Impact of CoronaVac on Covid-19 outcomes of elderly adults in a large and socially unequal Brazilian city: A target trial emulation study (preprint)

Background: Although CoronaVac was the only Covid-19 vaccine adopted in the first months of the Brazilian vaccination campaign, randomized clinical trials to evaluate its efficacy in elderly adults were limited. In this study, we use routinely collected surveillance and SARS-CoV-2 vaccination and testing data comprising the population of the fifth largest city of Brazil to evaluate the effectiveness of CoronaVac in adults 60+ years old against severe outcomes. Methods: Using large observational databases on vaccination and surveillance data from the city of Fortaleza, Brazil, we defined a retrospective cohort including 324,302 eligible adults aged [≥] 60 years to evaluate the effectiveness of the CoronaVac vaccine. The cohort included individuals vaccinated between January 21, 2021, and August 31, 2021, who were matched with unvaccinated persons at the time of rollout following a 1:1 ratio according to baseline covariates of age, sex, and Human Development Index of the neighborhood of residence. Only Covid-19-related severe outcomes were included in the analysis: hospitalization, ICU admission, and death. Vaccine effectiveness for each outcome was calculated by using the risk ratio between the two groups, with the risk obtained by the Kaplan-Meier estimator. Results: We obtained 62,643 matched pairs for assessing the effectiveness of the two-dose regimen of CoronaVac. The demographic profile of the matched population was statistically representative of the population of Fortaleza. Using the cumulative incidence as the risk associated with each group, starting at day 14 since the receipt of the second dose, we found an 82.3% (95% CI 66.3 - 93.9) effectiveness against Covid-19-related death, 68.4% (95% CI 42.3 - 86.4) against ICU admission, and 55.8% (95% CI 42.7 - 68.3) against hospital admission. Conclusions: Our results show that, despite critical delays in vaccine delivery and limited evidence in efficacy trial estimates, CoronaVac contributed to preventing deaths and severe morbidity due to Covid-19 in elderly adults.

Mortality by cause of death in Brazil: effects of the COVID-19 pandemic and contribution to changes in life expectancy at birth (preprint)

We investigate the consequences of the COVID-19 pandemic on other underlying causes of death in Brazil in 2020 and 2021. We estimate monthly age-standardized mortality rates for 2010-2021 and decompose those time series into three additive components: trend, seasonality, and remainder. Given the long-term trend and historical seasonal fluctuations, we assume that any impact from the pandemic will be left on the remainder. We also decompose the contributions of COVID-19 deaths (direct effect) and those from other causes (indirect effects) to the annual change in life expectancy at birth (e0) from 2017 to 2021. Broadly, the remainder mirrors the trajectory of pandemic waves. The impact of the COVID-19 pandemic on other causes of death was not limited to increases but also decreases. The direct effects of the pandemic reduced e0 by 1.89 years between 2019 and 2020 and 1.77 between 2020 and 2021. Indirect effects increased e0 by 0.44 between 2019 and 2020 and had virtually no impact on e0 between 2020 and 2021. Whether trajectories in mortality rates and annual gains in e0 will quickly return to pre-pandemic levels depends on governmental actions to mitigate the consequences of the COVID-19 pandemic.

Impact of the COVID-19 pandemic on maternal mental health, early childhood development, and parental practices: a global scoping review (preprint)

Background: In March 2020, the COVID-19 outbreak was declared a pandemic by the World Health Organization (WHO), generating stark economic and social repercussions that directly or indirectly affected families’ wellbeing and health status. Aims: This review aims at mapping the existing evidence on the impact of the COVID-19 pandemic on maternal mental health, early childhood development, and parental practices, worldwide, to identify evidence gaps and better inform future delivery of care and health policy measures. Methods: Following the protocol defined by PRISMA-ScR, this systematic review has searched for relevant studies published between January 2020 and June 2021, selecting evidence sources based on pre-established criteria. From a total of 2,308 articles, data were extracted from 537 publications from 35 countries on all three health domains. Results: The combined stressors brought forth by the pandemic have exerted a heavy burden on the mental health of mothers and the development of young children, partly mediated by its impact on parental practices. Conclusions: Despite remaining gaps, we have identified sufficient evidence pointing to an urgent need for more concerted global research efforts and rapid policy responses to timely address severe and pervasive negative impacts to the mental health of mothers and children at a key developmental stage.

COVID-19 is not an Independent Cause of Death (preprint)

The COVID-19 pandemic has had overwhelming global impacts with deleterious social, economic, and health consequences. To assess the COVID-19 death toll researchers have estimated declines in 2020 life expectancy at birth. Because data are often available only for COVID-19 deaths, the risks of dying from COVID-19 are assumed to be independent of those from other causes. We explore the soundness of this assumption based on data from the US and Brazil, the countries with the largest number of reported COVID-19 deaths. We use three methods. One estimates the difference between 2019 and 2020 life tables and therefore does not require the assumption of independence. The other two assume independence to simulate scenarios in which COVID-19 mortality is added to 2019 death rates or is eliminated from 2020 rates. Our results reveal that COVID-19 is not independent of other causes of death. The assumption of independence can lead to either an overestimate (Brazil) or an underestimate (US) of the decline in e0, depending on how the number of other reported causes of death changed in 2020.

Estimating the early impact of immunization against COVID-19 on deaths among elderly people in Brazil: analyses of secondary data on vaccine coverage and mortality. (preprint)

ABSTRACT Background Immunization against COVID-19 in Brazil started in January 2021, with health workers and the elderly as the priority groups. We assessed whether there was an impact of immunizations on the mortality of individuals aged 80+ years. Methods By April 22, 2021, 147,454 COVID-19 deaths had been reported to the Brazilian Mortality Information System. Denominators for mortality rates were calculated by correcting population estimates for all-cause deaths reported in 2020. Proportionate mortality at ages 80+ and 90+ years relative to deaths at all ages were calculated, and mortality rate ratios compared these two age groups with individuals aged 0-79 years. Vaccine coverage data were obtained from the Ministry of Health vaccination monitoring website. All results were tabulated by two-week periods from epidemiological weeks 1-14, 2021. Findings As the P.1 variant spread throughout Brazil, the total number of deaths increased over time starting in epidemiological week 9 of 2021. The proportion of all deaths occurring at ages 80+ years was over 25% in weeks 1-6 and declined rapidly to 13.1% in weeks 13-14. Mortality rates were over 13 times higher in the 80+ years age group compared to that of 0-79 year olds up to week 6, and declined to 6.9 times in weeks 13-14. Coronavac accounted for 77.3% and AstraZeneca for 15.9% of all doses administered. Vaccination coverage (first dose) increased rapidly among individuals aged 80+ years, reaching 49.1% in weeks 5-6 and over 90% after week 9. Interpretation Rapid scaling up of vaccination coverage among elderly Brazilians was associated with an important decline in relative mortality compared to younger individuals, in a setting where the P.1 variant predominates. Had mortality rates among the elderly remained proportionate to what was observed up to week 6, an estimated additional 13,824 deaths would have been expected up to week 14.

Reduction in the 2020 Life Expectancy in Brazil after COVID-19 (preprint)

Brazil has the second-largest number of COVID-19 deaths worldwide. We use data on reported deaths to measure and compare the death toll across states from a demographic perspective. We estimate a decline in 2020 life expectancy at birth of 1.94 years, resulting in a mortality level not seen since 2013. The reduction in life expectancy at age 65 was 1.58 years, setting Brazil back to 2009 levels. The decline was larger for males, widening by 2.3% and 5.4% the female-male gap in life expectancy at birth and at age 65, respectively. Among states, Amazonas lost 59.6% of the improvements in life expectancy at birth since 2000. With 2021 COVID-19 deaths at about 43% of the total 2020 figures (as of mid-March) the demographic effect is likely to be even higher this year.

Role of Heterogeneous Transmission in the Decline of COVID-19 Cases During Winter of 2020/2021 in Massachusetts (preprint)

Importance: Heterogeneity in transmission of COVID-19 is a significant multiscale phenomenon. However, the role of this heterogeneity in shaping the overall dynamics of disease transmission is not well understood. Objective: To investigate the role of heterogeneous transmission among different towns in Massachusetts in shaping the dynamics of COVID-19 transmission, especially the recent decline during winter of 2020/2021. Design, Setting, Participants: Analysis of COVID-19 data collected and archived by the Massachusetts Department of Public Health. Exposures: The entire population of the state of Massachusetts is exposed to the virus responsible for COVID-19, to varying degrees. This study quantifies this variation. Main outcome measures: Weekly observations, by town, on confirmed COVID-19 cases in Massachusetts, during the period (April 15th, 2020 to February 9th 2021). Results: The relative decline in COVID-19 cases, during January 12th, 2021 to February 9th, 2021, in the group of towns with higher total accumulated cases in the period before January 12th, 2021 is significantly larger than the corresponding relative decline in the group of towns with lower accumulated cases during the same period. Conclusions and Relevance: Heterogeneous nature of transmission is playing a significant role in shaping the rapid recent decline (January 12th to February 9th, 2021) in reported cases in Massachusetts, and probably around the country. These findings are relevant to how we estimate the threshold defining herd immunity, suggesting that we should account for effects due to heterogeneity.

Temporal and geographical variation of COVID-19 in-hospital fatality rate in Brazil (preprint)

Background: Previous studies have shown that COVID-19 In-Hospital Fatality Rate (IHFR) varies between regions and has been diminishing over time. It is believed that the continuous improvement in the treatment of patients, age group of hospitalized, and the availability of hospital resources might be affecting the temporal and regional variation of IHFR. In this study, we explored how the IHFR varied along time and among age groups and federative states in Brazil. In addition, we also assessed the relationship between hospital structure availability and peaks of IHFR. Methods: A retrospective analysis of all COVID-19 hospitalizations with confirmed outcomes in 21 states between March 01 and September 22, 2020 (N=345,281) was done. We fit GLM binomial models with additive and interaction effects between age groups, epidemiological weeks, and states. We also evaluated the association between the modeled peak of IHFR in each state and the variables of hospital structure using the Spearman rank correlation test. Results: We found that the temporal variation of the IHFR was heterogeneous among the states, and in general it followed the temporal trends in hospitalizations. In addition, the peak of IHFR was higher in states with a smaller number of doctors and intensivists, and in states in which a higher percentage of people relied on the Public Health System (SUS) for medical care. Conclusions: Our results suggest that the pressure over the healthcare system is affecting the temporal trends of IHFR in Brazil.

COVID-19 herd immunity in the Brazilian Amazon (preprint)

The herd immunity threshold is the proportion of a population that must be immune to an infectious disease, either by natural infection or vaccination such that, in the absence of additional preventative measures, new cases decline and the effective reproduction number falls below unity. This fundamental epidemiological parameter is still unknown for the recently-emerged COVID-19, and mathematical models have predicted very divergent results. Population studies using antibody testing to infer total cumulative infections can provide empirical evidence of the level of population immunity in severely affected areas. Here we show that the transmission of SARS-CoV-2 in Manaus, located in the Brazilian Amazon, increased quickly during March and April and declined more slowly from May to September. In June, one month following the epidemic peak, 44% of the population was seropositive for SARS-CoV-2, equating to a cumulative incidence of 52%, after correcting for the false-negative rate of the antibody test. The seroprevalence fell in July and August due to antibody waning. After correcting for this, we estimate a final epidemic size of 66%. Although non-pharmaceutical interventions, plus a change in population behavior, may have helped to limit SARS-CoV-2 transmission in Manaus, the unusually high infection rate suggests that herd immunity played a significant role in determining the size of the epidemic.

Baseline T cell immune phenotypes predict virologic and disease control upon SARS-CoV infection (preprint)

The COVID-19 pandemic has revealed that infection with SARS-CoV-2 can result in a wide range of clinical outcomes in humans, from asymptomatic or mild disease to severe disease that can require mechanical ventilation. An incomplete understanding of immune correlates of protection represents a major barrier to the design of vaccines and therapeutic approaches to prevent infection or limit disease. This deficit is largely due to the lack of prospectively collected, pre-infection samples from indiviuals that go on to become infected with SARS-CoV-2. Here, we utilized data from a screen of genetically diverse mice from the Collaborative Cross (CC) infected with SARS-CoV to determine whether circulating baseline T cell signatures are associated with a lack of viral control and severe disease upon infection. SARS-CoV infection of CC mice results in a variety of viral load trajectories and disease outcomes. Further, early control of virus in the lung correlates with an increased abundance of activated CD4 and CD8 T cells and regulatory T cells prior to infections across strains. A basal propensity of T cells to express IFNg and IL17 over TNFa also correlated with early viral control. Overall, a dysregulated, pro-inflammatory signature of circulating T cells at baseline was associated with severe disease upon infection. While future studies of human samples prior to infection with SARS-CoV-2 are required, our studies in mice with SARS-CoV serve as proof of concept that circulating T cell signatures at baseline can predict clinical and virologic outcomes upon SARS-CoV infection. Identification of basal immune predictors in humans could allow for identification of individuals at highest risk of severe clinical and virologic outcomes upon infection, who may thus most benefit from available clinical interventions to restrict infection and disease.

Comparative analysis reveals the species-specific genetic determinants of ACE2 required for SARS-CoV-2 entry (preprint)

Coronavirus interaction with viral receptor is a primary genetic determinant of host range and tissue tropism. SARS-CoV-2 utilizes ACE2 as the receptor to enter the host cell in a species-specific manner. We and others have previously shown that ACE2 orthologs from New World monkeys, koala and mouse cannot interact with SARS-CoV-2 to mediate viral entry, and this defect can be restored by humanization of the restrictive residues in New World monkey ACE2. To better understand the genetic determinants of susceptibility of ACE2 orthologs to viral entry, we compared koala and mouse ACE2 sequences with human ortholog, and identified the key residues in koala or mouse ACE2 that restrict its viral receptor activity. Humanization of these critical residues could render the capabilities of koala and mouse ACE2 to bind viral spike protein and facilitate the viral entry. Our work identifies the genetic determinant of ACE2 for SARS-CoV-2 susceptibility, and a single mutation could restore the mouse ACE2 receptor activity, providing a potential avenue for the development of mouse model of SARS-CoV-2.

Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19 (preprint)

Less than a year after its emergence, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over 22 million people worldwide with a death toll approaching 1 million. Vaccination remains the best hope to ultimately put this pandemic to an end. Here, using Trimer-Tag technology, we produced both wild-type (WT) and furin site mutant (MT) S-Trimers for COVID-19 vaccine studies. Cryo-EM structures of the WT and MT S-Trimers, determined at 3.2 Angstrom and 2.6 Angstrom respectively, revealed that both antigens adopt a tightly closed conformation and their structures are essentially identical to that of the previously solved full-length WT S protein in detergent. These results validate Trimer-Tag as a platform technology in production of metastable WT S-Trimer as a candidate for COVID-19 subunit vaccine.

SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism (preprint)

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 is thought to disable various features of host immunity and cellular defense. The SARS-CoV-2 nonstructural protein 1 (Nsp1) is known to inhibit host protein translation and could be a target for antiviral therapy against COVID-19. However, how SARS-CoV-2 circumvents this translational blockage for the production of its own proteins is an open question. Here, we report a bipartite mechanism of SARS-CoV-2 Nsp1 which operates by: (1) hijacking the host ribosome via direct interaction of its C-terminal domain (CT) with the 40S ribosomal subunit and (2) specifically lifting this inhibition for SARS-CoV-2 via a direct interaction of its N-terminal domain (NT) with the 5 untranslated region (5 UTR) of SARS-CoV-2 mRNA. We show that while Nsp1-CT is sufficient for binding to 40S and inhibition of host protein translation, the 5 UTR of SARS-CoV-2 mRNA removes this inhibition by binding to Nsp1-NT, suggesting that the Nsp1-NT-UTR interaction is incompatible with the Nsp1-CT-40S interaction. Indeed, lengthening the linker between Nsp1-NT and Nsp1-CT of Nsp1 progressively reduced the ability of SARS-CoV-2 5 UTR to escape the translational inhibition, supporting that the incompatibility is likely steric in nature. The short SL1 region of the 5 UTR is required for viral mRNA translation in the presence of Nsp1. Thus, our data provide a comprehensive view on how Nsp1 switches infected cells from host mRNA translation to SARS-CoV-2 mRNA translation, and that Nsp1 and 5 UTR may be targeted for anti-COVID-19 therapeutics.

An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2. (preprint)

COVID-19 vaccines are being rapidly developed and human trials are underway. Almost all of these vaccines have been designed to induce antibodies targeting spike protein of SARS-CoV-2 in expectation of neutralizing activities. However, non-neutralizing antibodies are at risk of causing antibody-dependent enhancement. Further, the longevity of SARS-CoV-2-specific antibodies is very short. Therefore, in addition to antibody-induced vaccines, novel vaccines on the basis of SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs) should be considered in the vaccine development. Here, we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Eighty-two peptides were firstly predicted as epitope candidates on bioinformatics. Fifty-four in 82 peptides showed high or medium binding affinities to HLA-A*02:01. HLA-A*02:01 transgenic mice were then immunized with each of the 54 peptides encapsulated into liposomes. The intracellular cytokine staining assay revealed that 18 out of 54 peptides were CTL epitopes because of the induction of IFN-{gamma}-producing CD8+ T cells. In the 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant CTL epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant over the other peptides. Surprisingly, all mice immunized with the liposomal 10 peptide mixture did not show the same reaction pattern to the 10 peptides. There were three pattern types that varied sequentially, suggesting the existence of an immunodominance hierarchy, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines. ImportanceFor the development of vaccines based on SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs), we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Out of 82 peptides predicted on bioinformatics, 54 peptides showed good binding affinities to HLA-A*02:01. Using HLA-A*02:01 transgenic mice, 18 in 54 peptides were found to be CTL epitopes in the intracellular cytokine staining assay. Out of 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant. Surprisingly, all immunized mice did not show the same reaction pattern to the 10 peptides. There were three pattern types that varied sequentially, suggesting the existence of an immunodominance hierarchy, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines.

Demand for hospitalization services for COVID-19 patients in Brazil (preprint)

COVID-19 is now a pandemic and many of the affected countries face severe shortages of hospital resources. In Brazil, the first case was reported on February 26. As the number of cases grows in the country, there is a concern that the health system may become overwhelmed, resulting in shortages of hospital beds, intensive care unit beds, and mechanical ventilators. The timing of shortage is likely to vary geographically depending on the observed onset and pace of transmission observed, on the availability of resources, and on the actions implemented. Here we consider the daily number of cases reported in municipalities in Brazil to simulate twelve alternative scenarios of the likely timing of shortage, based on parameters consistently reported for China and Italy, on rates of hospital occupancy for other health conditions observed in Brazil in 2019, and on assumptions of allocation of patients in public and private facilities. Results show that hospital services could start to experience shortages of hospital beds, ICU beds, and ventilators in early April, the most critical situation observed for ICU beds. Increasing the allocation of beds for COVID-19 (in lieu of other conditions) or temporarily placing all resources under the administration of the state delays the anticipated start of shortages by a week. This suggests that solutions adopted by the Brazilian government must aim at expanding the available capacity (e.g., makeshift hospitals), and not simply prioritizing the allocation of available resources to COVID-19.