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SARS-CoV-2, the virus that causes COVID-19, has had a major impact on human health worldwide; infect large numbers of people; causing serious illness and associated long-term health consequences; resulting in death and excessive mortality, especially among the elderly and vulnerable populations; interrupting routine health services; interruptions in travel, commerce, education, and many other social functions; and, in general, have a negative impact on people’s physical and mental health. Since the start of the COVID-19 pandemic, WHO has received several reports of unusual public health events possibly due to variants of SARS-CoV-2. WHO routinely assesses whether SARS-CoV-2 variants cause changes in transmissibility, clinical presentation and severity, or whether they have an impact on countermeasures, including diagnostics, therapeutics, and vaccines. Previous reports of the D614G mutation and recent reports of virus variants from the Kingdom of Denmark, the United Kingdom of Great Britain and Northern Ireland, and the Republic of South Africa have raised interest and concern about the impact of viral changes.
A SARS-CoV-2 variant with a D614G substitution in the gene encoding the spike protein emerged in late January or early February 2020. Over a period of several months, the D614G mutation replaced the initial SARS strain -CoV-2 identified in China and in June 2020 it became the dominant form of the virus circulating globally. Studies in human respiratory cells and in animal models demonstrated that, compared to the initial virus strain, the strain with the D614G substitution has higher infectivity and transmission. The SARS-CoV-2 virus with the D614G substitution does not cause more serious illness or alter the effectiveness of existing laboratory diagnostics, therapeutics, vaccines, or public health preventive measures.
In August and September 2020, a SARS-CoV-2 variant related to infection among brood mink and subsequently transmitted to humans was identified in North Jutland, Denmark. The variant, named the “Cluster 5” variant by the Danish authorities, has a combination of mutations not previously observed. Due to preliminary studies conducted in Denmark, there is concern that this variant may result in reduced virus neutralization in humans, which could decrease the extent and duration of immune protection after natural infection or vaccination. . Studies are underway to evaluate the neutralization of the virus among humans with this variant. To date, after extensive investigation and surveillance, Danish authorities have identified only 12 human cases of the Cluster 5 variant in September 2020, and it does not appear to have spread widely.
On 14 December 2020, the UK authorities notified the WHO of a variant named by the UK as SARS-CoV-2 VOC 202012/01 (Variant of Concern, year 2020, month 12, variant 01). This variant contains 23 nucleotide substitutions and is not phylogenetically related to the SARS-CoV-2 virus circulating in the UK at the time the variant was detected. It is unclear how and where the SARS-CoV-2 VOC 202012/01 originated. SARS-CoV-2 VOC 202012/01 initially appeared in south-east England, but within a few weeks it began to replace other virus lineages in this geographic area and in London. As of December 26, 2020, SARS-CoV-2 VOC 202012/01 has been identified from routine samples and genomic testing conducted across the UK. Preliminary epidemiological, modeling, phylogenetic, and clinical findings suggest that SARS-CoV-2 VOC 202012/01 has increased transmissibility. However, preliminary analyzes also indicate no change in disease severity (measured by length of hospitalization and 28-day case fatality), or occurrence of reinfection among variant cases compared to other SARS viruses. -CoV-2 circulating in the UK. .1 Another of the mutations in the VOC 202012/01 variant, the deletion at position 69 / 70del was found to affect the performance of some diagnostic PCR assays with an S gene target. Most PCR assays that used worldwide will utilize multiple targets and therefore the impact of the variant on diagnosis is not expected to be significant. Laboratory evaluation has not shown a significant impact on the performance of antigen-based lateral flow devices. As of December 30, variant VOC-202012/01 has been reported in another 31 countries / territories / areas in five of the six WHO regions.
On December 18, South African national authorities announced the detection of a new variant of SARS-CoV-2 that is spreading rapidly in three South African provinces. South Africa has named this variant 501Y.V2, due to a N501Y mutation. While SARS-CoV-2 VOC 202012/01 from the UK also has the N501Y mutation, phylogenetic analysis has shown that 501Y.V2 from South Africa are different virus variants. In the week beginning November 16, routine sequencing by South African health authorities found that this new variant of SARS-CoV-2 has largely replaced other SARS-CoV-2 viruses circulating in the provinces. from Eastern Cape, Western Cape and KwaZulu-Natal. While genomic data highlighted that the 501.V2 variant rapidly displaced other circulating lineages in South Africa, and preliminary studies suggest that the variant is associated with a higher viral load, which may suggest a potential for increased transmissibility, this, as well as other factors that influence transmissibility, are subject to further investigation. Also, at this stage, there is no clear evidence that the new variant is associated with more severe disease or worse outcomes. More research is needed to understand the impact on transmission, clinical severity of infection, laboratory diagnostics, therapeutics, vaccines, or public health preventive measures. As of December 30, South Africa’s 501Y.V2 variant has been reported from four other countries to date.
