Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020

Abstract

We whole-genome sequenced 55 SARS-CoV-2 isolates from Germany to investigate SARS-CoV-2 outbreaks in 2020 in the Heinsberg district and Düsseldorf. While the genetic structure of the Heinsberg outbreak indicates a clonal origin, reflecting superspreading dynamics from mid-February during the carnival season, distinct viral strains were circulating in Düsseldorf in March, reflecting the city’s international links. Limited detection of Heinsberg strains in the Düsseldorf area despite geographical proximity may reflect efficient containment and contact-tracing efforts.

Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches

“…Even though all four BiH sequences cluster mainly with European ones, the constructed phylogenetic tree indicates multiple independent introductions of COVID-19 in BiH. Those findings correspond with other COVID-19 WGS studies [13,14] and confirm the importance of travel-associated disease introduction events for BiH as well. The success of future mitigation measures related to this type of disease introduction will be highly challenging for BiH due to a significant proportion of BiH population living abroad.…”

The origin and early spread of SARS-CoV-2 in Europe

“…Genome sequence data indicates that prior to 8 March 2020, SARS-CoV-2 was introduced from Hubei province into France, Germany, Italy, and other European countries at least two to four times each ( Table 1 ). These estimates, which are based on genome sequence data and thus do not rely on having line list data for individual migration cases, provide a complementary account of introduction events compared to line list data ( 19 ) and phylogenetic inferences combining genome sequence and line list data ( 20 – 25 ). The introduction events we report here are inferred to have occurred along the transmission tree specific to the analyzed sequence set and are not attributable to individual cases.…”

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

“…Viral genomes can be used to estimate the rate of viral evolution, monitor circulating lineages as well as identifying any signs of adaptation to hosts, treatments or vaccines. Genome sequencing of SARS-CoV-2 has provided epidemiological insights into the early outbreak [7][8][9] and a number of studies have adopted our method [8,[10][11][12][13][14][15][16][17] . Rapid data sharing allows sequences to be compared across labs or public health authorities and can provide insight into routes of transmission and effectiveness of containment measures [18] .…”