Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy

Abstract

From February to April, 2020, Lombardy (Italy) was the area who worldwide registered the highest numbers of SARS-CoV-2 infection. By extensively analyzing 346 whole SARS-CoV-2 genomes, we demonstrated the simultaneous circulation in Lombardy of two major viral lineages, likely derived from multiple introductions, occurring since the second half of January. Seven single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. These two lineages, and the presence of two well defined clusters inside Lineage 1, revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy.

Effectiveness of infection-containment measures on SARS-CoV-2 seroprevalence and circulation from May to July 2020, in Milan, Italy

“…In our analysis, subjects residing in the Lombardy's provinces that suffered from a higher epidemic peak, such as Brescia, Bergamo or Cremona, had a higher risk of being anti-N reactive, compared to those residing in Milan. This is in agreement with very recent phylogenetic evidences of an effective containment of viral spread within specific geographical areas, with little mixing between different provinces in Lombardy [11].…”

“…Our region was the first, in Europe, to be intensively affected by SARS-CoV-2 infection. Recent phylogenetic estimates suggest that the introduction of SARS-CoV-2 in Lombardy occurred, with multiple hits, since the end of January 2020 [ 11 ], a hypothesis supported by the finding of a 2% serological positivity in blood donors who donated before February 20, 2020, in the Lodi area [ 12 ]. In our hospital, the largest of Milan and the second largest in Lombardy, the daily rates of new COVID-19 diagnoses reached their maximum around March 20, 2020, compatibly with a peak of contagions during the 1 st -2 nd week of the same month.…”

No evidence of SARS-CoV-2 circulation in the framework of influenza surveillance between October 2019 and February 2020 in Lombardy, Italy

“…The results of our retrospective analysis in respiratory samples collected from patients with respiratory symptoms are in keeping with those of others [ 2 ] and do not support evidence of widespread circulation for SARS-CoV-2 from October 2019 to January 2020 in Lombardy. This conclusion is also in agreement with data from a serologic analysis of the first SARS-CoV-2 outbreak (the Lodi Red Zone) [ 3 ] as well as a phylodynamic evaluation of SARS-CoV-2 genomes detected in the first epidemic wave, which both estimate (using different experimental approaches) the seeding of SARS-CoV-2 in Lombardy in early January 2020 [ 4 ]. In contrast, a study on stored sera from oncologic patients dated back early antibody seropositivity to SARS-CoV-2 to September 2019 [ 5 ].…”

Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants

“…In spite of these limitations, the data provide an image of the first epidemic wave in Madrid. The pattern of multiple and almost simultaneous virus entries from different origins suggested by the data is similar to those that have been described in several places and at different scales during this pandemic [ 3 , 4 , 5 , 6 , 9 ]. The lineage composition departs from the publicly available Spanish data and reflects the role of Madrid as a national and international travel and transportation hub, and the strong connections with European countries.…”

“…As part of the efforts to improve molecular diagnosis and to understand the population dynamics of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Madrid during the first pandemic wave, a collaboration was started between our three hospitals, for sequencing the genomes of a representative sample of the virus population circulating in the Madrid region. Several studies have explored the use of SARS-CoV-2 genome sequences to understand the spread of the epidemic at the local [ 3 ], regional [ 4 , 5 ] or higher levels [ 6 , 7 , 8 , 9 ]. We present here an analysis of the sequences of 224 viral genomes collected in Madrid from February to May 2020 coincident with the first pandemic wave in our country.…”