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SELECT REPORT LOCATIONS

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CURRENT LOCATIONS

South Africa United Kingdom United States

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CURRENT LOCATIONS

Worldwide South Africa United Kingdom United States



GENERATE CUSTOM MUTATION REPORT

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PANGO lineage
PANGO lineage + mutation(s)
Mutation(s)

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LINEAGE | MUTATION TRACKER


BA.2 LINEAGE REPORT

change mutation(s)
view on PANGO lineages
Updated 1d ago
with 18,751 sequences from GISAID
Enabled by data from
How to interpret these reports
Daily prevalenceGeographic prevalencePublications

CHARACTERISTIC MUTATIONS IN LINEAGE

Mutations in at least 75% of BA.2 sequences (read more)
Compare to other lineagesView S-gene mutations
ORF1aORF1bS61L24S203K1315C614G3395H679K681H223I969K655Y954H314L9I1307S3255I796Y1566V842I135R63T3027F3090I204R413R19I13L3201F84L213G764K2163I373P405N339D375F371F376A408S417N493R501Y498R505H484A478K477N142D440K19EΔ31:33Δ25:27Δ3675:3677



MUTATIONS

none

DELETIONS

none
ViewHide mutation table

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CHARACTERISTIC MUTATIONS OF BA.2

gene amino acid ORF1a S135R ORF1a T842I ORF1a G1307S ORF1a L3027F ORF1a T3090I
ORF1a L3201F ORF1a T3255I ORF1a P3395H ORF1a del3675/3677 ORF1b P314L ORF1b
R1315C ORF1b I1566V ORF1b T2163I S T19I S L24S S del25/27 S G142D S V213G S
G339D S S371F S S373P S S375F S T376A S D405N S R408S S K417N S N440K S S477N S
T478K S E484A S Q493R S Q498R S N501Y S Y505H S D614G S H655Y S N679K S P681H S
N764K S D796Y S Q954H S N969K ORF3a T223I E T9I M Q19E M A63T ORF6 D61L ORF8
S84L N P13L N del31/33 N R203K N G204R N S413R


SUMMARY

As of 27 January 2022 11:02 PM, 18,751 sequences in the BA.2 lineage have been
detected since the lineage was identified:

location BA.2 found when found** total cumulative prevalence* first last South
Africa 120 3% 17 Nov 2021 18 Jan 2022 United Kingdom 1,371 < 0.5% 6 Dec 2021 20
Jan 2022 Worldwide 18,751 < 0.5% 4 Jan 2021 24 Jan 2022 United States 127 < 0.5%
14 Dec 2021 18 Jan 2022

view change over timechange locations
* Apparent cumulative prevalence is the ratio of the sequences containing BA.2
to all sequences collected since the identification of BA.2 in that location.**
Dates are based on the sample collection date

Read about biases

The strain has been detected in at least 54 countries and 24 U.S. states.

view geographic prevalence

AVERAGE DAILY BA.2 PREVALENCE GLOBALLY

Based on reported sample collection date
WorldwideSouth AfricaUnited KingdomUnited StatesChange locations
7 day rolling average of percent of BA.2-positive sequences

95% confidence intervalmissing recent data
AprilJulyOctober20220%5%10%15%20%25%30%35%Latest dates are noisy due to fewer
samples, or missing from sequencing delays
2022045,517045,517
Total samples sequenced per dayBA.2 detected



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CUMULATIVE BA.2 PREVALENCE

WorldwideSouth AfricaUnited KingdomUnited StatesChange locations

Estimates are biased by sampling (read more)

Est. BA.2 prevalence since identification
0-11-55-1010-2020-3535-5050-7575-100%
sequenced < 25 samples not detectedno sequencing
minimum number of total samples252,379,170



No reported sequencing



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show not detected
sort by prevalencetotal sequencedname

CUMULATIVE PREVALENCE

Est. BA.2 prevalence since identification
0-11-55-1010-2020-3535-5050-7575-100%
95% confidence interval
0%1%2%3%4%5%0%1%2%3%4%5%DenmarkNepalSingaporeMyanmarGeorgiaBotswanaIndiaSri
LankaMoldovaQatarMaldivesHong KongSouth AfricaNew
ZealandIndonesiaArmeniaCambodiaPakistanSwedenJordanAustriaPhilippinesBangladeshMalawiMalaysiaThailandVietnamChinaUnited
KingdomBelgiumGermanyNorwayPortugalIsraelPolandJapanAustraliaNetherlandsSenegalSlovakiaKenyaSwitzerlandCzech
RepublicSpainItalyRomaniaFranceCanadaLuxembourgSouth KoreaUnited
StatesLithuaniaIrelandBrazil

NUMBER OF SAMPLES SEQUENCED


BA.2-positive samples

all sequenced samples
1100k1100kDenmarkNepalSingaporeMyanmarGeorgiaBotswanaIndiaSri
LankaMoldovaQatarMaldivesHong KongSouth AfricaNew
ZealandIndonesiaArmeniaCambodiaPakistanSwedenJordanAustriaPhilippinesBangladeshMalawiMalaysiaThailandVietnamChinaUnited
KingdomBelgiumGermanyNorwayPortugalIsraelPolandJapanAustraliaNetherlandsSenegalSlovakiaKenyaSwitzerlandCzech
RepublicSpainItalyRomaniaFranceCanadaLuxembourgSouth KoreaUnited
StatesLithuaniaIrelandBrazil14,371/321,34943/1,010233/12,4392/11420/1,16244/2,7451,249/100,65234/2,7402/19239/4,3695/1,00422/4,860120/27,07627/6,14454/13,9551/3046/2,2163/1,620247/142,1572/1,25125/15,76320/12,6406/4,2121/9499/8,60613/12,8172/2,4181/1,2311,371/1,795,10061/81,800269/364,12827/41,79515/26,10622/40,29323/48,92979/187,10522/58,96231/92,2141/3,1805/18,6541/5,73219/113,8314/25,52011/96,30010/91,8411/9,49520/194,11224/259,1832/22,1542/23,581127/2,379,1701/30,2251/50,3731/98,399



No reported sequencing



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BA.2 PUBLICATIONS & RESOURCES

3 results
10 results 50 results 100 results
Publication
The Geometry of ATG-Walks of the Omicron SARS CoV-2 Virus RNAs Guennadi Kouzaev
bioRxiv22 December 2021
Publication
Investigation of the N-shaped environmental Kuznets curve for COVID-19
mitigation in the KSA. Abdussalam Aljadani et al.Environmental science and
pollution research international13 August 2021
Publication
Aurintricarboxylic acid and its metal ion complexes in comparative virtual
screening versus Lopinavir and Hydroxychloroquine in fighting COVID-19 pandemic:
Synthesis and characterization. Moamen S Refat et al.Inorganic chemistry
communications14 January 2021
viewing results 1 − 3 of 3view all

METHODOLOGY

All SARS-CoV sequences are downloaded from the GISAID Initiative daily and
subsequently processed using Bjorn, which relies heavily on minimap2 and
datafunk. View full methods

SARS-CoV-2 (hCoV-19) sequencing is not a random sample of mutations. As a
result, this report does not indicate the true prevalence of the undefined but
rather our best estimate now. How to interpret this report

CITING THIS REPORT

BA.2 Lineage Report. Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Ginger
Tsueng, Marco Cano, Emily Haag, Jerry Zhou, Mark Zeller, Emory Hufbauer, Nate
Matteson, Chunlei Wu, Kristian G. Andersen, Andrew I. Su, Karthik Gangavarapu,
Laura D. Hughes, and the Center for Viral Systems Biology. outbreak.info,
(available at
https://outbreak.info/situation-reports?pango=BA.2&loc=ZAF&loc=GBR&loc=USA&selected=Worldwide&overlay=false).
Accessed 28 January 2022.

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We would like to thank the GISAID Initiative and are grateful to all of the data
contributors, i.e.the Authors, the Originating laboratories responsible for
obtaining the specimens, and the Submitting laboratories for generating the
genetic sequence and metadata and sharing via the GISAID Initiative, on which
this research is based. GISAID data provided on this website are subject to
GISAID’s Terms and Conditions.
Elbe, S., and Buckland-Merrett, G. (2017) Data, disease and diplomacy: GISAID’s
innovative contribution to global health. Global Challenges, 1:33-46. DOI:
10.1002/gch2.1018 PMCID: 31565258
This work was supported by the National Institute for Allergy and Infectious
Diseases (5 U19 AI135995-04S3), National Center for Data to Health (5 U24
TR00230), and Centers for Disease Control and Prevention (75D30120C09795).
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