Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification
Background This study aimed to compare the performance of Sanger-based SARS-CoV-2 spike gene sequencing and Next Generation Sequencing (NGS)-based full-genome sequencing for variant identification in saliva samples with low viral titer. Methods Using 241 stocked saliva samples collected from confirmed COVID-19 patients between November 2020 and March 2022 in Hiroshima, SARS-CoV-2 spike gene sequencing (nt22735-nt23532) was performed by nested RT-PCR and Sanger platform using in-house primers. The same samples underwent full-genome sequencing by NGS using Illumina NextSeq2000. Results Among 241 samples, 147 were amplified by both the Sanger and the Illumina NextSeq2000 NGS, 86 by Sanger only, and 8 were not amplified at all. The overall amplification rates of Illumina NextSeq2000 NGS and Sanger were 61% and 96.7%, respectively. At low viral titer (< $ 10^{3} $ copies/mL), Illumina NextSeq2000 NGS provided 19.2% amplification, while Sanger was 89.7% (p < 0.0001). Both platforms identified 38 wild type, 54 Alpha variants, 84 Delta variants, and 57 Omicron variants. Conclusions Our study provided evidence to expand the capacity of Sanger-based SARS-CoV-2 spike gene sequencing for variants identification over full-genome by Illumina NextSeq2000 NGS for mass screening. Therefore, the feasible and simple Sanger-based SARS-CoV-2 spike gene sequencing is practical for the initial variants screening, which might reduce the gap between the rapid evolution of SARS-CoV-2 and its molecular surveillance..
Medienart: |
E-Artikel |
---|
Erscheinungsjahr: |
2023 |
---|---|
Erschienen: |
2023 |
Enthalten in: |
Zur Gesamtaufnahme - volume:16 |
---|---|
Enthalten in: |
BMC medical genomics - 16(2023), 1 vom: 24. Aug. |
Sprache: |
Englisch |
---|
Beteiligte Personen: |
Ko, Ko [VerfasserIn] |
---|
Links: |
Volltext [kostenfrei] |
---|
Themen: |
Amplification |
---|
Anmerkungen: |
© BioMed Central Ltd., part of Springer Nature 2023 |
---|
doi: |
10.1186/s12920-023-01633-5 |
---|
funding: |
|
---|---|
Förderinstitution / Projekttitel: |
|
PPN (Katalog-ID): |
OLC2145211195 |
---|
LEADER | 01000caa a22002652 4500 | ||
---|---|---|---|
001 | OLC2145211195 | ||
003 | DE-627 | ||
005 | 20240324125626.0 | ||
007 | cr uuu---uuuuu | ||
008 | 240118s2023 xx |||||o 00| ||eng c | ||
024 | 7 | |a 10.1186/s12920-023-01633-5 |2 doi | |
035 | |a (DE-627)OLC2145211195 | ||
035 | |a (DE-He213)s12920-023-01633-5-e | ||
040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
041 | |a eng | ||
082 | 0 | 4 | |a 610 |q VZ |
100 | 1 | |a Ko, Ko |e verfasserin |4 aut | |
245 | 1 | 0 | |a Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification |
264 | 1 | |c 2023 | |
336 | |a Text |b txt |2 rdacontent | ||
337 | |a Computermedien |b c |2 rdamedia | ||
338 | |a Online-Ressource |b cr |2 rdacarrier | ||
500 | |a © BioMed Central Ltd., part of Springer Nature 2023 | ||
520 | |a Background This study aimed to compare the performance of Sanger-based SARS-CoV-2 spike gene sequencing and Next Generation Sequencing (NGS)-based full-genome sequencing for variant identification in saliva samples with low viral titer. Methods Using 241 stocked saliva samples collected from confirmed COVID-19 patients between November 2020 and March 2022 in Hiroshima, SARS-CoV-2 spike gene sequencing (nt22735-nt23532) was performed by nested RT-PCR and Sanger platform using in-house primers. The same samples underwent full-genome sequencing by NGS using Illumina NextSeq2000. Results Among 241 samples, 147 were amplified by both the Sanger and the Illumina NextSeq2000 NGS, 86 by Sanger only, and 8 were not amplified at all. The overall amplification rates of Illumina NextSeq2000 NGS and Sanger were 61% and 96.7%, respectively. At low viral titer (< $ 10^{3} $ copies/mL), Illumina NextSeq2000 NGS provided 19.2% amplification, while Sanger was 89.7% (p < 0.0001). Both platforms identified 38 wild type, 54 Alpha variants, 84 Delta variants, and 57 Omicron variants. Conclusions Our study provided evidence to expand the capacity of Sanger-based SARS-CoV-2 spike gene sequencing for variants identification over full-genome by Illumina NextSeq2000 NGS for mass screening. Therefore, the feasible and simple Sanger-based SARS-CoV-2 spike gene sequencing is practical for the initial variants screening, which might reduce the gap between the rapid evolution of SARS-CoV-2 and its molecular surveillance. | ||
650 | 4 | |a SARS-CoV-2 | |
650 | 4 | |a Sanger method | |
650 | 4 | |a Next generation sequencing | |
650 | 4 | |a Amplification | |
650 | 4 | |a Variants | |
650 | 4 | |a Screening | |
650 | 4 | |a Japan | |
700 | 1 | |a Takahashi, Kazuaki |4 aut | |
700 | 1 | |a Ito, Noriaki |4 aut | |
700 | 1 | |a Sugiyama, Aya |4 aut | |
700 | 1 | |a Nagashima, Shintaro |4 aut | |
700 | 1 | |a Miwata, Kei |4 aut | |
700 | 1 | |a Kitahara, Yoshihiro |4 aut | |
700 | 1 | |a Okimoto, Mafumi |4 aut | |
700 | 1 | |a Ouoba, Serge |4 aut | |
700 | 1 | |a Akuffo, Golda Ataa |4 aut | |
700 | 1 | |a E, Bunthen |4 aut | |
700 | 1 | |a Akita, Tomoyuki |4 aut | |
700 | 1 | |a Takafuta, Toshiro |4 aut | |
700 | 1 | |a Tanaka, Junko |4 aut | |
773 | 0 | 8 | |i Enthalten in |t BMC medical genomics |d BioMed Central, 2008 |g 16(2023), 1 vom: 24. Aug. |h Online-Ressource |w (DE-627)559080824 |w (DE-600)2411865-5 |w (DE-576)27922589X |x 1755-8794 |7 nnns |
773 | 1 | 8 | |g volume:16 |g year:2023 |g number:1 |g day:24 |g month:08 |
856 | 4 | 0 | |u https://dx.doi.org/10.1186/s12920-023-01633-5 |z kostenfrei |3 Volltext |
912 | |a GBV_USEFLAG_A | ||
912 | |a SYSFLAG_A | ||
912 | |a GBV_OLC | ||
912 | |a SSG-OLC-PHA | ||
912 | |a GBV_ILN_11 | ||
912 | |a GBV_ILN_20 | ||
912 | |a GBV_ILN_22 | ||
912 | |a GBV_ILN_23 | ||
912 | |a GBV_ILN_24 | ||
912 | |a GBV_ILN_31 | ||
912 | |a GBV_ILN_39 | ||
912 | |a GBV_ILN_40 | ||
912 | |a GBV_ILN_60 | ||
912 | |a GBV_ILN_62 | ||
912 | |a GBV_ILN_63 | ||
912 | |a GBV_ILN_65 | ||
912 | |a GBV_ILN_69 | ||
912 | |a GBV_ILN_73 | ||
912 | |a GBV_ILN_74 | ||
912 | |a GBV_ILN_95 | ||
912 | |a GBV_ILN_105 | ||
912 | |a GBV_ILN_110 | ||
912 | |a GBV_ILN_151 | ||
912 | |a GBV_ILN_161 | ||
912 | |a GBV_ILN_170 | ||
912 | |a GBV_ILN_206 | ||
912 | |a GBV_ILN_213 | ||
912 | |a GBV_ILN_230 | ||
912 | |a GBV_ILN_285 | ||
912 | |a GBV_ILN_293 | ||
912 | |a GBV_ILN_602 | ||
912 | |a GBV_ILN_2003 | ||
912 | |a GBV_ILN_2005 | ||
912 | |a GBV_ILN_2009 | ||
912 | |a GBV_ILN_2011 | ||
912 | |a GBV_ILN_2014 | ||
912 | |a GBV_ILN_2055 | ||
912 | |a GBV_ILN_2111 | ||
912 | |a GBV_ILN_2446 | ||
912 | |a GBV_ILN_4012 | ||
912 | |a GBV_ILN_4037 | ||
912 | |a GBV_ILN_4112 | ||
912 | |a GBV_ILN_4125 | ||
912 | |a GBV_ILN_4126 | ||
912 | |a GBV_ILN_4249 | ||
912 | |a GBV_ILN_4305 | ||
912 | |a GBV_ILN_4306 | ||
912 | |a GBV_ILN_4307 | ||
912 | |a GBV_ILN_4313 | ||
912 | |a GBV_ILN_4322 | ||
912 | |a GBV_ILN_4323 | ||
912 | |a GBV_ILN_4324 | ||
912 | |a GBV_ILN_4325 | ||
912 | |a GBV_ILN_4338 | ||
912 | |a GBV_ILN_4367 | ||
912 | |a GBV_ILN_4700 | ||
951 | |a AR | ||
952 | |d 16 |j 2023 |e 1 |b 24 |c 08 |