ABSTRACT
We report the coding-complete genome sequences of 25 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineage B.1.1.529 Omicron strains obtained from Bangladeshi individuals in samples collected between December 2021 and January 2022. Genomic data were generated by Nanopore sequencing using the amplicon sequencing approach developed by the ARTIC Network.
ANNOUNCEMENT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (family Coronaviridae, genus Betacoronavirus) is a positive-sense single-stranded RNA virus (1). The most recent emerging SARS-CoV-2 variant of concern (VOC), Omicron (B.1.1.529), was first reported in South Africa and Botswana and has gained considerable attention because of its high transmissibility and possible immune escape potential (2). Among the three sublineages of the Omicron variant (BA.1, BA.2, and BA.3), BA.1 and BA.3 possess the characteristic spike (S) gene target failure (SGTF) due to a deletion (Δ69–70) in the primer target site, while the BA.2 viral genome does not possess this deletion (3).
As part of the ongoing SARS-CoV-2 genomic surveillance (protocol IEDCR/IRB/2020/11) by the Institute of Epidemiology, Disease Control, and Research (IEDCR), Bangladesh, two specimens were obtained from individuals who had recently visited Africa and had reported coronavirus disease 2019 (COVID-19) symptoms on return to Bangladesh. These specimens were found to be positive for the SARS-CoV-2 nucleocapsid (N) gene but negative for the S gene by TaqPath COVID-19 Combo reverse transcription (RT)-PCR (Applied Biosystems, Bedford, MA, USA). Seventeen more SARS-CoV-2-positive specimens from the countrywide SARS-CoV-2 surveillance showed similar results. These specimens were further screened with the TaqMan SARS-CoV-2 mutation panel (Applied Biosystems), which indicated the presence of S:N501Y, one of the signature mutations of the SARS-CoV-2 Omicron variant. This S:N501Y mutation is not present in the S gene of the Delta variant, which was the predominant strain circulating in Bangladesh in the last few months of 2021. Overall, a total of 25 specimens were used as input for genome sequencing using the Oxford Nanopore Technologies sequencing platform. The detailed information for all 25 individuals is presented in Table 1.
TABLE 1.
Data for Bangladesh SARS-CoV-2 Sublineage B.1.1.529 isolates
| Sample | Date of sample collection (day/mo/yr) | Patient age (yr) | Sexa | Symptom(s)b | Name of vaccine received | Travel history outside Bangladesh |
Pangolin lineage | Genome size (bp) | Coverage (%)c | GC content (%) | SRA accession no. | GenBank accession no. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OIS-0630 | 6/12/2021 | 31 | F | + | AstraZeneca | Zimbabwe | B.1.1.529.1 | 29,743 | 99.5 | 40.7 | SRR17901911 | OM570259 |
| OIS-0631 | 6/12/2021 | 21 | F | + | AstraZeneca | Zimbabwe | B.1.1.529.1 | 29,743 | 99.5 | 42.3 | SRR17901910 | OM570260 |
| OIS-0633 | 8/12/2021 | 47 | F | − | AstraZeneca + Pfizer-BioNTech (booster dose) | Egypt | B.1.1.529.1 | 29,740 | 99.5 | 40.2 | SRR17901899 | OM570261 |
| OIS-0648 | 14/12/2021 | 18 | F | + | NA | United Kingdom | B.1.1.529.1 | 29,743 | 99.5 | 41.40 | SRR17901893 | OM570268 |
| OIS-0634 | 19/12/2021 | 30 | F | − | AstraZeneca | B.1.1.529.1 | 29,740 | 99.5 | 41.30 | SRR17901892 | OM570263 | |
| OIS-0637 | 19/12/2021 | 84 | M | + | Moderna | B.1.1.529.1 | 29,743 | 99.5 | 40.10 | SRR17901891 | OM570264 | |
| OIS-0649 | 22/12/2021 | 23 | F | + | Pfizer-BioNTech | United Kingdom | B.1.1.529.1 | 29,743 | 99.5 | 40.60 | SRR17901890 | OM570269 |
| IR-1955 | 23/12/2021 | 56 | M | + | Pfizer-BioNTech | Denmark | B.1.1.529.1 | 29,743 | 99.5 | 41.10 | SRR17901889 | OM570262 |
| OIS-0664 | 26/12/2021 | 65 | M | NA | Pfizer-BioNTech | B.1.1.529.1 | 29,743 | 99.5 | 40.70 | SRR17901888 | OM570270 | |
| OIS-0666 | 26/12/2021 | 53 | F | NA | NA | B.1.1.529.1 | 29,743 | 99.5 | 40.00 | SRR17901887 | OM570271 | |
| IR-1979 | 27/12/2021 | 49 | F | + | Pfizer-BioNTech | Denmark | B.1.1.529.1 | 29,743 | 99.5 | 40.30 | SRR17901909 | OM570265 |
| IR-1982 | 27/12/2021 | 65 | M | + | AstraZeneca | B.1.1.529.1 | 29,743 | 99.5 | 40.40 | SRR17901908 | OM570266 | |
| IR-1983 | 27/12/2021 | 65 | F | + | AstraZeneca | B.1.1.529.1 | 29,743 | 99.5 | 42.10 | SRR17901907 | OM570267 | |
| TND-07-0639 | 28/12/2021 | 35 | F | + | Sinopharm | B.1.1.529.1 | 29,743 | 99.5 | 40.80 | SRR17901906 | OM570275 | |
| OIS-686 | 30/12/2021 | 61 | M | + | AstraZeneca | B.1.1.529.1 | 29,743 | 99.5 | 40.70 | SRR17901905 | OM570272 | |
| TND-04-0674 | 2/1/2022 | 64 | M | NA | AstraZeneca | B.1.1.529.1 | 29,743 | 99.5 | 41.60 | SRR17901904 | OM570276 | |
| TND-04-0675 | 2/1/2022 | 29 | F | + | Pfizer-BioNTech | Germany | B.1.1.529.1 | 29,743 | 99.5 | 40.40 | SRR17901903 | OM570277 |
| OIS-688 | 3/1/2022 | 48 | F | NA | NA | B.1.1.529.1 | 29,743 | 99.5 | 40.10 | SRR17901902 | OM570273 | |
| IR-2027 | 3/1/2022 | 35 | F | + | AstraZeneca | UAE | B.1.1.529.1 | 29,743 | 99.5 | 40.80 | SRR17901901 | OM570274 |
| TND-09-0338 | 6/1/2022 | 49 | M | + | AstraZeneca | B.1.1.529.2 | 29,729 | 99.5 | 41.10 | SRR17901900 | OM570278 | |
| TND-05-0426 | 8/1/2022 | 60 | M | + | Sinopharm | B.1.1.529.2 | 29,729 | 99.5 | 40.30 | SRR17901898 | OM570279 | |
| TND-04-0735 | 9/1/2022 | 19 | M | + | Sinopharm | B.1.1.529.2 | 29,729 | 99.5 | 40.20 | SRR17901897 | OM570280 | |
| TND-04-0736 | 9/1/2022 | 43 | M | + | Sinopharm | B.1.1.529.2 | 29,729 | 99.5 | 40.50 | SRR17901896 | OM570281 | |
| TND-04-0747 | 10/1/2022 | 32 | M | + | AstraZeneca | B.1.1.529.2 | 29,714 | 99.5 | 40.90 | SRR17901895 | OM570282 | |
| TND-04-0748 | 10/1/2022 | 45 | M | + | Sinopharm | B.1.1.529.2 | 29,729 | 99.5 | 41.10 | SRR17901894 | OM570283 |
F, female; M, male.
+, present (fever, cough, or mild weakness); −, absent; NA, information not available.
With reference to the Wuhan Hu-1 genome (GenBank accession number NC_045512.2).
Viral RNA was extracted from nasopharyngeal swab samples using the QIAamp viral RNA minikit (Qiagen). Sequencing libraries were prepared using the multiplex PCR amplicon sequencing approach developed by the ARTIC Network (4, 5). Libraries were multiplexed and sequenced on an FLO-MIN106D flow cell (R9.4.1) for at least 6 h. Raw reads were base called and demultiplexed with MinKNOW v21.02.1. Processed reads were assembled using the artic gupplyplex script with Medaka v1.4 using the ARTIC EPI2ME v3.3.0 SARS-CoV-2 pipeline (FastQC plus ARTIC plus NextClade) (https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html). In total, 4,324,431 reads were obtained (range, 79,526 to 745,281 reads per sample; average length, 505 bp). Compared to the reference Wuhan Hu-1 genome (GenBank accession number NC_045512.2), the signature amino acid alterations in the spike protein matching the genetic markers of sublineages B1.1.529.1 and B1.1.529.2 were identified. Among the 25 sequences, Pangolin (github.com/cov-lineages/pangolin) assigned 19 sequences to lineage B.1.1.529.1 (BA.1), and six strains were found to be lineage B.1.1.529.2 (BA.2) (Table 1). These six BA.2 strains were SARS-CoV-2 S gene and S:N501Y positive by SARS-CoV-2 RT-PCR and TaqMan mutation PCR, respectively. SARS-CoV-2 lineage BA.2 lacks the characteristic SGTF-causing deletion (Δ69–70) by conventional quantitative PCR (qPCR), compared to BA.1 and BA.3; therefore, qPCR primarily targeting the absence of SGTF for detection of the Omicron variant will be insufficient for monitoring the spread of the Omicron variant. Here, we report the early detection of SARS-CoV-2 Omicron variant sublineages B.1.1.529.1 (BA.1) and B.1.1.529.2 (BA.2) in the Bangladeshi population, which will be helpful for mitigation of the potential fourth wave of COVID-19 in Bangladesh.
Data availability.
The data from this study can be found under GISAID accession numbers EPI_ISL_7404462, EPI_ISL_7404463, EPI_ISL_8146774, EPI_ISL_8414987, EPI_ISL_8146772, EPI_ISL_8146773, EPI_ISL_8414988, EPI_ISL_8096971, EPI_ISL_8414989, EPI_ISL_8414990, EPI_ISL_8215676, EPI_ISL_8215677, EPI_ISL_8415001, EPI_ISL_8215678, EPI_ISL_8414993, EPI_ISL_8415003, EPI_ISL_8415004, EPI_ISL_8414994, EPI_ISL_8414995, EPI_ISL_9456595, EPI_ISL_9456604, EPI_ISL_9456606, EPI_ISL_9456607, EPI_ISL_9456620, and EPI_ISL_9456621. The Sequence Read Archive (SRA) and GenBank accession numbers are listed in Table 1.
ACKNOWLEDGMENTS
The U.S. Agency for International Development (USAID) and the Wellcome Trust (grant 223613/Z/21/Z) funded the study. The International Centre for Diarrheal Disease Research, Bangladesh (icddr,b) acknowledges with gratitude the commitment of the Bill and Melinda Gates Foundation to its research efforts (grant INV-017556). The icddr,b is grateful to the governments of Bangladesh, Canada, Sweden, and the United Kingdom for providing core/unrestricted support. We are grateful for the funding and technical support of Fondation Merieux to the Institute for Developing Science and Health Initiatives (ideSHi) and the IEDCR.
We acknowledge physicians and diagnostic testing staff members at the IEDCR and the ideSHi who performed initial diagnostic testing of the SARS-CoV-2 samples.
Omar Hamza was involved in the sequencing work and wrote the first draft of the manuscript. Hassan Afrad supervised the laboratory work and reviewed the manuscript. Manjur Hossain coordinated the sample, data collection, and collected the metadata.
Contributor Information
Firdausi Qadri, Email: fqadri@icddrb.org.
Simon Roux, DOE Joint Genome Institute.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The data from this study can be found under GISAID accession numbers EPI_ISL_7404462, EPI_ISL_7404463, EPI_ISL_8146774, EPI_ISL_8414987, EPI_ISL_8146772, EPI_ISL_8146773, EPI_ISL_8414988, EPI_ISL_8096971, EPI_ISL_8414989, EPI_ISL_8414990, EPI_ISL_8215676, EPI_ISL_8215677, EPI_ISL_8415001, EPI_ISL_8215678, EPI_ISL_8414993, EPI_ISL_8415003, EPI_ISL_8415004, EPI_ISL_8414994, EPI_ISL_8414995, EPI_ISL_9456595, EPI_ISL_9456604, EPI_ISL_9456606, EPI_ISL_9456607, EPI_ISL_9456620, and EPI_ISL_9456621. The Sequence Read Archive (SRA) and GenBank accession numbers are listed in Table 1.