Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021.
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ABSTRACT:
SUBMITTER: Sam IC
PROVIDER: S-EPMC8661738 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Excess mortality has exceeded reported deaths from Covid-19 during the pandemic. This gap may be attributable to deaths that occurred among individuals with undiagnosed Covid-19 infections or indirect consequences of the pandemic response such as interruptions in medical care; distinguishing these possibilities has implications for public health responses. In the present study, we examined patterns of excess mortality over time and by setting (in-hospital or out-of-hospital) and cause of death using death certificate data from California. The estimated number of excess natural-cause deaths from 2020 March 1 to 2021 February 28 (69,182) exceeded the number of Covid-19 diagnosed deaths (53,667) by 29%. Nearly half, 47.4% (32,775), of excess natural-cause deaths occurred out of the hospital, where only 28.6% (9,366) of excess mortality was attributed to Covid-19. Over time, increases or decreases in excess natural non-Covid-19 mortality closely mirrored increases or decreases in Covid-19 mortality. The time series were positively correlated in out-of-hospital settings, particularly at time lags when excess natural-cause deaths preceded reported Covid-19 deaths; for example, when comparing Covid-19 deaths to excess natural-cause deaths in the week prior, the correlation was 0.73. The strong temporal association of reported Covid-19 deaths with excess out-of-hospital deaths from other reported natural-cause causes suggests Covid-19 deaths were undercounted during the first year of the pandemic.
| S-EPMC9272175 | biostudies-literature
Project description:ObjectiveUnderstanding COVID-19-related mortality among the large population of people experiencing homelessness (PEH) in Los Angeles County (LA County) may inform public health policies to protect this vulnerable group. We investigated the impact of COVID-19 on PEH compared with the general population in LA County.MethodsWe calculated crude COVID-19 mortality rates per 100 000 population and mortality rates adjusted for age, race, and sex/gender among PEH and compared them with the general population in LA County from March 1, 2020, through February 28, 2021.ResultsAmong adults aged ≥18 years, the crude mortality rate per 100 000 population among PEH was 20% higher than among the general LA County population (348.7 vs 287.6). After adjusting for age, the mortality rate among PEH was 570.7 per 100 000 population. PEH had nearly twice the risk of dying from COVID-19 as people in the general LA County population; PEH aged 18-29 years had almost 8 times the risk of dying compared with their peers in the general LA County population. PEH had a higher risk of mortality than the general population after adjusting for race (standardized mortality ratio [SMR] = 1.4; 95% CI, 1.2-1.6) and sex/gender (SMR = 1.3; 95% CI, 1.1-1.5).ConclusionsA higher risk of COVID-19-related death among PEH compared with the general population indicates the need for public health policies and interventions to protect this vulnerable group.
| S-EPMC9548447 | biostudies-literature
Project description:The COVID-19 pandemic has already reached more than 110 million people and is associated with 2.5 million deaths worldwide. Brazil is the third worst-hit country, with approximately 10.2 million cases and 250 thousand deaths. International efforts have been established to share information about Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemiology and evolution to support the development of effective strategies for public health and disease management. We aimed to analyze the high-quality genome sequences from Brazil from February 2020-2021 to identify mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages by using phylogenetics and phylodynamics analyses. We describe heterogeneous sequencing efforts, the progression of the different lineages along time, evaluating mutational spectra and frequency oscillations derived from the prevalence of specific lineages across different Brazilian regions. We found at least seven major (1-7) and two minor clades related to the six most prevalent lineages in the country and described its spatial distribution and dynamics. The emergence and recent frequency shift of lineages (P.1 and P.2) carrying mutations of concern in the spike protein (e. g., E484K, N501Y) draws attention due to their association with immune evasion and enhanced receptor binding affinity. Improvements in genomic surveillance are of paramount importance and should be extended in Brazil to better inform policy makers about better decisions to fight the COVID-19 pandemic.
| S-EPMC8654641 | biostudies-literature
Project description:BackgroundThe COVID-19 pandemic caused four waves of infection in Israel until October 2021. Israel was the first country to offer vaccinations to all the adult population followed by boosters. This study addresses how mortality rates reflect the effects of the pandemic.MethodsTotal mortality rates and rates of mortality without COVID-19 deaths (non-COVID-19 mortality) between March 2020 and October 2021 were compared with the average pre-COVID-19 rates in 2017-2019 by month, population group and by age group. In addition, a cohort vaccinated at least once by 31 March 2021 was followed up for mortality in the following seven months compared to the corresponding months in 2017-2019.ResultsA small number of excess deaths was found in the first wave and a greater excess in the following waves. The monthly mortality rate ratio was highest in October 2020, 23% higher than the average in 2017-2019, followed by August 2021 (22%), September 2021 (20%) and September 2020 (19%). Excess mortality in the Arab population was greater than for Jews and Others, and they had 65% and 43% higher mortality in September and October, 2020, 20-44% higher mortality between December 2020 and April 2021 and 33%, 45% and 22% higher mortality in August, September and October 2021, respectively. In most months of the pandemic, the non-COVID-19 mortality rates were not significantly different from those in 2017-2019. However, between November 2020 and March 2021, they were significantly lower for the total population and Jews and Others. They were significantly higher for the total population only in August 2021, and particularly for the Arab population. Non-COVID-19 mortality was also lower for most sex/age groups over the total study period. In a cohort of 5.07 million Israeli citizens vaccinated at least once by 31 March, 2021, age adjusted and age specific mortality rates for the following 7 months were lower than the average rates in 2017-2019 for these months, CONCLUSION: Israel has seen significant excess mortality during the COVID-19 pandemic, particularly in the Arab sector. Following lockdowns and administration of vaccinations excess mortality was reduced, and no excess mortality was seen amongst the vaccinated in the months after the vaccination campaign. These findings highlight the importance of public health measures such as mandating mask wearing and population vaccinations to control infection and reduce mortality.
| S-EPMC9153236 | biostudies-literature
Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presented numerous operational challenges to healthcare delivery networks responsible for implementing large scale detection of Coronavirus Disease 2019 (COVID-19), the infection caused by SARS-CoV-2. We describe testing performance, review data quality metrics, and summarize experiences during the scale up of laboratory-based detection of COVID-19 in the Veterans Health Administration, the largest healthcare system in the United States. During March 2020 to February 2021, we observed rapid increase in testing volume, decreases in test turnaround time, improvements in testing of hospitalized persons, changes in test positivity, and varying utilization of different tests. Though performance metrics improved over time, surges challenged testing capacity and data quality remained suboptimal. Future planning efforts should focus on fortifying supply chains for consumables and equipment repair, optimizing distribution of testing workload across laboratories, and improving informatics to accurately monitor operations and intent for testing during a public health emergency.
| S-EPMC8665666 | biostudies-literature
Project description:BackgroundThe incidence of multisystem inflammatory syndrome in children (MIS-C) varies by race and ethnicity. This study assessed whether disparities in MIS-C in the United States by race and ethnicity exceed known disparities in coronavirus disease 2019 (COVID-19) incidence.MethodsWe compared the distribution of race and ethnicity among patients with MIS-C (<21 years of age, termed children) with onset March 2020 to February 2021 to that of children with COVID-19 and in the general population. Analysis was restricted to 369 counties with high completeness of race and ethnicity reporting for MIS-C and COVID-19. For each racial and ethnic group, observed numbers of patients with MIS-C were compared with expected numbers (observed/expected ratio) in children with COVID-19 and in the general population within these counties.ResultsCompared with children in the general population, MIS-C was more frequent among Hispanic (139% of expected) and non-Hispanic Black children (183%) and less frequent among non-Hispanic White (64%) and non-Hispanic Asian children (48%). Compared with children with COVID-19, MIS-C was more frequent in non-Hispanic Black children (207% of expected) and less frequent in non-Hispanic White children (68%); however, frequency was not different among Hispanic (102%) and non-Hispanic Asian (74%) children.ConclusionsDisparities in MIS-C by race and ethnicity exist, even after controlling for COVID-19 disparities and geographic variations. The high proportion of MIS-C among Hispanic children and low proportion among non-Hispanic Asian children align with COVID-19 rates, while the high proportion among non-Hispanic Black children and low proportion among non-Hispanic White children are not explainable by COVID-19 rates.
| S-EPMC8505134 | biostudies-literature
Project description:BackgroundAfter a pneumonia outbreak in late 2019 in China, a new virus related to the Coronaviridae strain, called Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2), was identified as the pathogen of an emerging disease known as COronaVIrus Disease 19 (COVID-19). Preliminary evidence outlines a higher prevalence in adults and lower susceptibility in children. However, recent epidemiologic research highlighted that transmissibility and susceptibility among children and adolescents become higher due to new virus variants. Infections among youth arises with mainly respiratory and gastrointestinal symptoms and malaise. Nevertheless, critical illness affects new-borns and fragile children, requiring hospitalization and possibly intensive care support. Aim of this study was to examine the impact of COVID-19 pandemic on hospital admissions among children and adolescents aged 0 to 17 years over three waves of COVID-19 (from February 2020 to May 2021) in Piedmont, a large Italian region, and to investigate the possible determinants of hospitalizations.MethodsA meta-analysis for risk assessment was performed over three waves of COVID-19 (from February 2020 to May 2021). Data were extracted from the official Italian National Information System and ISTAT.ResultsOverall, 442 paediatric patients were enrolled and admissions concerned mostly the age group 0-4 years (60.2%). Trends of hospitalization showed a slight increase of paediatric admissions already in March 2020 and a rise during second and third waves (November 2020, March 2021). Paediatric age-grouped hospitalizations (0-4; 12-17; 5-11) reproduced an analogous trend. The children and adolescent hospitalization rate appeared lower than overall population with a moderate slope of increase in comparison with population slope. Monthly hospitalization rate (per 100,000) of children and adolescents aged 0-17 years reproduced the increasing trend of hospitalization numbers. This trend was influenced, in particular, by the trend of hospitalization rates for children aged 0-4 years. The meta-analysis for risk assessment showed a decreased likelihood of rescue of hospitalizations in female, 5-11 and 12-17 age groups. Conversely, the meta-analysis showed a positive association between foreign nationality and hospitalizations.ConclusionsOur results show a comparable trend of paediatric hospital admissions for COVID-19 and of the entire population hospitalizations over three waves. COVID-19 hospital admissions increase with a bimodal age distribution and the most admissions are among patients aged ≤4 or 5-11 years. Significant predictive factors of hospitalization are identified.
| S-EPMC10292193 | biostudies-literature
Project description:The emergence of SARS-CoV-2 variants has led to several cases among children. However, limited information is available from North African countries. This study describes the SARS-CoV-2 strains circulating in Tunisian pediatric population during successive waves. A total of 447 complete sequences were obtained from individuals aged from 13 days to 18 years, between March 2020 and September 2022: 369 sequences generated during this study and 78 ones, available in GISAID, previously obtained from Tunisian pediatric patients. These sequences were compared with 354 and 274 ones obtained from Tunisian adults and a global dataset, respectively. The variant circulation dynamics of predominant variants were investigated during the study period using maximum-likelihood phylogenetic analysis. Among the studied population, adolescents were the predominant age group, comprising 55.26% of cases. Twenty-three lineages were identified; seven of which were not previously reported in Tunisia. Phylogenetic analysis showed a close relationship between the sequences from Tunisian adults and children. The connections of sequences from other countries were variable according to variants: close relationships were observed for Alpha, B1.160 and Omicron variants, while independent Tunisian clusters were observed for Delta and B.1.177 lineages. These findings highlight the pivotal role of children in virus transmission and underscore the impact of vaccination on virus spread. Vaccination of children, with booster doses, may be considered for better management of future emergences.
| S-EPMC10966772 | biostudies-literature
Project description:BackgroundSouth Africa experienced four waves of SARS-CoV-2 infection, dominated by Wuhan-Hu, Beta, Delta, and Omicron (BA.1/BA.2). We describe the trends in SARS-CoV-2 testing, cases, admissions, and deaths among children and adolescents in South Africa over successive waves.MethodsWe analyzed national SARS-CoV-2 testing, case, and admissions data from March 2020 to February 2022 and estimated cumulative rates by age group for each endpoint. The severity in the third versus the fourth wave was assessed using multivariable logistic regression.ResultsIndividuals ≤18 years comprised 35% (21,008,060/60,142,978) of the population but only 12% (424,394/3,593,644) of cases and 6% (26,176/451,753) of admissions. Among individuals ≤18 years, infants had the highest admission (505/100,000) rates. Testing, case, and admission rates generally increased successively in the second (Beta) and third (Delta) waves among all age groups. In the fourth (Omicron BA.1/BA.2) wave, the case rate dropped among individuals ≥1 year but increased among those <1 year. Weekly admission rates for children <1 year (169/100,000) exceeded rates in adults (124/100,000) in the fourth wave. The odds of severe COVID-19 in all admitted cases were lower in the fourth wave versus the third wave in each age group, but they were twice as high in admitted cases with at least one comorbidity than those without.ConclusionsThe admission rate for children <5 years was higher in the fourth wave than in previous waves, but the overall outcomes were less severe. However, children with at least one comorbidity had increased odds of severe disease, warranting consideration of prioritizing this group for vaccination.
| S-EPMC10112681 | biostudies-literature
Project description:We report phylogenetic and mutational analysis of severe acute respiratory syndrome coronavirus 2 virus strains from the Lazio region of Italy and provide information about the dynamics of virus spread. Data suggest effective containment of clade V strains, but subsequently, multiple waves of clade G strains were circulating widely in Europe.
| S-EPMC7392408 | biostudies-literature