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Article: Insights into Omicron's Low Fusogenicity through

Mondol, Spencer Mark / Hasib, Md / Limon, Md Belayet Hasan / Alam, A S M Rubayet Ul

2023 Volume 17, Page(s) 11779322231189371

Abstract: The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these ... ...

Abstract	The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we
Language	English
Publishing date	2023-07-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/11779322231189371
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Article: Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology.

Hasan, Md Shazid / Rahman, M Shaminur / Das, Prosanto Kumar / Ul Alam, A S M Rubayet / Islam, Ovinu Kibria / Al-Emran, Hassan M / Hossain, M Anwar / Jahid, Iqbal Kabir

MethodsX

2024 Volume 12, Page(s) 102646

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 ... ...

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.
Language	English
Publishing date	2024-03-11
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2830212-6
ISSN	2215-0161
ISSN	2215-0161
DOI	10.1016/j.mex.2024.102646
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Article ; Online: Unique mutations in SARS-CoV-2 Omicron subvariants' non-spike proteins: Potential impacts on viral pathogenesis and host immune evasion.

Hossain, Anamica / Akter, Shammi / Rashid, Alfi Anjum / Khair, Sabik / Alam, A S M Rubayet Ul

Microbial pathogenesis

2022 Volume 170, Page(s) 105699

Abstract: ... BA.4, BA.5, and BA.2.12.1). The mutations such as in NSP3, NSP6, NSP13, M protein, ORF7b, and ORF9b ...

Abstract	SARS-CoV-2 is the causative agent behind the ongoing COVID-19 pandemic. This virus is a cumulative outcome of mutations, leading to frequent emergence of new variants and their subvariants. Some of them are a matter of high concern, while others are variants of interest for studying the mutational effect. The major five variants of concern (VOCs) are Alpha (B.1.1.7), Beta (B.1.315), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529./BA.). Omicron itself has >100 subvariants at present, among which BA.1 (21K), BA.2 (21L), BA.4 (22A), BA.5 (22B), and BA.2.12.1 (22C) are the dominant ones. Undoubtedly, these variants and sometimes their progeny subvariants have significant differences in their spike region that impart them the unique properties they harbor. But alongside, the mutations in their non-spike regions could also be responsible elements behind their characteristics, such as replication time, virulence, survival, host immune evasion, and such. There exists a probability that these mutations of non-spike proteins may also impart epistatic effects that are yet to be brought to light. The focus of this review encompasses the non-spike mutations of Omicron, especially in its widely circulating subvariants (BA.1, BA.2, BA.4, BA.5, and BA.2.12.1). The mutations such as in NSP3, NSP6, NSP13, M protein, ORF7b, and ORF9b are mentioned few of all, which might have led to the varying properties, including growth advantages, higher transmission rate, lower infectivity, and most importantly better host immune evasion through natural killer cell inactivation, autophagosome-lysosome fusion prevention, host protein synthesis disruption, and so on. This aspect of Omicron subvariants has not yet been explored. Further study of alteration of expression or interaction profile of these non-spike mutations bearing proteins, if present, can add a great deal of knowledge to the current understanding of the viral properties and thus effective prevention strategies.
MeSH term(s)	COVID-19 ; Humans ; Immune Evasion ; Mutation ; Pandemics ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-08-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2022.105699
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Article ; Online: Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern.

Dip, Sourav Dutta / Sarkar, Shovon Lal / Setu, Md Ali Ahasan / Das, Prosanto Kumar / Pramanik, Md Hasan Ali / Alam, A S M Rubayet Ul / Al-Emran, Hassan M / Hossain, M Anwar / Jahid, Iqbal Kabir

Scientific reports

2023 Volume 13, Issue 1, Page(s) 2342

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 ...

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.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; Reverse Transcriptase Polymerase Chain Reaction ; RNA, Viral/genetics ; RNA, Viral/analysis ; Sensitivity and Specificity ; COVID-19 Testing
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-02-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-28275-y
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Article: Unique mutations in SARS-CoV-2 Omicron subvariants' non-spike proteins: Potential impacts on viral pathogenesis and host immune evasion

Hossain, Anamica / Akter, Shammi / Rashid, Alfi Anjum / Khair, Sabik / Alam, A.S.M. Rubayet Ul

Microbial pathogenesis. 2022 Sept., v. 170

2022

Abstract: ... BA.4, BA.5, and BA.2.12.1). The mutations such as in NSP3, NSP6, NSP13, M protein, ORF7b, and ORF9b ...

Abstract	SARS-CoV-2 is the causative agent behind the ongoing COVID-19 pandemic. This virus is a cumulative outcome of mutations, leading to frequent emergence of new variants and their subvariants. Some of them are a matter of high concern, while others are variants of interest for studying the mutational effect. The major five variants of concern (VOCs) are Alpha (B.1.1.7), Beta (B.1.315), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529./BA.). Omicron itself has >100 subvariants at present, among which BA.1 (21K), BA.2 (21L), BA.4 (22A), BA.5 (22B), and BA.2.12.1 (22C) are the dominant ones. Undoubtedly, these variants and sometimes their progeny subvariants have significant differences in their spike region that impart them the unique properties they harbor. But alongside, the mutations in their non-spike regions could also be responsible elements behind their characteristics, such as replication time, virulence, survival, host immune evasion, and such. There exists a probability that these mutations of non-spike proteins may also impart epistatic effects that are yet to be brought to light. The focus of this review encompasses the non-spike mutations of Omicron, especially in its widely circulating subvariants (BA.1, BA.2, BA.4, BA.5, and BA.2.12.1). The mutations such as in NSP3, NSP6, NSP13, M protein, ORF7b, and ORF9b are mentioned few of all, which might have led to the varying properties, including growth advantages, higher transmission rate, lower infectivity, and most importantly better host immune evasion through natural killer cell inactivation, autophagosome-lysosome fusion prevention, host protein synthesis disruption, and so on. This aspect of Omicron subvariants has not yet been explored. Further study of alteration of expression or interaction profile of these non-spike mutations bearing proteins, if present, can add a great deal of knowledge to the current understanding of the viral properties and thus effective prevention strategies.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; epistasis ; etiological agents ; immune evasion ; natural killer cells ; pathogenesis ; probability ; progeny ; protein synthesis ; virulence ; viruses
Language	English
Dates of publication	2022-09
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2022.105699
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Author Correction: Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity.

Islam, M Rafiul / Hoque, M Nazmul / Rahman, M Shaminur / Alam, A S M Rubayet Ul / Akther, Masuda / Puspo, J Akter / Akter, Salma / Sultana, Munawar / Crandall, Keith A / Hossain, M Anwar

Scientific reports

2021 Volume 11, Issue 1, Page(s) 20568

Language	English
Publishing date	2021-10-12
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-00133-9
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Article ; Online: Initial reports of the SARS-CoV-2 Delta variant (B.1.617.2 lineage) in Bangladeshi patients: Risks of cross-border transmission from India.

Hasan, Md Shazid / Islam, Md Tanvir / Alam, A S M Rubayet Ul / Sarkar, Shovon Lal / Rahman, M Shaminur / Islam, Ovinu Kibria / Setu, Md Ali Ahsan / Chakrovarty, Tanay / Al-Emran, Hassan M / Jahid, Iqbal Kabir / Hossain, M Anwar

Health science reports

2021 Volume 4, Issue 3, Page(s) e366

Language	English
Publishing date	2021-09-08
Publishing country	United States
Document type	Journal Article
ISSN	2398-8835
ISSN (online)	2398-8835
DOI	10.1002/hsr2.366
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Article ; Online: Understanding the possible origin and genotyping of the first Bangladeshi SARS-CoV-2 strain.

Alam, A S M Rubayet Ul / Islam, M Rafiul / Rahman, M Shaminur / Islam, Ovinu Kibria / Hossain, M Anwar

Journal of medical virology

2020 Volume 93, Issue 1, Page(s) 1–4

Abstract: ... Therefore, long-awaited questions regarding the possible origin and typing of the strain(s) can now be answered ...

Abstract	The novel coronavirus, SARS-CoV-2, has caused the most unfathomable pandemic in the history of humankind. Bangladesh is also a victim of this critical situation. To investigate the genomic features of the pathogen from Bangladesh, the first complete genome of the virus has very recently been published. Therefore, long-awaited questions regarding the possible origin and typing of the strain(s) can now be answered. Here, we endeavor to mainly discuss the published reports or online-accessed data (results) regarding those issues and present a comprehensive picture of the typing of the virus alongside the probable origin of the subclade containing the Bangladeshi strain. Our observation suggested that this strain might have originated from the United Kingdom or the other European countries epidemiologically linked to the United Kingdom. According to different genotyping classification schemes, this strain belongs to the A2a clade under the G major clade, is of B and/or L type, and is a SARS-CoV-2a substrain. In the future, randomized genomic data will certainly increase in Bangladesh, however because of globalization and immigrant movement, we urgently need a mass regional sequencing approach targeting the partial or complete genome that can link the epidemiological data and may help in further clinical intervention.
MeSH term(s)	Bangladesh/epidemiology ; COVID-19/epidemiology ; COVID-19/virology ; Genotype ; Humans ; Phylogeny ; SARS-CoV-2/genetics
Keywords	covid19
Language	English
Publishing date	2020-09-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26115
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Article: In silico

Mishu, Israt Dilruba / Akter, Salma / Alam, A S M Rubayet Ul / Hossain, M Anwar / Sultana, Munawar

Frontiers in veterinary science

2020 Volume 7, Page(s) 592

Abstract: Foot-and-mouth disease (FMD) is an economically devastating disease of the livestock worldwide and caused by the FMD virus (FMDV), which has seven immunologically distinct serotypes (O, A, Asia1, C, and SAT1-SAT3). Studies suggest that VP2 is relatively ... ...

Abstract	Foot-and-mouth disease (FMD) is an economically devastating disease of the livestock worldwide and caused by the FMD virus (FMDV), which has seven immunologically distinct serotypes (O, A, Asia1, C, and SAT1-SAT3). Studies suggest that VP2 is relatively conserved among three surface-exposed capsid proteins (VP1-VP3) of FMDV, but the level of conservation has not yet been reported. Here we analyzed the comparative evolutionary divergence of VP2 and VP1 to determine the level of conservation in VP2 at different hierarchical levels of three FMDV serotypes (O, A, and Asia1) currently circulating in Asia through an in-depth computational analysis of 14 compiled datasets and designed a consensus VP2 protein that can be used for the development of a serotype-independent FMDV detection tool. The phylogenetic analysis clearly represented a significant level of conservation in VP2 over VP1 at each subgroup level. The protein variability analysis and mutational study showed the presence of 67.4% invariant amino acids in VP2, with the N-terminal end being highly conserved. Nine inter-serotypically conserved fragments located on VP2 have been identified, among which four sites showed promising antigenicity value and surface exposure. The designed 130 amino acid long consensus VP2 protein possessed six surface-exposed B cell epitopes, which suggests the possible potentiality of the protein for the development of a serotype-independent FMDV detection tool in Asia. Conclusively, this is the first study to report the comparative evolutionary divergence between VP2 and VP1, along with proposing the possible potentiality of a designed protein candidate in serotype-independent FMDV detection.
Language	English
Publishing date	2020-09-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2834243-4
ISSN	2297-1769
ISSN	2297-1769
DOI	10.3389/fvets.2020.00592
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Article ; Online: Identification and qualitative characterization of new therapeutic targets in Stenotrophomonas maltophilia through in silico proteome exploration.

Chakrabarty, Ram Prosad / Alam, A S M Rubayet Ul / Shill, Dipok Kumer / Rahman, Arafat

Microbial pathogenesis

2020 Volume 149, Page(s) 104293

Abstract: Stenotrophomonas maltophilia is an emerging opportunistic pathogen, and immunocompromised patients are at a higher risk of getting infected with this nosocomial bacterium. The biggest concern is its inherent resistance to most of the commonly used ... ...

Abstract	Stenotrophomonas maltophilia is an emerging opportunistic pathogen, and immunocompromised patients are at a higher risk of getting infected with this nosocomial bacterium. The biggest concern is its inherent resistance to most of the commonly used antibiotics, leaving a few options for treatment. Moreover, recent studies have reported the emergence of its resistance to trimethoprim/sulfamethoxazole (TMP/SMX), the drugs of choice against this pathogen. In this study, we employed a subtractive proteome analysis approach to identify new drug targets against Stenotrophomonas maltophilia K279a. We identified 56 proteins to be essential for the survival of this pathogen, 33 of which are exclusively involved in its metabolism. We identified their subcellular locations and performed broad-spectrum analysis, interactome analysis, and functional analysis. Drug targeting properties and docking energy showed that 29 out of 33 proteins have the potential to serve as potential new therapeutic targets, and four proteins (dCTP deaminase, NAD(P)H:quinone oxidoreductase, dihydroneopterin aldolase, and α, α-trehalose-phosphate synthase) bind with high affinity to already approved or experimental drugs. Based on the broad-spectrum analysis and interactome analysis, we identified NAD(P)H:quinone oxidoreductase, dCTP deaminase, Phosphotransferase, and ATP-dependent Clp protease adapter (ClpS) as the most potential therapeutic targets. Notably, phosphotransferase and ClpS are new targets, i.e., they do not interact with any experimental or approved drugs. Overall, our study will guide the development of new and effective drugs for the treatment of Stenotrophomonas maltophilia infection.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Computer Simulation ; Gram-Negative Bacterial Infections/drug therapy ; Humans ; Proteome ; Stenotrophomonas maltophilia ; Trimethoprim, Sulfamethoxazole Drug Combination
Chemical Substances	Anti-Bacterial Agents ; Proteome ; Trimethoprim, Sulfamethoxazole Drug Combination (8064-90-2)
Language	English
Publishing date	2020-06-10
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2020.104293
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