Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletion
Abstract Background: SARS-CoV-2 variant tracking is key to the genomic surveillance of the COVID-19 pandemic. While next-generation sequencing (NGS) is commonly used for variant determination, it is expensive and time-consuming. Variant-specific PCR (vsPCR) is a faster, cheaper method that detects s...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-10-01
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| Series: | Virology Journal |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12985-022-01883-2 |
| _version_ | 1811198035244351488 |
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| author | Carlos Daviña-Nuñez Sonia Pérez-Castro Lucía Martínez-Lamas Jorge Julio Cabrera-Alvargonzález Sonia Rey-Cao Raquel Carballo-Fernandez Montse Godoy-Diz Leticia López-Bóveda Victor del Campo-Pérez Silvia Suárez-Luque Benito Regueiro-García |
| author_facet | Carlos Daviña-Nuñez Sonia Pérez-Castro Lucía Martínez-Lamas Jorge Julio Cabrera-Alvargonzález Sonia Rey-Cao Raquel Carballo-Fernandez Montse Godoy-Diz Leticia López-Bóveda Victor del Campo-Pérez Silvia Suárez-Luque Benito Regueiro-García |
| author_sort | Carlos Daviña-Nuñez |
| collection | DOAJ |
| description | Abstract Background: SARS-CoV-2 variant tracking is key to the genomic surveillance of the COVID-19 pandemic. While next-generation sequencing (NGS) is commonly used for variant determination, it is expensive and time-consuming. Variant-specific PCR (vsPCR) is a faster, cheaper method that detects specific mutations that are considered variant-defining. These tests usually rely on specific amplification when a mutation is present or a specific melting temperature peak after amplification. Case presentation: A discrepant result between vsPCR and NGS was found in seventeen SARS-CoV-2 samples from Galicia, Spain. A cluster of BA.1 Omicron SARS-CoV-2 variant showed a BA.2-like melting temperature pattern due to a point mutation (C21772T) downstream the deletion of the spike amino acids 69/70. As the 69/70 deletion is widely used for differentiation between BA.1 and BA.2 by vsPCR, C21772T can cause BA.1 samples to be misinterpreted as BA.2. Over a thousand BA.1 sequences in the EpiCoV database contain this mutation. Conclusions: To our knowledge, this is the first case of a point mutation causing a vsPCR algorithm to misclassify BA.1 samples as BA.2. This is an example of how mutations in the probe target area of vsPCR tests based on melting curve analysis can lead to variant misclassification. NGS confirmation of vsPCR results is relevant for the accuracy of the epidemiological surveillance. In order to overcome the possible impact of novel mutations, diagnostic tools must be constantly updated. |
| first_indexed | 2024-04-12T01:24:10Z |
| format | Article |
| id | doaj.art-726e7f6e9bbf4d02b73d4ad77775215f |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-04-12T01:24:10Z |
| publishDate | 2022-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-726e7f6e9bbf4d02b73d4ad77775215f2022-12-22T03:53:42ZengBMCVirology Journal1743-422X2022-10-011911610.1186/s12985-022-01883-2Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletionCarlos Daviña-Nuñez0Sonia Pérez-Castro1Lucía Martínez-Lamas2Jorge Julio Cabrera-Alvargonzález3Sonia Rey-Cao4Raquel Carballo-Fernandez5Montse Godoy-Diz6Leticia López-Bóveda7Victor del Campo-Pérez8Silvia Suárez-Luque9Benito Regueiro-García10Universidade de Vigo. Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur)Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGASMicrobiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGASMicrobiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGASMicrobiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGASMicrobiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGASMicrobiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGASMicrobiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGASRheumatology and Immune-mediated Diseases Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). Preventive Medicine Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGASDirección Xeral de Saúde Pública, Xunta de Galicia, Consellería de SanidadeMicrobiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur)Abstract Background: SARS-CoV-2 variant tracking is key to the genomic surveillance of the COVID-19 pandemic. While next-generation sequencing (NGS) is commonly used for variant determination, it is expensive and time-consuming. Variant-specific PCR (vsPCR) is a faster, cheaper method that detects specific mutations that are considered variant-defining. These tests usually rely on specific amplification when a mutation is present or a specific melting temperature peak after amplification. Case presentation: A discrepant result between vsPCR and NGS was found in seventeen SARS-CoV-2 samples from Galicia, Spain. A cluster of BA.1 Omicron SARS-CoV-2 variant showed a BA.2-like melting temperature pattern due to a point mutation (C21772T) downstream the deletion of the spike amino acids 69/70. As the 69/70 deletion is widely used for differentiation between BA.1 and BA.2 by vsPCR, C21772T can cause BA.1 samples to be misinterpreted as BA.2. Over a thousand BA.1 sequences in the EpiCoV database contain this mutation. Conclusions: To our knowledge, this is the first case of a point mutation causing a vsPCR algorithm to misclassify BA.1 samples as BA.2. This is an example of how mutations in the probe target area of vsPCR tests based on melting curve analysis can lead to variant misclassification. NGS confirmation of vsPCR results is relevant for the accuracy of the epidemiological surveillance. In order to overcome the possible impact of novel mutations, diagnostic tools must be constantly updated.https://doi.org/10.1186/s12985-022-01883-2SARS-CoV-2OmicronNext generation sequencingVariant-specific PCRSurveillanceBA.1 |
| spellingShingle | Carlos Daviña-Nuñez Sonia Pérez-Castro Lucía Martínez-Lamas Jorge Julio Cabrera-Alvargonzález Sonia Rey-Cao Raquel Carballo-Fernandez Montse Godoy-Diz Leticia López-Bóveda Victor del Campo-Pérez Silvia Suárez-Luque Benito Regueiro-García Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletion Virology Journal SARS-CoV-2 Omicron Next generation sequencing Variant-specific PCR Surveillance BA.1 |
| title | Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletion |
| title_full | Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletion |
| title_fullStr | Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletion |
| title_full_unstemmed | Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletion |
| title_short | Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletion |
| title_sort | case report ba 1 subvariant showing a ba 2 like pattern using a variant specific pcr assay due to a single point mutation downstream the spike 69 70 deletion |
| topic | SARS-CoV-2 Omicron Next generation sequencing Variant-specific PCR Surveillance BA.1 |
| url | https://doi.org/10.1186/s12985-022-01883-2 |
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