Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Jun:39:100578.
doi: 10.1016/j.epidem.2022.100578. Epub 2022 May 13.

Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern

Laura Amato  1 , Luca Candeloro  2 , Arturo Di Girolamo  3 , Lara Savini  4 , Ilaria Puglia  5 , Maurilia Marcacci  6 , Marialuigia Caporale  7 , Iolanda Mangone  8 , Cesare Cammà  9 , Annamaria Conte  10 , Giuseppe Torzi  11 , Adamo Mancinelli  12 , Francesca Di Giallonardo  13 , Alessio Lorusso  14 , Giacomo Migliorati  15 , Thomas Schael  16 , Nicola D'Alterio  17 , Paolo Calistri  18
Affiliations

Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern

Laura Amato et al. Epidemics. 2022 Jun.

Abstract

From 24 December 2020 to 8 February 2021, 163 cases of SARS-CoV-2 Alpha variant of concern (VOC) were identified in Chieti province, Abruzzo region. Epidemiological data allowed the identification of 14 epi-clusters. With one exception, all the epi-clusters were linked to the town of Guardiagrele: 149 contacts formed the network, two-thirds of which were referred to the family/friends context. Real data were then used to estimate transmission parameters. According to our method, the calculated Re(t) was higher than 2 before the 12 December 2020. Similar values were obtained from other studies considering Alpha VOC. Italian sequence data were combined with a random subset of sequences obtained from the GISAID database. Genomic analysis showed close identity between the sequences from Guardiagrele, forming one distinct clade. This would suggest one or limited unspecified viral introductions from outside to Abruzzo region in early December 2020, which led to the diffusion of Alpha VOC in Guardiagrele and in neighbouring municipalities, with very limited inter-regional mixing.

Keywords: Abruzzo; Epidemiology; Genomic surveillance; Reproduction number; SARS-CoV-2, Alpha variant.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Network based on epidemiological data. 14 apparently unrelated epi-clusters were identified, with 163 cases (circles) and 149 transmission links (arrows). Epi-clusters are numbered (number located on the index case) and circles’ diameter is proportional to the number of secondary cases. Color of the circles represent date of symptoms' onset: recorded (black circles) or not (grey circles). Arrows represent the transmission chain, from the infector to the infected.
Fig. 2
Fig. 2
Epi-clusters and nature of connections between cases. One-hundred contacts happened in the family/friends context; 25 connections were related to working locations, 15 connections were linked to a residential medical center; three cases were associated to a fourth one because of attending the same school; spatial analysis highlighted two connections between cases, and, lastly, the nature of four connections reported by the Local Health Authorities was not specified.
Fig. 3
Fig. 3
Infection incidence and estimated incidence. The vertical dashed blue line represents the first symptom onset (12 Dec, blue line). Upper panel: infection incidence (bars). Lower panel: Re(t) and 95% CI estimated by Cori model (grey area), and from case reproduction number (blue area); the dashed red line represents Re(t)= 1.
Fig. 4
Fig. 4
Phylogeny of B.1.1.7 in Italy. (A) Maximum likelihood tree showing 1097 full-genome SARS-CoV-2 sequences. Branches are colored according to Italian regions; global data is shown in grey. For the five main Italian clusters the proportion of sequences per region is shown as a pie chart. (B) The largest clusters containing all sequences from Guardiagrele is shown enlarged (n = 383). Branches are colored according to the province in Abruzzo. Sequences from Guardiagrele are marked with white. (C) The provinces in Abruzzo and the proportion of sequences from each province in the large cluster. Branch length shows nucleotide substitutions per site.
See this image and copyright information in PMC

References

    1. Abbott, S., 2020. epiforecasts/EpiNow2: Initial release [WWW Document]. 10.5281/ZENODO.3957490. - DOI
    1. Abbott S., Hellewell J., Sherratt K., Gostic K., Hickson J., Badr H.S., DeWitt M., Thompson R., EpiForecasts, Funk S. (2020a). EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters. doi: 10.5281/zenodo.3957489.
    1. Abbott S., Hellewell J., Thompson R.N., Sherratt K., Gibbs H.P., Bosse N.I., Munday J.D., Meakin S., Doughty E.L., Chun J.Y., Chan Y.-W.D., Finger F., Campbell P., Endo A., Pearson C.A.B., Gimma A., Russell T., Flasche S., Kucharski A.J., Eggo R.M., Funk S. Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts. Wellcome Open Res. 2020;5:112. doi: 10.12688/wellcomeopenres.16006.2. - DOI
    1. Amato L., Jurisic L., Puglia I., Di Lollo V., Curini V., Torzi G., Di Girolamo A., Mangone I., Mancinelli A., Decaro N., Calistri P., Di Giallonardo F., Lorusso A., D’Alterio N. Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Emerging Microbes & Infections. 2021:1148–1155. doi: 10.1080/22221751.2021.1933609. - DOI - PMC - PubMed
    1. Bager P., Wohlfahrt J., Fonager J., Rasmussen M., Albertsen M., Michaelsen T.Y., Møller C.H., Ethelberg S., Legarth R., Button M.S.F., Gubbels S., Voldstedlund M., Mølbak K., Skov R.L., Fomsgaard A., Krause T.G. Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study. Lancet Infect. Dis. 2021 doi: 10.1016/s1473-3099(21)00290-5. - DOI - PMC - PubMed

Supplementary concepts