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23-10-2022 22:07 | Basic reproduction number of the COVID-19 Delta variant: Estimation from multiple transmission datasets | The basic reproduction number, R0, plays a central role in measuring the transmissibility of an infectious disease, and it thus acts as the fundamental index for planning control strategies. In the present study, we apply a branching process model to meticulously observed contact tracing data from Wakayama Prefecture, Japan, obtained in early 2020 and mid-2021. This allows us to efficiently estimate R0 and the dispersion parameter k of the wild-type COVID-19, as well as the relative transmissibility of the Delta variant and relative transmissibility among fully vaccinated individuals, from a very limited data. R0 for the wild type of COVID-19 is estimated to be 3.78 (95% confidence interval [CI]: 3.72–3.83), with k = 0.236 (95% CI: 0.233–0.240). For the Delta variant, the relative transmissibility to the wild type is estimated to be 1.42 (95% CI: 0.94–1.90), which gives R0 = 5.37 (95% CI: 3.55–7.21). Vaccine effectiveness, determined by the reduction in the number of secondary transmissions among fully vaccinated individuals, is estimated to be 91% (95% CI: 85%–97%). The present study highlights that basic reproduction numbers can be accurately estimated from the distribution of minor outbreak data, and these data can provide further insightful epidemiological estimates including the dispersion parameter and vaccine effectiveness regarding the prevention of transmission. |
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23-10-2022 22:06 | The importance of booster vaccination in the context of Omicron wave | Omicron (B.1.1.529) was first detected in a sample collected in Botswana on November 11, 2021, and has rapidly replaced Delta as the dominant global variant given the robust transmissibility. Moreover, it displays a lower virulence than other variants. However, the pathogenicity of Omicron appears to be underestimated in view of the increasing levels of herd immunity through natural infection or vaccination. Additionally, the volume of hospitalizations and deaths increase in proportion to the number of cases due to the high transmissibility of Omicron. Therefore, vaccination remains an important public health priority. Notably, a series of important mutations in the Omicron spike protein, especially in the receptor-binding domain and N-terminal domain, appears to be associated with immune escape capacity, reducing the willingness of people to receive vaccines. Herein, we provide an in-depth discussion to assess the effectiveness of the second and third vaccination against Omicron variant. On the one hand, the two-dose vaccination program adopted by many countries is insufficient to prevent Omicron infection given the mutations correlated with immune escape and the decline in vaccine efficacy over time. On the other hand, booster dose significantly increases the protective efficacy against Omicron infection. Most importantly, heterologous third dose vaccination induces a more robust immune response than homologous booster dose. Therefore, under the special background of this pandemic, there is an urgent need to accelerate the third dose of vaccination, especially providing better booster vaccination strategies, to combat emerging Omicron variant. |
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23-10-2022 22:06 | Testing behaviour may bias observational studies of vaccine effectiveness | BACKGROUND: Recent observational studies suggest that vaccines may have little effect in preventing infection with the Omicron variant of severe acute respiratory syndrome coronavirus 2. However, the observed effects may be confounded by patient factors, preventive behaviours, or differences in testing behaviour. To assess potential confounding, we examined differences in testing behaviour between unvaccinated and vaccinated populations. METHODS: We recruited 1,526 Australian adults for an online randomized study about coronavirus disease 2019 (COVID-19) testing in late 2021, collecting self-reported vaccination status and three measures of COVID-19 testing behaviour: testing in past month or ever and test intention if they woke with a sore throat. We examined the association between testing intentions and vaccination status in the trial's baseline data. RESULTS: Of the 1,526 participants (mean age 31 y), 22% had a COVID-19 test in the past month and 61% ever;17% were unvaccinated, 11% were partially vaccinated (one dose), and 71% were fully vaccinated (two or more doses). Fully vaccinated participants were twice as likely as those who were unvaccinated (relative risk [RR] 2.2, 95% CI 1.8 to 2.8, p < 0.001) to report positive COVID testing intentions. Partially vaccinated participants had less positive intentions than fully vaccinated participants (RR 0.68, 95% CI 0.52 to 0.89, p < 0.001) but higher intentions than unvaccinated participants (RR 1.5, 95% CI 1.4 to 1.6, p = 0.002). DISCUSSION: Vaccination predicted greater COVID-19 testing intentions and would substantially bias observed vaccine effectiveness. To account for differential testing behaviours, test-negative designs are currently the preferred option, but their assumptions need more thorough examination. HISTORIQUE: Selon de récentes études observationnelles, les vaccins peuvent avoir peu d'effet sur la prévention de l'infection par le variant Omicron du coronavirus 2 du syndrome respiratoire aigu sévère. Cependant, les effets observés peuvent être biaisés par des facteurs liés aux patients, des comportements préventifs ou des différences de comportements liés aux tests. Pour évaluer les facteurs confusionnels potentiels, les auteurs ont examiné les différences de comportements liés aux tests entre les populations non vaccinées et vaccinées. MÉTHODOLOGIE : Les auteurs ont recruté 1 526 adultes australiens en vue d'une étude randomisée en ligne sur les tests de la maladie à coronavirus 2019 (COVID-19) à la fin de 2021, afin de colliger l'état vaccinal autodéclaré et trois mesures sur les comportements liés aux tests de la COVID-19 : test au cours du mois précédent ou jamais auparavant et intention de se soumettre à un test en cas de mal de gorge. Ils ont examiné l'association entre les intentions de se soumettre à un test et l'état vaccinal dans les données de référence de l'étude. RÉSULTATS : Sur les 1 526 participants (d'un âge moyen de 31 ans), 22 % avaient subi un test de COVID-19 au cours du mois précédent et 61 % n'en avaient jamais subi;17 % n'étaient pas vaccinés, 11 % l'étaient partiellement (une dose) et 71 % l'étaient pleinement (au moins deux doses). Les participants pleinement vaccinés étaient deux fois plus susceptibles que ceux qui ne l'étaient pas (risque relatif [RR] 2,2, IC à 95 % 1,8 à 2,8, p < 0,001) de déclarer des intentions de se faire tester contre la COVID-19. Les participants partiellement vaccinés avaient des intentions moins positives que les participants pleinement vaccinés (RR 0,68, IC à 95 % 0,52 à 0,89, p < 0,001), mais plus élevées que ceux qui ne l'étaient pas du tout (RR 1,5, IC à 95 % 1,4 à 1,6, p = 0,002). DISCUSSION : La vaccination était prédictive de plus grandes intentions de subir un test de COVID-19 et établissait un biais important à l'égard de l'efficacité réelle des vaccins. Pour tenir compte des comportements différentiels vis-à-vis des tests, les méthodologies de tests négatifs constituent actuellement la solution privilégiée, mais cette hypothèse doit être approfondie. |
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23-10-2022 22:06 | Effectiveness of CoronaVac vaccination against COVID-19 development in healthcare workers: real-life data | Background: This study was designed to investigate the effectiveness of CoronaVac in preventing COVID-19 in healthcare workers (HCWs) during the Alpha variant-dominant period. Materials & methods: Follow-up was initiated 14 days after the second dose for double-dose vaccinated HCWs and on 25 February 2021, for the unvaccinated group. The incidence rate ratio was calculated to estimate the unadjusted effectiveness. Cox regression was used to adjust the effectiveness of CoronaVac. Results & Conclusion: The adjusted effectiveness of CoronaVac against COVID-19 was 65% (95% CI: 50-75%). Compared with the results of the phase III trial conducted in Turkey, a lower effectiveness of CoronaVac against COVID-19 was detected in this real-life study. This finding suggests that mass vaccination and booster doses are needed. |
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23-10-2022 22:06 | Possible Autoimmune Encephalitis Associated with the Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant Successfully Treated with Steroids: A Case Report | We encountered a 55-year-old woman with possible autoimmune encephalitis associated with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant. She was not vaccinated against coronavirus disease 2019 (COVID-19). Consciousness disturbance, myoclonic-like movements and gait disturbance occurred 10 days after the COVID-19 symptom onset. Her neurological symptoms improved two days after methylprednisolone pulse therapy. Cerebrospinal fluid (CSF) was negative for SARS-CoV-2 reverse transcription-polymerase chain reaction, the CSF-to-serum albumin quotient was mildly elevated, and interleukin 6 and 8 levels were normal in serum but mildly elevated in CSF. Omicron variant infection may increase blood-brain barrier permeability and intrathecal inflammation, causing autoimmune encephalitis. |
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21-10-2022 22:26 | Shedding of infectious SARS-CoV-2 despite vaccination | The SARS-CoV-2 Delta Variant of Concern is highly transmissible and contains mutations that confer partial immune escape. The emergence of Delta in North America caused the first surge in COVID-19 cases after SARS-CoV-2 vaccines became widely available. To determine whether individuals infected despite vaccination might be capable of transmitting SARS-CoV-2, we compared RT-PCR cycle threshold (Ct) data from 20,431 test-positive anterior nasal swab specimens from fully vaccinated (n = 9,347) or unvaccinated (n = 11,084) individuals tested at a single commercial laboratory during the interval 28 June- 1 December 2021 when Delta variants were predominant. We observed no significant effect of vaccine status alone on Ct value, nor when controlling for vaccine product or sex. Testing a subset of low-Ct (<25) samples, we detected infectious virus at similar rates, and at similar titers, in specimens from vaccinated and unvaccinated individuals. These data indicate that vaccinated individuals infected with Delta variants are capable of shedding infectious SARS-CoV-2 and could play a role in spreading COVID-19. |
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21-10-2022 22:26 | A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern | Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key DELTAH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes. |
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21-10-2022 22:26 | Outcomes of Monoclonal Antibody Infusion Treatment During Delta (B.1.617.2) and Omicron (B.1.1.529) COVID 19 Variant Surges among Vaccinated and Unvaccinated Patients | Background: Coronavirus infection of 2019 (COVID-19) is associated with significant morbidity and mortality. Vaccines supplement public health and social measures in preventing severe illness and mortality from COVID-19;however, vaccination rates remain inadequate in many regions. It is important to continuously explore the effective treatment due to the insufficient vaccination rate and increasing number of patients infected with virus. The emergence of new variants has led to multiple surges throughout the world requiring changes to treatment protocols. Method: We conducted a single-center observational study on all adult patients who received monoclonal antibody (mAb) infusion as a treatment for COVID-19 infection. Based on the predominant variant, patients were either offered Casirivimab (600 mg)/imdevimab (600 mg) or Sotrovimab (500 mg). Forty-six patients were given mAbs;24 were vaccinated, and the remaining unvaccinated. Result: The mean age was 56 years, and the majority (63.04%) of the patients were female. Clinical symptoms of COVID-19 improved within 3 days of infusion in the majority of the patients (70%). None of the patients who received mAb showed progression of disease or required hospitalization at 30 days follow-up. There were no deaths at 30 days follow-up. Monoclonal antibodies are highly effective in reducing hospitalizations and mortality when given within 7 days of symptoms onset in patients with high-risk factors for progression to severe COVID-19 infection. The mean number of days after the onset at which the mAbs were administered to the patient was 4. Conclusion: Monoclonal antibodies should be considered in both vaccinated and unvaccinated patients with COVID-19 infection if newer antiviral agents are contraindicated. Our study highlights the effectiveness of monoclonal antibody infusions when given early in the course of COVID-19 infection regardless of vaccination status |
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21-10-2022 22:26 | The Omicron Variant BA.1.1 Presents a Lower Pathogenicity than B.1 D614G and Delta Variants in a Feline Model of SARSCoV-2 Infection | Omicron (B.1.1.529) is the most recent SARS-CoV-2 variant of concern, which emerged in late 2021 and rapidly achieved global predominance by early 2022. In this study, we compared the infection dynamics, tissue tropism, and pathogenesis and pathogenicity of SARS-CoV-2 D614G (B.1), Delta (B.1.617.2), and Omicron BA.1.1 (B.1.1.529) variants in a highly susceptible feline model of infection. Although D614G- and Delta-inoculated cats became lethargic and showed increased body temperatures between days 1 and 3 postinfection (pi), Omicron-inoculated cats remained subclinical and, similar to control animals, gained weight throughout the 14-day experimental period. Intranasal inoculation of cats with D614G- and the Delta variants resulted in high infectious virus shedding in nasal secretions (up to 6.3 log10 TCID50.Ml21), whereas strikingly lower level of viruses shedding (,3.1 log10 TCID50.Ml-1) was observed in Omicron-inoculated animals. In addition, tissue distribution of the Omicron variant was markedly reduced in comparison to the D614G and Delta variants, as evidenced by lower in situ viral RNA detection, in situ viral immunofluorescence staining, and viral loads in tissues on days 3, 5, and 14 pi. Nasal turbinate, trachea, and lung were the main--but not the only--sites of replication for all three viral variants. However, only scarce virus staining and lower viral titers suggest lower levels of viral replication in tissues from Omicron-infected animals. Notably, while D614G- and Delta-inoculated cats presented pneumonia, histologic examination of the lungs from Omicron-infected cats revealed mild to modest inflammation. Together, these results demonstrate that the Omicron variant BA.1.1 is less pathogenic than D614G and Delta variants in a highly susceptible feline model. [ FROM AUTHOR] Copyright of Journal of Virology is the property of American Society for Microbiology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . |
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21-10-2022 19:09 | A new, stealthy coronavirus variant is spreading fast, spooking scientists and Wall Street ... |  -
XBB is a new version of Omicron that is evading existing treatments and immunity. -
It is spreading quickly in Singapore, and virus-watchers are worried it could spread in the US. -
BQ.1.1 is also emerging. Experts say: prepare for more COVID infections this winter. As Halloween approaches, murmurs of another "nightmare" COVID variant on the way are spooking reporters and Wall Street analysts alike. The new variant is called XBB, and it's already triggering a new wave of infections and hospitalizations in some south Asian countries, including India and Singapore. XBB is just one of "multiple more-immune evasive Omicron subvariants on the rise around the world," infectious disease expert Dr. Celine Gounder, a Senior Fellow at the Kaiser Family Foundation, told Insider. But "among the new variants, XBB has the most significant immune evasion properties," market forecasters at Morgan Stanley said Thursday in a memo. Given that we've now seen nearly three full years of COVID variants — and nearly a year of different Omicrons before XBB emerged from them — how worried, really, should we be about this new version of the virus? Experts say we should expect many more infections this fall and winter, including infections in vaccinated, boosted Americans. But there are some simple things you can do to prepare to battle XBB and other evasive COVID variants on the horizon. What is XBB? XBB is a recombinant variant – meaning that it's a combination of two other BA.2 Omicron subvariants (specifically, BA.2.10.1 + BA.2.75). Like other Omicrons we've seen before, XBB is "finding ways to evade the way we get immunity from vaccines and previous infection, with changes on the spike protein," UC Berkeley infectious disease expert John Swartzberg told the San Francisco Chronicle. |
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19-10-2022 14:11 | Broadly neutralizing antibodies to SARS-CoV-2 and other human coronaviruses | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged pathogenic human coronavirus that belongs to the sarbecovirus lineage of the genus Betacoronavirus. The ancestor strain has evolved into a number of variants of concern, with the Omicron variant of concern now having many distinct sublineages. The ongoing COVID-19 pandemic caused by SARS-CoV-2 has caused serious damage to public health and the global economy, and one strategy to combat COVID-19 has been the development of broadly neutralizing antibodies for prophylactic and therapeutic use. Many are in preclinical and clinical development, and a few have been approved for emergency use. Here we summarize neutralizing antibodies that target four key regions within the SARS-CoV-2 spike (S) protein, namely the N-terminal domain and the receptor-binding domain in the S1 subunit, and the stem helix region and the fusion peptide region in the S2 subunit. Understanding the characteristics of these broadly neutralizing antibodies will accelerate the development of new antibody therapeutics and provide guidance for the rational design of next-generation vaccines. |
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19-10-2022 14:10 | Increased household transmission and immune escape of the SARS-CoV-2 Omicron compared to Delta variants | Understanding the epidemic growth of the novel SARS-CoV-2 Omicron variant is critical for public health. We compared the ten-day secondary attack rate (SAR) of the Omicron and Delta variants in households using Norwegian contact tracing data, December 2021 - January 2022. Omicron SAR was higher than Delta, with a relative risk (RR) of 1.41 (95% CI 1.27-1.56). We observed increased susceptibility to Omicron infection in household contacts compared to Delta, independent of contacts' vaccination status. Among three-dose vaccinated contacts, the mean SAR was lower for both variants. We found increased Omicron transmissibility from primary cases to contacts in all vaccination groups, except 1-dose vaccinated, compared to Delta. Omicron SAR of three-dose vaccinated primary cases was high, 46% vs 11 % for Delta. In conclusion, three-dose vaccinated primary cases with Omicron infection can efficiently spread in households, while three-dose vaccinated contacts have a lower risk of being infected by Delta and Omicron. |
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18-10-2022 11:02 | New Mongolia-Born Omicron Variant BF.7 Found in India; Here's All We Know About Its Symptoms, Transmissibility and More |  The monsoon rains are slowly retreating, and Diwali is peering at us from out of the corner, which means that air pollution is likely to be at an all-time high for most of the upcoming week. Combined with inevitably large crowds, these factors set an unfortunate stage for Omicron’s latest highly infectious variant BF.7 to make waves over the coming days. But what is this variant, and how does it differ from its predecessors? Listed below are answers to some FAQs, so we stay updated and safe from the disease that doesn’t seem to quit. What is the Omicron BF.7 variant? The BF.7 variant is the newest Omicron strain to surface and was initially detected in China’s Mongolia region on October 4. After rapidly spreading through many districts of China, it found its way into the UK, Germany, France, the US, and now, India. Many of these countries have classified it as a variant of concern, with it already constituting a significant share of total positive cases. Some experts believe this variant is a contender to replace the dominant one worldwide. Where has the Omicron BF.7 variant been found in India? The Gujarat Biotechnology Centre discovered the first case of the new BF.7 subvariant in Gandhinagar, Gujarat. Is the new Omicron BF.7 variant more transmissible? The BF.7 is highly transmissible and requires a far less viral load to infect someone, primarily due to its ability to bind much more effectively than previous variants. In addition, this variant can evade immunity from prior infections, and might even be able to infect fully vaccinated people. What are the symptoms and the severity of an Omicron BF.7 infection? Most reported symptoms of patients infected by the new subvariant remain the same as before — sore throat, congestion, bodily fatigue, cough, runny nose, loss of smell, etc. As before, carriers of the virus can also be asymptomatic. Aside from these symptoms, we aren’t sure of the exact severity or any additional symptoms inflicted by the virus since scientists are still sequencing the data. We will receive more information in the coming days, as more positive people are tested. Will this new Omicron BF.7 variant trigger a new wave? While there is a good chance India might be in for a new COVID-19 wave, we cannot purely attribute it to the new variant. Large crowds and a lack of compliance with COVID-19 protective measures during the festival season means that all variants have an increased chance of jumping from patient to patient. What precautions can we take against the new coronavirus variant? Maintain social distancing as much as possible, wear a reliable mask, and maintain cough etiquette and basic hygiene to protect the most vulnerable groups (such as pregnant people and the elderly) as much as possible. Currently, India’s weekly positivity rate stands around 1.02% per cent, and we must try to make sure that the figure isn’t the thing blowing up during the festival of joy. |
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17-10-2022 16:29 | Identification and assessment of TCR-T cells targeting an epitope conserved in SARS-CoV-2 variants for the treatment of COVID-19 | Background Coronavirus disease 2019 (COVID-19) continues to be a major global public health challenge, with the emergence of variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Current vaccines or monoclonal antibodies may not well be protect against infection with new SARS-CoV-2 variants. Unlike antibody-based treatment, T cell-based therapies such as TCR-T cells can target epitopes that are highly conserved across different SARS-CoV-2 variants. Reportedly, T cell-based immunity alone can restrict SARS-CoV-2 replication. Methods In this study, we identified two TCRs targeting the RNA-dependent RNA polymerase (RdRp) protein in CD8+ T cells. Functional evaluation by transducing these TCRs into CD8+ or CD4+ T cells confirmed their specificity. Results Combinations of inflammatory and anti-inflammatory cytokines secreted by CD8+ and CD4+ T cells can help control COVID-19 in patients. Moreover, the targeted epitope is highly conserved in all emerged SARS-CoV-2 variants, including the Omicron. It is also conserved in the seven coronaviruses that infect humans and more broadly in the subfamily Coronavirinae. Conclusions The pan-genera coverage of mutant epitopes from the Coronavirinae subfamily by the two TCRs highlights the unique strengths of TCR-T cell therapies in controlling the ongoing pandemic and in preparing for the next coronavirus outbreak. |
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17-10-2022 16:29 | Efficacy, immunogenicity and safety of COVID-19 vaccines in older adults: a systematic review and meta-analysis | Background Older adults are more susceptible to severe health outcomes for coronavirus disease 2019 (COVID-19). Universal vaccination has become a trend, but there are still doubts and research gaps regarding the COVID-19 vaccination in the elderly. This study aimed to investigate the efficacy, immunogenicity, and safety of COVID-19 vaccines in older people aged ≥ 55 years and their influencing factors. Methods Randomized controlled trials from inception to April 9, 2022, were systematically searched in PubMed, EMBASE, the Cochrane Library, and Web of Science. We estimated summary relative risk (RR), rates, or standardized mean difference (SMD) with 95% confidence interval (CI) using random-effects meta-analysis. This study was registered with PROSPERO (CRD42022314456). Results Of the 32 eligible studies, 9, 21, and 25 were analyzed for efficacy, immunogenicity, and safety, respectively. In older adults, vaccination was efficacious against COVID-19 (79.49%, 95% CI: 60.55−89.34), with excellent seroconversion rate (92.64%, 95% CI: 86.77−96.91) and geometric mean titer (GMT) (SMD 3.56, 95% CI: 2.80−4.31) of neutralizing antibodies, and provided a significant protection rate against severe disease (87.01%, 50.80−96.57). Subgroup and meta-regression analyses consistently found vaccine types and the number of doses to be primary influencing factors for efficacy and immunogenicity. Specifically, mRNA vaccines showed the best efficacy (90.72%, 95% CI: 86.82−93.46), consistent with its highest seroconversion rate (98.52%, 95% CI: 93.45−99.98) and GMT (SMD 6.20, 95% CI: 2.02−10.39). Compared to the control groups, vaccination significantly increased the incidence of total adverse events (AEs) (RR 1.59, 95% CI: 1.38−1.83), including most local and systemic AEs, such as pain, fever, chill, etc. For inactivated and DNA vaccines, the incidence of any AEs was similar between vaccination and control groups (p > 0.1), while mRNA vaccines had the highest risk of most AEs (RR range from 1.74 to 7.22). Conclusion COVID-19 vaccines showed acceptable efficacy, immunogenicity and safety in older people, especially providing a high protection rate against severe disease. The mRNA vaccine was the most efficacious, but it is worth surveillance for some AEs it caused. Increased booster coverage in older adults is warranted, and additional studies are urgently required for longer follow-up periods and variant strains. |
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17-10-2022 16:29 | Evolving trend change during the COVID-19 pandemic | Coronavirus disease (COVID-19) has caused unimaginable damage to public health and socio-economic structures worldwide;thus, an epidemiological depiction of the global evolving trends of this disease is necessary. As of March 31, 2022, the number of cases increased gradually over the four waves of the COVID-19 pandemic, indicating the need for continuous countermeasures. The highest total cases per million and total deaths per million were observed in Europe (240,656.542) and South America (2,912.229), despite these developed countries having higher vaccination rates than other continents, such as Africa. In contrast, the lowest of the above two indices were found in undeveloped African countries, which had the lowest number of vaccinations. These data indicate that the COVID-19 pandemic is positively related to the socio-economic development level;meanwhile, the data suggest that the vaccine currently used in these continents cannot completely prevent the spread of COVID-19. Thus, rethinking the feasibility of a single vaccine to control the disease is needed. Although the number of cases in the fourth wave increased exponentially compared to those of the first wave, ~43.1% of deaths were observed during the first wave. This was not only closely linked to multiple factors, including the inadequate preparation for the initial response to the COVID-19 pandemic, the gradual reduction in the severity of additional variants, and the protection conferred by prior infection and/or vaccination, but this also indicated the change in the main driving dynamic in the fourth wave. Moreover, at least 12 variants were observed globally, showing a clear spatiotemporal profile, which provides the best explanation for the presence of the four waves of the pandemic. Furthermore, there was a clear shift in the trend from multiple variants driving the spread of disease in the early stage of the pandemic to a single Omicron lineage predominating in the fourth wave. These data suggest that the Omicron variant has an advantage in transmissibility over other contemporary co-circulating variants, demonstrating that monitoring new variants is key to reducing further spread. We recommend that public health measures, along with vaccination and testing, are continually implemented to stop the COVID-19 pandemic. |
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17-10-2022 16:29 | Cohort-Specific Serological Recognition of SARS-CoV-2 Variant RBD Antigens | OBJECTIVE: Estimating the response of different population cohorts to new SARS-CoV-2 variants is important to customize measures of control. Our goal was to evaluate how antibodies from sera of infected and vaccinated people recognize antigens expressed by different SARS-CoV-2 variants. METHODS: We compared sera from vaccinated donors and four patient/donor cohorts: Sera from critically ill patients collected 2-7 days and more than 10 days after admission to an intensive care unit, a NIBSC/WHO reference panel of SARS-CoV-2 positive individuals, and ambulatory or hospitalized (but not critically ill) positive donors. Samples were tested with an anti-SARS-CoV-2 ELISA kit coated with SARS-CoV-2 RBD recombinant antigens including mutations present in eleven of the most widespread variants. RESULTS: Sera from vaccinated individuals exhibited higher antibody binding (P<0.001) than sera from infected (but not critically ill) individuals when tested against the wild type (WT) and each of 11 variants' receptor binding domain (RBD). Antibodies' binding to the SARS-CoV-2 antigens of at least 6 variants, including Variants of Concern (VOCs), was reduced in comparison to the WT in vaccinated and non-critically ill convalescence individuals. CONCLUSION: Understanding differences between population cohorts in the antibody titers against WT vs variant RBD antigens can help design variant-specific immunoassays for surveillance and evaluation of the epidemiology of new variants. |
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17-10-2022 16:29 | The Omicron Variant of Concern: Diversification and Convergent Evolution in Spike Protein, and Escape From Anti-spike Monoclonal Antibodies | WHO-defined SARS-CoV-2 variants of concern (VOC) drive therapeutics and vaccine development. The Omicron VOC is dominating the arena since November 2021, but the number of its sublineages is growing in complexity. Omicron represent a galaxy with a myriad of stars that suddenly rise and expand before collapsing into apparent extinction when a more fit sublineage appears. This has already happened with BA.1, BA.2, and BA.4/5 and is happening with BA.2.75. We review here the current PANGO phylogeny, focusing on sublineages with Spike mutations, and show how common convergent evolution has occurred in these sublineages. We finally summarize how Omicron evolution has progressively defeated the anti-Spike monoclonal antibodies authorized so far, leaving clinicians to again fall back on COVID19 convalescent plasma from vaccinated donors as the only antibody-based therapy available. |
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17-10-2022 13:12 | New Subvariant Of Omicron Found To Escape Most Antibodies: Study In Lancet | Omicron sublineage BA.2.75.2 escapes most antibodies, a study published in The Lancet Infectious Diseases journal says. The study, led by researchers at Karolinska Institutet in Sweden, suggests a risk of increased Covid-19 infections this winter. This is likely to happen unless the new updated bivalent vaccines help to boost immunity in the population. Bivalent Covid-19 vaccines include a component of the original virus strain to provide broad protection against Covid-19 and a component of the Omicron variant to provide better protection against Covid-19 caused by the Omicron variant, according to the Food and Drug Administration (FDA). The new study was conducted in collaboration with researchers at ETH Zürich, Switzerland and Imperial College London, United Kingdom. Why is BA.2.75.2 more resistant to antibodies than its predecessor? In a statement released by Karolinska Institutet, Ben Murrell, the corresponding author on the paper, said while antibody immunity is not completely gone, BA.2.75.2 exhibited far more dramatic resistance than variants previously studied. This resistance is largely driven by two mutations in the receptor binding domain of the spike protein. Time points at which samples were collected Antibodies in random serum samples from 75 blood donors in Stockholm, Sweden were approximately only one-sixth as effective at neutralising BA.2.75.2 compared with the now-dominant variant BA.5, the study says. The researchers collected the serum samples at three time points. Some samples were collected in November last year, before the emergence of Omicron, some were collected in April, 2022 after a large wave of infections in Sweden, and some were collected at the end of August to early September this year after the BA.5 variant became dominant. Which monoclonal antibody was able to neutralise the new variant? Bebtelovimab was one of the clinically available monoclonal antibody treatments tested. Monoclonal antibodies are engineered in a laboratory and are given to a person directly in an infusion. These antibodies are used as antiviral treatments for people at high risk of developing severe Covid-19. Bebtelovimab was observed to be able to potently neutralise the new Omicron subvariant. According to the study, BA.2.75.2 is a mutated version of another Omicron variant, BA.2.75, and was first discovered earlier this fall. Since then, the variant has spread to several countries but so far represents only a minority of registered cases. Covid-19 infections are likely to increase this winter Murrell said in the statement that the new subvariant is just one of a constellation of emerging variants with similar mutations that will likely come to dominate in the near future. He added that people should expect infections to increase this winter. However, some questions remain. For instance, it is not known whether these new variants will drive an increase in hospitalisation rates. In general, current vaccines have had a protective effect against severe disease for Omicron infections. But there is no data which shows the degree to which the updated bivalent Covid-19 vaccines provide protection from new variants. Murrell said the vaccines are expected to be beneficial, but the extent to which they provide protection against Covid-19 variants is not known. |
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