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Spatiotemporal Analyses of 2 Co-Circulating SARS-CoV-2 Variants, New York State, USA.

ABSTRACT: The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in late 2020 and early 2021 raised alarm worldwide because of their potential for increased transmissibility and immune evasion. Elucidating the evolutionary and epidemiologic dynamics among novel SARS-CoV-2 variants is essential for understanding the trajectory of the coronavirus disease pandemic. We describe the interplay between B.1.1.7 (Alpha) and B.1.526 (Iota) variants in New York State, USA, during December 2020-April 2021 through phylogeographic analyses, space-time scan statistics, and cartographic visualization. Our results indicate that B.1.526 probably evolved in New York City, where it was displaced as the dominant lineage by B.1.1.7 months after its initial appearance. In contrast, B.1.1.7 became dominant earlier in regions with fewer B.1.526 infections. These results suggest that B.1.526 might have delayed the initial spread of B.1.1.7 in New York City. Our combined spatiotemporal methodologies can help disentangle the complexities of shifting SARS-CoV-2 variant landscapes.

SUBMITTER: Russell A

PROVIDER: S-EPMC8888210 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Spatiotemporal Analyses of 2 Co-Circulating SARS-CoV-2 Variants, New York State, USA.

Russell Alexis A O'Connor Collin C Lasek-Nesselquist Erica E Plitnick Jonathan J Kelly John P JP Lamson Daryl M DM St George Kirsten K

Emerging infectious diseases 20220208 3

The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in late 2020 and early 2021 raised alarm worldwide because of their potential for increased transmissibility and immune evasion. Elucidating the evolutionary and epidemiologic dynamics among novel SARS-CoV-2 variants is essential for understanding the trajectory of the coronavirus disease pandemic. We describe the interplay between B.1.1.7 (Alpha) and B.1.526 (Iota) variants in New York State, USA, durin ...[more]

PMID: 35133957

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Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that was first reported in Wuhan, China in December of 2019 and has since caused a global pandemic resulting in millions of deaths and tens of millions of patients testing positive for infection. Analysis of different viral strains has identified a D614G change in the spike protein that is correlated with the virus becoming more transmissible. While studies have shown G614 viruses to be more transmissible, the effects of this mutation on the host response, especially on the cellular level, are yet to be fully elucidated. In this experiment we infected NHBE cells with the Washington (D614) strain or the New York (G614) strains of SARS-CoV-2. We generated RNA sequencing data at three different time points to improve our understanding of how the intracellular host response differs between infections with these two strains. We analyzed these data with a bioinformatics pipeline that identifies differentially expressed genes, enriched Gene Ontology terms and dysregulated signaling pathways. We detected over 2,000 differentially expressed genes, over 600 Gene Ontology terms, and 29 affected pathways between the two treatments. Many of these entities play a role in immune signaling and response. When comparing the different strains and different time points we found more overall similarities between matched time points than across different time points with the same strain. When specifically comparing the affected pathways, we saw that the 24hr time point of the New York strain was more similar to the 12hr time point of the Washington strain with a large number of pathways related to translation being inhibited in both strains at these time points. These results suggest that D614G substitution in the spike protein, combined with other nonsynonymous changes in the viral gene products cause distinct responses in infected host cells, especially relating to how quickly translation is dysregulated after infection. These observed differences in the intracellular host response to infection could play a role in driving the increase in pathogenicity and mortality seen in the New York outbreaks versus the Washington outbreaks at the beginning of the SARS-CoV-2 pandemic.

Project description:IntroductionThe coronavirus disease 2019 (COVID-19) pandemic has caused significant public health and socioeconomic crises across Africa; however, the prevalent patterns of COVID-19 and the circulating characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the continent remain insufficiently documented.MethodsIn this study, national data on case numbers, infection incidences, mortality rates, the circulation of SARS-CoV-2 variants, and key health indexes were collected from various official and professional sources between January 2020 and December 2023 were analyzed with SaTScan and geographically weighted regression (GWR).ResultsThe prevalent profiles and circulating features of SARS-CoV-2 across the African continent, including its five regions and all African countries, were analyzed. Four major waves of the epidemic were observed. The first wave was closely associated with the introduction of the early SARS-CoV-2 strain while the subsequent waves were linked to the emergence of specific variants, including variants of concern (VOCs) Alpha, Beta, variants of interest (VOIs) Eta (second wave), VOC Delta (third wave), and VOC Omicron (fourth wave). SaTScan analysis identified four large spatiotemporal clusters that affected various countries. A significant number of countries (50 out of 56) reported their first cases during February 2020 and March 2020, predominantly involving individuals with confirmed cross-continental travel histories, mainly from Europe. In total, 12 distinct SARS-CoV-2 VOCs and VOIs were identified, with the most prevalent being VOCs Omicron, Delta, Beta, Alpha, and VOI Eta. Unlike the dominance of VOC Delta during the third wave and Omicron during the fourth wave, VOC Alpha was relatively rare in the Southern regions but more common in the other four regions. At the same time, Beta predominated in the Southern region and Eta in the Western region during the second wave. Additionally, relatively higher COVID-19 case incidences and mortalities were reported in the Southern and Northern African regions. Spearman rank correlation and geographically weighted regression (GWR) analyses of COVID-19 incidences against health indexes in 52 African countries indicate that countries with higher national health expenditures and better personnel indexes tended to report higher case incidences.DiscussionThis study offers a detailed overview of the COVID-19 pandemic in Africa. Strengthening the capacity of health institutions across African countries is essential for the timely detection of new SARS-CoV-2 variants and, consequently, for preparedness against future COVID-19 pandemics and other potentially infectious disease outbreaks.

Dataset Information

Spatiotemporal Analyses of 2 Co-Circulating SARS-CoV-2 Variants, New York State, USA.

Publications

Spatiotemporal Analyses of 2 Co-Circulating SARS-CoV-2 Variants, New York State, USA.

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