Alignment updated: 2022-10-12

Last run: 2022-10-14

Notes

  • The situation with SARS-CoV-2 is constantly changing. The numbers given here reflect the most recent three months of sequences available as of 12th October 2022, and not the number of cases or prevalence. There are a number of potential sources of bias, including, but not limited to:
    • changing lineage definitions
    • QC rejections, e.g. due to frameshifts
    • sampling strategy
    • unidentified non-independent sequences.
  • Non-synonymous mutations are defined against WIV04 as a reference sequence. Insertions are not currently considered.
  • Mutation frequencies only count those with a known amino acid or gap (denoted “-”), and exclude the ambiguous “X”.
  • Caution should be taken in interpreting data where sequence numbers are low, especially in the most recent past which is particularly liable to be impacted by the lag between sampling and sequencing.

Geography

Global sequences

There are 243,243 deduplicated sequences from 18 countries.

US sequences

All US sequences

CDC surveillance sequences

Sampling through time

Globally

By region

Lineage overview

Variants through time

Global

Africa

Asia

Europe

North America

Oceania

South America

There are no sequences for this region in the alignment.

Variants of concern

Global

Africa

Asia

Europe

North America

Oceania

There are no VOC lineages present.

South America

There are no VOC lineages present.

Most common other lineages

Global

Africa

There are no non-VOC lineages present.

Asia

Europe

North America

Oceania

South America

There are no non-VOC lineages present.

Complete lineage list

Global

Africa

Asia

Europe

North America

Oceania

South America

Diversity

Across Spike

NTD

RBD

Non-synonymous mutation list

Acknowledgements

The analyses in this report use data from NCBI GenBank, preprocessed and made available by NextStrain following Open Data principles. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences and metadata for submitting their work to open databases.