Genomic epidemiology of the early stages of SARS-CoV-2 outbreak in Russia

Abstract

The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from 67 closely timed introductions into Russia, mostly in late February to early March. All but one of these introductions came from non-Chinese sources, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia. These introductions resulted in at least 9 distinct Russian lineages corresponding to domestic transmission. A notable transmission cluster corresponded to a nosocomial outbreak at the Vreden hospital in Saint Petersburg; phylodynamic analysis of this cluster reveals multiple (2-4) introductions each giving rise to a large number of cases, with a high initial effective reproduction number of 3.7 (2.5-5.0).

A novel computational approach to reconstruct SARS-CoV-2 infection dynamics through the inference of unsampled sources of infection

“…This is backed up by the presence of Moscow-derived samples appearing at a large portion of larger cluster junctions in our diagram, indicating travel that may have led to outbreaks in other cities such as Omsk and Saint Petersburg. Additionally, Komissarov et al [38] have identified nine distinct transmission networks within the Russian Federation, making use of similar data obtained from GISAID [38]. Several of the transmission networks deduced by Komissarov et al include transmissions from Moscow to Yakutia, from Krasnodar to Orenburg, and from Moscow to Sverdlovsk.…”

“…3) also shares several similarities with the literature, despite the difficulty in making more concrete comparisons due to the lack of extensive epidemiological data. Kozlovskaya et al [37] state that the first several cases identified in Russia for the latter transmission pathway [38]. Additionally, several large outbreaks are seen in Saint Petersburg, since similar data has been used, these outbreaks may contribute to outbreaks at the Vreden Hospital which occurred somewhere from late-March to early-April [38].…”

Epidemic trends of SARS-CoV-2 modulated by economic activity, ethnicity, and vaccination

“…The Russian epidemic was characterized by influx from other countries. 19 In areas where crude oil exports are active, the virus may spread due to inflows from other countries even in remote areas with a small population.…”

“…Moreover, it is unclear how industrial structure and affluence affect infection trends in countries with large regional economic disparities, such as Russia. It also remains enigmatic whether policy is the only factor behind the success of countries resilient to coronavirus disease 2019 (COVID- 19), such as New Zealand 10 and Taiwan.…”

PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak

“…In the ongoing pandemic, large scale whole genome sequencing initiatives in other countries are being used to establish the origins of the spreading infections as well as to determine how the virus has mutated during its transmission (9). Viral genome sequencing and epidemiological data have also been successfully used to estimate the impact of informed public health decisions on the spread of the virus and contact tracing of cluster cases (10). Hence, large scale generation of whole-genome sequence data on SARS-CoV-2 from clinical samples collected from multiple geographic locations and at different time points of the outbreak and rapid dissemination of the same in public databases like the Global Initiative on Sharing All Influenza Data (GISAID) (11), is expected to provide valuable information.…”