The spatiotemporal estimation of the risk and the international transmission of COVID-19: a global perspective

Lin, Yingtong; Ju, Wan; Lin, Yu; Lai, Chun Yeh

doi:10.1038/s41598-020-77242-4

Cited by 8 publications

(5 citation statements)

References 16 publications

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“…Generally speaking, it was observed that government-imposed mobility restrictions were successful in mitigating COVID-19 transmission [ 61 , 138 ]. At a global level, a positive correlation was found between human mobility and COVID-19 infections [ 45 , 92 , 75 , 76 , 139 ]. At a national scale, several studies found that mobility reduction generally implies a restrain on infections [ 59 , 140 , 141 ].…”

Section: Resultsmentioning

confidence: 99%

Conditioning factors in the spreading of Covid-19 – Does geography matter?

Vandelli,

Palandri,

Coratza

et al. 2024

Heliyon

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Section: Resultsmentioning

confidence: 99%

Conditioning factors in the spreading of Covid-19 – Does geography matter?

Vandelli,

Palandri,

Coratza

et al. 2024

Heliyon

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“…Surveillance data, including phylogenomic analysis of clinical infections, has shown that the virus has evolved with highly transmissible variants, i.e., variants of concern (VOCs), including Alpha, Beta, Gamma, Delta, and Omicron. These variants have driven successive waves of transmission in different continents and territories [ 3 , 4 , 5 ]. Other reports have associated variant-specific outbreaks with different demographics and clinical forms of COVID-19, but whether these factors can explain the case disparities reported globally has not been thoroughly investigated [ 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

Contrasting Epidemiology and Population Genetics of COVID-19 Infections Defined by Multilocus Genotypes in SARS-CoV-2 Genomes Sampled Globally

Chan

Ataíde

Richards

et al. 2022

Viruses

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Since its emergence in 2019, SARS-CoV-2 has spread and evolved globally, with newly emerged variants of concern (VOCs) accounting for more than 500 million COVID-19 cases and 6 million deaths. Continuous surveillance utilizing simple genetic tools is needed to measure the viral epidemiological diversity, risk of infection, and distribution among different demographics in different geographical regions. To help address this need, we developed a proof-of-concept multilocus genotyping tool and demonstrated its utility to monitor viral populations sampled in 2020 and 2021 across six continents. We sampled globally 22,164 SARS-CoV-2 genomes from GISAID (inclusion criteria: available clinical and demographic data). They comprised two study populations, “2020 genomes” (N = 5959) sampled from December 2019 to September 2020 and “2021 genomes” (N = 16,205) sampled from 15 January to 15 March 2021. All genomes were aligned to the SARS-CoV-2 reference genome and amino acid polymorphisms were called with quality filtering. Thereafter, 74 codons (loci) in 14 genes including orf1ab polygene (N = 9), orf3a, orf8, nucleocapsid (N), matrix (M), and spike (S) met the 0.01 minimum allele frequency criteria and were selected to construct multilocus genotypes (MLGs) for the genomes. At these loci, 137 mutant/variant amino acids (alleles) were detected with eight VOC-defining variant alleles, including N KR203&204, orf1ab (I265, F3606, and L4715), orf3a H57, orf8 S84, and S G614, being predominant globally with > 35% prevalence. Their persistence and selection were associated with peaks in the viral transmission and COVID-19 incidence between 2020 and 2021. Epidemiologically, older patients (≥20 years) compared to younger patients (<20 years) had a higher risk of being infected with these variants, but this association was dependent on the continent of origin. In the global population, the discriminant analysis of principal components (DAPC) showed contrasting patterns of genetic clustering with three (Africa, Asia, and North America) and two (North and South America) continental clusters being observed for the 2020 and 2021 global populations, respectively. Within each continent, the MLG repertoires (range 40–199) sampled in 2020 and 2021 were genetically differentiated, with ≤4 MLGs per repertoire accounting for the majority of genomes sampled. These data suggested that the majority of SARS-CoV-2 infections in 2020 and 2021 were caused by genetically distinct variants that likely adapted to local populations. Indeed, four GISAID clade-defined VOCs - GRY (Alpha), GH (Beta), GR (Gamma), and G/GK (Delta variant) were differentiated by their MLG signatures, demonstrating the versatility of the MLG tool for variant identification. Results from this proof-of-concept multilocus genotyping demonstrates its utility for SARS-CoV-2 genomic surveillance and for monitoring its spatiotemporal epidemiology and evolution, particularly in response to control interventions including COVID-19 vaccines and chemotherapies.

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“…The local gravity model based on power-law decay can effectively describe the diffusion patterns and process of COVID-19 in Hubei Province [16]. On a global scale, the risk of COVID-19 in each country decreased exponentially with the input of the first imported case and the time of onset [17]. At present, many types of COVID-19 vaccines are on the market.…”

Section: Introductionmentioning

confidence: 99%

The Analysis of Patterns of Two COVID-19 Outbreak Clusters in China

Gong

Zhou

et al. 2022

IJERPH

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Since the emergence of COVID-19, there have been many local outbreaks with foci at shopping malls in China. We compared and analyzed the epidemiological and spatiotemporal characteristics of local COVID-19 outbreaks in two commercial locations, a department store building (DSB) in Baodi District, Tianjin, and the Xinfadi wholesale market (XFD) in Fengtai District, Beijing. The spread of the infection at different times was analyzed by the standard deviation elliptical method. The spatial transfer mode demonstrated that outbreaks started at the center of each commercial location and spread to the periphery. The number of cases and the distance from the central outbreak showed an inverse proportional logarithmic function shape. Most cases were distributed within a 10 km radius; infected individuals who lived far from the outbreak center were mainly infected by close-contact transmission at home or in the workplace. There was no efficient and rapid detection method at the time of the DSB outbreak; the main preventative measure was the timing of COVID-19 precautions. Emergency interventions (closing shopping malls and home isolation) were initiated five days before confirmation of the first case from the shopping center. In contrast, XFD closed after the first confirmed cases appeared, but those infected during this outbreak benefitted from efficient nucleic acid testing. Quick results and isolation of infected individuals were the main methods of epidemic control in this area. The difference in the COVID-19 epidemic patterns between the two shopping malls reflects the progress of Chinese technology in the prevention and control of COVID-19.

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The spatiotemporal estimation of the risk and the international transmission of COVID-19: a global perspective

Cited by 8 publications

References 16 publications

Conditioning factors in the spreading of Covid-19 – Does geography matter?

Conditioning factors in the spreading of Covid-19 – Does geography matter?

Contrasting Epidemiology and Population Genetics of COVID-19 Infections Defined by Multilocus Genotypes in SARS-CoV-2 Genomes Sampled Globally

The Analysis of Patterns of Two COVID-19 Outbreak Clusters in China

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