scholarly journals Molecular Analysis and Genome Sequencing of SARS-Cov-2 during Second Wave 2021 Revealed Variant Diversity in India

2021 ◽  
Author(s):  
Rupinder Bakshi ◽  
Satinder Kaur ◽  
Karashdeep Kaur ◽  
Ramanpreet Kaur ◽  
Jaspreet Kaur Boparai ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Immune Escape ◽  
Age Group ◽  
Wild Type ◽  
Rt Pcr ◽  
Dominant Trait ◽  
Male Population ◽  
Second Wave ◽  
Rapid Emergence ◽  
Critical Challenge

SARS-CoV-2 variants rapid emergence has posed critical challenge of higher transmission and immune escape causing serious threats to control the pandemic. The present study was carried out in confirmed cases of SARS-CoV-2 patients to elucidate the prevalence of SARS-CoV-2 variant strain. We performed RT-PCR using extracted RNA from the nasopharyngeal swabs of suspected Covid-19 patients. Confirmed positive cases with CT<25 were subjected to whole-genome sequencing to track the prevalence of the virus in the Malwa region of Punjab. The presence of B.1, B.1.1.7, B.1.351, B.1.617.1, B.1.617.2, AY.1 and other unidentified variants of SARS-CoV-2 was found in the studied population. Among all the variants, B.1.1.7 (UK variant) and B.1.617.2 (delta-Indian variant) was found to be the most dominant variant in the population and was found majorly in Patiala followed by Ludhiana, SBS Nagar, Mansa and Sangrur. In addition to this, sequencing results also observed that the dominant trait was more prevalent in male population and age group 21-40 years. The B.1.1.7 and B.1.617.2 variant of SARS-CoV-2 is replacing the wild type (Wuhan Strain) and emerging as the dominant variant in Punjab.

scholarly journals Evaluation of the SARS-CoV-2 positivity ratio and upper respiratory tract viral load among asymptomatic individuals screened before hospitalization or surgery in Flanders, Belgium

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259908
Author(s):  
Laura Heireman ◽  
Steven Abrams ◽  
Peggy Bruynseels ◽  
Reinoud Cartuyvels ◽  
Lize Cuypers ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Age Group ◽  
Test Results ◽  
Rt Pcr ◽  
Median Viral Load ◽  
Viral Loads ◽  
Asymptomatic Patients ◽  
Positivity Ratio ◽  
Second Wave

Introduction The incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in the Belgian community is mainly estimated based on test results of patients with coronavirus disease (COVID-19)-like symptoms. The aim of this study was to investigate the evolution of the SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) positivity ratio and distribution of viral loads within a cohort of asymptomatic patients screened prior hospitalization or surgery, stratified by age category. Materials/Methods We retrospectively studied data on SARS-CoV-2 real-time RT-PCR detection in respiratory tract samples of asymptomatic patients screened pre-hospitalization or pre-surgery in nine Belgian hospitals located in Flanders over a 12-month period (1 April 2020–31 March 2021). Results In total, 255925 SARS-CoV-2 RT-PCR test results and 2421 positive results for which a viral load was reported, were included in this study. An unweighted overall SARS-CoV-2 real-time RT-PCR positivity ratio of 1.27% was observed with strong spatiotemporal differences. SARS-CoV-2 circulated predominantly in 80+ year old individuals across all time periods except between the first and second COVID-19 wave and in 20–30 year old individuals before the second COVID-19 wave. In contrast to the first wave, a significantly higher positivity ratio was observed for the 20–40 age group in addition to the 80+ age group compared to the other age groups during the second wave. The median viral load follows a similar temporal evolution as the positivity rate with an increase ahead of the second wave and highest viral loads observed for 80+ year old individuals. Conclusion There was a high SARS-CoV-2 circulation among asymptomatic patients with a predominance and highest viral loads observed in the elderly. Moreover, ahead of the second COVID-19 wave an increase in median viral load was noted with the highest overall positivity ratio observed in 20–30 year old individuals, indicating they could have been the hidden drivers of this wave.

scholarly journals Possible link between higher transmissibility of B.1.617 and B.1.1.7 variants of SARS-CoV-2 and increased structural stability of its spike protein and hACE2 affinity

2021 ◽  
Author(s):  
Vipul Kumar ◽  
Jasdeep Singh ◽  
Seyed E. Hasnain ◽  
Durai Sundar
Keyword(s):  
Binding Energy ◽  
Immune Escape ◽  
Spike Protein ◽  
Wild Type ◽  
Rt Pcr ◽  
Dynamic Simulations ◽  
Human Antibodies ◽  
Global Pandemic ◽  
Hydrogen Interaction ◽  
The Stability

AbstractThe Severe Acute syndrome corona Virus 2 (SARS-CoV-2) outbreak in December 2019 has caused a global pandemic. The rapid mutation rate in the virus has caused alarming situations worldwide and is being attributed to the false negativity in RT-PCR tests, which also might lead to inefficacy of the available drugs. It has also increased the chances of reinfection and immune escape. We have performed Molecular Dynamic simulations of three different Spike-ACE2 complexes, namely Wildtype (WT), B.1.1.7 variant (N501Y Spike mutant) and B.1.617 variant (L452R, E484Q Spike mutant) and compared their dynamics, binding energy and molecular interactions. Our result shows that mutation has caused the increase in the binding energy between the Spike and hACE2. In the case of B.1.617 variant, the mutations at L452R and E484Q increased the stability and intra-chain interactions in the Spike protein, which may change the interaction ability of human antibodies to this Spike variant. Further, we found that the B.1.1.7 variant had increased hydrogen interaction with LYS353 of hACE2 and more binding affinity in comparison to WT. The current study provides the biophysical basis for understanding the molecular mechanism and rationale behind the increase in the transmissivity and infectivity of the mutants compared to wild-type SARS-CoV-2.

scholarly journals SARS-CoV-2 PCR positivity rate and seroprevalence of related antibodies among a sample of patients in Cairo: Pre-wave 2 results of a screening program in a university hospital

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254581
Author(s):  
Samia A. Girgis ◽  
Hala M. Hafez ◽  
Hoda Ezz Elarab ◽  
Basma Sherif ◽  
Moshira H. Sabry ◽  
...  
Keyword(s):  
Screening Program ◽  
University Hospital ◽  
Screening Tests ◽  
Age Group ◽  
Rt Pcr ◽  
High Seroprevalence ◽  
University Hospitals ◽  
Antibody Assay ◽  
Second Wave ◽  
Interview Questionnaire

Background Research has revealed that asymptomatic and pre-symptomatic infections are important contributors to the transmission of SARS-CoV-2 in populations. In Egypt, the true prevalence of infections is veiled due to the low number of screening tests. The aim of this study was to determine the SARS-CoV-2 PCR positivity rate as well the seroprevalence of the SARS-CoV-2 antibodies before the ultimate development of a second wave of the epidemic in Cairo, Egypt. Methods Our study was carried out between May 5 and the end of October 2020. It included all patients requiring admission to Ain Shams University hospitals. An interview questionnaire was used to collect demographic and clinical data. Laboratory tests for all participants included RT-PCR and total antibody assay for SARS-CoV-2. Results A total of 4,313 subjects were enrolled in our study, with females representing 56% of the sample. Adults and middle-aged individuals represented around 60% of the study sample. The positivity rate of SARS-CoV-2 PCR was 3.84% (95% CI 3.29–4.48), and the SARS-CoV-2 antibody seroprevalence was 29.82% (95% CI: 28.16–31.51). Males showed a higher risk for getting the COVID-19 infection, while middle-age group had significantly higher antibody seroprevalence rates. Conclusion SARS-CoV-2 infection imposes a high burden on the community as detected by high seroprevalence rates.

scholarly journals Impact of B.1.617 and RBD SARS-CoV-2 Variants on Vaccine Efficacy: An In-silico Approach

2021 ◽  
Author(s):  
Prashant Ranjan ◽  
Neha ◽  
Chandra Devi ◽  
Garima Jain ◽  
Chandana Basu Mallick ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Immune Escape ◽  
Conformational Dynamics ◽  
Structural Alteration ◽  
Spike Protein ◽  
Wild Type ◽  
Factors Affecting ◽  
And Function ◽  
Replication Fitness ◽  
Second Wave

Abstract The existing panels of COVID-19 vaccines are based on the spike protein of earlier SARS-CoV-2 strain that emerged in Wuhan, China. However, the evolving nature of SARS-CoV-2 has resulted in emergence of new variants, thereby, posing a greater challenge in the management of the disease. India faced a deadlier second wave of infections very recently and genomic surveillance revealed that B.1.617 variant and its sub lineages are responsible for majority of the cases. These are highly infectious and possibly more lethal and therefore labelled as variants of concern by WHO. Hence, it’s crucial to determine if the current vaccines available can be effective against these variants. To address this, we performed molecular dynamics (MD) simulation on B.1.617 along with K417G variants and other RBD variants. We studied structural alteration of the spike protein and factors affecting antibody neutralization and immune escape. We found in seven of the 12 variants studied, there was a structural alteration in RBD region further affecting its stability and function. Docking analysis of RBD variants and wild type strain demonstrated increase in binding affinity with ACE2 (angiotensin 2 altered enzymes) receptor in these variants. Molecular interaction with CR3022 antibody revealed that binding affinity was less in comparison to wild type, with B.1.617 showing the least binding affinity. These findings from the extensive simulations provides novel mechanistic insights on the conformational dynamics and improves our understanding of the enhanced properties of these variants in terms of infectivity, transmissibility, neutralization potential, virulence and host-viral replication fitness.

scholarly journals S Gene Target Failure (SGTF) in Commercial Multiplex RT-PCR assay as indicator to detect SARS-CoV-2 VOC B.1.1.7 lineage in Tamil Nadu, India

2021 ◽  
Author(s):  
Vidhya N M ◽  
Kumaresan A ◽  
Kalaivani V ◽  
Rajesh Kumar A ◽  
Gurunathan Subramanian ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tamil Nadu ◽  
Immune Escape ◽  
Whole Genome ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Gene Target ◽  
S Gene ◽  
Significant Public Health

Emergence of Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) Variants of Concern (VOC) possessing improved virulence, transmissibility and/or immune-escape capabilities has raised significant public health concerns. In order to identify VOCs, WHO recommends Whole-Genome Sequencing approach, which is costly and involves longer completion time. Hence, potential role of commercial multiplex RT-PCR kit to screen variants rapidly is being attempted in this study. A total of 1200 suspected COVID samples from different districts of Tamil Nadu State (India) were screened with Thermo TaqPath RT-PCR kit and Altona Realstar RT-PCR Assay kit. Among 1200 screened, S-gene target failure (SGTF) phenomenon were identified in 112 samples while testing with TaqPath RT-PCR Kit. 100% concordant results were observed between SGTF phenomenon and whole-genome sequencing (WGS) results in detecting SARS-CoV-2 VOC B.1.1.7. TaqPath RT-PCR assay testing can be utilized by laboratories to screen rapidly the VOC B.1.1.7 variants, thus enabling early detection of B.1.1.7 variant infection and transmission in population. This in turn will pave way to implement suitable preventive measures by appropriate authorities to control the transmission of the viral variant.

scholarly journals To Establish A Normal Range of Inter-Incisal Opening - A Study of 756 Subjects of Age Group 20-50 Years in Yamunanagar City, Haryana.

2013 ◽  
Vol 01 (01) ◽  
pp. 001-003
Author(s):  
Aruna Singh ◽  
Nymphea Pandit ◽  
Monica Sharma
Keyword(s):  
Pearson Correlation ◽  
Mouth Opening ◽  
Clinical History ◽  
P Value ◽  
Age Group ◽  
Male Population ◽  
Female Population ◽  
Odontogenic Infections ◽  
Anterior Teeth ◽  
Average Maximum

Abstract Aim- 1. The aim of this study was to investigate the average maximum range of inter-incisal mouth opening in a representative sample of the adult subjects of Haryana. 2. To see any correlation between maximal inter-incisal opening with age. Methods- Maximum mouth opening was studied in 756 adult subjects with age range of 20-50 years in Yamunanagar, Haryana. Age limit was further divided into three groups (20-30, 31-40, 41-50). Those with clinical history of TMJ involvement, OSMF, any trauma, odontogenic and non-odontogenic infections, dental prosthesis on the anterior teeth, congenital anomalies in the maxillofacial region were excluded from this study. The measurements were recorded twice and mean of the two values were taken. Statistical Analysis- Independent sample t-test was calculated to compare age and mouth opening in both male and females respectively. Bivariate pearson correlation was used to see any relationship between age and mouth opening. P-value ≤ 0.05 and CI (confidence interval) at 95% were considered statistically significant. The Results- The average mouth opening of males (45.36±6.70 mm) subjects was higher as compared to female (41.27 ± 6.75 mm) with significant, p-value 0.000. The mean mouth opening ± SD for both sexes combined was 43.39 ± 7.02 mm. The corresponding values for mean inter-incisal opening in male population aged 20-30, 31-40, 41-50 were 45.52 ± 7.15, 46.16 ± 5.47, 42.96 ± 6.82 mm and in female population aged 20-30, 31-40, 41-50 were 41.40 ± 7.08, 41.60 ± 6.29 and 40.03 ± 6.38 mm respectively. Conclusion- Maximal mouth opening differ significantly with gender. There is a decrease in MMO with older age group.

scholarly journals The Cloning and Molecular Analysis of pawn-B in Paramecium tetraurelia

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1105-1117 ◽  
Author(s):  
W John Haynes ◽  
Kit-Yin Ling ◽  
Robin R Preston ◽  
Yoshiro Saimi ◽  
Ching Kung
Keyword(s):  
Genomic Library ◽  
Open Reading Frame ◽  
Paramecium Tetraurelia ◽  
Wild Type ◽  
Rt Pcr ◽  
Reading Frame ◽  
Close Proximity ◽  
In The Wild ◽  
Dna Fragment ◽  
Alternative Sites

Abstract Pawn mutants of Paramecium tetraurelia lack a depolarization-activated Ca2+ current and do not swim backward. Using the method of microinjection and sorting a genomic library, we have cloned a DNA fragment that complements pawn-B (pwB/pwB). The minimal complementing fragment is a 798-bp open reading frame (ORF) that restores the Ca2+ current and the backward swimming when expressed. This ORF contains a 29-bp intron and is transcribed and translated. The translated product has two putative transmembrane domains but no clear matches in current databases. Mutations in the available pwB alleles were found within this ORF. The d4-95 and d4-96 alleles are single base substitutions, while d4-662 (previously pawn-D) harbors a 44-bp insertion that matches an internal eliminated sequence (IES) found in the wild-type germline DNA except for a single C-to-T transition. Northern hybridizations and RT-PCR indicate that d4-662 transcripts are rapidly degraded or not produced. A second 155-bp IES in the wild-type germline ORF excises at two alternative sites spanning three asparagine codons. The pwB ORF appears to be separated from a 5′ neighboring ORF by only 36 bp. The close proximity of the two ORFs and the location of the pwB protein as indicated by GFP-fusion constructs are discussed.

scholarly journals FGFR3 overexpression is a useful detection tool for FGFR3 fusions and sequence variations in glioma

2020 ◽  
Author(s):  
Jens Schittenhelm ◽  
Lukas Ziegler ◽  
Jan Sperveslage ◽  
Michel Mittelbronn ◽  
David Capper ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Growth Factor Receptor ◽  
Gene Mutations ◽  
Diagnostic Tools ◽  
Wild Type ◽  
Rt Pcr ◽  
Fgfr3 Gene ◽  
Detection Tool ◽  
Sequence Variations ◽  
Gene Panel Sequencing

Abstract Background Fibroblast growth factor receptor (FGFR) inhibitors are currently used in clinical development. A subset of glioblastomas carries gene fusion of FGFR3 and transforming acidic coiled-coil protein 3. The prevalence of other FGFR3 alterations in glioma is currently unclear. Methods We performed RT-PCR in 101 glioblastoma samples to detect FGFR3-TACC3 fusions (“RT-PCR cohort”) and correlated results with FGFR3 immunohistochemistry (IHC). Further, we applied FGFR3 IHC in 552 tissue microarray glioma samples (“TMA cohort”) and validated these results in two external cohorts with 319 patients. Gene panel sequencing was carried out in 88 samples (“NGS cohort”) to identify other possible FGFR3 alterations. Molecular modeling was performed on newly detected mutations. Results In the “RT-PCR cohort,” we identified FGFR3-TACC3 fusions in 2/101 glioblastomas. Positive IHC staining was observed in 73/1024 tumor samples of which 10 were strongly positive. In the “NGS cohort,” we identified FGFR3 fusions in 9/88 cases, FGFR3 amplification in 2/88 cases, and FGFR3 gene mutations in 7/88 cases in targeted sequencing. All FGFR3 fusions and amplifications and a novel FGFR3 K649R missense mutation were associated with FGFR3 overexpression (sensitivity and specificity of 93% and 95%, respectively, at cutoff IHC score &gt; 7). Modeling of these data indicated that Tyr647, a residue phosphorylated as a part of FGFR3 activation, is affected by the K649R mutation. Conclusions FGFR3 IHC is a useful screening tool for the detection of FGFR3 alterations and could be included in the workflow for isocitrate dehydrogenase (IDH) wild-type glioma diagnostics. Samples with positive FGFR3 staining could then be selected for NGS-based diagnostic tools.

scholarly journals Estimating effective infection fatality rates during the course of the COVID-19 pandemic in Germany

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Christian Staerk ◽  
Tobias Wistuba ◽  
Andreas Mayr
Keyword(s):  
Age Distribution ◽  
Age Groups ◽  
Case Fatality ◽  
Time Dependent ◽  
Temporary Increase ◽  
International Studies ◽  
Age Group ◽  
Fatality Rate ◽  
Substantial Fraction ◽  
Second Wave

Abstract Background The infection fatality rate (IFR) of the Coronavirus Disease 2019 (COVID-19) is one of the most discussed figures in the context of this pandemic. In contrast to the case fatality rate (CFR), the IFR depends on the total number of infected individuals – not just on the number of confirmed cases. In order to estimate the IFR, several seroprevalence studies have been or are currently conducted. Methods Using German COVID-19 surveillance data and age-group specific IFR estimates from multiple international studies, this work investigates time-dependent variations in effective IFR over the course of the pandemic. Three different methods for estimating (effective) IFRs are presented: (a) population-averaged IFRs based on the assumption that the infection risk is independent of age and time, (b) effective IFRs based on the assumption that the age distribution of confirmed cases approximately reflects the age distribution of infected individuals, and (c) effective IFRs accounting for age- and time-dependent dark figures of infections. Results Effective IFRs in Germany are estimated to vary over time, as the age distributions of confirmed cases and estimated infections are changing during the course of the pandemic. In particular during the first and second waves of infections in spring and autumn/winter 2020, there has been a pronounced shift in the age distribution of confirmed cases towards older age groups, resulting in larger effective IFR estimates. The temporary increase in effective IFR during the first wave is estimated to be smaller but still remains when adjusting for age- and time-dependent dark figures. A comparison of effective IFRs with observed CFRs indicates that a substantial fraction of the time-dependent variability in observed mortality can be explained by changes in the age distribution of infections. Furthermore, a vanishing gap between effective IFRs and observed CFRs is apparent after the first infection wave, while an increasing gap can be observed during the second wave. Conclusions The development of estimated effective IFR and observed CFR reflects the changing age distribution of infections over the course of the COVID-19 pandemic in Germany. Further research is warranted to obtain timely age-stratified IFR estimates, particularly in light of new variants of the virus.

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