scholarly journals Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

2021 ◽  
Vol 9 (5) ◽  
pp. 1035
Author(s):  
Rokshana Parvin ◽  
Sultana Zahura Afrin ◽  
Jahan Ara Begum ◽  
Salma Ahmed ◽  
Mohammed Nooruzzaman ◽  
...  
Keyword(s):  
Virus Transmission ◽  
Genomic Diversity ◽  
Evolutionary Analysis ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
Community Transmission ◽  
Amino Acid Diversity ◽  
Significant Amino Acid ◽  
Mutation Analyses ◽  
Lineage Diversity

Virus evolution and mutation analyses are crucial for tracing virus transmission, the potential variants, and other pathogenic determinants. Despite continuing circulation of the SARS-CoV-2, very limited studies have been conducted on genetic evolutionary analysis of the virus in Bangladesh. In this study, a total of 791 complete genome sequences of SARS-CoV-2 from Bangladesh deposited in the GISAID database during March 2020 to January 2021 were analyzed. Phylogenetic analysis revealed circulation of seven GISAID clades G, GH, GR, GRY, L, O, and S or five Nextstrain clades 20A, 20B, 20C, 19A, and 19B in the country during the study period. The GISAID clade GR or the Nextstrain clade 20B or lineage B.1.1.25 is predominant in Bangladesh and closely related to the sequences from India, USA, Canada, UK, and Italy. The GR clade or B.1.1.25 lineage is likely to be responsible for the widespread community transmission of SARS-CoV-2 in the country during the first wave of infection. Significant amino acid diversity was observed among Bangladeshi SARS-CoV-2 isolates, where a total of 1023 mutations were detected. In particular, the D614G mutation in the spike protein (S_D614G) was found in 97% of the sequences. However, the introduction of lineage B.1.1.7 (UK variant/S_N501Y) and S_E484K mutation in lineage B.1.1.25 in a few sequences reported in late December 2020 is of particular concern. The wide genomic diversity indicated multiple introductions of SARS-CoV-2 into Bangladesh through various routes. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS-CoV-2 in Bangladesh.

scholarly journals A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

2020 ◽  
Author(s):  
Xianding Deng ◽  
Wei Gu ◽  
Scot Federman ◽  
Louis du Plessis ◽  
Oliver G. Pybus ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
The United States ◽  
Contact Tracing ◽  
Northern California ◽  
Cruise Ship ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
The Usa ◽  
Community Transmission ◽  
Virus Genomes

AbstractThe COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.

scholarly journals Genomic epidemiology of SARS-CoV-2 in Colombia

2020 ◽  
Author(s):  
Katherine Laiton-Donato ◽  
Christian Julián Villabona-Arenas ◽  
José A. Usme-Ciro ◽  
Carlos Franco-Muñoz ◽  
Diego A. Álvarez-Díaz ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Human Mobility ◽  
Virus Transmission ◽  
Genetic Data ◽  
Air Travel ◽  
Transmission Dynamics ◽  
Clinical Samples ◽  
Epidemiological Investigation ◽  
Multiple Introductions ◽  
Genomic Epidemiology

AbstractCoronavirus disease 2019 (COVID-19) was first diagnosed in Colombia from a traveler arriving from Italy on February 26, 2020. To date, available data on the origins and number or introductions of SARS-CoV-2 into the country are limited. Here, we sequenced SARS-CoV-2 from 43 clinical samples and—together with another 73 genomes sequences available from the country—we investigated the emergence and the routes of importation of COVID-19 into Colombia using epidemiological, historical air travel and phylogenetic observations. Our study provided evidence of multiple introductions, mostly from Europe, with at least 12 lineages being documented. Phylogenetic findings validated the linkage of epidemiologically-linked transmission chains. Our results demonstrate the advantages of genome sequencing to complement COVID-19 outbreak investigation and underscores that human mobility and genetic data are relevant to complete epidemiological investigation and better characterize virus transmission dynamics at local scales.

scholarly journals Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

2021 ◽  
Author(s):  
Vinícius Bonetti Franceschi ◽  
Gabriel Dickin Caldana ◽  
Amanda de Menezes Mayer ◽  
Gabriela Bettella Cybis ◽  
Carla Andretta Moreira Neves ◽  
...  
Keyword(s):  
South African ◽  
Viral Evolution ◽  
Temporal Correlation ◽  
Representative Sampling ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
Viral Spread ◽  
Frequent Mutations ◽  
Community Transmission

AbstractBrazil is the third country most affected by Covid-19 pandemic. In spite of this, viral evolution in municipality resolution is poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We identified four main circulating lineages in Esteio (Southern Brazil) and their relationship with global, national and regional lineages using phylogenetics and phylodynamics inferences from 21 SARS-CoV-2 genome sequences. We provided a comprehensive view of viral mutations from a time- and age-representative sampling from May to October 2020, in Esteio (RS, Brazil), highlighting two frequent mutations in Spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in Spike Receptor Binding Domain (RBD) characteristic of the South African lineage B.1.351, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). A significant viral diversity was evidenced with the identification of 80 different SNPs. The E484K replacement was found in two genomes (9.5%) from samples obtained in mid-October, which is to our best knowledge the earliest description of E484K harboring SARS-CoV-2 in South Brazil. This mutation identified in a small municipality from the RS state demonstrates that it was probably widely distributed in the Brazilian territory, but went unnoticed so far by the lack of genomic surveillance in Brazil. The introduction of E484K mutants shows temporal correlation with later increases in new cases in our state. Importantly, since it has been associated with immune evasion and enhanced interaction with hACE-2, lineages containing this substitution must be the subject of intense surveillance. Our date demonstrates multiple introductions of the most prevalent lineages (B.1.1.33 and B.1.1.248) and the major role of community transmission in viral spreading and the establishment of Brazilian lineages. This represents an important contribution to the epidemiology of SARS-CoV-2.

scholarly journals Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy

2020 ◽  
Author(s):  
Claudia Alteri ◽  
Valeria Cento ◽  
Antonio Piralla ◽  
Valentino Costabile ◽  
Monica Tallarita ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
Glycosylation Sites ◽  
Community Transmission

From February to April, 2020, Lombardy (Italy) was the area who worldwide registered the highest numbers of SARS-CoV-2 infection. By extensively analyzing 346 whole SARS-CoV-2 genomes, we demonstrated the simultaneous circulation in Lombardy of two major viral lineages, likely derived from multiple introductions, occurring since the second half of January. Seven single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. These two lineages, and the presence of two well defined clusters inside Lineage 1, revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy.

scholarly journals Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

2020 ◽  
Author(s):  
Jemma L Geoghegan ◽  
Xiaoyun Ren ◽  
Matthew Storey ◽  
James Hadfield ◽  
Lauren Jelley ◽  
...  
Keyword(s):  
Public Health ◽  
New Zealand ◽  
Epidemiological Data ◽  
Genomic Diversity ◽  
Reproductive Number ◽  
Genomic Epidemiology ◽  
Aotearoa New Zealand ◽  
Time Period ◽  
Community Transmission ◽  
Health And Disease

New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nation-wide lockdown of all non-essential services to curb the spread of COVID-19. New Zealand experienced 102 days without community transmission before a new outbreak in August 2020. Here, we generated 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected from the 'first wave' between 26 February and 22 May 2020, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. The proportion of D614G variants in the virus spike protein increased over time due to an increase in their importation frequency, rather than selection within New Zealand. These data also helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re, of New Zealand's largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in a transmission lineage of more than one additional case. Most of the cases that resulted in a transmission lineage originated from North America, rather than from Asia where the virus first emerged or from the nearest geographical neighbour, Australia. Genomic data also helped link more infections to a major transmission cluster than through epidemiological data alone, providing probable sources of infections for cases in which the source was unclear. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.

scholarly journals Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

2021 ◽  
Vol 6 (3) ◽  
pp. 414-414
Author(s):  
Ana da Silva Filipe ◽  
◽  
James G. Shepherd ◽  
Thomas Williams ◽  
Joseph Hughes ◽  
...  
Keyword(s):  
Multiple Introductions ◽  
Genomic Epidemiology

scholarly journals Molecular Phylogenetics and Evolutionary Analysis of a Highly Recombinant Begomovirus, Cotton Leaf Curl Multan Virus and Associated Satellites

2021 ◽  
Author(s):  
Tahir Farooq ◽  
Muhammad Umar ◽  
Xiaoman She ◽  
Yafei Tang ◽  
Zifu He
Keyword(s):  
Molecular Phylogenetics ◽  
Management Strategies ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Cotton Leaf ◽  
Evolutionary Analysis ◽  
Cotton Production ◽  
Evolutionary Patterns ◽  
Satellite Sequences ◽  
Leaf Curl

Abstract Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite’s virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite (CLCuMuA) and Cotton leaf curl Multan betasatellite (CLCuMuB) populations arising from distinct regions exhibit high mutation rates. Though evolutionary linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.

scholarly journals State-wide Genomic Epidemiology Investigations of COVID-19 Infections in Healthcare Workers: Insights for Future Pandemic Preparedness

2021 ◽  
Author(s):  
Anne E Watt ◽  
Norelle L Sherry ◽  
Patiyan Andersson ◽  
Courtney R Lane ◽  
Sandra Johnson ◽  
...  
Keyword(s):  
Healthcare Workers ◽  
Genomic Analysis ◽  
Epidemiological Data ◽  
Pandemic Preparedness ◽  
Transmission Networks ◽  
Healthcare Facilities ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
Sequencing Coverage ◽  
Healthcare Settings

Background COVID-19 has resulted in many infections in healthcare workers (HCWs) globally. We performed state-wide SARS-CoV-2 genomic epidemiological investigations to identify HCW transmission dynamics and provide recommendations to optimise healthcare system preparedness for future outbreaks. Methods Genome sequencing was attempted on all COVID-19 cases in Victoria, Australia. We combined genomic and epidemiologic data to investigate the source of HCW infections across multiple healthcare facilities (HCFs) in the state. Phylogenetic analysis and fine-scale hierarchical clustering were performed for the entire Victorian dataset including community and healthcare cases. Facilities provided standardised epidemiological data and putative transmission links. Findings Between March and October 2020, approximately 1,240 HCW COVID-19 infection cases were identified; 765 are included here. Genomic sequencing was successful for 612 (80%) cases. Thirty-six investigations were undertaken across 12 HCFs. Genomic analysis revealed that multiple introductions of COVID-19 into facilities (31/36) were more common than single introductions (5/36). Major contributors to HCW acquisitions included mobility of staff and patients between wards and facilities, and characteristics and behaviours of individual patients including super-spreading events. Key limitations at the HCF level were identified. Interpretation Genomic epidemiological analyses enhanced understanding of HCW infections, revealing unsuspected clusters and transmission networks. Combined analysis of all HCWs and patients in a HCF should be conducted, supported by high rates of sequencing coverage for all cases in the population. Established systems for integrated genomic epidemiological investigations in healthcare settings will improve HCW safety in future pandemics.

scholarly journals Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jemma L. Geoghegan ◽  
Xiaoyun Ren ◽  
Matthew Storey ◽  
James Hadfield ◽  
Lauren Jelley ◽  
...  
Keyword(s):  
Public Health ◽  
New Zealand ◽  
Health Interventions ◽  
Genomic Diversity ◽  
Reproductive Number ◽  
Genomic Epidemiology ◽  
Aotearoa New Zealand ◽  
Time Period ◽  
Essential Services ◽  
Health And Disease

AbstractNew Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide ‘lockdown’ of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected during the ‘first wave’, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. These data helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re of New Zealand’s largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.

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