Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Report of SARS-CoV-2 BA.1 Lineage in Morocco.

ABSTRACT: Here, we report the near-complete genome sequence and genetic variations of a clinical sample of SARS-CoV-2 for the newly emerged Omicron variant (BA.1). The sample was collected from a nasopharyngeal swab of a Moroccan patient, and the sequencing was done using Ion S5 technology.

SUBMITTER: El Mazouri S

PROVIDER: S-EPMC9119083 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Report of SARS-CoV-2 BA.1 Lineage in Morocco.

El Mazouri Safae S Bendani Houda H Boumajdi Nasma N Chaoui Roqai Mhammed M Aanniz Tarik T Seffar Myriam M Kabbaj Hakima H El Amin Ghizlane G Zouaki Amal A Amzazi Saaïd S Ouadghiri Mouna M Belyamani Lahcen L Ibrahimi Azeddine A

Microbiology resource announcements 20220413 5

Here, we report the near-complete genome sequence and genetic variations of a clinical sample of SARS-CoV-2 for the newly emerged Omicron variant (BA.1). The sample was collected from a nasopharyngeal swab of a Moroccan patient, and the sequencing was done using Ion S5 technology. ...[more]

PMID: 35416694

Similar Datasets

Report of SARS-CoV-2 B1.1.7 Lineage in Morocco.

Project description:Here, we report the near-complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring the N501Y mutation assigned to the B.1.1.7 lineage. The sample was collected from a nasopharyngeal swab of a female patient from Temara, Morocco, and the sequencing was done using Ion S5 technology.

| S-EPMC8063648 | biostudies-literature

Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines.

Project description:The Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant led to a dramatic global epidemic wave following detection in South Africa in November 2021. The BA.1 Omicron lineage was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021-January 2022, while other Omicron lineages, including BA.2, accounted for the minority of global isolates. Here, we describe the Omicron wave in the Philippines by analysing genomic data. Our results identify the presence of both BA.1 and BA.2 lineages in the Philippines in December 2021, before cases surged in January 2022. We infer that only the BA.2 lineage underwent sustained transmission in the country, with an estimated emergence around 18 November 2021 (95 per cent highest posterior density: 6-28 November), while despite multiple introductions, BA.1 transmission remained limited. These results suggest that the Philippines was one of the earliest areas affected by BA.2 and reiterate the importance of whole genome sequencing for monitoring outbreaks.

| S-EPMC9452094 | biostudies-literature

Hospitalisation and mortality risk of SARS-COV-2 variant omicron sub-lineage BA.2 compared to BA.1 in England.

Project description:The Omicron variant of SARS-CoV-2 became the globally dominant variant in early 2022. A sub-lineage of the Omicron variant (BA.2) was identified in England in January 2022. Here, we investigated hospitalisation and mortality risks of COVID-19 cases with the Omicron sub-lineage BA.2 (n = 258,875) compared to BA.1 (n = 984,337) in a large cohort study in England. We estimated the risk of hospital attendance, hospital admission or death using multivariable stratified proportional hazards regression models. After adjustment for confounders, BA.2 cases had lower or similar risks of death (HR = 0.80, 95% CI 0.71-0.90), hospital admission (HR = 0.88, 95% CI 0.83-0.94) and any hospital attendance (HR = 0.98, 95% CI 0.95-1.01). These findings that the risk of severe outcomes following infection with BA.2 SARS-CoV-2 was slightly lower or equivalent to the BA.1 sub-lineage can inform public health strategies in countries where BA.2 is spreading.

| S-EPMC9559149 | biostudies-literature

Case Report: Omicron BA.2 Subvariant of SARS-CoV-2 Outcompetes BA.1 in Two Co-infection Cases.

Project description:Trends from around the world suggest that the omicron BA.2 subvariant is increasing in proportion to the original BA.1 subvariant. Here we report two cases of co-infection with omicron BA.1 and omicron BA.2 in co-exposed individuals. In both individuals, genome sequencing and/or S-gene specific PCR identified omicron BA.1 at early time-points, which was replaced by omicron BA.2 at later time-points of the infection. The timeline of our data supports the proposition that BA.2 outcompetes BA.1 in a real-life scenario, and in time becomes the dominant variant in the upper respiratory tract of the host.

| S-EPMC9041751 | biostudies-literature

Coding-Complete Sequence of a SARS-CoV-2 Strain from an Omicron (B.1.1.529+BA.1) Variant Detected in Morocco.

Project description:Here, we describe the coding-complete sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain HM36, identified as a strain of concern of B.1.1.529+BA (Omicron).

| S-EPMC9119047 | biostudies-literature

Immune escape and attenuated severity associated with the SARS-CoV-2 BA.2.86/JN.1 lineage.

Project description:The SARS-CoV-2 BA.2.86 lineage, and its sublineage JN.1 in particular, achieved widespread transmission in the US during winter 2023-24. However, this surge in infections was not accompanied by COVID-19 hospitalizations and mortality commensurate with prior waves. To understand shifts in COVID-19 epidemiology associated with JN.1 emergence, we compared characteristics and clinical outcomes of time-matched cases infected with BA.2.86 lineages (predominantly representing JN.1) versus co-circulating XBB-derived lineages in December, 2023 and January, 2024. Cases infected with BA.2.86 lineages received greater numbers of COVID-19 vaccine doses, including XBB.1.5-targeted boosters, in comparison to cases infected with XBB-derived lineages. Additionally, cases infected with BA.2.86 lineages experienced greater numbers of documented prior SARS-CoV-2 infections. Cases infected with BA.2.86 lineages also experienced lower risk of progression to severe clinical outcomes requiring emergency department consultations or hospital admission. Sensitivity analyses suggested under-ascertainment of prior infections could not explain this apparent attenuation of severity. Our findings implicate escape from immunity acquired from prior vaccination or infection in the emergence of the JN.1 lineage and suggest infections with this lineage are less likely to experience clinically-severe disease. Monitoring of immune escape and clinical severity in emerging SARS-CoV-2 variants remains a priority to inform responses.

| S-EPMC11450198 | biostudies-literature

mouse ACE2 receptor bound to SARS-CoV-2 variant Omicron BA.2.12.1 Spike

Project description: Not available

| EMPIAR-11180 | biostudies-other

mouse ACE2 receptor bound to SARS-CoV-2 variant Omicron BA.1 Spike

Project description: Not available

| EMPIAR-11179 | biostudies-other

Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases.

Project description:BackgroundThroughout the SARS-CoV-2 pandemic, multiple waves of variants of concern have swept across populations, leading to a chain of new and yet more contagious variants dominating COVID-19 cases. Here, we tracked the remarkably rapid shift from Omicron BA.1 to BA.2 sublineage dominance in the Swedish population in early 2022 at a day-by-day basis.MethodsUsing a custom SARS-CoV-2 Omicron BA.1 lineage-typing RT-PCR assay, we analyzed 174,933 clinical upper airway samples collected during January to March 2022.FindingsOur study demonstrates the feasibility and reliability of parallel lineage assignment of select variants at population scale, tracking the dominant sublineage transition from BA.1 to BA.2 at day-to-day resolution and uncovering nearly 2-fold higher levels of viral RNA in cases infected with Omicron BA.2 relative to BA.1.ConclusionsOur data provide unique insights into the Omicron BA.1 to BA.2 transition that occurred in Sweden during early 2022, and later, across the world. This may help to understand the increased transmissibility of the BA.2 variant.

| S-EPMC9359497 | biostudies-literature

Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR.

Project description:Whole genome sequencing (WGS) is considered the best instrument to track both virus evolution and the spread of new, emerging variants. However, WGS still does not allow the analysis of as many samples as qPCR does. Epidemiological and clinical research needs to develop advanced qPCR methods to identify emerging variants of SARS-CoV-2 while collecting data on their spreading in a faster and cheaper way, which is critical for introducing public health measures. This study aimed at designing a one-step RT-qPCR assay for multiplex detection of the Omicron lineage and providing additional data on its subvariants in clinical samples. The RT-qPCR assay demonstrated high sensitivity and specificity on multiple SARS-CoV-2 variants and was cross-validated by WGS.

| S-EPMC9784567 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data