SARS-CoV-2 lineages of potential epidemiological interest in Italy
Published: 05 February 2021
At present (Feb 5th 2020) 3 lineages of SARS-CoV-2, known as the “English (B.1.1.7)”, “South African (501Y.V2)” and “Brazilian (P.1)” variants have been reported to represent a potential risk and are under scrutiny by national and supranational health authorities. The top panel indicates the prevalence (pie charts) of these variants in different regions of our country. The histogram indicates prevalence nationwide, per week. To facilitate future comparisons, other variants that are not currently considered to be of epidemiological significance (Spanish variant B.1.177), or for which there is limited evidence of potential epidemiological risk (under observation) are also displayed. It should be stressed that these do not currently represent a source of concern. “Altro” (other in Italian) is used to collectively indicate all those lineages that are not associated with mutations of potential epidemiological relevance.
IMPORTANT: Since available data are fragmented and not homogeneous between different Italian regions, the information reported in this analysis is purely descriptive, and does not necessarily represent the real situation in our country.
IMPORTANT: while these analyses are based on recent data, and probably represent the most up to date overview of the distribution of different viral lineages in our country we want to stress that they do not offer a complete overview of the current situation. Indeed, data are in general fragmented and only some regions provide up to date data.
The information reported in this analysis is purely descriptive and does not necessarily represent the real situation. In other words, it is like looking at a very low-res image: details are blurred and it is nearly impossible to know with a sufficient degree of precision what is the real situation. Furthermore, it is like some bits of the image have been shot in spring, a few in summer and fall and some more in winter. That is, we have both spatial and temporal blurriness. Improving the resolution of the image both at the spatial and temporal levels, that is increasing the number of viral genomes regularly sequenced and shared in public repositories in our country, will provide a clearer picture.
Variants of potential epidemiological relevance
English variant (lineage B.1.1.7)
Emerged in the South of the UK in mid December 2020, B.1.1.7 is currently the predominant lineage in that country. In the UK, the incidence of COVID-19 cases increased from early December 2020 until reaching a peak in early January 2021; A decreasing trend was observed from January 11th to 24th, likely due to the implementation of rigorous health control measures and social distancing. Similar dynamics were also recorded in Denmark, Ireland and the Netherlands, where this lineage was subsequently isolated. In the UK and Northern Ireland, B.1.1.7 has been shown to have a higher transmissibility. Moreover preliminary observations suggest also a greater severity of the disease, although further experimental tests and clinical investigations are necessary [4].
At present, for Italy, 146 genomic sequences of this lineage have been deposited in the GISAID database, all isolated starting from 14/12/2020. However, since the data have not been collected in a geographically or temporally uniform and homogeneous manner, it is currently not possible to provide accurate estimates of the prevalence of this lineage in our country. The relevant increase in the number of viral genomes of this type is probably due, at least in part, to the growing attention that has been registered in the last 2 months for this lineage,also by the media.
South African variant (lineage 501Y.V2)
The 501Y.V2 lineage was first identified in South Africa in December 2020, where it is currently the most widespread viral type. As of January 25, 2021, it has been reported in 31 countries. In South Africa, weekly cases have increased since early November, and reached a peak in early January. In the last two weeks the trend has been decreasing. Preliminary data indicate that this lineage may also be characterized by greater transmissibility; while it is currently unclear whether it is associated with more severe clinical manifestations.
At present no viral sequences of this type are represented in the GISAID database for our country. Although a case has been identified in Varese.
Brazilian variant (lineage P.1)
The P.1 lineage was first reported in Japan on 10/01/2021, where it was isolated in 4 travellers arriving from Brazil, and subsequently identified also in South Korea, again in travellers from Brazil. As of January 25th 2021, the P.1 lineage was reported in 8 countries, including Italy. In Brazil, the number of new weekly cases in the last two weeks is reported to be higher compared to September-November 2020, and COVID-19 related deaths have increased since the beginning of November. Preliminary investigations in Manaus, Amazonas state, report an increase in the proportion of COVOD-19 cases associated with P.1, from 52.2% (35/67) in December 2020 to 85.4% (41/48) in January 2021. Highlighting ongoing local transmission and suggesting potential greater transmissibility or propensity for reinfection, although available data are limited. There is no evidence of increased severity of the disease.
Three viral genomes of this type from our country are currently present in the GISAID database.
Other variants
Spanish variant (lineage B.1.177)
Lineage B.1.177 reached a high prevalence in several European countries last summer. However, its widespread diffusion does not seem to be associated with increased infectivity or an improved ability to evade the immune system [5]. Therefore it is not considered a source for concern. At the present time, 928 genomes of this type are recorded in our country in the GISAID database.
Variants of limited concern
Recent in vitro studies have highlighted some mutations in the spike protein that could be associated with a reduced immune response [5]. These mutations are not associated with particular viral lineages and represent a limited concern at present. However, they are still monitored for safety reasons. The figures show the cumulative number of variants of this type observed in our country.
Other (Altro)
For the sake of completeness, the figures also display all the viral lineages that are not associated with particular characteristics or that make them interesting from an epidemiological point of view. These are flagged under “altro” (other in Italian)
Source: https://www.gisaid.org/ (genomic data)
Source: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports (epidemiological data)
Please see https://cov-lineages.org/global_report.html for daily updates on the prevalence of SARS-CoV-2 lineages worldwide
Bibliography
[1] “Weekly epidemiological update -27January 2021” (https://www.who.int/publications/m/item/weekly-epidemiological-update—27-january-2021)
[2] “European Centre for Disease Prevention and Control. Risk related to spread of new SARS-CoV-2 variants of concern in the EU/EEA, first update –21 January 2021. ECDC: Stockholm; 2021.” (https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA-first-update.pdf)
[3] “European Centre for Disease Prevention and Control. Sequencing of SARS-CoV-2: first update. 18 January 2021. ECDC: Stockholm; 2021. (https://www.ecdc.europa.eu/sites/default/files/documents/Sequencing-of-SARS-CoV-2-first-update.pdf)
[4] NERVTAG paper on COVID-19 variant of concern B.1.1.7. The Government of the United Kingdom of Great Britain and Northern Ireland; 2021. Available at: https://www.gov.uk/government/publications/nervtag-paper-on-covid-19-variant-of-concern-b117
[5] COG-UK report on SARS-CoV-2 Spike mutations of interest in the UK — 15th January 2021. Available at: https://www.cogconsortium.uk/wp-content/uploads/2021/01/Report-2_COG-UK_SARS-CoV-2-Mutations.pdf