The Ellerslie School Health and Safety Committee: Epidemiological update: Occurrence of variants of SARS-CoV-2 in the Americas

20 January 2021

Introduction

The appearance of mutations is a natural and expected event within the evolution of the virus. In fact, some specific mutations define the viral genetic groups (also called lineages) that are currently circulating globally. Due to various microevolution processes and selection pressures, some additional mutations may appear, generating differences within each genetic group (called variants).

Genomic characterization of SARS-CoV-2

Recent reports of different variants of SARS-CoV-2 have reawakened interest and concern about the impact of viral changes. In recent months, two different variants of SARS -CoV-2 have been reported to WHO as unusual public health events: VOC 202012/01, lineage B.1.1.7 in the United Kingdom (U.K.) and Northern Ireland and 501Y.V2, lineage B.1.351, in South Africa.

VOC 202012/01 variant, B.1.1.7 lineage

On 14 December 2020, the U.K. authorities notified WHO of a variant named by the U.K. as SARSCoV-2 VOC 202012/01. This variant contains 23 nucleotide substitutions and is not phylogenetically related to the SARS-CoV-2 virus circulating in the United Kingdom at the time it was detected. It is unclear how and where it originated.

Findings and preliminary data, as much epidemiological, modeling, phylogenetic and clinical, suggest that SARS-CoV-2 VOC 202012/01 has higher transmissibility. However, preliminary analysis currently available suggest that there are no changes in the severity of the disease (measured by the duration of hospitalization and the 28-day case fatality rate), or the occurrence of reinfection among cases positive for this variant compared to cases by other SARS-CoV-2 lineages circulating in the U.K. Although no higher severity is observed among cases, the increase in transmissibility is of concern; the increase in cases in a limited time-period is associated with a significant public health impact.

As of 19 January 2021, 60 countries and territories outside of the U.K. in all six WHO Regions have reported either imported cases or community transmission of VOC 202012/013; this represents 20 additional countries and territories since the publication of the “Occurrence of variants of SARS-CoV-2 in the Americas, Preliminary Information as of 11 January 2021.”

Variant 501.V2, lineage B.1.351

On 18 December 2020, 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 the VOC 202012/01 variant also has the N501Y mutation, phylogenetic analysis has shown that the 501Y.V2 detected in South Africa is a different variant.

Genomic data highlighted that the 501.V2 variant rapidly displaced other lineages circulating in South Africa. Preliminary studies suggest that this variant is associated with a higher viral load, which could suggest a potential for greater transmissibility. However, further investigation of this and other factors that influence transmissibility is necessary.

Also, at this stage of ongoing research, there is no clear evidence that the new variant is associated with more severe disease or worse outcome. More research is needed to understand the impact on transmission, clinical severity of infection, laboratory diagnostics, therapeutics, vaccines, or public health preventive measures. Although this new variant does not appear to cause more serious disease, the rapid increase in the number of cases has put health systems under pressure.

As of 19 January 2021, 23 countries outside of South Africa in four of the six WHO Regions have reported cases of 501Y.V2; this represents 17 additional countries and territories since the publication of the “Occurrence of variants of SARS-CoV-2 in the Americas, Preliminary Information as of 11 January 2021.” However, no increase in circulation or sustained increase in the spread of this variant has been reported in these countries or territories.

Other variants of potential public health interest

In addition to the variants already mentioned, Brazil, Japan, and the United States of America, have reported the detection of variants.

Lineage B.1.1.28

The lineage was described for the first time in Brazil on 5 March 2020 by the Adolfo Lutz Institute in a 22-year-old patient. This lineage has been circulating in the U.K (3.0%, in Australia (1.0%), in the United States (1.0%), and in Portugal (1.0%).

Variant P.1, lineage B.1.1.28

On 9 January 2021, Japan notified WHO about a new variant of SARS-CoV-2, B.1.1.28 (initially reported as B.1.1.248), detected in four travelers from Brazil. This variant is not closely related to the SARS-CoV-2 VOC 202012/01 variant or to the 501Y.V2 variant.

This variant has 12 mutations to the spike protein, including three mutations of concern in common with 501Y.V2, i.e.: K417N/T, E484K and N501Y, which may impact transmissibility and host immune response.

On 12 January 2021, researchers in Brazil reported on the detection of a variant of the B.1.1.28 lineage that, like the P.1 variant, has the E484K mutation, which has probably evolved independently of the variant detected among the travelers reported by Japan. The detection was carried out in the state of Amazonas.

Additionally, other researchers from Brazil reported 148 sequences of the complete SARS -CoV2 genome from the state of Amazonas, in which 69 (47%) B.1.1.28 sequences were identified among the samples from different municipalities between 13 April and 13 November 2020, making this variant the most prevalent variant in that Brazilian state.

Variant L452R

In the United States, the California Department of Public Health (CDPH), in coordination with Santa Clara County and the University of California, San Francisco (UCSF), announced on 17 January 2021 that the SARS-CoV-2 variant, L452R, is detected more frequently, by genomic sequencing of the virus in several counties of the state of California.

Genetic variants of SARS-CoV-2 in the Americas

The Region of the Americas has contributed to the generation of genomic sequencing data through the Regional Network for Genomic Surveillance of COVID-1913, which is open to all countries in the region, through the National Public Health Laboratories or equivalent public institutions. This Network includes two Regional Sequencing Laboratories (Fiocruz-Brazil and the Institute of Public Health-Chile), which provide external sequencing for participating laboratories in the network that do not have the capacity to sequence.

As of 19 January 2021, countries and territories of the Americas have published 87,851 SARSCoV-2 genomes on the GISAID platform, collected between February 2020 and January 2021. The countries and territories that have contributed are Antigua and Barbuda, Argentina, Aruba, Belize, Bermuda, Bolivia, Brazil, Canada, Chile, Colombia, Costa Rica, Cuba, Curaçao, the Dominican Republic, Ecuador, El Salvador, Guadeloupe, Guatemala, Jamaica, Mexico, Panama, Peru, Saint Barthelemy, Saint Eustatius, Saint Kitts and Nevis, Saint Martin, Saint Vincent and the Grenadines, Suriname, Trinidad and Tobago, United States of America, Uruguay, and Venezuela.

As of 19 January 2021, the United States is the country in the Region of the Americas that has reported the highest number of cases in which the variant SARS -CoV-2 VOC 202012/01 has been detected (122 cases), distributed among 20 states; California and Florida States concentrate 70% of the reported cases.

As of 15 January 2021, Canada and Chile have reported 23 cases and 20 cases of the variant SARS-CoV-2 VOC 202012/01, respectively.

Additionally, as of 15 January 2021 in the Region of the Americas, only in Canada has the 501.V2 variant, lineage B.1.35, been detected (2 cases).

Conclusions and guidance for national authorities

National and local authorities should continue to strengthen existing disease control activities, including monitoring their epidemics closely through ongoing epidemiological surveillance and strategic testing; conducting outbreak investigation and contact tracing; and where appropriate, adjusting public health and social measures to reduce transmission of SARS -CoV2.

The data and information available indicate that both variants of interest (VOC 202012/01 and 501Y.V2) have been identified in the Americas. The frequency of detection of these variants is still very limited to date. Nonetheless, there is a possibility that the detection of these variants will gradually increase in the coming weeks and months.

PAHO/WHO has supported strengthening the capacity of each country to carry out genomic surveillance since March 2020 within the framework of the Regional Network for Genomic Surveillance of COVID-19 and urges Member States to participate in this Network and carry out sequencing, in accordance with the recommended samples and the technical approaches of this Network.

PAHO/WHO recommends that in the event of symptoms suggesting acute respiratory illness during or after travel, travelers are advised to seek medical attention and share their travel history with their healthcare provider. Health authorities should work with the transport and tourism sectors to provide travelers with information to reduce the risk of infection.

In line with the advice provided by the Emergency Committee on COVID-19 at its most recent meeting, WHO recommends that States Parties should regularly re-consider measures applied to international travel in compliance with Article 43 of the International Health Regulations (2005) and continue to provide information and rationale to WHO on measures that significantly interfere with international traffic. Countries are encouraged to implement coordinated, timelimited, risk-based, and evidence-based approaches for health measures in relation to international travel.

In all circumstances, essential travel (e.g., emergency responders; providers of public health technical support; critical personnel in transport and security sector such as seafarers; repatriations; and cargo transport for essential supplies such as food, medicines and fuel) identified by countries should always be prioritized and facilitated.

The following are links to a series of guides, scientific reports, and other resources published by PAHO/WHO and WHO.