The emergence of novel SARS-CoV-2 variant P.1 in Amazonas (Brazil) was temporally associated with a change in the age and sex profile of COVID-19 mortality: A population based ecological study

Epidemiological profile of patients hospitalized with Crohn's disease due to severe acute respiratory infection during the COVID-19 pandemic: a 2-year report from Brazil

Background and aims

The novel coronavirus-induced severe acute respiratory syndrome (COVID-19) led to one of the most significant global pandemics of the 21st century, causing substantial challenges for healthcare systems worldwide, including those in Brazil. This study aimed to investigate the demographic and clinical profiles of hospitalized patients in Brazil who had both COVID-19 and Crohn's disease (CD) over a 2-year period.

Methods

An epidemiological analysis was conducted using data from Open-Data-SUS. The study focused on describing the demographic characteristics, clinical manifestations, comorbidities, and hospitalization details of patients afflicted with severe acute respiratory syndrome due to COVID-19 and CD, with the aim of predicting mortality risk.

Results

The states of São Paulo, Paraná, and Minas Gerais accounted for 50% of the reported COVID-19 cases. The most affected racial group consisted of individuals who self-declared as mixed race. Common comorbidities included heart disease, diabetes mellitus, and obesity. The age group most affected was 25 to 60 years old, particularly among hospitalized patients with both CD and COVID-19 who ultimately succumbed to the illness. A multivariable analysis was conducted to identify the following significant risk factors for death: (a) the presence of neurological disorder (OR = 6.716; 95% CI = 1.954-23.078), (b) the need for intensive care (OR = 3.348; 95% CI = 1.770-6.335), and (c) the need for invasive mechanical ventilation (OR = 59.017; 95% CI = 19.796-175.944).

Conclusion

There was no discernible gender-based prevalence among hospitalized patients with CD and COVID-19; however, individuals of mixed race were disproportionately affected. The 25 to 60 age group emerged as the most vulnerable demographic group, with high risks of hospitalization and mortality. Moreover, the study highlights the potential for COVID-19 to induce systemic pathologies that may result in long-term degenerative effects and sequelae.

COVID-19 mortality: educational inequalities and socio-spatial context in two provinces of Argentina

Motivation for the study. There are very few studies on the educational inequalities in COVID-19 mortality, taking into account social contextual factors. Main findings. We found educational inequalities of COVID-19 mortality during both the 2020 and 2021 waves, regardless of the level of poverty and urbanization in the departments of Mendoza and San Juan provinces (Argentina). Implications. Preventive policies should focus not only in areas with high levels of poverty, but also in areas with adults of low educational level. With the aim of describing the association between sociodemographic characteristics and contextual factors with COVID-19 mortality during 2020-2021 in the provinces of Mendoza and San Juan in Argentina, we conducted an ecological study, which included the sociodemographic factors: age, sex and educational level, and the contextual factors: poverty and urbanization at the departmental level. The analyses were estimated using negative binomial Bayesian hierarchical models. Educational inequalities existed regardless of socioeconomic context and level of urbanization. The exception was the age group 65 years and older during 2021, which, regardless of educational level, showed a higher risk of death by COVID-19 in departments with high levels of structural poverty. In conclusion, educational inequality is an indicator of social inequality that increases vulnerability to COVID-19 mortality.

Hospitalizations for coronavirus disease 2019: an analysis of the occurrence waves

The pandemic has been characterized by several waves defined by viral strains responsible for the predominance of infections. We aimed to analyze the mean length of hospital stay for patients with COVID-19 during the first three waves of the pandemic and its distribution according to sociodemographic and clinical variables. This retrospective study used the notifications of patients hospitalized for COVID-19 in a Brazilian state during the period of the three waves of the disease as the data source. There were 13,910 hospitalizations for confirmed COVID-19 cases. The first wave was the longest, with 4101 (29.5%) hospitalizations, while the third, although shorter, had a higher number of hospitalized patients (N = 6960). The average length of stay in the hospital in all waves was associated with age groups up to 60 years old., elementary, high school and higher education, residents of the periurban area Regarding the presence of comorbidities, there was a statistically significant difference in the mean number of days of hospitalization among patients with chronic cardiovascular disease and obesity (P < 0.001). In conclusion, the COVID-19 pandemic has been distinctly revealed among the waves.

Impact of COVID-19 vaccination: a global perspective

Introduction

The COVID-19 pandemic has caused widespread morbidity, mortality, and socio-economic disruptions worldwide. Vaccination has proven to be a crucial strategy in controlling the spread of the virus and mitigating its impact.

Objective

The study focuses on assessing the effectiveness of COVID-19 vaccination in reducing the incidence of positive cases, hospitalizations, and ICU admissions. The presented study is focused on the COVID-19 fully vaccinated population by considering the data from the first positive case reported until 20 September 2021.

Methods

Using data from multiple countries, time series analysis is deployed to investigate the variations in the COVID-19 positivity rates, hospitalization rates, and ICU requirements after successful vaccination campaigns at the country scale.

Results

Analysis of the COVID-19 positivity rates revealed a substantial decline in countries with high pre-vaccination rates. Within 1-3 months of vaccination campaigns, these rates decreased by 20-44%. However, certain countries experienced an increase in positivity rates with the emergence of the new Delta variant, emphasizing the importance of ongoing monitoring and adaptable vaccination strategies. Similarly, the analysis of hospitalization rates demonstrated a steady decline as vaccination drive rates rose in various countries. Within 90 days of vaccination, several countries achieved hospitalization rates below 200 per million. However, a slight increase in hospitalizations was observed in some countries after 180 days of vaccination, underscoring the need for continued vigilance. Furthermore, the ICU patient rates decreased as vaccination rates increased across most countries. Within 120 days, several countries achieved an ICU patient rate of 20 per million, highlighting the effectiveness of vaccination in preventing severe cases requiring intensive care.

Conclusion

COVID-19 vaccination has proven to be very much effective in reducing the incidence of cases, hospitalizations, and ICU admissions. However, ongoing surveillance, variant monitoring, and adaptive vaccination strategies are crucial for maximizing the benefits of vaccination and effectively controlling the spread of the virus.

Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study

The analyses of genetic traits, dispersion patterns and phylogenomics are essential for understanding the evolutionary forces driving SARS-CoV-2 viruses in these three years of COVID-19 pandemics. Brazil is one of the most affected countries in the world and not sufficient genomic studies have been performed. The emergence of P.1 lineage led to one of the most serious public health crises on record. Our study presents the genomic sequencing and characterization of 412 samples from Rio Grande do Sul state, in the Brazilian Southern region, during Gamma and Delta epidemic waves, in 2021. Additionally, molecular evolution tests were performed to identify positively selected sites in Brazil between 2020 and 2022, as well as offer some evolutionary perspective about the maintenance of multiple spike mutations in Omicron lineages. Genomic epidemiology analysis has indicated an intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil.

Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity

Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.

Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus

Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad ACE2 usage and that RBD mutations further expand receptor promiscuity and enable human ACE2 utilization. We determined a cryoEM structure of the PRD-0038 RBD bound to R. alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryoEM and monoclonal antibody reactivity revealed its distinct antigenicity relative to SARS-CoV-2 and identified PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicited greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared to SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.

Transmission dynamics of SARS-CoV-2 variants in the Brazilian state of Pará

Introduction

After three years since the beginning of the pandemic, the new coronavirus continues to raise several questions regarding its infectious process and host response. Several mutations occurred in different regions of the SARS-CoV-2 genome, such as in the spike gene, causing the emergence of variants of concern and interest (VOCs and VOIs), of which some present higher transmissibility and virulence, especially among patients with previous comorbidities. It is essential to understand its spread dynamics to prevent and control new biological threats that may occur in the future. In this population_based retrospective observational study, we generated data and used public databases to understand SARS-CoV-2 dynamics.

Methods

We sequenced 1,003 SARS-CoV-2 genomes from naso-oropharyngeal swabs and saliva samples from Pará from May 2020 to October 2022. To gather epidemiological data from Brazil and the world, we used FIOCRUZ and GISAID databases.

Results

Regarding our samples, 496 (49.45%) were derived from female participants and 507 (50.55%) from male participants, and the average age was 43  years old. The Gamma variant presented the highest number of cases, with 290 (28.91%) cases, followed by delta with 53 (5.28%). Moreover, we found seven (0.69%) Omicron cases and 651 (64.9%) non-VOC cases. A significant association was observed between sex and the clinical condition (female, p = 8.65e-08; male, p = 0.008961) and age (p = 3.6e-10).

Discussion

Although gamma had been officially identified only in December 2020/January 2021, we identified a gamma case from Belém (capital of Pará State) dated May 2020 and three other cases in October 2020. This indicates that this variant was circulating in the North region of Brazil several months before its formal identification and that Gamma demonstrated its actual transmission capacity only at the end of 2020. Furthermore, the public data analysis showed that SARS-CoV-2 dispersion dynamics differed in Brazil as Gamma played an important role here, while most other countries reported a new infection caused by the Delta variant. The genetic and epidemiological information of this study reinforces the relevance of having a robust genomic surveillance service that allows better management of the pandemic and that provides efficient solutions to possible new disease-causing agents.

A beta regression analysis of COVID-19 mortality in Brazil

Brazil was one of the countries most impacted by the COVID-19 pandemic, with a cumulative total of nearly 700,000 deaths by early 2023. The country's federative units were unevenly affected by the pandemic and adopted mitigation measures of different scopes and intensity. There was intense conflict between the federal government and state governments over the relevance and extent of such measures. We build a simple regression model with good predictive power on state COVID-19 mortality rates in Brazil. Our results reveal that the federative units' urbanization rate and per capita income are important for determining their mean mortality rate and that the number of physicians per 100,000 inhabitants is important for modeling the mortality rate precision. Based on the fitted model, we obtain approximations for the levels of administrative efficiency of local governments in dealing with the pandemic.

The origins of new SARS-COV-2 variants in immunocompromised individuals

PURPOSE OF REVIEW

To explore the origins of new severe acute respiratory coronavirus 2 (SARS-CoV-2) variants in immunocompromised individuals and whether the emergence of novel mutations in these individuals is responsible for the development of variants of concern (VOC).

RECENT FINDINGS

Next generation sequencing of samples from chronically infected immunocompromised patients has enabled identification of VOC- defining mutations in individuals prior to the emergence of these variants worldwide. Whether these individuals are the source of variant generation is uncertain. Vaccine effectiveness in immunocompromised individuals and with respect to VOCs is also discussed.

SUMMARY

Current evidence on chronic SARS-CoV-2 infection in immunocompromised populations is reviewed including the relevance of this to the generation of novel variants. Continued viral replication in the absence of an effective immune response at an individual level or high levels of viral infection at the population level are likely to have contributed to the appearance of the main VOC.

CRISPR techniques and potential for the detection and discrimination of SARS-CoV-2 variants of concern

The continuing evolution of the SARS-CoV-2 virus has led to the emergence of many variants, including variants of concern (VOCs). CRISPR-Cas systems have been used to develop techniques for the detection of variants. These techniques have focused on the detection of variant-specific mutations in the spike protein gene of SARS-CoV-2. These sequences mostly carry single-nucleotide mutations and are difficult to differentiate using a single CRISPR-based assay. Here we discuss the specificity of the Cas9, Cas12, and Cas13 systems, important considerations of mutation sites, design of guide RNA, and recent progress in CRISPR-based assays for SARS-CoV-2 variants. Strategies for discriminating single-nucleotide mutations include optimizing the position of mismatches, modifying nucleotides in the guide RNA, and using two guide RNAs to recognize the specific mutation sequence and a conservative sequence. Further research is needed to confront challenges in the detection and differentiation of variants and sublineages of SARS-CoV-2 in clinical diagnostic and point-of-care applications.

Resolving the enigma of Iquitos and Manaus: A modeling analysis of multiple COVID-19 epidemic waves in two Amazonian cities

The two nearby Amazonian cities of Iquitos and Manaus endured explosive COVID-19 epidemics and may well have suffered the world's highest infection and death rates over 2020, the first year of the pandemic. State-of-the-art epidemiological and modeling studies estimated that the populations of both cities came close to attaining herd immunity (>70% infected) at the termination of the first wave and were thus protected. This makes it difficult to explain the more deadly second wave of COVID-19 that struck again in Manaus just months later, simultaneous with the appearance of a new P.1 variant of concern, creating a catastrophe for the unprepared population. It was suggested that the second wave was driven by reinfections, but the episode has become controversial and an enigma in the history of the pandemic. We present a data-driven model of epidemic dynamics in Iquitos, which we also use to explain and model events in Manaus. By reverse engineering the multiple epidemic waves over 2 y in these two cities, the partially observed Markov process model inferred that the first wave left Manaus with a highly susceptible and vulnerable population (≈40% infected) open to invasion by P.1, in contrast to Iquitos (≈72% infected). The model reconstructed the full epidemic outbreak dynamics from mortality data by fitting a flexible time-varying reproductive number [Formula: see text] while estimating reinfection and impulsive immune evasion. The approach is currently highly relevant given the lack of tools available to assess these factors as new SARS-CoV-2 virus variants appear with different degrees of immune evasion.

Molecular evolution of SARS-CoV-2 from December 2019 to August 2022

Severe acute respiratorysyndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning worldwide, presenting more than 590 million coronavirus disease 2019 cases and 6.4 million deaths. The emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide during the pandemic. The present study review and summarizes the temporal spreading and molecular evolution of SARS-CoV-2 clades and variants worldwide. The evaluation of these data is important for understanding the evolutionary histories of SARSCoV-2 lineages, allowing us to identify the origins of each lineage of this virus responsible for one of the biggest pandemics in history. A total of 2897 SARS-CoV-2 whole-genome sequences with available information from the country and sampling date (December 2019 to August 2022), were obtained and were evaluated by Bayesian approach. The results demonstrated that the SARS-CoV-2 the time to the most recent common ancestor (tMRCA) in Asia was 2019-12-26 (highest posterior density 95% [HPD95%]: 2019-12-18; 2019-12-29), in Oceania 2020-01-24 (HPD95%: 2020-01-15; 2020-01-30), in Africa 2020-02-27 (HPD95%: 2020-02-21; 2020-03-04), in Europe 2020-02-27 (HPD95%: 2020-02-20; 2020-03-06), in North America 2020-03-12 (HPD95%: 2020-03-05; 2020-03-18), and in South America 2020-03-15 (HPD95%: 2020-03-09; 2020-03-28). Between December 2019 and June 2020, 11 clades were detected (20I [Alpha] and 19A, 19B, 20B, 20C, 20A, 20D, 20E [EU1], 20F, 20H [Beta]). From July to December 2020, 4 clades were identified (20J [Gamma, V3], 21 C [Epsilon], 21D [Eta], and 21G [Lambda]). Between January and June 2021, 3 clades of the Delta variant were detected (21A, 21I, and 21J). Between July and December 2021, two variants were detected, Delta (21A, 21I, and 21J) and Omicron (21K, 21L, 22B, and 22C). Between January and June 2022, the Delta (21I and 21J) and Omicron (21K, 21L, and 22A) variants were detected. Finally, between July and August 2022, 3 clades of Omicron were detected (22B, 22C, and 22D). Clade 19A was first detected in the SARS-CoV-2 pandemic (Wuhan strain) with origin in 2019-12-16 (HPD95%: 2019-12-15; 2019-12-25); 20I (Alpha) in 2020-11-24 (HPD95%: 2020-11-15; 2021-12-02); 20H (Beta) in 2020-11-25 (HPD95%: 2020-11-13; 2020-11-29); 20J (Gamma) was 2020-12-21 (HPD95%: 2020-11-05; 2021-01-15); 21A (Delta) in 2020-09-20 (HPD95%: 2020-05-17; 2021-02-03); 21J (Delta) in 2021-02-26 (2020-11-02; 2021-04-24); 21M (Omicron) in 2021-01-25 (HPD95%: 2020-09-16; 2021-08-08); 21K (Omicron) in 2021-07-30 (HPD95%: 2021-05-30; 2021-10-19); 21L (Omicron) in 2021-10-03 (HPD95%: 2021-04-16; 2021-12-23); 22B (Omicron) in 2022-01-25 (HPD95%: 2022-01-10; 2022-02-05); 21L in 2021-12-20 (HPD95%: 2021-05-16; 2021-12-31). Currently, the Omicron variant predominates worldwide, with the 21L clade branching into 3 (22A, 22B, and 22C). Phylogeographic data showed that Alpha variant originated in the United Kingdom, Beta in South Africa, Gamma in Brazil, Delta in India, Omicron in South Africa, Mu in Colombia, Epsilon in the United States of America, and Lambda in Peru. The COVID-19 pandemic has had a significant impact on global health worldwide and the present study provides an overview of the molecular evolution of SARS-CoV-2 lineage clades (from the Wuhan strain to the currently circulating lineages of the Omicron).

COVID-19 mortality in Brazil, 2020-21: consequences of the pandemic inadequate management

BACKGROUND

The COVID-19 pandemic brought countless challenges to public health and highlighted the Brazilian health system vulnerabilities in facing the emergency. In this article, we analyze data on COVID-19-related deaths in 2020-21 to show the epidemic consequences in Brazil.

METHODS

The Mortality Information System and the Live Birth Information System were the primary information sources. We used population estimates in 2020-21 to calculate COVID-19 specific mortality rates by age, sex, and educational level. Considering the total number of COVID-19 deaths in 2020-21, the COVID-19 proportional mortality (%) was estimated for each age group and sex. A graph of the daily number of deaths from January 2020 to December 2021 by sex was elaborated to show the temporal evolution of COVID-19 deaths in Brazil. In addition, four indicators related to COVID-19 mortality were estimated: infant mortality rate (IMR); maternal mortality ratio (MMR); number and rate of orphans due to mother's COVID-19 death; the average number of years lost.

RESULTS

The overall COVID-19 mortality rate was 14.8 (/10,000). The mortality rates increase with age and show a decreasing gradient with higher schooling. The rate among illiterate people was 38.8/10,000, three times higher than a college education. Male mortality was 31% higher than female mortality. COVID-19 deaths represented 19.1% of all deaths, with the highest proportions in the age group of 40-59 years. The average number of years lost due to COVID-19 was 19 years. The MMR due to COVID-19 was 35.7 per 100,000 live births (LB), representing 37.4% of the overall MMR. Regarding the number of orphans due to COVID-19, we estimated that 40,830 children under 18 lost their mothers during the epidemic, with an orphans' rate of 7.5/10,000 children aged 0-17 years. The IMR was 11.7 per 1000 LB, with 0.2 caused by COVID-19. The peak of COVID-19 deaths occurred in March 2021, reaching almost 4000 COVID-19 deaths per day, higher than the average number of deaths per day from all causes in 2019.

CONCLUSIONS

The delay in adopting public health measures necessary to control the epidemic has exacerbated the spread of the disease, resulting in several avoidable deaths.

Impact of Vaccination and Control Measures on the Fatality of COVID-19: An Ecological Study

BACKGROUND

During the COVID-19 pandemic, reducing the case fatality rate (CFR) becomes an urgent goal.

OBJECTIVE

This study explored the effect of vaccination and variants on COVID-19 fatality and provide a basis for the adjustment of control measures.

METHODS

This study collected epidemiological information on COVID-19 from January to October 2021. By setting different lag times, we calculated the adjusted CFR. The Spearman correlation coefficient and beta regression were used to explore factors that may affect COVID-19 fatality.

RESULTS

Every 1% increase in the percentage of full vaccinations may reduce the 3 weeks lagging CFR by 0.66%. Increasing the restrictions on internal movement from level 0 to 1, restrictions on international travel controls from level 2 to 3, and stay-at-home restrictions from level 0 to 2 were associated with an average reduction in 3 weeks lagging CFR of 0.20%, 0.39%, and 0.36%, respectively. Increasing strictness in canceling public events from level 0 to 1 and 2 may reduce the 3 weeks lagging CFR by 0.49% and 0.37, respectively. Increasing the severity of school and workplace closures from level 1 or level 0 to 3 may increase the 3 weeks lagging CFR of 0.39% and 0.83, respectively. Every 1-point increase in the Global Health Security (GHS) index score may increase the 3 weeks lagging CFR by 0.12%.

CONCLUSION

A higher percentage of full vaccinations, higher levels of internal movement restrictions, international travel control restrictions, cancelations of public events, and stay-at-home restrictions are factors that may reduce the adjusted CFR.

Profile of coronavirus disease enlightened asthma as a protective factor against death: An epidemiology study from Brazil during the pandemic

INTRODUCTION

The possibility that asthma is not a risk factor for the worst outcomes due to coronavirus disease (COVID-19) is encouraged. The increase in Th2 response dominance can downregulate the late phase of hyperinflammation, which is typically the hallmark of more severe respiratory viral infections, alongside lower angiotensin-converting enzyme receptors in patients with asthma due to chronic inflammation. Few studies associated asthma diagnosis and COVID-19 outcomes. In this context, we aimed to associate the asthma phenotype with the clinical signs, disease progression, and outcomes in patients with COVID-19.

METHODS

We performed an epidemiologic study using patients' characteristics from OpenDataSUS to verify the severity of COVID-19 among Brazilian hospitalized patients with and without the asthma phenotype according to the need for intensive care units, intubation, and deaths. We also evaluated the demographic data (sex, age, place of residence, educational level, and race), the profile of clinical signs, and the comorbidities.

RESULTS

Asthma was present in 43,245/1,129,838 (3.8%) patients. Among the patients with asthma, 74.7% who required invasive ventilatory support evolved to death. In contrast, 78.0% of non-asthmatic patients who required invasive ventilatory support died (OR = 0.83; 95% CI = 0.79-0.88). Also, 20.0% of the patients with asthma that required non-invasive ventilatory support evolved to death, while 23.5% of non-asthmatic patients evolved to death (OR = 0.81; 95% CI = 0.79-0.84). Finally, only 11.2% of the patients with asthma who did not require any ventilatory support evolved to death, while 15.8% of non-asthmatic patients evolved to death (OR = 0.67; 95% CI = 0.62-0.72). In our multivariate analysis, one comorbidity and one clinical characteristic stood out as protective factors against death during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Patients with asthma were less prone to die than other patients (OR = 0.79; 95% CI = 0.73-0.85), just like puerperal patients (OR = 0.74; 95% CI = 0.56-0.97) compared to other patients.

CONCLUSION

Asthma was a protective factor for death in hospitalized patients with COVID-19 in Brazil. Despite the study's limitations on patients' asthma phenotype information and corticosteroid usage, this study brings to light information regarding a prevalent condition that was considered a risk factor for death in COVID-19, being ultimately protective.

COVID-19 and its genomic variants: Molecular pathogenesis and therapeutic interventions

Coronavirus disease-19 (COVID-19), caused by a β-coronavirus and its genomic variants, is associated with substantial morbidities and mortalities globally. The COVID-19 virus and its genomic variants enter host cells upon binding to the angiotensin converting enzyme 2 receptors that are expressed in a variety of tissues, but predominantly in the lungs, heart, and blood vessels. Patients afflicted with COVID-19 may be asymptomatic or present with critical symptoms possibly due to diverse lifestyles, immune responses, aging, and underlying medical conditions. Geriatric populations, especially men in comparison to women, with immunocompromised conditions, are most vulnerable to severe COVID-19 associated infections, complications, and mortalities. Notably, whereas immunomodulation, involving nutritional consumption, is essential to protecting an individual from COVID-19, immunosuppression is detrimental to a person with this aggressive disease. As such, immune health is inversely correlated to COVID-19 severity and resulting consequences. Advances in genomic and proteomic technologies have helped us to understand the molecular events underlying symptomatology, transmission and, pathogenesis of COVID-19 and its genomic variants. Accordingly, there has been development of a variety of therapeutic interventions, ranging from mask wearing to vaccination to medication. This review summarizes the current understanding of molecular pathogenesis of COVID-19, effects of comorbidities on COVID-19, and prospective therapeutic strategies for the prevention and treatment of this contagious disease.

Clinical and demographic characteristics of COVID-19 cases in Brunei Darussalam: comparison between the first and second waves, 2020 and 2021

Objective

Differences in clinical manifestations between strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported. This retrospective descriptive study compares the clinical and demographic characteristics of all confirmed coronavirus disease (COVID-19) cases admitted to the National Isolation Centre (NIC) in the first wave and at the beginning of the second wave of the pandemic in Brunei Darussalam.

Methods

All COVID-19 cases admitted to the NIC between 9 March and 6 May 2020 (first wave) and 7-17 August 2021 (second wave) were included. Data were obtained from NIC databases and case characteristics compared using Student's t-tests and χ² tests, as appropriate.

Results

Cases from the first wave were significantly older than those from the second wave (mean 37.2 vs 29.7 years, P < 0.001), and a higher proportion reported comorbidities (30.5% vs 20.3%, P = 0.019). Cases from the second wave were more likely to be symptomatic at admission (77.7% vs 63.1%, P < 0.001), with a higher proportion reporting cough, anosmia, sore throat and ageusia/dysgeusia; however, myalgia and nausea/vomiting were more common among symptomatic first wave cases (all P < 0.05). There was no difference in the mean number of reported symptoms (2.6 vs 2.4, P = 0.890).

Discussion

Our study showed clear differences in the profile of COVID-19 cases in Brunei Darussalam between the first and second waves, reflecting a shift in the predominating SARS-CoV-2 strain. Awareness of changes in COVID-19 disease manifestation can help guide adjustments to management policies such as duration of isolation, testing strategies, and criteria for admission and treatment.

Characterization of demographic data, clinical signs, comorbidities, and outcomes according to the race in hospitalized individuals with COVID-19 in Brazil: An observational study

Background

Brazil is a multiracial country with five major official races: White, Black, individuals with multiracial backgrounds, Asian, and Indigenous. Brazil is also one of the epicentres of the Coronavirus Disease (COVID)-19 pandemic. Thus, we evaluated how the races of the Brazilian population contribute to the outcomes in hospitalized individuals with COVID-19, and we also described the clinical profile of the five official Brazilian races.

Methods

We performed an epidemiological analysis for the first 67 epidemiological weeks of the COVID-19 pandemic in Brazil (from February 22, 2020, to April 04, 2021) using the data available at OpenDataSUS of the Brazilian Ministry of Health, a data set containing data from Brazilian hospitalized individuals. We evaluated more than 30 characteristics, including demographic data, clinical symptoms, comorbidities, need for intensive care unit and mechanical ventilation, and outcomes.

Results

In our data, 585 655 hospitalized individuals with a positive result in SARS-CoV-2 real-time chain reaction (RT-PCR) were included. Of these total, 309 646 (52.9%) identified as White, 31 872 (5.4%) identified as Black, 7108 (1.2%) identified as Asian, 235 108 (40.1%) identified as individuals with multiracial background, and 1921 (0.3%) identified as Indigenous. The multivariate analysis demonstrated that race was significative to predict the death being that Black (OR = 1.43; 95% CI = 1.39-1.48), individuals with multiracial background (OR = 1.36; 95% CI = 1.34-1.38), and Indigenous (OR = 1.91; 95% CI = 1.70-2.15) races were more prone to die compared to the White race. The Asian individuals did not have a higher chance of dying due to SARS-CoV-2 infection compared to White individuals (OR = 0.99; 95% CI = 0.94-1.06). In addition, other characteristics contributed as such as being male (OR = 1.17; 95% CI = 1.16-1.19), age (mainly, +85 years old – OR = 23.02; 95% CI = 20.05-26.42) compared to 1-year-old individuals, living in rural areas (OR = 1.22; 95% CI = 1.18-1.26) or in peri-urban places (OR = 1.25; 95% CI = 1.11-1.40), and the presence of nosocomial infection (OR = 1.91; 95% CI = 1.82-2.01). Among the clinical symptoms, the main predictors were dyspnoea (OR = 1.25; 95% CI = 1.23-1.28), respiratory discomfort (OR = 1.30; 95% CI = 1.28-1.32), oxygen saturation <95% (OR = 1.40; 95% CI = 1.38-1.43). Also, among the comorbidities, the main predictors were the presence of immunosuppressive disorder (OR = 1.44; 95% CI = 1.39-1.49), neurological disorder (OR = 1.21; 95% CI = 1.17-1.25), hepatic disorder (OR = 1.41; 95% CI = 1.34-1.50), diabetes mellitus (OR = 1.40; 95% CI = 1.37-1.42), cardiopathy (OR = 1.13; 95%CI = 1.11-1.14), hematologic disorder (OR = 1.34; 95% CI = 1.24-1.43), Down syndrome (OR = 1.61; 95% CI = 1.43-1.81), renal disease (OR = 1.15; 95% CI = 1.11-1.18), and obesity (OR = 1.18; 95% CI = 1.15-1.21). Individuals on intensive care unit (OR = 2.25; 95% CI = 2.22-2.29) and on invasive (OR = 10.92; 95% CI = 10.66-11.18) or non-invasive (OR = 1.33; 95% CI = 1.30-1.35) mechanical ventilation were more prone to die.

Conclusions

Alongside several clinical symptoms and comorbidities, we associated race with an enhanced risk of death in Black individuals, individuals with multiracial backgrounds, and Indigenous peoples.

Induction of Broadly Cross-Reactive Antibody Responses to SARS-CoV-2 Variants by S1 Nanoparticle Vaccines

Despite the rapid deployment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines, the emergence of SARS-CoV-2 variants and reports of their immune evasion characteristics have led to an urgent need for novel vaccines that confer potent cross-protective immunity. In this study, we constructed three different SARS-CoV-2 spike S1-conjugated nanoparticle vaccine candidates that exhibited high structural homogeneity and stability. Notably, these vaccines elicited up to 50-times-higher neutralizing antibody titers than the S1 monomer in mice. Crucially, it was found that the S1-conjugated nanoparticle vaccine could elicit comparable levels of neutralizing antibodies against wild-type or emerging variant SARS-CoV-2, with cross-reactivity to SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), the effect of which could be further enhanced using our designed nanoparticles. Our results indicate that the S1-conjugated nanoparticles are promising vaccine candidates with the potential to elicit potent and cross-reactive immunity against not only wild-type SARS-CoV-2, but also its variants of concern, variants of interest, and even other pathogenic betacoronaviruses. IMPORTANCE The emergence of SARS-CoV-2 variants led to an urgent demand for a broadly effective vaccine against the threat of variant infection. The spike protein S1-based nanoparticle designed in our study could elicit a comprehensive humoral response toward different SARS-CoV-2 variants of concern and variants of interest and will be helpful to combat COVID-19 globally.

The Impact of the Highly Virulent SARS-CoV-2 Gamma Variant on Young Adults in the State of São Paulo: Was It Inevitable?

Background

The coronavirus disease 2019 (COVID-19) pandemic had and is still having a tremendous impact on people all over the world, but it has been particularly harsh in South America. Nine out of 13 South American countries are among the 50 countries with the highest COVID-19 death rates. The gamma severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant that emerged by the end of 2020 in the Brazilian Amazon quickly spread throughout the country causing the harsh COVID-19 second wave. This variant displayed high viral loads, high transmissibility, and increased virulence as compared to previous variants.

Aims

The aim of this retrospective study is to revisit and analyse the epidemiology of the COVID-19 second wave in the state of São Paulo, the most populous Brazilian state. In addition to examining the possible factors that led to the emergence and propagation of the gamma variant, measures that could have prevented its spread and that of other highly virulent variants were also investigated.

Materials and methods

Data from São Paulo's official sources on morbidity, mortality, age distribution, and testing prior to and during the COVID-19 second wave (February - June 2021) and data regarding the distribution of SARS-CoV-2 variants in the country were parsed, analyzed, and compared to the period that anteceded the eruption of the second COVID-19 wave.

Results

In the state of São Paulo, the toll of the COVID-19 second wave surpassed that of the first 11 months of the pandemic (from March 2020 to January 2021), as 56% of the deaths occurred in the five months of the second wave between February and June 2021. The mean age of COVID-19 victims, which was already below life expectancy in the state dropped even further in the pandemic's second wave, reaching an average of 60 years of age. The years of life lost per death per month doubled and the case-fatality rate (CFR) of young adults (20-39 years old) more than trebled during this period. A number of hypotheses have been raised that might explain the emergence and spread of the gamma variant and the measures that could have been taken to prevent it and minimise its impact on the population.

Conclusions

Over 142,000 people died as a result of the SARS-CoV-2 gamma variant sweep in São Paulo in the first semester of 2021. Due to its high viral load, the gamma variant displayed high transmissibility and a high degree of virulence resulting in increased case fatality rates across most age tiers. Notably, this second wave was marked by a very significant increase in deaths among young adults. This increase was at least partially due to a deterioration in general health provoked by non-pharmaceutical interventions. In hindsight, a safer and more effective measure might have been to allow the free spread of the virus among the young and healthy in the first wave, thus conferring immunity against more virulent variants that emerged later on.

Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant of concern has spread rapidly across Brazil since late 2020, causing substantial infection and death waves. Here we used individual-level patient records after hospitalization with suspected or confirmed coronavirus disease 2019 (COVID-19) between 20 January 2020 and 26 July 2021 to document temporary, sweeping shocks in hospital fatality rates that followed the spread of Gamma across 14 state capitals, during which typically more than half of hospitalized patients aged 70 years and older died. We show that such extensive shocks in COVID-19 in-hospital fatality rates also existed before the detection of Gamma. Using a Bayesian fatality rate model, we found that the geographic and temporal fluctuations in Brazil's COVID-19 in-hospital fatality rates were primarily associated with geographic inequities and shortages in healthcare capacity. We estimate that approximately half of the COVID-19 deaths in hospitals in the 14 cities could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization and pandemic preparedness are critical to minimize population-wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.

Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status

The emergence and global dissemination of Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) variants of concern (VOCs) have been described as the main factor driving the Coronavirus Disease 2019 pandemic. In Brazil, the Gamma variant dominated the epidemiological scenario during the first period of 2021. Many Brazilian regions detected the Delta variant after its first description and documented its spread. To monitor the introduction and spread of VOC Delta, we performed Polymerase Chain Reaction (PCR) genotyping and genome sequencing in ten regional sentinel units from June to October 2021 in the State of Minas Gerais (MG). We documented the introduction and spread of Delta, comprising 70 per cent of the cases 8 weeks later. Comparing the viral loads of the Gamma and Delta dominance periods, we provide additional evidence that the latter is more transmissible. The spread and dominance of Delta did not culminate in the increase in cases and deaths, suggesting that the vaccination may have restrained the epidemic growth. Analysis of 224 novel Delta genomes revealed that Rio de Janeiro state was the primary source for disseminating this variant in the state of MG. We present the establishment of Delta, providing evidence of its enhanced transmissibility and showing that this variant shift did not aggravate the epidemiological scenario in a high immunity setting.

Epidemiologic Profile of Severe Acute Respiratory Infection in Brazil During the COVID-19 Pandemic: An Epidemiological Study

Background

The COVID-19 is a significant public health issue, and monitoring confirmed cases and deaths is an essential epidemiologic tool. We evaluated the features in Brazilian hospitalized patients due to severe acute respiratory infection (SARI) during the COVID-19 pandemic in Brazil. We grouped the patients into the following categories: Influenza virus infection (G1), other respiratory viruses' infection (G2), other known etiologic agents (G3), SARS-CoV-2 infection (patients with COVID-19, G4), and undefined etiological agent (G5).

Methods

We performed an epidemiological study using data from DataSUS (https://opendatasus.saude.gov.br/) from December 2019 to October 2021. The dataset included Brazilian hospitalized patients due to SARI. We considered the clinical evolution of the patients with SARI during the COVID-19 pandemic according to the SARI patient groups as the outcome. We performed the multivariate statistical analysis using logistic regression, and we adopted an Alpha error of 0.05.

Results

A total of 2,740,272 patients were hospitalized due to SARI in Brazil, being the São Paulo state responsible for most of the cases [802,367 (29.3%)]. Most of the patients were male (1,495,416; 54.6%), aged between 25 and 60 years (1,269,398; 46.3%), and were White (1,105,123; 49.8%). A total of 1,577,279 (68.3%) patients recovered from SARI, whereas 701,607 (30.4%) died due to SARI, and 30,551 (1.3%) did not have their deaths related to SARI. A major part of the patients was grouped in G4 (1,817,098; 66.3%) and G5 (896,207; 32.7%). The other groups account for &lt;1% of our sample [G1: 3,474 (0.1%), G2: 16,627 (0.6%), and G3: 6,866 (0.3%)]. The deaths related to SARI were more frequent in G4 (574,887; 34.7%); however, the deaths not related to SARI were more frequent among the patients categorized into the G3 (1,339; 21.3%) and G5 (25,829; 4.1%). In the multivariate analysis, the main predictors to classify the patients in the G5 when compared with G4 or G1-G4 were female sex, younger age, Black race, low educational level, rural place of residence, and the use of antiviral to treat the clinical signs. Furthermore, several features predict the risk of death by SARI, such as older age, race (Black, Indigenous, and multiracial background), low educational level, residence in a flu outbreak region, need for intensive care unit, and need for mechanical ventilatory support.

Conclusions

The possible COVID-19 underreporting (G5) might be associated with an enhanced mortality rate, more evident in distinct social groups. In addition, the patients' features are unequal between the patients' groups and can be used to determine the risk of possible COVID-19 underreporting in our population. Patients with a higher risk of death had a different epidemiological profile when compared with patients who recovered from SARI, like older age, Black, Indigenous, and multiracial background races, low educational level, residence in a flu outbreak region, need for intensive care unit and need for mechanical ventilatory support.

Clinical characteristics and comorbidities of COVID-19 in unvaccinated patients with Down syndrome: first year report in Brazil

Patients with Down syndrome (DS) are more affected by the Coronavirus Disease (COVID)-19 pandemic when compared with other populations. Therefore, the primary aim of our study was to report the death (case fatality rate) from SARS-CoV-2 infection in Brazilian hospitalized patients with DS from 03 January 2020 to 04 April 2021. The secondary objectives were (i) to compare the features of patients with DS and positive for COVID-19 (G1) to those with DS and with a severe acute respiratory infection (SARI) from other etiological factors (G2) to tease apart the unique influence of COVID-19, and (ii) to compare the features of patients with DS and positive for COVID-19 to those without DS, but positive for COVID-19 (G3) to tease apart the unique influence of DS. We obtained the markers for demographic profile, clinical symptoms, comorbidities, and the clinical features for SARI evolution during hospitalization in the first year of the COVID-19 pandemic in Brazil from a Brazilian open-access database. The data were compared between (i) G1 [1619 (0.4%) patients] and G2 [1431 (0.4%) patients]; and between (ii) G1 and G3 [222,181 (64.8%) patients]. The case fatality rate was higher in patients with DS and COVID-19 (G1: 39.2%), followed by individuals from G2 (18.1%) and G3 (14.0%). Patients from G1, when compared to G2, were older (≥ 25 years of age), presented more clinical symptoms related to severe illness and comorbidities, needed intensive care unit (ICU) treatment and non-invasive mechanical ventilation (MV) more frequently, and presented a nearly two fold-increased chance of death (OR = 2.92 [95% CI 2.44–3.50]). Patients from G1, when compared to G3, were younger (< 24 years of age), more prone to nosocomial infection, presented an increased chance for clinical symptoms related to a more severe illness; frequently needed ICU treatment, and invasive and non-invasive MV, and raised almost a three fold-increased chance of death (OR = 3.96 [95% CI 3.60–4.41]). The high case fatality rate in G1 was associated with older age (≥ 25 years of age), presence of clinical symptoms, and comorbidities, such as obesity, related to a more severe clinical condition. Unvaccinated patients with DS affected by COVID-19 had a high case fatality rate, and these patients had a different profile for comorbidities, clinical symptoms, and treatment (such as the need for ICU and MV) when compared with other study populations.

Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants

The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.

Clinical Characteristics, Transmissibility, Pathogenicity, Susceptible Populations, and Re-infectivity of Prominent COVID-19 Variants

In addition to the rapid, global spread of SARS-CoV-2, new and comparatively more contagious variants are of considerable concern. These emerging mutations have become a threat to the global public health, creating COVID-19 surges in different countries. However, information on these emerging variants is limited and scattered. In this review, we discuss new variants that have emerged worldwide and identify several variants of concern, such as B.1.1.7, B.1.351, P.1, B.1.617.2 and B.1.1.529, and their basic characteristics. Other significant variants such as C.37, B.1.621, B.1.525, B.1.526, AZ.5, C.1.2, and B.1.617.1 are also discussed. This review highlights the clinical characteristics of these variants, including transmissibility, pathogenicity, susceptible population, and re-infectivity. It provides the latest information on the recent variants of SARS-CoV-2. The summary of this information will help researchers formulate reasonable strategies to curb the ongoing COVID-19 pandemic.

Age-specific rate of severe and critical SARS-CoV-2 infections estimated with multi-country seroprevalence studies

BACKGROUND

Knowing the age-specific rates at which individuals infected with SARS-CoV-2 develop severe and critical disease is essential for designing public policy, for infectious disease modeling, and for individual risk evaluation.

METHODS

In this study, we present the first estimates of these rates using multi-country serology studies, and public data on hospital admissions and mortality from early to mid-2020. We combine these under a Bayesian framework that accounts for the high heterogeneity between data sources and their respective uncertainties. We also validate our results using an indirect method based on infection fatality rates and hospital mortality data.

RESULTS

Our results show that the risk of severe and critical disease increases exponentially with age, but much less steeply than the risk of fatal illness. We also show that our results are consistent across several robustness checks.

CONCLUSION

A complete evaluation of the risks of SARS-CoV-2 for health must take non-fatal disease outcomes into account, particularly in young populations where they can be 2 orders of magnitude more frequent than deaths.

Age-specific rate of severe and critical SARS-CoV-2 infections estimated with multi-country seroprevalence studies

BACKGROUND

Knowing the age-specific rates at which individuals infected with SARS-CoV-2 develop severe and critical disease is essential for designing public policy, for infectious disease modeling, and for individual risk evaluation.

METHODS

In this study, we present the first estimates of these rates using multi-country serology studies, and public data on hospital admissions and mortality from early to mid-2020. We combine these under a Bayesian framework that accounts for the high heterogeneity between data sources and their respective uncertainties. We also validate our results using an indirect method based on infection fatality rates and hospital mortality data.

RESULTS

Our results show that the risk of severe and critical disease increases exponentially with age, but much less steeply than the risk of fatal illness. We also show that our results are consistent across several robustness checks.

CONCLUSION

A complete evaluation of the risks of SARS-CoV-2 for health must take non-fatal disease outcomes into account, particularly in young populations where they can be 2 orders of magnitude more frequent than deaths.

Epidemiology of COVID-19 after Emergence of SARS-CoV-2 Gamma Variant, Brazilian Amazon, 2020-2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant has been hypothesized to cause more severe illness than previous variants, especially in children. Successive SARS-CoV-2 IgG serosurveys in the Brazilian Amazon showed that age-specific attack rates and proportions of symptomatic SARS-CoV-2 infections were similar before and after Gamma variant emergence.

Emergence of SARS-CoV-2 Variants in the World: How Could This Happen?

The COVID-19 pandemic has had a significant global impact, with more than 280,000,000 people infected and 5,400,000 deaths. The use of personal protective equipment and the anti-SARS-CoV-2 vaccination campaigns have reduced infection and death rates worldwide. However, a recent increase in infection rates has been observed associated with the appearance of SARS-CoV-2 variants, including the more recently described lineage B.1.617.2 (Delta variant) and lineage B.1.1.529/BA.1 (Omicron variant). These new variants put the effectiveness of international vaccination at risk, with the appearance of new outbreaks of COVID-19 throughout the world. This emergence of new variants has been due to multiple predisposing factors, including molecular characteristics of the virus, geographic and environmental conditions, and the impact of social determinants of health that favor the genetic diversification of SARS-CoV-2. We present a literature review on the most recent information available on the emergence of new variants of SARS-CoV-2 in the world. We analyzed the biological, geographical, and sociocultural factors that favor the development of these variants. Finally, we evaluate the surveillance strategies for the early detection of new variants and prevent their distribution outside these regions.

Deciphering Multifactorial Correlations of COVID-19 Incidence and Mortality in the Brazilian Amazon Basin

Amazonas suffered greatly during the COVID-19 pandemic. The mortality and fatality rates soared and scarcity of oxygen and healthcare supplies led the health system and funerary services to collapse. Thus, we analyzed the trends of incidence, mortality, and lethality indicators of COVID-19 and the dynamics of their main determinants in the state of Amazonas from March 2020 to June 2021. This is a time-series ecological study. We calculated the lethality, mortality, and incidence rates with official and public data from the Health Department. We used the Prais-Winsten regression and trends were classified as stationary, increasing, or decreasing. The effective reproduction number (Rt) was also estimated. Differences were considered significant when p < 0.05. We extracted 396,772 cases of and 13,420 deaths from COVID-19; 66% of deaths were in people aged over 60; 57% were men. Cardiovascular diseases were the most common comorbidity (28.84%), followed by diabetes (25.35%). Rural areas reported 53% of the total cases and 31% of the total deaths. The impact of COVID-19 in the Amazon is not limited to the direct effects of the pandemic itself; it may present characteristics of a syndemic due to the interaction of COVID-19 with pre-existing illnesses, endemic diseases, and social vulnerabilities.

SARS-CoV-2 Variants, Vaccines, and Host Immunity

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new beta coronavirus that emerged at the end of 2019 in the Hubei province of China. SARS-CoV-2 causes coronavirus disease 2019 (COVID-19) and was declared a pandemic by the World Health Organization (WHO) on 11 March 2020. Herd or community immunity has been proposed as a strategy to protect the vulnerable, and can be established through immunity from past infection or vaccination. Whether SARS-CoV-2 infection results in the development of a reservoir of resilient memory cells is under investigation. Vaccines have been developed at an unprecedented rate and 7 408 870 760 vaccine doses have been administered worldwide. Recently emerged SARS-CoV-2 variants are more transmissible with a reduced sensitivity to immune mechanisms. This is due to the presence of amino acid substitutions in the spike protein, which confer a selective advantage. The emergence of variants therefore poses a risk for vaccine effectiveness and long-term immunity, and it is crucial therefore to determine the effectiveness of vaccines against currently circulating variants. Here we review both SARS-CoV-2-induced host immune activation and vaccine-induced immune responses, highlighting the responses of immune memory cells that are key indicators of host immunity. We further discuss how variants emerge and the currently circulating variants of concern (VOC), with particular focus on implications for vaccine effectiveness. Finally, we describe new antibody treatments and future vaccine approaches that will be important as we navigate through the COVID-19 pandemic.

The Disease Severity and Clinical Outcomes of the SARS-CoV-2 Variants of Concern

With the continuation of the pandemic, many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have appeared around the world. Owing to a possible risk of increasing the transmissibility of the virus, severity of the infected individuals, and the ability to escape the antibody produced by the vaccines, the four SARS-CoV-2 variants of Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) have attracted the most widespread attention. At present, there is a unified conclusion that these four variants have increased the transmissibility of SARS-CoV-2, but the severity of the disease caused by them has not yet been determined. Studies from June 1, 2020 to October 15, 2021 were considered, and a meta-analysis was carried out to process the data. Alpha, Beta, Gamma, and Delta variants are all more serious than the wild-type virus in terms of hospitalization, ICU admission, and mortality, and the Beta and Delta variants have a higher risk than the Alpha and Gamma variants. Notably, the random effects of Beta variant to the wild-type virus with respect to hospitalization rate, severe illness rate, and mortality rate are 2.16 (95% CI: 1.19-3.14), 2.23 (95% CI: 1.31-3.15), and 1.50 (95% CI: 1.26-1.74), respectively, and the random effects of Delta variant to the wild-type virus are 2.08 (95% CI: 1.77-2.39), 3.35 (95% CI: 2.5-4.2), and 2.33 (95% CI: 1.45-3.21), respectively. Although, the emergence of vaccines may reduce the threat posed by SARS-CoV-2 variants, these are still very important, especially the Beta and Delta variants.

Report 46: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital fatality rates that followed Gamma's spread across 14 state capitals, and in which more than half of hospitalised patients died over sustained time periods. We show that extensive fluctuations in COVID-19 in-hospital fatality rates also existed prior to Gamma's detection, and were largely transient after Gamma's detection, subsiding with hospital demand. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil's COVID-19 in-hospital fatality rates are primarily associated with geographic inequities and shortages in healthcare capacity. We project that approximately half of Brazil's COVID-19 deaths in hospitals could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.

NOTE

The following manuscript has appeared as 'Report 46 - Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals' at https://spiral.imperial.ac.uk:8443/handle/10044/1/91875 .

ONE SENTENCE SUMMARY

COVID-19 in-hospital fatality rates fluctuate dramatically in Brazil, and these fluctuations are primarily associated with geographic inequities and shortages in healthcare capacity.

Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil

In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion.

The real-life impact of vaccination on COVID-19 mortality in Europe and Israel

OBJECTIVES

This study aimed at estimating the real-life impact of vaccination on COVID-19 mortality, with adjustment for SARS-CoV-2 variants spread and other factors across Europe and Israel.

STUDY DESIGN

Time series analysis.

METHODS

Time series analysis of the daily number of COVID-19 deaths was performed using non-linear Poisson mixed regression models. Variables such as variants' frequency, demographics, climate, health, and mobility characteristics of thirty-two countries between January 2020 and April 2021 were considered as potentially relevant adjustment factors.

RESULTS

The analysis revealed that vaccination efficacy in terms of protection against deaths was 72%, with a lower reduction of the number of deaths for B.1.1.7 vs non-B.1.1.7 variants (70% and 78%, respectively). Other factors significantly related to mortality were arrivals at airports, mobility change from the prepandemic level, and temperature.

CONCLUSIONS

Our study confirms a strong effectiveness of COVID-19 vaccination based on real-life public data, although lower than expected from clinical trials. This suggests the absence of indirect protection for non-vaccinated individuals. Results also show that vaccination effectiveness against mortality associated with the B.1.1.7 variant is slightly lower than that with other variants. Lastly, this analysis confirms the role of mobility reduction, within and between countries, as an effective way to reduce COVID-19 mortality and suggests the possibility of seasonal variations in COVID-19 incidence.

Effectiveness of the CoronaVac vaccine in older adults during a gamma variant associated epidemic of covid-19 in Brazil: test negative case-control study

OBJECTIVE

To estimate the effectiveness of the inactivated whole virus vaccine, CoronaVac (Sinovac Biotech), against symptomatic covid-19 in the elderly population of São Paulo state, Brazil during widespread circulation of the gamma variant.

DESIGN

Test negative case-control study.

SETTING

Community testing for covid-19 in São Paulo state, Brazil.

PARTICIPANTS

43 774 adults aged ≥70 years who were residents of São Paulo state and underwent reverse transcription polymerase chain reaction (RT-PCR) testing for SARS-CoV-2 from 17 January to 29 April 2021. 26 433 cases with symptomatic covid-19 and 17 622 test negative controls with covid-19 symptoms were formed into 13 283 matched sets, one case with to up to five controls, according to age, sex, self-reported race, municipality of residence, previous covid-19 status, and date of RT-PCR test (±3 days).

INTERVENTION

Vaccination with a two dose regimen of CoronaVac.

MAIN OUTCOME MEASURES

RT-PCR confirmed symptomatic covid-19 and associated hospital admissions and deaths.

RESULTS

Adjusted vaccine effectiveness against symptomatic covid-19 was 24.7% (95% confidence interval 14.7% to 33.4%) at 0-13 days and 46.8% (38.7% to 53.8%) at ≥14 days after the second dose. Adjusted vaccine effectiveness against hospital admissions was 55.5% (46.5% to 62.9%) and against deaths was 61.2% (48.9% to 70.5%) at ≥14 days after the second dose. Vaccine effectiveness ≥14 days after the second dose was highest for the youngest age group (70-74 years)-59.0% (43.7% to 70.2%) against symptomatic disease, 77.6% (62.5% to 86.7%) against hospital admissions, and 83.9% (59.2% to 93.7%) against deaths-and declined with increasing age.

CONCLUSIONS

Vaccination with CoronaVac was associated with a reduction in symptomatic covid-19, hospital admissions, and deaths in adults aged ≥70 years in a setting with extensive transmission of the gamma variant. Vaccine protection was, however, low until completion of the two dose regimen, and vaccine effectiveness was observe to decline with increasing age among this elderly population.