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Tasnim, N.

Publications and source records attributed to Tasnim, N..

2 recordsLinked to original sources

Seroprevalence of IgG Antibody against SARS-CoV-2 Nucleocapsid protein and Associated Risk Factors

Estimation of antibody development against SARS-CoV-2 is essential means for understanding the immune response against the virus. We reported IgG antibody development status against Nucleocapsid protein of the virus and compared with lifestyle (health and food habits), co-existing diseases, vaccination and COVID-19 infection status. ELISA (Enzyme Linked Immunosorbent Assay) was performed to assess IgG antibodies targeted against the Nucleocapsid protein of SARS-CoV-2 in participants (n=500). In this seroprevalence study, serological data were estimated for a period of 10 months in the participants who were aged 10 years and above. Sociodemographic and risk factors related data were collected through a written questionnaire and chi-square test was performed to determine the association with seropositivity. The overall seroprevalence of anti-SARS-CoV-2 antibodies among the study subjects was 47.8%. Estimates were highest among the participants of 21-40 years old (55.1%), and lowest in older aged (>60 years) participants (39.5%). Among the Sinopharm vaccinated individuals 81.8% had developed anti-Nucleocapsid antibody. Physical exercise and existence of comorbidities like hypertension and diabetes were the distinguishing factors between seropositive and seronegative individuals. Seropositivity rate largely varied among symptomatic (67%) and asymptomatic (33.1%) COVID-19 infected participants. The findings suggest that residents of Dhaka city had a higher prevalence of anti-nucleocapsid antibody in the second year of the pandemic. This indicates the improvement of immunological status among the population. Finally, the study emphasizes on maintaining active and healthy lifestyle to improve immunity. However, the absence of IgG antibodies in many cases of COVID-19 infected individuals suggests that antibodies wane with time. Key messagesO_LIThe overall seroprevalence of anti-Nucleocapsid IgG among the study subjects was determined to be 47.8%. C_LIO_LIAge, regular physical exercise, existence of comorbidities were the identified parameters associated with seroprevalence. C_LIO_LIThis study observed lower prevalence of Anti-Nucleocapsid antibody among asymptomatic cases of COVID-19 infected individuals compared to symptomatic cases. C_LI

immunology↗

Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants

BackgroundCoronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic following its initial emergence in China. Using next-generation sequencing technologies, a large number of SARS-CoV-2 genomes are being sequenced at an unprecedented rate and being deposited in public repositories. For the de novo assembly of the SARS-CoV-2 genomes, a myriad of assemblers is being used, although their impact on the assembly quality has not been characterized for this virus. In this study, we aim to understand the variabilities on assembly qualities due to the choice of the assemblers. ResultsWe performed 6,648 de novo assemblies of 416 SARS-CoV-2 samples using 8 different assemblers with different k-mers. We used Illumina paired-end sequencing reads and compared the genome assembly quality to that of different assemblers. We showed the choice of assemblers plays a significant role in reconstructing the SARS-CoV-2 genome. Two metagenomic assemblers e.g. MEGAHIT and metaSPAdes performed better compared to others in most of the assembly quality metrics including, recovery of a larger fraction of the genome, constructing larger contigs and higher N50, NA50 values etc. We showed that at least 09% (259/2,873) of the variants present in the assemblies between MEGAHIT and metaSPAdes are unique to the assembly methods. ConclusionOur analyses indicate the critical role of assembly methods for assembling SARS-CoV-2 genome using short reads and their impact on variant characterization. This study could help guide future studies to determine which assembler is best suited for the de novo assembly of virus genomes.

bioinformatics↗