Global transmission network of SARS-CoV-2: from outbreak to pandemic

Abstract

Background. The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is straining health systems around the world. Although the Chinese government implemented a number of severe restrictions on people's movement in an attempt to contain its local and international spread, the virus had already reached many areas of the world in part due to its potent transmissibility and the fact that a substantial fraction of infected individuals develop little or no symptoms at all. Following its emergence, the virus started to generate sustained transmission in neighboring countries in Asia, Western Europe, Australia, Canada and the United States, and finally in South America and Africa. As the virus continues its global spread, a clear and evidence-based understanding of properties and dynamics of the global transmission network of SARS-CoV-2 is essential to design and put in place efficient and globally coordinated interventions. Methods. We employ molecular surveillance data of SARS-CoV-2 epidemics for inference and comprehensive analysis of its global transmission network before the pandemic declaration. Our goal was to characterize the spatial-temporal transmission pathways that led to the establishment of the pandemic. We exploited a network-based approach specifically tailored to emerging outbreak settings. Specifically, it traces the accumulation of mutations in viral genomic variants via mutation trees, which are then used to infer transmission networks, revealing an up-to-date picture of the spread of SARS-CoV-2 between and within countries and geographic regions. Results and Conclusions. The analysis suggest multiple introductions of SARS-CoV-2 into the majority of world regions by means of heterogeneous transmission pathways. The transmission network is scale-free, with a few genomic variants responsible for the majority of possible transmissions. The network structure is in line with the available temporal information represented by sample collection times and suggest the expected sampling time difference of few days between potential transmission pairs. The inferred network structural properties, transmission clusters and pathways and virus introduction routes emphasize the extent of the global epidemiological linkage and demonstrate the importance of internationally coordinated public health measures.

Settings of virus exposure and their implications in the propagation of transmission networks in a COVID-19 outbreak

“…Heterogeneity is the hallmark of the transmission pattern of SARS-CoV-2, as inferred from global molecular epidemiologic studies. [18] Its propagation varies by the rate and extent of secondary transmission in the population, which is in turn dependent on the settings of virus exposure. Our results reported, for the first time, the association between exposure settings and the propagation of transmission clusters using real world surveillance and contact tracing data.…”

“…With a daily increase of over 0·2 million new cases, the ultimate toll of the pandemic may surpass many of the previous influenza pandemics. Amidst the widespread dissemination of COVID-19, marked heterogeneity of SARS-CoV-2’s transmission pattern is noted, [1] as has been described for the related virus causing SARS over a decade ago [2] . Modelling studies suggested the phenomenon of overdispersion, with 80% of the secondary transmission caused by a very small fraction of proportion of SARS-CoV-2 infected patients, [3] which explains the characteristics of outbreaks attributed to a single patient exposure, [4 , 5] or inferred from some big clusters as reported in South Korea [6] and Germany [7] .…”

Large scale genomic and evolutionary study reveals SARS-CoV-2 virus isolates from Bangladesh strongly correlate with European origin and not with China

“…The virus was later designated as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) based on taxonomic and genetic relationship with the previously identified SARS-CoV virus 4 . It’s high rate of transmissibility 5,6 allowed the virus to achieve global transmission rapidly 7,8 . The World Health Organization (WHO) announced COVID-19 as a pandemic on March 11, 2020 9 .…”

Transmission route and introduction of pandemic SARS‐CoV‐2 between China, Italy, and Spain

“…1,2 By the time China was the epicenter of this pandemic, a stringent framework for maintaining the distribution of these people had been placed in place, whether at local or international level, the virus had gained ground in many countries around the world, Partly because of its strong transmissibility, and also because a small fraction of infected persons experience little to no symptoms. 3 This global spread suggests a clear and actual understanding of this pathogen's dynamic properties, through modeling, adapting a phylogeographic method that allows for joint estimation of phylogeny and epidemiological parameters of interest. 4 By applying this discipline in this research, which is the most recent field of phylodynamics, 5 we can map the current SARS-CoV-2 migration scenario, between and within the three countries selected in this research (China [Shanghai], Italy, Spain), that we assume reflects what is happening around the world.…”

“…The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic (2019) has placed health systems around the world on high alert, many governments have declared a strengthening of measures at their borders to prevent this virus from spreading 1,2 . By the time China was the epicenter of this pandemic, a stringent framework for maintaining the distribution of these people had been placed in place, whether at local or international level, the virus had gained ground in many countries around the world, Partly because of its strong transmissibility, and also because a small fraction of infected persons experience little to no symptoms 3 . This global spread suggests a clear and actual understanding of this pathogen's dynamic properties, through modeling, adapting a phylogeographic method that allows for joint estimation of phylogeny and epidemiological parameters of interest 4 .…”