Prevalence of SARS-CoV-2 lineages of potential epidemiological concern
Published: 24 June 2021
Two distinct non-overlapping time intervals are compared to illustrate the circulation of VOCs in space and time and possible increases/decreases in their prevalence. Table 1 incorporates data from April 29th (last update) to June 15th 2021, while Table 2 reports equivalent for the interval considered in the previous update (from February 27th to April 28th 2021).
The tables report the prevalence of four different lineages of SARS-CoV-2, known as the Alpha variant (B.1.1.7), Beta variant (B.1.351), Gamma variant (P.1) and Delta variant (B.1.617.2) that are considered to represent a potential risk and are under scrutiny by national and supranational health authorities. For these reasons they are defined as Variants of Concern or VOC. Additional information about the nomenclature and characteristics of these variants, can be found here, in a recent publication by the World Health Organization (WHO).
Table 1 reports the prevalence of the four VOCs in different countries (both European and extra-European) between April 29th and June 15th 2021.
Table 2 shows equivalent data but for the interval considered in the previous update (from February 27th to April 28th 2021). In both tables the last row indicates the total numbers of genomic sequences available at the time of analysis.
Table 3 reports equivalent data for different italian administrative regions. The column “Total genomes” reports the total number of genomes considered.
IMPORTANT: Since available data are fragmented and not homogeneous between different italian regions and different counties, the information reported in this analysis is purely descriptive, and does not necessarily represent the real.
IMPORTANT: despite being as complete and up to date as possible, the analyses reported here can not provide a precise overview of the real epidemiological situation. In fact, available data are fragmented and do not possess the same level of completeness and accuracy for different geographic regions. Increasing the number of viral genomes regularly sequenced and shared in public open access repositories, would be exential to improve the above-mentioned issue in the future.
Variants of potential epidemiological relevance
B.1.1.7 (Alpha variant)
B.1.1.7 was first detected in the South of the UK in mid-December 2020. This lineage is currently predominant in most European countries. B.1.1.7 has been shown to have higher transmissibility. Moreover, preliminary observations suggest also a greater severity of the disease, although further experimental tests and clinical investigations are required.
As of June 15th 2021, B.1.1.7 presence was verified in 164 countries in the world.
Comparison between the values reported in Table 1 and Table 2, highlights how the prevalence of B.1.1.7 in Italy has basically remained steady between the two intervals of time considered in our analyses (current: from April 29th to June 15h 2021; previous: from February 27th to April 28th). Conversely a slight increase in the prevalence of this lineage can still be observed in other European countries: 72.45% to 79.60% in France and from 86.52% to 92.67% in Germany. Interestingly, in theUnited Kingdom, where B.1.1.7 was the most prevalent lineage as of last update, the prevalence of the Alpha variant dropped from 96.83% to 36.89%. This decrease in prevalence of B.1.1.7 could be linked with the contemporary spread of the Delta variant (B.1.617.2) in the UK. Regarding extra-European countries, B.1.1.7 further increased its prevalence in the United States (from 51.14% to 66.75%), whereas it is scarcely detected in Brazil and South Africa. Finally, India presents a decrease trend similar to that observed in the UK, with a decrease in the prevalence of the Alpha variant (B.1.1.7) from 18.07% to 1.67%.
For Italian administrative regions, data reported in Table 3 suggest that, also when the the number of available genomic sequence is taken into account, the circulation of, B.1.1.7 does not seem to be uniform in our country. This notwithstanding a generalized increase in the prevalence of B.1.1.7 can still be observed.
Finally, it is important to remark that data reported in Table 3 represent an estimate of the prevalence of B.1.1.7 based on currently available data. Despite the recent increase in the number of publicly available genomic sequences, data are still highly fragmented between different Italian regions, and a lack of homogeneity in genomic data collection and sharing can result in possible biases in the estimation of the prevalence of thic VOC.
P.1 (Gamma variant)
The P.1 lineage was first reported in Japan on January 19th 2021 where it was isolated in four travellers arriving from Brazil, and subsequently identified also in South Korea, again in travellers from the same country. Preliminary investigations in Manaus, Amazonas state, report an increase in the proportion of COVID-19 cases associated with P.1, from 52.2% (35/67) in December 2020 to 85.4% (41/48) in January 2021. The P.1 VOC is considered to have a greater transmissibility and propensity for reinfection, although available data are still limited. There is no evidence of increased severity of the disease.
As of June 15th 2021, P.1 was detected in 68 countries in the world.
The comparison between Table 1 and Table 2 shows how this lineage is still predominant in Brazil (where it was first identified) and its prevalence settled down around 60%.
Regarding other countries considered in this analysis, a mild increase in the number of P.1 sequenced genomes was observed. The overall prevalence of this variant remains generally low.
B.1.351 (Beta variant)
The B.1.351 lineage was first identified in South Africa in December 2020, where it is currently the most widespread viral type. 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.
As of June 15th 2021, B.1.351 presence was verified in 115 countries in the world.
As it can be clearly observed from data reported in Table 1 and Table 2, B.1.351 shows a limited prevalence outside of South Africa where it represents the predominant lineage.
B.1.617.2 (Delta variant)
B.1.617.2 was first identified in India during December 2020 and rapidly became the most prevalent lineage in the country, leading, as of April 2021, to a wide increase in daily hospitalization cases and deaths and, consequently, to a health system overload.
As of June 15th 2021, B.1.617.2 was recorded in at least 80 countries in the world.
It is immediately evident from data reported in Table 1 and Table 2 that B.1.617.2 is the most represented lineage in India (where it was first isolated) and that its prevalence more than doubled from 32.02% to 76.87% between 29th April and 15th June 2021 with respect to the interval of time considered in our previous analysis (from 27th February to 28th April 2021). A similar increase can be observed also in the United Kingdom, where B.1.617.2 increased from a little less than 1% to 61.33% in the last two months. All the countries herein considered, both European and extra-European, show a reduced circulation of this lineaged, although slight but systematic increase in its prevalence can be observed.
Sources: GISAID (genomic data), ECDC (Variants of Concern), WHO (epidemiological data)