SARS-CoV-2

Background

Pathogen : SARS CoV 2 is a virus belonging to the coronavirus family. Many variants of SARS-CoV-2 have circulated in humans since December 2019, when the pathogen became capable of human to human transmission.
Transmission: Transmission is primarily via respiratory droplets and aerosols when infected individuals breathe, talk, cough, or sneeze. Indirect transmission via contaminated surfaces (fomites) is possible, but less likely. The virus can spread from symptomatic, presymptomatic, or asymptomatic individuals.
Sources and risk factors: The risk of infection is higher when encountering infected individuals in close proximity, poorly ventilated indoor spaces, or crowded settings. Some variants exhibit increased transmissibility or allow immune escape, both of which can increase the risk of infection. Individuals with waning immunity or suboptimal vaccine responses (e.g. immunocompromised individuals) are also at greater risk of infection. The risk of serious illness is higher in individuals lacking prior immunity (gained through vaccination or previous infection), though it is possible for otherwise healthy individuals to become seriously ill.
Seasonality: After the pandemic came to a close, the number of cases has been relatively higher during winter months.

Brief Summary of the Outbreak

SARS-CoV-2 emerged in humans in late 2019, but existed in animals prior to this. The first cases of the novel coronavirus (nCoV) were identified in China in December 2019, and the virus quickly spread worldwide. In response, the World Health Organization (WHO) declared a Public Health Emergency of International Concern (PHEIC) on 30th January 2020, and later reclassified the outbreak as a pandemic on 11th March 2020.

Since then, many variants infecting humans have appeared. Variants are monitored by health agencies, who use multiple tools for tracking, sharing, and processing data (e.g. Nextstrain, GISAID). In May 2021, WHO adopted the Greek alphabet nomenclature (Alpha, Beta, Gamma, Delta, Omicron, etc.) for naming variants. Variants were categorised as Variants of Concern (VOC), Variants of Interest (VOI), and Variants under Monitoring (VUM), depending on their impact on society (transmissibility, severity, immunity evasion, detection). For example, variants were categorised as VOCs if there was clear evidence that they would have a marked negative impact on the population. Multiple variants were classified as VOCs between 2019 and 2023, including Alpha, Beta, Gamma, Delta, and Omicron variants.

On 5th May 2023, the WHO Emergency Committee on COVID-19 advised that the situation no longer met the criteria for a PHEIC. The WHO Director-General accepted this recommendation, marking the end of COVID-19’s classification as a global health emergency. A review committee began drafting recommendations to support countries in managing COVID-19 as an established, long-term health challenge.

In 2023, WHO refined variant classification definitions. VOC status became reserved for variants posing new, added risk. After this point, sublineages of Omicron were more often classified as VOIs or VUMs. Since then, multiple newer variants (e.g. JN.1, NB.1.8.1, XFG, LP.8.1, etc.) have been tracked, with risk assessments and monitoring by the World Health Organization (WHO) and the European Centre for Disease Prevention and Control (ECDC).

Outbreak Timeline

YEAR	DATE	OBSERVATION
2019	December	SARS-CoV-2 was first detected in humans in Wuhan, China.
2020	September	Alpha Variant (20I/501Y.V1, lineage B.1.1.7) was first identified in the UK and later spread to 114 countries
2020	October	Beta variant (B.1.351) was first identified in South Africa.
2020	December	Gamma variant (P.1) was first identified in Brazil (initially detected in travellers).
2021	February	Delta variant (B.1.617.2) was first detected in India, and later became globally dominant.
2021	November	Omicron variant (B.1.1.529) was first detected in South Africa / Botswana. WHO designated it as a VOC on 26th November 2021.
2022	Early 2022 (Jan)	Omicron became dominant globally. Subvariant BA.1 peaked and was soon replaced by BA.2 in many regions.
2022	February	Subvariant BA.2 overtook BA.1 as the dominant variant in many regions. BA.2 was estimated to be more transmissible and better at immune escape than BA.1.
2022	Mid / Late 2022	Omicron sublineages such as BA.4, BA.5 increased in prevalence followed by emergence of further descendants (e.g. BQ.1, BQ.1.1) in late 2022.
2023	Overall	Continued circulation and diversification of the Omicron variant led to recombinants and subvariants (XBB, etc.). WHO shifted classification practices (VOC was reserved for new threats, subvariants were handled as VOIs/VUMs). ECDC released documentation in regard the these variant changes.
2023	July -August	BA.2.86 (and derivative JN.1) was first detected in Germany. JN.1 was later designated as VOI.
2024	Jan–Mid 2024	While JN.1 was circulating, the other emerging lineages were monitored (VOIs/VUMs).
2024	March	WHO launched CoViNet, a global network for coronavirus variant surveillance and coordination.
2024	Late 2024	New lineage designations and risk evaluations were published. (e.g. JN.1, LP.8.1, etc.)
2025	Early 2025	Detection and monitoring of sublineages such as NB.1.8.1 and XFG were in progress.
2025	June	XFG was categorised by WHO as a variant under monitoring (VUM) and NB.1.8.1 was also under evaluation.
2025	Mid 2025 onwards	Variant competition continues, new mutations and subvariants are monitored as pandemic evolves.

Data Visualisations

This Nextstrain build, maintained by the Neher lab and Nextstrain team, focuses specifically on sequences from Sweden.
ECDC created a dashboard that shows a variants of SARS-CoV-2 in EU/EEA.
The Swedish Pathogens Portal offers interactive dashboards on SARS‑CoV‑2, including data on wastewater quantification, variant dynamics, serology testing, and vaccine coverage. It also visualises whole genome sequencing data and highlights trends in variant growth.