Abstract
In this letter, we report a large-scale synchronized replacement pattern of the Alpha strain by the Delta strain. We argue that this phenomenon is associated with the invasion timing and transmissibility advantage of the Delta strain. Alpha strain skipped some countries/regions, e.g. India and neighboring countries/regions, which led to a mild first wave before the invasion of the Delta strain, in term of reported COVID-deaths per capita.
Keyword: variants of concern, Delta strain, Alpha variant, synchronization
Dear Editor:
The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has seriously affected public health worldwide. As of February 2021, more than 100 million people had been diagnosed with SARS-COV-2 and more than 2 million deaths have been attributed to COVID-19 1. The virus evolved rapidly and several variants have emerged. In March 2021, the Alpha variant began to spread in Cambodia and Thailand, in some clusters in Thailand, the positive rate of SARS-CoV-2 testing is as much as 60-90%.2 According to 3, besides a higher transmissibility than the previous wild strain, patients infected with the Alpha COVID-19 variant were at a higher risk of hospitalization than those infected with the previous wild strain, reflecting the increased virulence of the Alpha variant.
At the same time, Kappa (B.1.617.2) and Delta (B.1.617.2) variants appeared in Maharashtra, India and resulting in a resurgence of cases in the country. Different from Alpha variant, the Delta variant lineage is defined by eight non-synonymous mutations in S protein. The Delta variant which spread around 200 countries/regions has been classified as a variant of concern by the CDC. 4 Besides a higher transmissibility than Alpha strain, patients with the Delta variant were more than twice as likely to be hospitalized as those with the Alpha variant, according to5. The Delta variant is replacing all the other SARS-COV-2 variants.
Starting from June 2020, India has implemented 11 stages of unlocking, phase 11 of which was announced at the end of March, 202 and remains in effect until April 30, 2020. But since mid-April, 2020, India has seen a severe surge in the pandemic. As of May 10, 2020, more than 388,000 people had been affected.6 And according to another report 7, characteristic mutations of the Delta variant were observed in sequences obtained in India in April and May 2021, and the Delta variant became the dominant transmission variant in May and June, 2021 in India.
In this letter, we visualize the replacement of previous strain with Alpha strain and the replacement of Alpha strain with Delta strains globally. We find that the Alpha strain only dominated for a short period of 3-4 months and the replacement of Alpha with Delta show surprisingly synchronous pattern in a large number of countries/regions.