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Hasan MS, Rahman MS, Das PK, Ul Alam AR, Islam OK, Al-Emran HM, Hossain MA, Jahid IK. Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology. MethodsX 2024; 12:102646. [PMID: 38524302 PMCID: PMC10957433 DOI: 10.1016/j.mex.2024.102646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
A thorough understanding of SARS-CoV-2 genetic features is compulsory to track the ongoing pandemic across multiple geographical locations of the world. Thermo Fisher Scientific USA has developed the Ion AmpliSeq SARS-CoV-2 Research Panel for the targeted sequencing of SARS-CoV-2 complete genome with high coverage and lower error rate. In this study an alternative approach of complete genome sequencing has been validated using different commercial sequencing kits to sequence the SARS-CoV-2. Amplification of cDNA with the SARS-CoV-2 primer pool was performed separately using two different master mixes: 2X environmental master mix (EM) and Platinum™ PCR SuperMix High Fidelity master mix (PM) instead of 5X Ion AmpliSeq™ HiFi Mix whereas NEBNext® Fast DNA Library Prep Set for Ion Torrent™ kit was used as an alternative to Ion AmpliSeq Library Kit Plus for other reagents. This study demonstrated a successful procedure to sequence the SARS-CoV-2 whole genome with average ∼2351 depth and 98.1% of total the reads aligned against the reference sequence (SARS-CoV-2, isolate Wuhan-Hu-1, complete genome). Although genome coverage varied, complete genomes were retrieved for both reagent sets with a reduced cost. This study proposed an alternative approach of high throughput sequencing using Ion torrent technology for the sequencing of SARS-CoV-2 in developing countries where sequencing facilities are low. This blended sequencing technique also offers a low cost protocol in developing countries like Bangladesh.
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Affiliation(s)
- Md. Shazid Hasan
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M. Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Prosanto Kumar Das
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - A.S.M. Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Ovinu Kibria Islam
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Hassan M. Al-Emran
- Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M. Anwar Hossain
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Iqbal Kabir Jahid
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
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Kabir MF, Yin KN, Jeffree MS, Ahmedy FB, Jahan S, Islam MW, Jahid IK, Sivan M, Chakrovorty SK, Hossain KMA. Profile of long COVID symptoms needing rehabilitation: a cross-sectional household survey of 12,925 SARS-CoV-2 cases between July and December 2021 in Bangladesh. Arch Public Health 2023; 81:132. [PMID: 37461092 PMCID: PMC10351147 DOI: 10.1186/s13690-023-01140-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND AND AIMS It is important to determine the profile of long COVID (LC) symptoms within the scope of rehabilitation in Bangladesh. This study's objective was to estimate the newly experienced long COVID symptoms needing rehabilitation by determining the prevalence and spectrum of impairments due to LC in Bangladesh. METHODS A Cross-sectional household survey of 12,925 COVID-19 patients confirmed by RT-PCR from 24 testing facilities in Bangladesh. LC was diagnosed according to WHO working group definition. COVID-19 Yorkshire Rehabilitation Scale (C19-YRS) was used to determine the symptom responses, symptom severity, new long COVID symptoms, and scope of rehabilitation. RESULTS The population proportion of LC symptoms requiring rehabilitation interventions are 0.22 [95% CI, 0.20-0.24] in Bangladeshi people diagnosed with SARS-CoV-2. Among them, 0.08 [95% CI, 0.07-0.09] had mild, 0.07 [95% CI, 0.06-0.09] had moderate, and 0.05 [95% CI, 0.04-0.06] had severe long COVID symptoms (LCS). There was a significant positive correlation between LCS and functional disabilities (r = 0.889, p < 0.001), while a negative correlation was observed between the severity of symptoms and overall health (r=-0.658, p < 0.001). In comparison to the pre-COVID status, 17 new LCS were observed and the increase in the scope of rehabilitation intervention among LCS ranged between 0.01 [95% CI, 0.001-0.01] and 0.21 [95% CI, 0.19-0.22]. In Bangladesh, 59% (n = 334) of the LC cases are out of reach for any rehabilitation interventions. CONCLUSION Nearly one-fourth of Bangladeshi Post-COVID-19 have long COVID (LC). Seventeen symptoms (LCS) were observed and more than half of the populations having long COVID are out of reach of any rehabilitation facilities.
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Affiliation(s)
- Md Feroz Kabir
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
- Department of Physiotherapy and Rehabilitation, Jashore University of Science and Technology (JUST), Jashore, Bangladesh
| | - Khin Nyein Yin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia.
| | - Mohammad Saffree Jeffree
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
| | - Fatimah Binti Ahmedy
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
| | - Sharmila Jahan
- Department of Physiotherapy and Rehabilitation, Jashore University of Science and Technology (JUST), Jashore, Bangladesh
| | - Md Waliul Islam
- Department of Physiotherapy, Centre for the Rehabilitation of the Paralysed (CRP), Savar, Dhaka, Bangladesh
| | - Iqbal Kabir Jahid
- Department of Microbiology, Jashore University of Science and Technology (JUST), Jashore, Bangladesh
| | - Manoj Sivan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Sonjit Kumar Chakrovorty
- Department of Microbiology, Jashore University of Science and Technology (JUST), Jashore, Bangladesh
| | - K M Amran Hossain
- Department of Physiotherapy and Rehabilitation, Jashore University of Science and Technology (JUST), Jashore, Bangladesh
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Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern. Sci Rep 2023; 13:2342. [PMID: 36759632 PMCID: PMC9910272 DOI: 10.1038/s41598-023-28275-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been considered with great importance on correct screening procedure. The detection efficiency of recent variants of concern were observed by comparing 5 commercial RT-PCR kits and a SYBR-green method developed and validated in our laboratory. The RNA was extracted from nasopharyngeal samples from suspected COVID-19 patients and RT-PCR assay was performed according to the instruction of the respective manufacturers. The specificity and sensitivity of Maccura kit was 81.8% and 82.5%, A*Star kit was 100% and 75.4%, Da An Gene kit was 100% and 68.4%, Sansure kit was 54.5% and 91.2% and TaqPath kit was 100% and 70.2% respectively. Our in house SYBR-Green method showed a consistent detection result with 90.9% specificity and 91.2% sensitivity. We also found that detection kits targeting more genes showed better accuracy which facilitates less false positive results (< 20%). Our study found a significant difference (p < 0.005) in Ct value reported for common target genes shared by the RT-PCR kits in relation with different variants of COVID-19 infection. Recent variants of concerns contain more than 30 mutations in the spike proteins including 2 deletion and a unique insertion mutation by which makes detection of these variants difficult and these facilitates the variants to escape from being detected.
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Health-related quality of life and coping strategies adopted by COVID-19 survivors: A nationwide cross-sectional study in Bangladesh. PLoS One 2022; 17:e0277694. [PMID: 36383545 PMCID: PMC9668139 DOI: 10.1371/journal.pone.0277694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/02/2022] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION This study aims to investigate the health-related quality of life and coping strategies among COVID-19 survivors in Bangladesh. METHODS This is a cross-sectional study of 2198 adult, COVID-19 survivors living in Bangladesh. Data were collected from previously diagnosed COVID-19 participants (confirmed by an RT-PCR test) via door-to-door interviews in the eight different divisions in Bangladesh. For data collection, Bengali-translated Brief COPE inventory and WHO Brief Quality of Life (WHO-QoLBREF) questionnaires were used. The data collection period was from October 2020 to March 2021. RESULTS Males 72.38% (1591) were more affected by COVID-19 than females 27.62% (607). Age showed significant correlations (p<0.005) with physical, psychological and social relationships, whereas gender showed only a significant correlation with physical health (p<0.001). Marital status, occupation, living area, and co-morbidities showed significant co-relation with all four domains of QoL (p<0.001). Education and affected family members showed significant correlation with physical and social relationship (p<0.001). However, smoking habit showed a significant correlation with both social relationship and environment (p<0.001). Age and marital status showed a significant correlation with avoidant coping strategies (p<0.001); whereas gender and co-morbidities showed a significant correlation with problem-focused coping strategies (p<0.001). Educational qualification, occupation and living area showed significant correlation with all three coping strategies(p<0.001). CONCLUSION Survivors of COVID-19 showed mixed types of coping strategies; however, the predominant coping strategy was avoidant coping, followed by problem-focused coping, with emotion-focused coping reported as the least prevalent. Marital status, occupation, living area and co-morbidities showed a greater effect on QoL in all participants. This study represents the real scenario of nationwide health-associated quality of life and coping strategies during and beyond the Delta pandemic.
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Moradi J, Moradi P, Alvandi AH, Abiri R, Moghoofei M. Variation analysis of SARS-CoV-2 complete sequences from Iran. Future Virol 2022. [PMID: 36312039 PMCID: PMC9594980 DOI: 10.2217/fvl-2021-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/30/2022] [Indexed: 11/21/2022]
Abstract
Aim: SARS-CoV-2 is an emerging coronavirus that was discovered in China and rapidly spread throughout the world. The authors looked at nucleotide and amino acid variations in SARS-CoV-2 genomes, as well as phylogenetic and evolutionary events in viral genomes, in Iran. Materials & methods: All SARS-CoV-2 sequences that were publicly released between the start of the pandemic and 15 October 2021 were included. Results: The majority of mutations were found in vaccine target proteins, Spike and Nucleocapsid proteins, and nonstructural proteins. The majority of the viruses that circulated in the early stages of the pandemic belonged to the B.4 lineage. Conclusion: We discovered the prevalence of viral populations in Iran. As a result, tracking the virus’s variation in Iran and comparing it with a variety of nearby neighborhoods may reveal a pattern for future variant introductions.
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Affiliation(s)
- Jale Moradi
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parnia Moradi
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amir H Alvandi
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Moghoofei
- Infectious Diseases Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Khairullin B, Zakarya K, Orynbayev M, Abduraimov Y, Kassenov M, Sarsenbayeva G, Sultankulova K, Chervyakova O, Myrzakhmetova B, Nakhanov A, Nurpeisova A, Zhugunissov K, Assanzhanova N, Nurabayev S, Kerimbayev A, Yershebulov Z, Burashev Y, Kulmagambetov I, Davlyatshin T, Sergeeva M, Buzitskaya Z, Stukova M, Kutumbetov L. Efficacy and safety of an inactivated whole-virion vaccine against COVID-19, QazCovid-in®, in healthy adults: A multicentre, randomised, single-blind, placebo-controlled phase 3 clinical trial with a 6-month follow-up. EClinicalMedicine 2022; 50:101526. [PMID: 35770251 PMCID: PMC9233449 DOI: 10.1016/j.eclinm.2022.101526] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/16/2022] [Accepted: 06/01/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Vaccination remains the primary measure to prevent the spread of the SARS-CoV-2 virus, further necessitating the use of effective licensed vaccines. METHODS From Dec 25, 2020, to July 11, 2021, we conducted a multicenter, randomised, single-blind, placebo-controlled phase 3 efficacy trial of the QazCovid-in® vaccine with a 180-day follow-up period in three clinical centres in Kazakhstan. A total of 3000 eligible participants aged 18 years or older were randomly assigned (4:1) to receive two doses of the vaccine (5 μg each, 21 days apart) or placebo administered intramuscularly. QazCovid-in® is a whole-virion formaldehyde-inactivated anti-COVID-19 vaccine, adjuvanted with aluminium hydroxide. The primary endpoint was the incidence of symptomatic cases of the SARS-CoV-2 infection confirmed by RT-PCR starting from day 14 after the first immunisation. The trial was registered with ClinicalTrials.gov NCT04691908. FINDINGS The QazCovid-in® vaccine was safe over the 6-month monitoring period after two intramuscular immunisations inducing only local short-lived adverse events. The concomitant diseases of participants did not affect the vaccine safety. Out of 2400 vaccinated participants, 31 were diagnosed with COVID-19; 43 COVID-19 cases were recorded in 600 placebo participants with onset of 14 days after the first dose within the 180-day observation period. Only one severe COVID-19 case was identified in a vaccine recipient with a comorbid chronic heart failure. The protective efficacy of the QazCovid-in® vaccine reached 82·0% (95% CI 71.1-88.5) within the 180-day observation period. INTERPRETATION Two immunisations with the inactivated QazCovid-in® vaccine achieved 82·0% (95% CI 71.1-88.5) protective efficacy against COVID-19 within a 180-day follow-up period. FUNDING The work was funded by the Science Committee of the Ministry of Education and Science of Kazakhstan within the framework of the Scientific and Technical Program "Development of a vaccine against coronavirus infection COVID-19". State registration number 0.0927.
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Affiliation(s)
- Berik Khairullin
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
- Corresponding author at: Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, 080409, Kazakhstan.
| | - Kunsulu Zakarya
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Mukhit Orynbayev
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Yergali Abduraimov
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Markhabat Kassenov
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Gulbanu Sarsenbayeva
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Kulyaisan Sultankulova
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Olga Chervyakova
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Balzhan Myrzakhmetova
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Aziz Nakhanov
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Ainur Nurpeisova
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Kuandyk Zhugunissov
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Nurika Assanzhanova
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Sergazy Nurabayev
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Aslan Kerimbayev
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Zakir Yershebulov
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | - Yerbol Burashev
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
| | | | | | - Maria Sergeeva
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Zhanna Buzitskaya
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Marina Stukova
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Lespek Kutumbetov
- Research Institute of Biological Safety Problems of the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Gvardeysk, Kazakhstan
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In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12020665] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In October 2020, the SARS-CoV-2 B.1.617 lineage was discovered in India. It has since become a prominent variant in several Indian regions and 156 countries, including the United States of America. The lineage B.1.617.2 is termed the delta variant, harboring diverse spike mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD), which may heighten its immune evasion potentiality and cause it to be more transmissible than other variants. As a result, it has sparked substantial scientific investigation into the development of effective vaccinations and anti-viral drugs. Several efforts have been made to examine ancient medicinal herbs known for their health benefits and immune-boosting action against SARS-CoV-2, including repurposing existing FDA-approved anti-viral drugs. No efficient anti-viral drugs are available against the SARS-CoV-2 Indian delta variant B.1.617.2. In this study, efforts were made to shed light on the potential of 603 phytocompounds from 22 plant species to inhibit the Indian delta variant B.1.617.2. We also compared these compounds with the standard drug ceftriaxone, which was already suggested as a beneficial drug in COVID-19 treatment; these compounds were compared with other FDA-approved drugs: remdesivir, chloroquine, hydroxy-chloroquine, lopinavir, and ritonavir. From the analysis, the identified phytocompounds acteoside (−7.3 kcal/mol) and verbascoside (−7.1 kcal/mol), from the plants Clerodendrum serratum and Houttuynia cordata, evidenced a strong inhibitory effect against the mutated NTD (MT-NTD). In addition, the phytocompounds kanzonol V (−6.8 kcal/mol), progeldanamycin (−6.4 kcal/mol), and rhodoxanthin (−7.5 kcal/mol), from the plant Houttuynia cordata, manifested significant prohibition against RBD. Nevertheless, the standard drug, ceftriaxone, signals less inhibitory effect against MT-NTD and RBD with binding affinities of −6.3 kcal/mol and −6.5 kcal/mol, respectively. In this study, we also emphasized the pharmacological properties of the plants, which contain the screened phytocompounds. Our research could be used as a lead for future drug design to develop anti-viral drugs, as well as for preening the Siddha formulation to control the Indian delta variant B.1.617.2 and other future SARS-CoV-2 variants.
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Rahaman MM, Sarkar MMH, Rahman MS, Islam MR, Islam I, Saha O, Akter S, Banu TA, Jahan I, Habib MA, Goswami B, Bari L, Malek MA, Khan MS. Genomic characterization of the dominating Beta variant carrying vaccinated (Oxford-AstraZeneca) and non-vaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole genome approach. J Med Virol 2021; 94:1670-1688. [PMID: 34939673 DOI: 10.1002/jmv.27537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/11/2022]
Abstract
Bangladesh experiences a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approach. Screening for SARS-CoV-2 by RT-PCR and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated=10, non-vaccinated=7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the co-infected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta,V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthy, the RBD region of S protein of all the isolates harbored similar substitutions including K417N, E484K and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS=0.621). Furthermore, we found different bacterial co-infection like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoni and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and non-vaccinated patients in Bangladesh. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Md Murshed Hasan Sarkar
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science Technology, Jashore, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Shahina Akter
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Tanjian Akhtar Banu
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Iffat Jahan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Md Ahasan Habib
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Barna Goswami
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Latiful Bari
- Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Abdul Malek
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Salim Khan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
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