scholarly journals Surge of severe acute respiratory syndrome coronavirus 2 infections linked to single introduction of a virus strain in Myanmar, 2020

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Myat Htut Nyunt ◽  
Hnin Ohnmar Soe ◽  
Kay Thi Aye ◽  
Wah Wah Aung ◽  
Yi Yi Kyaw ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Early Phase ◽  
International Travel ◽  
Health Concern ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genomic Epidemiology ◽  
Local Spread ◽  
Control And Prevention ◽  
Local Transmission

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major health concern globally. Genomic epidemiology is an important tool to assess the pandemic of coronavirus disease 2019 (COVID-19). Several mutations have been reported by genome analysis of the SARS-CoV-2. In the present study, we investigated the mutational and phylogenetic analysis of 30 whole-genome sequences for the virus's genomic characteristics in the specimens collected in the early phase of the pandemic (March–June, 2020) and the sudden surge of local transmission (August–September, 2020). The four samples in the early phase of infection were B.6 lineage and located within a clade of the samples collected at the same time in Singapore and Malaysia, while five returnees by rescue flights showed the lineage B. 1.36.1 (three from India), B.1.1 (one from India) and B.1.80 (one from China). However, there was no evidence of local spread from these returnees. Further, all 19 whole-genome sequences collected in the sudden surge of local transmission showed lineage B.1.36. The surge of the second wave on SARS-CoV-2 infection was linked to the single-introduction of a variant (B.1.36) that may result from the strict restriction of international travel and containment efforts. These genomic data provides the useful information to disease control and prevention strategy.

scholarly journals Surge of Severe Acute Respiratory Syndrome Coronavirus 2 Infections Linked to Single Introduction of a Virus Strain in Myanmar, 2020

2020 ◽  
Author(s):  
Myat Htut Nyunt ◽  
Hnin Ohnmar Soe ◽  
Kay Thi Aye ◽  
Wah Wah Aung ◽  
Yi Yi Kyaw ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Severe Acute Respiratory Syndrome ◽  
Early Stage ◽  
International Travel ◽  
Health Concern ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genomic Epidemiology ◽  
Control And Prevention ◽  
Local Transmission

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major health concern globally. Genomic epidemiology is an important tool to assess the pandemic of the coronavirus disease 2019 (COVID-19). Several mutations have been reported by genome analysis of the SARS-CoV-2. In the present study, we investigate mutational and phylogenetic analysis of 30 whole genome sequences for genomic characteristics of the virus in the specimens collected early phase of pandemic, (March-June, 2020) and sudden surge of infection (August-September, 2020). Phylogenetic analysis revealed that 4 samples of L strain and 1 GR strain in early stage of local transmission, while 6 returnees by rescue flights showed GH (India) and GR strains (China and Philippines) with no evidence of local spread. However, all 19 whole genome sequences in sudden surge of local transmission showed genetically distinct clade GH (Lineage B.1.36). Surge of second wave on SARS-CoV-2 infection was linked to the single-introduction of the GH strain that may be a result of strict restriction of international travel and containment efforts. These genomic data provides the useful information to disease control and prevention strategy.

scholarly journals One year of SARS-CoV-2: Genomic characterization of COVID-19 outbreak in Qatar

2021 ◽  
Author(s):  
Fatiha M. Benslimane ◽  
Hebah A. AlKhatib ◽  
Ola Al-Jamal ◽  
Dana Albatesh ◽  
Sonia Boughattas ◽  
...  
Keyword(s):  
International Travel ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Genome Sequences ◽  
Short Period ◽  
National Response ◽  
Genomic Characterization ◽  
One Year ◽  
Local Transmission

The state of Qatar has emerged as a major transit hub connecting all parts of the globe, making it as a hotspot for infectious disease introduction and providing an ideal setting to monitor the emergence and spread of variants. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population's genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number in the mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. This raises the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor SARS-CoV-2 profile and re-emergence in Qatar.

scholarly journals Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Early Manifestations of COVID-19 in Israel

2020 ◽  
Vol 9 (28) ◽  
Author(s):  
Inbar Cohen-Gihon ◽  
Ofir Israeli ◽  
Ohad Shifman ◽  
Dana Stein ◽  
Hagit Achdout ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Complete Genome ◽  
Genome Sequences ◽  
Local Spread

ABSTRACT We announce the genome sequences of two strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated in Israel, one imported by a traveler who returned from Japan and the second strain collected from a patient infected by a traveler returning from Italy. The sequences obtained are valuable as early manifestations for future follow-up of the local spread of the virus in Israel.

scholarly journals Whole-Genome Sequences of SARS-CoV-2 Isolates from Ethiopian Patients

2021 ◽  
Vol 10 (38) ◽  
Author(s):  
Dawit Hailu Alemayehu ◽  
Bethlehem Adnew ◽  
Fekadu Alemu ◽  
Dessalegn Abeje Tefera ◽  
Tamrayehu Seyoum ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Genetic Group ◽  
The Other ◽  
Whole Genome ◽  
Genome Sequences

Three complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Ethiopian patients were compared with deposited global genomes. Two genomes belonged to genetic group 20A/B.1/GH, and the other belonged to genetic group 20A/B.1.480/GH. Enhancing genomic capacity is important to investigate the transmission and to monitor the evolution and mutational patterns of SARS-CoV-2 in this country.

scholarly journals Whole Genome Sequence Analysis of SARS-CoV-2 Strains Circulating in Malaysia During First Wave and Early Second Wave of Infections.

2020 ◽  
Author(s):  
Zarina Mohd Zawawi ◽  
Jeyanthi Suppiah ◽  
Jeevanathan Kalyanasundram ◽  
Muhammad Afif Azizan ◽  
Shuhaila Mat-Sharani ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Health Concern ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Full Genome ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Synonymous Mutations

Abstract Background: Since December 2019, the outbreak of COVID-19 has raised a great public health concern globally. Here, we report the whole genome sequencing analysis of SARS-CoV-2 strains in Malaysia isolated from six patients diagnosed with COVID-19.Methods: The SARS-CoV-2 viral RNA extracted from clinical specimens and isolates were subjected to whole genome sequencing using NextSeq 500 platform. The sequencing data were assembled to full genome sequences using Megahit and phylogenetic tree was constructed using Mega X software.Results: Six full genome sequences of SARS-CoV-2 comprising of strains from 1st wave (25th January 2020) and 2nd wave (27th February 2020) infection were obtained. Downstream analysis demonstrated diversity among the Malaysian strains with several synonymous and non-synonymous mutations in four of the six cases, affecting the genes M, orf1ab, and S of the SARS-CoV-2 virus. The phylogenetic analysis revealed viral genome sequences of Malaysian SARS-CoV-2 strains clustered under the ancestral Type B.Conclusion: This study comprehended the SARS-CoV-2 virus evolution during its circulation in Malaysia. Continuous monitoring and analysis of the whole genome sequences of confirmed cases would be crucial to further understand the genetic evolution of the virus.

scholarly journals First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016

2022 ◽  
Vol 12 ◽  
Author(s):  
Ronza Hadad ◽  
Daniel Golparian ◽  
Inga Velicko ◽  
Anna-Karin Ohlsson ◽  
Ylva Lindroth ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Health Agency ◽  
Epidemiological Data ◽  
Health Concern ◽  
Dynamic Evolution ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
The Public ◽  
Genomic Epidemiology ◽  
Sequence Types

The increasing transmission and antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health concern with worrying trends of decreasing susceptibility to also the last-line extended-spectrum cephalosporin (ESC) ceftriaxone. A dramatic increase of reported gonorrhea cases has been observed in Sweden from 2016 and onward. The aim of the present study was to comprehensively investigate the genomic epidemiology of all cultured N. gonorrhoeae isolates in Sweden during 2016, in conjunction with phenotypic AMR and clinical and epidemiological data of patients. In total, 1279 isolates were examined. Etest and whole-genome sequencing (WGS) were performed, and epidemiological data obtained from the Public Health Agency of Sweden. Overall, 51.1%, 1.7%, and 1.3% resistance to ciprofloxacin, cefixime, and azithromycin, respectively, was found. No isolates were resistant to ceftriaxone, however, 9.3% of isolates showed a decreased susceptibility to ceftriaxone and 10.5% to cefixime. In total, 44 penA alleles were found of which six were mosaic (n = 92). Using the typing schemes of MLST, NG-MAST, and NG-STAR; 133, 422, and 280 sequence types, respectively, and 93 NG-STAR clonal complexes were found. The phylogenomic analysis revealed two main lineages (A and B) with lineage A divided into two main sublineages (A1 and A2). Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were predominantly found in sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.

scholarly journals Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy

Vaccines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1195
Author(s):  
Sindhu Ramesh ◽  
Manoj Govindarajulu ◽  
Rachel S. Parise ◽  
Logan Neel ◽  
Tharanath Shankar ◽  
...  
Keyword(s):  
United States ◽  
Severe Acute Respiratory Syndrome ◽  
Vaccine Efficacy ◽  
Severe Disease ◽  
The United States ◽  
Health Concern ◽  
Close Monitoring ◽  
The World ◽  
Control And Prevention ◽  
Significant Health

The widespread increase in multiple severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants is causing a significant health concern in the United States and worldwide. These variants exhibit increased transmissibility, cause more severe disease, exhibit evasive immune properties, impair neutralization by antibodies from vaccinated individuals or convalescence sera, and reinfection. The Centers for Disease Control and Prevention (CDC) has classified SARS-CoV-2 variants into variants of interest, variants of concern, and variants of high consequence. Currently, four variants of concern (B.1.1.7, B.1.351, P.1, and B.1.617.2) and several variants of interests (B.1.526, B.1.525, and P.2) are characterized and are essential for close monitoring. In this review, we discuss the different SARS-CoV-2 variants, emphasizing variants of concern circulating the world and highlight the various mutations and how these mutations affect the characteristics of the virus. In addition, we discuss the most common vaccines and the various studies concerning the efficacy of these vaccines against different variants of concern.

scholarly journals Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yvan Butera ◽  
Enatha Mukantwari ◽  
Maria Artesi ◽  
Jeanne d’arc Umuringa ◽  
Áine Niamh O’Toole ◽  
...  
Keyword(s):  
Genomic Sequencing ◽  
Whole Genome ◽  
Genome Sequences ◽  
Durable Response ◽  
Travel History ◽  
Transmission Rates ◽  
Spatio Temporal ◽  
Local Transmission ◽  
Lineage Diversity

AbstractCOVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.

scholarly journals One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar

2021 ◽  
Vol 11 ◽  
Author(s):  
Fatiha M. Benslimane ◽  
Hebah A. Al Khatib ◽  
Ola Al-Jamal ◽  
Dana Albatesh ◽  
Sonia Boughattas ◽  
...  
Keyword(s):  
International Travel ◽  
Genomic Diversity ◽  
Diverse Population ◽  
Genome Sequences ◽  
Short Period ◽  
National Response ◽  
Genomic Characterization ◽  
One Year ◽  
Local Transmission

Qatar, a country with a strong health system and a diverse population consisting mainly of expatriate residents, has experienced two large waves of COVID-19 outbreak. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population’s genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number of mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. These findings raise the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor the SARS-CoV-2 profile and re-emergence in Qatar.

scholarly journals Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

2021 ◽  
Author(s):  
Bernardo Gutierrez ◽  
Sully Marquez ◽  
Belen Prado-Vivar ◽  
Monica Becerra-Wong ◽  
Juan Jose Guadalupe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Clock ◽  
Transmission Dynamics ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genomic Epidemiology ◽  
Early Stages ◽  
Spatiotemporal Distributions ◽  
Space And Time ◽  
Pharmaceutical Interventions

Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.

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