the SARS-CoV-2. To limit the spread of the virus, rigorous implementation of large-scale SARS-CoV-2 vaccination and anti-SARS-CoV-2 serological testing strategies should be empowered.

SARS-CoV-2-specicific humoral immunity in convalescent patients with mild COVID-19 is supported by CD4+ T-cell help and negatively correlated with Alphacoronavirus-specific antibody titer

This study aimed at investigating the nature of SARS-CoV-2-specific immunity in patients with mild COVID-19 and sought to identify parameters most relevant for the generation of neutralizing antibody responses in convalescent COVID-19 patients. In the majority of the examined patients a cellular as well as humoral immune response directed to SARS-CoV-2 was detected. The finding of an anti-SARS-CoV-2-reactive cellular immune response in healthy individuals suggests a pre-existing immunity to various common cold HCoVs which share close homology with SARS-CoV-2. The humoral immunity to the S protein of SARS-CoV-2 detected in convalescent COVID-19 patients correlates with the presence of SARS-CoV-2-reactive CD4⁺ T cells expressing T_h1 cytokines. Remarkably, an inverse correlation of SARS-CoV-2 S protein-specific IgGs with HCoV-NL63 and HCoV-229E S1 protein-specific IgGs suggests that pre-existing immunity to Alphacoronaviruses might have had an inhibitory imprint on the immune response to SARS-CoV-2-infection in the examined patients with mild COVID-19.

Susceptibility to SARS-CoV-2 omicron following ChAdOx1 nCoV-19 and BNT162b2 versus CoronaVac vaccination

The emergence of SARS-CoV-2 variants raises concerns of reduced COVID-19 vaccine efficacy. We investigated the humoral immunity in uninfected and previously infected ChAdOx1 nCoV-19, BNT162b2 and CoronaVac vaccinees, who have received complete regimes of vaccines by means of a SARS-CoV-2 surrogate virus blocking test. The ChAdOx1 nCoV-19 (p = 0.0013) and BNT162b2 (p = 0.0005) vaccines induced significant higher blocking activity with longer durability against the Spike (S) protein receptor binding domain (RBD) of wild type SARS-CoV-2 than the CoronaVac vaccine in uninfected vaccinees. Prior infection improved protection in the CoronaVac vaccinees. Subsequent investigation on the breadth of SARS-CoV-2 vaccine-induced antibody blocking responses, revealed that all vaccine platforms cross-protected uninfected vaccinees against all variant of concerns, except Omicron. Prior infection protected the ChAdOx1 nCoV-19 and BNT162b2 vaccinees against Omicron but not CoronaVac vaccinees. Our study suggests that vaccines that induce broader sterilizing immunity are essential to fight against fast-emerging variants.

Concordance of B- and T-cell responses to SARS-CoV-2 infection, irrespective of symptoms suggestive of COVID-19

This study assessed T-cell responses in individuals with and without a positive antibody response to SARS-CoV-2, in symptomatic and asymptomatic individuals during the COVID-19 pandemic. Participants were drawn from the TwinsUK cohort, grouped by (a) presence or absence of COVID-associated symptoms (S+, S-), logged prospectively through the COVID Symptom Study app, and (b) anti-IgG Spike and anti-IgG Nucleocapsid antibodies measured by ELISA (Ab+, Ab-), during the first wave of the UK pandemic. T-cell helper and regulatory responses after stimulation with SARS-CoV-2 peptides were assessed. Thirty-two participants were included in the final analysis. Fourteen of 15 with IgG Spike antibodies had a T-cell response to SARS-CoV-2-specific peptides; none of 17 participants without IgG Spike antibodies had a T-cell response (χ2 : 28.2, p < 0.001). Quantitative T-cell responses correlated strongly with fold-change in IgG Spike antibody titer (ρ = 0.79, p < 0.0001) but not to symptom score (ρ = 0.17, p = 0.35). Humoral and cellular immune responses to SARS-CoV-2 are highly correlated. We found no evidence of cellular immunity suggestive of SARS-CoV2 infection in individuals with a COVID-19-like illness but negative antibodies.

Immune response induced by novel coronavirus infection

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV)-2 has been prominent around the world since it was first discovered, affecting more than 100 million people. Although the symptoms of most infected patients are not serious, there is still a considerable proportion of patients who need hospitalization and even develop fatal symptoms such as cytokine storms, acute respiratory distress syndrome and so on. Cytokine storm is usually described as a collection of clinical manifestations caused by overactivation of the immune system, which plays an important role in tissue injury and multiorgan failure. The immune system of healthy individuals is composed of two interrelated parts, the innate immune system and the adaptive immune system. Innate immunity is the body's first line of defense against viruses; it can quickly perceive viruses through pattern recognition receptors and activate related inflammatory pathways to clear pathogens. The adaptive immune system is activated by specific antigens and is mainly composed of CD4+ T cells, CD8+ T cells and B cells, which play different roles in viral infection. Here, we discuss the immune response after SARS-CoV-2 infection. In-depth study of the recognition of and response of innate immunity and adaptive immunity to SARS-CoV-2 will help to prevent the development of critical cases and aid the exploration of more targeted treatments.

Recent advances in the vaccine development for the prophylaxis of SARS Covid-19

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused Coronavirus Disease 2019 (COVID-19) is currently a global pandemic that has wreaked havoc on public health, lives, and the global economy. The present COVID-19 outbreak has put pressure on the scientific community to develop medications and vaccinations to combat COVID-19. However, according to highly optimistic forecasts, we could not have a COVID-19 vaccine until September 2020. This is due to the fact that a successful COVID-19 vaccine will necessitate a careful validation of effectiveness and adverse reactivity given that the target vaccine population includes high-risk people over 60, particularly those with severe co-morbid conditions, frontline healthcare professionals, and those involved in essential industrial sectors. For passive immunization, which is being considered for Covid-19, there are several platforms for vaccine development, each with its own advantages and disadvantages. The COVID-19 pandemic, which is arguably the deadliest in the last 100 years after the Spanish flu, necessitates a swift assessment of the various approaches for their ability to incite protective immunity and safety to prevent unintended immune potentiation, which is crucial to the pathogenesis of this virus. Considering the pandemic's high fatality rate and rapid spread, an efficient vaccination is critical for its management. As a result, academia, industry, and government are collaborating in unprecedented ways to create and test a wide range of vaccinations. In this review, we summarize the Covid-19 vaccine development initiatives, recent trends, difficulties, comparison between traditional vaccines development and Covid-19 vaccines development also listed the approved/authorized, phase-3 and pre-clinical trials Covid-19 vaccines in different countries.

Clinical outcomes and immune responses to SARS-CoV-2 vaccination in severe aplastic anaemia

Patients with severe aplastic anaemia (SAA) are often not vaccinated against viruses due to concerns of ineffective protective antibody response and potential for pathogenic global immune system activation, leading to relapse. We evaluated the impact of COVID‐19 vaccination on haematological indices and disease status and characterized the humoural and cellular responses to vaccination in 50 SAA patients, who were previously treated with immunosuppressive therapy (IST). There was no significant difference in haemoglobin (p = 0.52), platelet count (p = 0.67), absolute lymphocyte (p = 0.42) and neutrophil (p = 0.98) counts prior to and after completion of vaccination series. Relapse after vaccination, defined as a progressive decline in counts requiring treatment, occurred in three patients (6%). Humoural response was detectable in 90% (28/31) of cases by reduction in an in‐vitro Angiotensin II Converting Enzyme (ACE2) binding and neutralization assay, even in patients receiving ciclosporin (10/11, 90.1%). Comparison of spike‐specific T‐cell responses in 27 SAA patients and 10 control subjects revealed qualitatively similar CD4⁺ Th1‐dominant responses to vaccination. There was no difference in CD4⁺ (p = 0.77) or CD8⁺ (p = 0.74) T‐cell responses between patients on or off ciclosporin therapy at the time of vaccination. Our data highlight appropriate humoural and cellular responses in SAA previously treated with IST and true relapse after vaccination is rare.

SARS-CoV-2 infection: Pathogenesis, Immune Responses, Diagnosis

COVID-19 has emerged as the most alarming infection of the present time instigated by the virus SARS-CoV-2. In spite of advanced research technologies, the exact pathophysiology and treatment of the condition still need to be explored. However, SARS-CoV-2 has several structural and functional similarities that resemble SARS-CoV and MERS-CoV which may be beneficial in exploring the possible treatment and diagnostic strategies for SARS-CoV-2. This review discusses the pathogen phenotype, genotype, replication, pathophysiology, elicited immune response and emerging variants of SARS-CoV-2 and their similarities with other similar viruses. SARS-CoV-2 infection is detected by a number of diagnostics techniques, their advantages and limitations are also discussed in detail. The review also focuses on nanotechnology-based easy and fast detection of SARS-CoV-2 infection. Various pathways which might play a vital role during SARS-CoV-2 infection have been elaborately discussed since immune response plays a major role during viral infections.

Immune response to SARS-CoV-2 vaccination in relation to peripheral immune cell profiles among patients with multiple sclerosis receiving ocrelizumab

BACKGROUND

Vaccination has proven to be effective in preventing SARS-CoV-2 transmission and severe disease courses. However, immunocompromised patients have not been included in clinical trials and real-world clinical data point to an attenuated immune response to SARS-CoV-2 vaccines among patients with multiple sclerosis (MS) receiving immunomodulatory therapies.

METHODS

We performed a retrospective study including 59 ocrelizumab (OCR)-treated patients with MS who received SARS-CoV-2 vaccination. Anti-SARS-CoV-2-antibody titres, routine blood parameters and peripheral immune cell profiles were measured prior to the first (baseline) and at a median of 4 weeks after the second vaccine dose (follow-up). Moreover, the SARS-CoV-2-specific T cell response and peripheral B cell subsets were analysed at follow-up. Finally, vaccination-related adverse events were assessed.

RESULTS

After vaccination, we found anti-SARS-CoV-2(S) antibodies in 27.1% and a SARS-CoV-2-specific T cell response in 92.7% of MS cases. T cell-mediated interferon (IFN)-γ release was more pronounced in patients without anti-SARS-CoV-2(S) antibodies. Antibody titres positively correlated with peripheral B cell counts, time since last infusion and total IgM levels. They negatively correlated with the number of previous infusion cycles. Peripheral plasma cells were increased in antibody-positive patients. A positive correlation between T cell response and peripheral lymphocyte counts was observed. Moreover, IFN-γ release was negatively correlated with the time since the last infusion.

CONCLUSION

In OCR-treated patients with MS, the humoral immune response to SARS-CoV-2 vaccination is attenuated while the T cell response is preserved. However, it is still unclear whether T or B cell-mediated immunity is required for effective clinical protection. Nonetheless, given the long-lasting clinical effects of OCR, monitoring of peripheral B cell counts could facilitate individualised treatment regimens and might be used to identify the optimal time to vaccinate.

SARS-CoV-2 vaccine-induced antibody and T cell response in SARS-CoV-1 survivors

Preexisting immunity cross-reactive to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in SARS-CoV-1 survivors suggests that a coronavirus disease 2019 vaccine may boost such preexisting cross-reactive memory T cells. We measure SARS-CoV-2 and SARS-CoV-1 spike-specific neutralizing antibody and T cell responses in a single dose of Ad5-nCoV-immunized SARS-CoV-1 survivors 6 months after vaccination. Compared with Ad5-nCoV-immunized naive healthy individuals (NHIs), vaccination of Ad5-nCoV in SARS-CoV-1 survivors boosts the antibody response against SARS-CoV-1 but induces a limited neutralizing antibody that is capable of neutralizing SARS-CoV-2 variants of concern, and nearly all serum samples lose neutralization to Omicron subvariants. Immunized SARS-CoV-1 survivors produce a T cell response to SARS-CoV-2 comparable with that of Ad5-nCoV-immunized NHIs. However, a robust cross-reactive T cell response to SARS-CoV-1 is identified in immunized SARS-CoV-1 survivors compared with Ad5-nCoV-immunized NHIs. These findings suggest that vaccination with Ad5-nCoV elicits a stronger neutralizing antibody and cross-reactive T cell responses against SARS-CoV-1 in SARS-CoV-1 survivors.

Differential persistence of neutralizing antibody against SARS-CoV-2 in post immunized Bangladeshi population

Development of effective vaccines have been immensely welcomed by the world to prevent the transmission of SARS-CoV-2. However, the duration and clinical implications of antibody-mediated natural immunity in SARS-CoV-2 have not been adequately elucidated alongside some other immune system transforming factors. In a cohort study, we measured NAb titer following the 2nd immunization dosage of the CoviShield (AZD1222) vaccine. The enzyme-linked immunoassay was used to look for SARS-CoV-2—specific NAb. We measured NAb at 30 days after the 2nd dosage of immunization and > 96% titer was detected in 42.9% of subjects, but only 5.1% of subjects retained the same level after 180 days. The median NAb titer dropped significantly, from 92% at 30 days to 58% at 180 days (p < 0.001). Besides, there were significant differences observed in NAb titer after 180 days by age, sex, COVID-19 infection, tobacco use, and asthma patients. However, SARS-CoV-2 infection along with two dosages of immunization upheld NAb titer (p < 0.001) even at the end of the study period.

Two-years antibody responses following SARS-CoV-2 infection in humans: A study protocol

The long-term antibody response to the novel SARS-CoV-2 in infected patients and their residential neighborhood remains unknown in Indonesia. This information will provide insights into the antibody kinetics over a relatively long period as well as transmission risk factors in the community. We aim to prospectively observe and determine the kinetics of the anti-SARS-CoV-2 antibody for 2 years after infection in relation to disease severity and to determine the risk and protective factors of SARS CoV-2 infections in the community. A cohort of RT-PCR confirmed SARS-CoV-2 patients (case) will be prospectively followed for 2 years and will be compared to a control population. The control group comprises SARS-CoV-2 non-infected people who live within a one-kilometer radius from the corresponding case (location matching). This study will recruit at least 165 patients and 495 controls. Demographics, community variables, behavioral characteristics, and relevant clinical data will be collected. Serum samples taken at various time points will be tested for IgM anti-Spike protein of SARS-CoV-2 and IgG anti-Spike RBD of SARS-CoV-2 by using Chemiluminescent Microparticle Immunoassay (CMIA) method. The Kaplan-Meier method will be used to calculate cumulative seroconversion rates, and their association with disease severity will be estimated by logistic regression. The risk and protective factors associated with the SARS-CoV-2 infection will be determined using conditional (matched) logistic regression and presented as an odds ratio and 95% confidence interval.

T cell perturbations persist for at least 6 months following hospitalization for COVID-19

COVID-19 is being extensively studied, and much remains unknown regarding the long-term consequences of the disease on immune cells. The different arms of the immune system are interlinked, with humoral responses and the production of high-affinity antibodies being largely dependent on T cell immunity. Here, we longitudinally explored the effect COVID-19 has on T cell populations and the virus-specific T cells, as well as neutralizing antibody responses, for 6-7 months following hospitalization. The CD8⁺ TEMRA and exhausted CD57⁺ CD8⁺ T cells were markedly affected with elevated levels that lasted long into convalescence. Further, markers associated with T cell activation were upregulated at inclusion, and in the case of CD69⁺ CD4⁺ T cells this lasted all through the study duration. The levels of T cells expressing negative immune checkpoint molecules were increased in COVID-19 patients and sustained for a prolonged duration following recovery. Within 2-3 weeks after symptom onset, all COVID-19 patients developed anti-nucleocapsid IgG and spike-neutralizing IgG as well as SARS-CoV-2-specific T cell responses. In addition, we found alterations in follicular T helper (TFH) cell populations, such as enhanced TFH-TH2 following recovery from COVID-19. Our study revealed significant and long-term alterations in T cell populations and key events associated with COVID-19 pathogenesis.

SARS-CoV-2 Infection: Host Response, Immunity, and Therapeutic Targets

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in a global pandemic with severe socioeconomic effects. Immunopathogenesis of COVID-19 leads to acute respiratory distress syndrome (ARDS) and organ failure. Binding of SARS-CoV-2 spike protein to human angiotensin-converting enzyme 2 (hACE2) on bronchiolar and alveolar epithelial cells triggers host inflammatory pathways that lead to pathophysiological changes. Proinflammatory cytokines and type I interferon (IFN) signaling in alveolar epithelial cells counter barrier disruption, modulate host innate immune response to induce chemotaxis, and initiate the resolution of inflammation. Here, we discuss experimental models to study SARS-CoV-2 infection, molecular pathways involved in SARS-CoV-2-induced inflammation, and viral hijacking of anti-inflammatory pathways, such as delayed type-I IFN response. Mechanisms of alveolar adaptation to hypoxia, adenosinergic signaling, and regulatory microRNAs are discussed as potential therapeutic targets for COVID-19.

COVID-19 and plasma cells: Is there long-lived protection?

Infection with SARS-CoV-2, the etiology of the ongoing COVID-19 pandemic, has resulted in over 450 million cases with more than 6 million deaths worldwide, causing global disruptions since early 2020. Memory B cells and durable antibody protection from long-lived plasma cells (LLPC) are the mainstay of most effective vaccines. However, ending the pandemic has been hampered by the lack of long-lived immunity after infection or vaccination. Although immunizations offer protection from severe disease and hospitalization, breakthrough infections still occur, most likely due to new mutant viruses and the overall decline of neutralizing antibodies after 6 months. Here, we review the current knowledge of B cells, from extrafollicular to memory populations, with a focus on distinct plasma cell subsets, such as early-minted blood antibody-secreting cells and the bone marrow LLPC, and how these humoral compartments contribute to protection after SARS-CoV-2 infection and immunization.

Progress in COVID research and developments during pandemic

The pandemic respiratory disease COVID-19 has spread over the globe within a small span of time. Generally, there are two important points are being highlighted and considered towards the successful diagnosis and treatment process. The first point includes the reduction of the rate of infections and the next one is the decrease of the death rate. The major threat to public health globally progresses due to the absence of effective medication and widely accepted immunization for the COVID-19. Whereas, understanding of host susceptibility, clinical features, adaptation of COVID-19 to new environments, asymptomatic infection is difficult and challenging. Therefore, a rapid and an exact determination of pathogenic viruses play an important role in deciding treatments and preventing pandemic to save the people's lives. It is urgent to fix a standardized diagnostic approach for detecting the COVID-19. Here, this systematic review describes all the current approaches using for screening and diagnosing the COVID-19 infectious patient. The renaissance in pathogen due to host adaptability and new region, facing creates several obstacles in diagnosis, drug, and vaccine development process. The study shows that adaptation of accurate and affordable diagnostic tools based on candidate biomarkers using sensor and digital medicine technology can deliver effective diagnosis services at the mass level. Better prospects of public health management rely on diagnosis with high specificity and cost-effective manner along with multidisciplinary research, specific policy, and technology adaptation. The proposed healthcare model with defined road map represents effective prognosis system.

SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development

The pandemic caused by the SARS-CoV-2 virus, the agent responsible for the COVID-19 disease, has affected millions of people worldwide. There is constant search for new therapies to either prevent or mitigate the disease. Fortunately, we have observed the successful development of multiple vaccines. Most of them are focused on one viral envelope protein, the spike protein. However, such focused approaches may contribute for the rise of new variants, fueled by the constant selection pressure on envelope proteins, and the widespread dispersion of coronaviruses in nature. Therefore, it is important to examine other proteins, preferentially those that are less susceptible to selection pressure, such as the nucleocapsid (N) protein. Even though the N protein is less accessible to humoral response, peptides from its conserved regions can be presented by class I Human Leukocyte Antigen (HLA) molecules, eliciting an immune response mediated by T-cells. Given the increased number of protein sequences deposited in biological databases daily and the N protein conservation among viral strains, computational methods can be leveraged to discover potential new targets for SARS-CoV-2 and SARS-CoV-related viruses. Here we developed SARS-Arena, a user-friendly computational pipeline that can be used by practitioners of different levels of expertise for novel vaccine development. SARS-Arena combines sequence-based methods and structure-based analyses to (i) perform multiple sequence alignment (MSA) of SARS-CoV-related N protein sequences, (ii) recover candidate peptides of different lengths from conserved protein regions, and (iii) model the 3D structure of the conserved peptides in the context of different HLAs. We present two main Jupyter Notebook workflows that can help in the identification of new T-cell targets against SARS-CoV viruses. In fact, in a cross-reactive case study, our workflows identified a conserved N protein peptide (SPRWYFYYL) recognized by CD8⁺ T-cells in the context of HLA-B7⁺. SARS-Arena is available at https://github.com/KavrakiLab/SARS-Arena.

Clinical status of patients 1 year after hospital discharge following recovery from COVID-19: a prospective cohort study

Background

The long-term clinical status of coronavirus disease 2019 (COVID-19) in recovered patients remains largely unknown. This prospective cohort study evaluated clinical status of COVID-19 and explored the associated risk factors.

Methods

At the outpatient visit, patients underwent routine blood tests, physical examinations, pulmonary function tests, 6-min walk test, high-resolution computed tomography (CT) of the chest, and extrapulmonary organ function tests.

Results

230 patients were analyzed. Half (52.7%) reported at least one symptom, most commonly fatigue (20.3%) and sleep difficulties (15.8%). Anxiety (8.2%), depression (11.3%), post-traumatic symptoms (10.3%), and sleep disorders (26.3%) were also reported. Diffusion impairments were found in 35.4% of the patients. Abnormal chest CT scans were present in 63.5% of the patients, mainly reticulation and ground-glass opacities. Further, a persistent decline in kidney function was observed after discharge. SARS-CoV-2-specific antibodies of IgA, IgG, and IgM were positive in 56.4%, 96.3%, and 15.2% of patients, respectively. Multivariable logistic regression showed that disease severity, age, and sex were closely related to patient recovery.

Conclusions

One year after hospital discharge, patients recovered from COVID-19 continued to experience both pulmonary and extrapulmonary dysfunction. While paying attention to pulmonary manifestations of COVID-19, follow-up studies on extrapulmonary manifestations should be strengthened.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13613-022-01034-4.

Seasonal coronaviruses and SARS-CoV-2: effects of preexisting immunity during the COVID-19 pandemic

Although the coronavirus disease 2019 (COVID-19) epidemic is still ongoing, vaccination rates are rising slowly and related treatments and drugs are being developed. At the same time, there is increasing evidence of preexisting immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans, mainly consisting of preexisting antibodies and immune cells (including T cells and B cells). The presence of these antibodies is mainly due to the seasonal prevalence of four common coronavirus types, especially OC43 and HKU1. The accumulated relevant evidence has suggested that the target of antibodies is mainly the S2 subunit of S protein, followed by evolutionary conservative regions such as the nucleocapsid (N) protein. Additionally, preexisting memory T and B cells are also present in the population. Preexisting antibodies can help the body protect against SARS-CoV-2 infection, reduce the severity of COVID-19, and rapidly increase the immune response post-infection. These multiple effects can directly affect disease progression and even the likelihood of death in certain individuals. Besides the positive effects, preexisting immunity may also have negative consequences, such as antibody-dependent enhancement (ADE) and original antigenic sin (OAS), the prevalence of which needs to be further established. In the future, more research should be focused on evaluating the role of preexisting immunity in COVID-19 outcomes, adopting appropriate policies and strategies for fighting the pandemic, and vaccine development that considers preexisting immunity.

Seroprevalence of immunoglobulin G antibodies against SARS-CoV-2 in Cyprus

Monitoring the levels of IgG antibodies against the SARS-CoV-2 is important during the coronavirus disease 2019 (COVID-19) pandemic, to plan an adequate and evidence-based public health response. After this study we report that the plasma levels of IgG antibodies against SARS-CoV-2 spike protein were higher in individuals with evidence of prior infection who received at least one dose of either an mRNA-based vaccine (Comirnaty BNT162b2/Pfizer-BioNTech or Spikevax mRNA-1273/Moderna) or an adenoviral-based vaccine (Vaxzervia ChAdOx1 nCoV-19 /Oxford-Astra Zeneca) (n = 39) compared to i) unvaccinated individuals with evidence of prior infection with SARS-CoV-2 (n = 109) and ii) individuals without evidence of prior infection with SARS-CoV-2 who received one or two doses of one of the aforementioned vaccines (n = 342). Our analysis also revealed that regardless of the vaccine technology (mRNA-based and adenoviral vector-based) two doses achieved high anti- SARS-CoV-2 IgG responses. Our results indicate that vaccine-induced responses lead to higher levels of IgG antibodies compared to those produced following infection with the virus. Additionally, in agreement with previous studies, our results suggest that among individuals previously infected with SARS-CoV-2, even a single dose of a vaccine is adequate to elicit high levels of antibody response.

Antibody- and T Cell-Dependent Responses Elicited by a SARS-CoV-2 Adenoviral-Based Vaccine in a Socially Vulnerable Cohort of Elderly Individuals

BACKGROUND

In spite of compelling evidence demonstrating safety and immunogenicity of adenoviral-based SARS-CoV-2 vaccines in the general population, its effects in socially vulnerable elderly individuals are poorly understood. Here we aimed to investigate the efficacy of two doses of combined vector vaccine, the Gam-COVID-Vac (Sputnik-V vaccine), at 14, 42, and 180 days after immunization, in a nursing home for underprivileged population and homeless individuals.

METHODS

A phase 3, open-label clinical trial involving administration of two adenoviral vectors (Ad26-Ad5) vaccine, in elderly individuals over the ages of 60 years was performed. SARS-CoV-2 Spike RBD-specific IgG antibodies at days 21-, 42- and 180 post-vaccination was analyzed in sera of individuals receiving two doses of the Sputnik-V vaccine with an interval of 21 days. SARS-CoV-2-specific CD8+ T cell responses, measured by intracellular tumor necrosis factor (TNF) was determined by flow cytometry following antigen-specific cultures.

RESULTS

A total of 72 elderly adults with a mean age of 72.6 ± 9.5 years-old was selected after applying the inclusion criteria, all corresponding to an underprivileged population. Two-doses vaccination with Sputnik-V vaccine elicited an antibody-mediated immune response (revealed by quantitative detection of SARS-CoV-2-specific IgG antibodies, CMIA) 70% at day 21, 90% at day 42, and 66.1% at day 180. Fully vaccinated individuals had robust SARS-CoV-2-specific T cell responses, evidenced by TNF production in CD4+ and CD8+ T cells in all time periods analyzed.

CONCLUSION

Six months after receipt of the second dose of the Gam-COVID-Vac vaccine, SARS-CoV-2-specific IgG levels declined substantially among the tested population, whereas CD4+ and CD8+ T-cell-mediated immunity remained at high levels. These data suggest that two doses of combined adenoviral-based vaccine elicits a considerable level of SARS-CoV-2 immune responses in elderly individuals, highlighting its safety and immunogenicity in this highly vulnerable population.

The Pre-Vaccination Donated Blood Is Free from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) but Is Rich with Anti-SARS-CoV-2 Antibodies: A Cross-Section Saudi Study

(1) Backgrounds and Objectives: Since its discovery, information about the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has spread rapidly. However, many issues remain unresolved. Coronaviruses are primarily transmitted through respiratory secretions. The possibility of transmission via donated blood transfusion deserves studying. This is the first study in Saudi Arabia to look at pre-vaccination donated blood anti-SARS-CoV-2 antibody content as a marker for virus transmission via viral RNA positive blood and/or the potential therapeutic value of convalescent plasma. (2) Methods: A total of 300 blood samples were sequentially collected from unvaccinated donors who donated blood to the blood bank of Prince Mutaib Bin Abdulaziz Hospital in Sakaka, Al-Jouf, Saudi Arabia. Specific ELISA was used to detect anti-SARS-CoV-2 IgG and IgM antibodies. SARS-CoV-2 was detected using specific real-time reverse-transcription PCR (rRT-PCR). (3) Results: The prevalence of anti-SARS-CoV-2 IgG was low (9%), whereas the prevalence of anti-SARS-CoV-2 IgM was high (65%). Relevant demographics, anthropometrics, and lifestyle factors revealed significant associations (p < 0.05) between IgM-positivity only vs. age (age group 21−30 years), postgraduate education, no history of international travel, IgG-negativity, and absence of experience with COVID-19-like symptoms. Furthermore, there are significant associations (p < 0.05) between IgG-positivity only vs. age (age group 21−30 years), postgraduate education, and being a non-healthcare worker. All donors in the anti-SARS-CoV-2 IgG-positive group (n = 27) had previously experienced symptoms similar to COVID-19 (p < 0.001) and most of them (n = 24) showed anti-SARS-CoV-2 IgM-positive test (p = 0.006). However, all the samples tested negative for SARS-CoV-2 RNA using rRT-PCR. (4) Conclusion: Our findings add to the growing body of evidence that donated blood is safe, with the added benefit of convalescent plasma rich in potentially neutralizing IgG and IgM against SARS-CoV-2.

COVID-19 hastalarının semptomlarına ve pnömoni varlığına göre antikor tepkileri

Introduction: The aim of the study was to examine the 30-day total SARS-CoV-2 antibody positivity in patients across a clinical spectrum ranging from asymptomatic to pneumonia.Methods: This prospective cohort study consisted of 51 consecutive patients who were RT-PCR positive and diagnosed COVID-19 pneumonia (Group 1) and 58 consecutive patients who were also RT-PCR positive but were asymptomatic or had mild symptoms (Group 2). On the 30th day from the date of symptom onset, the patients were called for examination and blood samples were taken for the detection of SARS-CoV-2 antibodies.Results: Patients with pneumonia, fever, muscle pain, and loss of taste and smell had significantly higher rates of antibody positivity (p= 0.001, 0.003, 0.030, and 0.018, respectively). Antibody positivity was found to be significantly higher in patients with at least one symptom on admission compared to asymptomatic patients (p = 0.001). While the antibody positivity rate was 96.1% in Group 1 (patients with pneumonia), it was 50% in Group 2 (patients without pneumonia), and 77.7% in patients with at least one symptom on admission compared to 33.3% in asymptomatic patients (p=0.001).Conclusions: Patients with COVID-19 pneumonia have significantly higher disease-specific total antibody positivity rates than patients without pneumonia. Considering the 50% antibody positivity in patients who had COVID-19 infection who were asymptomatic or had symptoms other than pneumonia, the issue of COVID-19 re-infection and immunity is much more important than it appears. 

A framework for reconstructing SARS-CoV-2 transmission dynamics using excess mortality data

The transmission dynamics and burden of SARS-CoV-2 in many regions of the world is still largely unknown due to the scarcity of epidemiological analyses and lack of testing to assess the prevalence of disease. In this work, we develop a quantitative framework based on excess mortality data to reconstruct SARS-CoV-2 transmission dynamics and assess the level of underreporting in infections and deaths. Using weekly all-cause mortality data from Iran, we are able to show a strong agreement between our attack rate estimates and seroprevalence measurements in each province and find significant heterogeneity in the level of exposure across the country with 11 provinces reaching near 100% attack rates. Despite having a young population, our analysis reveals that incorporating limited access to medical services in our model, coupled with undercounting of COVID-19-related deaths, leads to estimates of infection fatality rate in most provinces of Iran that are comparable to high-income countries.

Risk of COVID-19 re-infection and its predictors (CORES): protocol for a community-based longitudinal cohort study in Vellore, India

INTRODUCTION

The incidence of SARS-CoV-2 re-infection has not been widely evaluated in low-income and middle-income countries. Understanding immune responses elicited by SARS-CoV-2 natural infection and factors that lead to re-infection in a community setting is important for public health policy. We aim to investigate the risk of primary infection and re-infection among those without and with evidence of prior infection as defined by the presence of antibodies to SARS-CoV-2 spike protein.

METHODS AND ANALYSIS

A baseline seroprevalence survey will test for SARS-CoV-2 antibodies among healthy adults in Vellore, India. Based on an expected seropositivity rate of 50% in the general population, with annual attack rates of 12%, 6%, 4.8% and 4% among those unvaccinated and seronegative, vaccinated and seronegative, unvaccinated and seropositive, and vaccinated and seropositive, respectively, we will recruit 1200 adults who will be followed up for a total of 24 months. Weekly self-collected saliva samples will be tested by reverse transcription-PCR (RT-PCR) to detect SARS-CoV-2 infections, for a period of 1 year. For any person testing RT-PCR positive, blood samples will be collected within 2 days of RT-PCR positivity and on days 30 and 90 to assess the kinetics and longevity of the antibody responses, B cell memory and T cell memory post-infection. The data will be analysed to estimate seroprevalence at baseline and over time, the risk factors for infection, rates of primary infection and re-infection, and provide a comparison of the rates across groups based on infection and vaccination status.

ETHICS AND DISSEMINATION

The study has been approved by the Institutional Review Board (IRB No: 13585) of Christian Medical College and Hospital, Vellore. The results of the study will be made available through journal publications and conference presentations.

TRIAL REGISTRATION NUMBER

Central Trial Registry of India: CTRI/2020/11/029438.

Possible Cross-Reactivity of Feline and White-Tailed Deer Antibodies against the SARS-CoV-2 Receptor Binding Domain

In late 2019, a novel coronavirus began circulating within humans in central China. It was designated SARS-CoV-2 because of its genetic similarities to the 2003 SARS coronavirus (SARS-CoV). Now that SARS-CoV-2 has spread worldwide, there is a risk of it establishing new animal reservoirs and recombination with native circulating coronaviruses. To screen local animal populations in the United States for exposure to SARS-like coronaviruses, we developed a serological assay using the receptor binding domain (RBD) from SARS-CoV-2. SARS-CoV-2's RBD is antigenically distinct from common human and animal coronaviruses, allowing us to identify animals previously infected with SARS-CoV or SARS-CoV-2. Using an indirect enzyme-linked immunosorbent assay (ELISA) for SARS-CoV-2's RBD, we screened serum from wild and domestic animals for the presence of antibodies against SARS-CoV-2's RBD. Surprisingly prepandemic feline serum samples submitted to the University of Tennessee Veterinary Hospital were ∼50% positive for anti-SARS RBD antibodies. Some of these samples were serologically negative for feline coronavirus (FCoV), raising the question of the etiological agent generating anti-SARS-CoV-2 RBD cross-reactivity. We also identified several white-tailed deer from South Carolina with anti-SARS-CoV-2 antibodies. These results are intriguing, as cross-reactive antibodies toward SARS-CoV-2 RBD have not been reported to date. The etiological agent responsible for seropositivity was not readily apparent, but finding seropositive cats prior to the current SARS-CoV-2 pandemic highlights our lack of information about circulating coronaviruses in other species. IMPORTANCE We report cross-reactive antibodies from prepandemic cats and postpandemic South Carolina white-tailed deer that are specific for that SARS-CoV RBD. There are several potential explanations for this cross-reactivity, each with important implications to coronavirus disease surveillance. Perhaps the most intriguing possibility is the existence and transmission of an etiological agent (such as another coronavirus) with similarity to SARS-CoV-2's RBD region. However, we lack conclusive evidence of prepandemic transmission of a SARS-like virus. Our findings provide impetus for the adoption of a One Health Initiative focusing on infectious disease surveillance of multiple animal species to predict the next zoonotic transmission to humans and future pandemics.