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

Alteri, Claudia; Cento, Valeria; Piralla, Antonio; Costabile, Valentino; Tallarita, Monica; Colagrossi, Luna; Renica, Silvia; Giardina, Federica; Novazzi, Federica; Gaiarsa, Stefano; Matarazzo, E.; Antonello, Maria; Vismara, Chiara; Fumagalli, Roberto; Epis, Oscar Massimiliano; Puoti, Massimo; Perno, Carlo Federico; Baldanti, Fausto

doi:10.1038/s41467-020-20688-x

Cited by 118 publications

(103 citation statements)

References 45 publications

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“…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.…”

Section: Discussionsupporting

confidence: 71%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Madrid, Spain, on 25 February 2020. It increased in frequency very fast and by the end of May more than 70,000 cases had been confirmed by reverse transcription-polymerase chain reaction (RT-PCR). To study the lineages and the diversity of the viral population during this first epidemic wave in Madrid we sequenced 224 SARS-CoV-2 viral genomes collected from three hospitals from February to May 2020. All the known major lineages were found in this set of samples, though B.1 and B.1.5 were the most frequent ones, accounting for more than 60% of the sequences. In parallel with the B lineages and sublineages, the D614G mutation in the Spike protein sequence was detected soon after the detection of the first coronavirus disease 19 (COVID-19) case in Madrid and in two weeks became dominant, being found in 80% of the samples and remaining at this level during all the study periods. The lineage composition of the viral population found in Madrid was more similar to the European population than to the publicly available Spanish data, underlining the role of Madrid as a national and international transport hub. In agreement with this, phylodynamic analysis suggested multiple independent entries before the national lockdown and air transportation restrictions.

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Section: Discussionsupporting

confidence: 71%

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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“… 18 Previous studies have reported relevant differences in the geographical distribution of the three most represented lineages (B.1, B.1.1, and B.1.5) in Lombardy, Italy. 22 Conversely, in our study, Lima‐Callao presents all nine lineages found in Peru, whereas the rest of the region's harbor lineages B.1, B.1.1, B.1.1.1, and B.1.5 (Figure 1B ). Additionally, until March 2020, we observed the nine PANGOLIN lineages in Lima‐Callao including A lineages; however, after April 2020, only B.1.1.1, B.1.1, B.1, and B.5 were registered by WGS (Figure 2A ).…”

Section: Resultscontrasting

confidence: 57%

Phylogenomics reveals multiple introductions and early spread of SARS‐CoV‐2 into Peru

Juscamayta-López

Carhuaricra

Tarazona

et al. 2021

Journal of Medical Virology

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Peru has become one of the countries with the highest mortality rates from the current coronavirus disease 2019 (COVID‐19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). To investigate early transmission events and the genomic diversity of SARS‐CoV‐2 isolates circulating in Peru in the early COVID‐19 pandemic, we analyzed 3472 viral genomes, of which 149 were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia and a high diversity of genetic lineages circulating in Peru. In addition, we found evidence for community‐driven transmission of SARS‐CoV‐2 as suggested by clusters of related viruses found in patients living in different regions of Peru.

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“…(1) , (2) , (3) , (4) , (5) )) the following data are needed: quanta emission rate (ER q ), deposition rate (k), inactivation rate (λ), inhalation rate (IR), room volume (V), air exchange rate (AER), time of exposure (T). The quanta emission rate was investigated in our previous papers where we highlighted that uncertainty relates to the quality of data on viral load, infectious dose and particle volume: such data, at least for SARS-CoV-2, are not definitive [ 47 , 55 , 73 ] also due to the presence of different viral lineages [ 74 ]. Therefore, even if the ER q data provided by our model are much more suitable than those typically estimated based on retrospective assessments of infectious outbreaks, a not negligible uncertainty exists.…”

Section: Resultsmentioning

confidence: 99%

Ventilation procedures to minimize the airborne transmission of viruses in classrooms

Stabile

Pacitto

Mikszewski

et al. 2021

Building and Environment

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Reducing the transmission of SARS-CoV-2 through indoor air is the key challenge of the COVID-19 pandemic. Crowded indoor environments, such as schools, represent possible hotspots for virus transmission since the basic non-pharmaceutical mitigation measures applied so far (e.g. social distancing) do not eliminate the airborne transmission mode. There is widespread consensus that improved ventilation is needed to minimize the transmission potential of airborne viruses in schools, whether through mechanical systems or ad-hoc manual airing procedures in naturally ventilated buildings. However, there remains significant uncertainty surrounding exactly what ventilation rates are required, and how to best achieve these targets with limited time and resources. This paper uses a mass balance approach to quantify the ability of both mechanical ventilation and ad-hoc airing procedures to mitigate airborne transmission risk in the classroom environment. For naturally-ventilated classrooms, we propose a novel feedback control strategy using CO 2 concentrations to continuously monitor and adjust the airing procedure. Our case studies show how such procedures can be applied in the real world to support the reopening of schools during the pandemic. Our results also show the inadequacy of relying on absolute CO 2 concentration thresholds as the sole indicator of airborne transmission risk.

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

Cited by 118 publications

References 45 publications

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

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

Phylogenomics reveals multiple introductions and early spread of SARS‐CoV‐2 into Peru

Ventilation procedures to minimize the airborne transmission of viruses in classrooms

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