Circulating SARS-CoV-2 variants in Italy, October 2020-March 2021.
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ABSTRACT:
SUBMITTER: Lai A
PROVIDER: S-EPMC8364297 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:In early 2020, the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the human population quickly developed into a global pandemic. SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19) which has a broad range of respiratory illnesses. As the virus circulates, it acquires nucleotide changes. These mutations are potentially due to the inherent differences in the selection pressures within the human population compared to the original zoonotic reservoir of SARS-CoV-2 and formerly naïve humans. The acquired mutations will most likely be neutral, but some may have implications for viral transmission, disease severity, and resistance to therapies or vaccines. This is a follow-up study from our early report (Hartley et al. J Genet Genomics. 01202021;48(1):40-51) which detected a rare variant (nsp12, RdRp P323F) circulating within Nevada in mid 2020 at high frequency. The primary goals of the current study were to determine the phylogenetic relationship of the SARS-CoV-2 genomes within Nevada and to determine if there are any unusual variants within Nevada compared to the current database of SARS-CoV-2 sequences. Whole genome sequencing and analysis of SARS-CoV-2 from 425 positively identified nasopharyngeal/nasal swab specimens were performed from October 2020 to August 2021 to determine any variants that could result in potential escape from current therapeutics. Our analysis focused on nucleotide mutations that generated amino acid variations in the viral Spike (S) protein, Receptor binding domain (RBD), and the RNA-dependent RNA-polymerase (RdRp) complex. The data indicate that SARS-CoV-2 sequences from Nevada did not contain any unusual variants that had not been previously reported. Additionally, we did not detect the previously identified the RdRp P323F variant in any of the samples. This suggests that the rare variant we detected before was only able to circulate because of the stay-at-home orders and semi-isolation experience during the early months of the pandemic. IMPORTANCE: SARS-COV-2 continues to circulate in the human population. In this study, SARS-CoV-2 positive nasopharyngeal/nasal swab samples were used for whole genome sequencing to determine the phylogenetic relationship of SARS-CoV-2 sequences within Nevada from October 2020 to August 2021. The resulting data is being added to a continually growing database of SARS-CoV-2 sequences that will be important for understanding the transmission and evolution of the virus as it spreads around the globe.
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Project description:Epidemiological and virological studies have revealed that SARS-CoV-2 variants of concern (VOCs) are emerging globally, including in Europe. The aim of this study was to evaluate the spread of B.1.1.7-lineage SARS-CoV-2 in southern Italy from December 2020-March 2021 through the detection of the S gene target failure (SGTF), which could be considered a robust proxy of VOC B.1.1.7. SGTF was assessed on 3075 samples from week 52/2020 to week 10/2021. A subset of positive samples identified in the Apulia region during the study period was subjected to whole-genome sequencing (WGS). A descriptive and statistical analysis of the demographic and clinical characteristics of cases according to SGTF status was performed. Overall, 20.2% of samples showed SGTF; 155 strains were confirmed as VOC 202012/01 by WGS. The proportion of SGTF-positive samples rapidly increased over time, reaching 69.2% in week 10/2021. SGTF-positive cases were more likely to be symptomatic and to result in hospitalization (p < 0.0001). Despite the implementation of large-scale non-pharmaceutical interventions (NPIs), such as the closure of schools and local lockdowns, a rapid spread of VOC 202012/01 was observed in southern Italy. Strengthened NPIs and rapid vaccine deployment, first among priority groups and then among the general population, are crucial both to contain the spread of VOC 202012/01 and to flatten the curve of the third wave.
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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.
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