Genetic drift versus regional spreading dynamics of COVID-19

Alberti, Saverio; Pietro, Roberta Di; Basile, Mariangela; Antolini, Laura

doi:10.1101/2020.05.08.20095448

Cited by 4 publications

(6 citation statements)

References 40 publications

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“…Some mutations could be the result of the virus adapting to specific environmental conditions in a given geographic area, such as the climate [ 39 ]. However, the potential geoclimatic effects on the mutations observed must be evaluated by clinical and/or experimental studies.…”

Section: Discussionmentioning

confidence: 99%

“…Amino acid changes may play an important role in increasing the virulence of viral strains by inducing conformational changes in discontinuous neutralizing epitopes [35]. Some mutations could be the result of the virus adapting to specific environmental conditions in a given geographic area, such as the climate [39]. However, the potential geoclimatic effects on the mutations observed must be evaluated by clinical and/or experimental studies.…”

Section: Period Of Collectionmentioning

confidence: 99%

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Relevant SARS‐CoV‐2 Genome Variation through Six Months of Worldwide Monitoring

Hakmaoui

Khan

Liacini

et al. 2021

BioMed Research International

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Real-time genome monitoring of the SARS-CoV-2 pandemic outbreak is of utmost importance for designing diagnostic tools, guiding antiviral treatment and vaccination strategies. In this study, we present an accurate method for temporal and geographical comparison of mutational events based on GISAID database genome sequencing. Among 42523 SARS-CoV-2 genomes analyzed, we found 23202 variants compared to the reference genome. The Ti/Tv (transition/transversion) ratio was used to filter out possible false-positive errors. Transition mutations generally occurred more frequently than transversions. Our clustering analysis revealed remarkable hotspot mutation patterns for SARS-CoV-2. Mutations were clustered based on how their frequencies changed over time according to each geographical location. We observed some clusters showing a clear variation in mutation frequency and continuously evolving in the world. However, many mutations appeared in specific periods without a clear pattern over time. Various important nonsynonymous mutations were observed, mainly in Oceania and Asia. More than half of these mutations were observed only once. Four hotspot mutations were found in all geographical locations at least once: T265I (NSP2), P314L (NSP12), D614G (S), and Q57H (ORF3a). The current analysis of SARS-CoV-2 genomes provides valuable information on the geographical and temporal mutational evolution of SARS-CoV-2.

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Section: Discussionmentioning

confidence: 99%

Section: Period Of Collectionmentioning

confidence: 99%

Relevant SARS‐CoV‐2 Genome Variation through Six Months of Worldwide Monitoring

Hakmaoui

Khan

Liacini

et al. 2021

BioMed Research International

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“…Specifically, Araujo and Naimi (2020) submitted that immediate physical environment can mediate human-to-human transmission of COVID-19 and that unsuitable climates can cause the virus to destabilize quickly, hence reducing its capacity to become epidemic. Further, the strong association of COVID-19 to a sharp North/South climate gradient, with a faster spread in warm and cold temperate climates have been reported ( Araujo and Naimi, 2020 ; Briz-Redón and Serrano-Aroca, 2020 ; Di Pietro et al, 2020 ; Méndez-Arriaga, 2020 ). Similarly, Mishra and Wargocki (2020) , Sajadi et al (2020) and Wang et al (2020a) suggested a close relationship between the incidence of COVID-19 epidemics and climate with countries in high latitudes (characterized by temperate and/or continental climate) exhibiting a high incidence of the disease.…”

Section: Introductionmentioning

confidence: 88%

“…Climate is one of many factors likely affecting the spread of the virus ( Briz-Redón and Serrano-Aroca, 2020 ; Di Pietro et al, 2020 ; Mishra and Wargocki, 2020 ) and that the host's behaviour ( Kraemer et al, 2019 ) and population density ( Geoghegan and Holmes, 2017 ) are important predictors of the capacity of the virus to spread ( Araujo and Naimi, 2020 ). Recent studies suggested that infected humans can be asymptomatic and transmit the virus to others, generating substantial uncertainties regarding the overall risk of epidemic outbreaks under a variety of different climate, ecological and social settings ( Li et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Spatio-temporal variations in COVID-19 in relation to the global climate distribution and fluctuations

Matthew

Eludoyin

Oluwadiya

2021

Spatial and Spatio-temporal Epidemiology

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This study investigates the spatio-temporal variations in the occurrence of COVID-19 (confirmed cases and deaths) in relation to climate fluctuations in 61 countries scattered around the world from December 31, 2019 to May 28, 2020. Logarithm transformation of the count variable (COVID-19 cases) was used in a multiple linear regression model to predict the potential effects of weather variables on the prevalence of the disease. The study revealed strong associations (-0.510 ≤ r ≤ -0.967; 0.519 ≤ r ≤0.999) between climatic variables and confirmed cases of COVID-19 in majority (68.85%) of the selected countries. It showed evidences of 1 to 7-day delays in the response of the infection to changes in weather pattern. Model simulations suggested that a unit fall in temperature and humidity could increase (0.04 -18.70%) the infection in 19.67% and 16.39% of the countries respectively while a general reduction (-0.05 —9.40%) in infection cases was projected in 14.75% countries with a unit drop in precipitation. In conclusion, the study suggests that effective public health interventions are crucial contain the projected upsurge in COVID-19 cases during both cold and warm seasons in the southern and northern hemispheres.

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“…Over a year into the pandemic, sequencing analysis has shown that SARS-CoV-2 variants are being selected as the ongoing uncontrolled spreading of the SARS-CoV-2. While many mutations represent neutral genetic drift [ 2 ], a subset may alter its pathogenic potential and possibly reduce the efficacy of drugs and of immunity elicited by current vaccines. Since isolated, complete viral genome sequences have been periodically uploaded into the Global Initiative on Sharing Avian Influenza Data (GISAID; https://www.gisaid.org ) database.…”

Section: Introductionmentioning

confidence: 99%

Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia

et al. 2021

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In-depth study of the entire SARS-CoV-2 genome has uncovered many mutations, which have replaced the lineage that characterized the first wave of infections all around the world. In December 2020, the outbreak of variant of concern (VOC) 202012/01 (lineage B.1.1.7) in the United Kingdom defined a turning point during the pandemic, immediately posing a worldwide threat on the Covid-19 vaccination campaign. Here, we reported the evolution of B.1.1.7 lineage-related infections, analyzing samples collected from January 1st 2021, until April 15th 2021, in Friuli Venezia Giulia, a northeastern region of Italy. A cohort of 1508 nasopharyngeal swabs was analyzed by High Resolution Melting (HRM) and 479 randomly selected samples underwent Next Generation Sequencing analysis (NGS), uncovering a steady and continuous accumulation of B.1.1.7 lineage-related specimens, joined by sporadic cases of other known lineages (i.e. harboring the Spike glycoprotein p.E484K mutation). All the SARS-CoV-2 genome has been analyzed in order to highlight all the rare mutations that may eventually result in a new variant of interest. This work suggests that a thorough monitoring of the SARS-CoV-2 genome by NGS is essential to contain any new variant that could jeopardize all the efforts that have been made so far to resolve the emergence of the pandemic.

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Genetic drift versus regional spreading dynamics of COVID-19

Abstract: ObjectiveTo delineate the genetic and environmental determinants of COVID-19 spreading.

Cited by 4 publications

References 40 publications

Relevant SARS‐CoV‐2 Genome Variation through Six Months of Worldwide Monitoring

Relevant SARS‐CoV‐2 Genome Variation through Six Months of Worldwide Monitoring

Spatio-temporal variations in COVID-19 in relation to the global climate distribution and fluctuations

Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia

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