scholarly journals Dynamic Zero-Covid strategy curtails mutagenesis and emergence of new variants of the SARS-CoV-2

2021 ◽  
Author(s):  
Lunbiao Cui ◽  
Liguo Zhu ◽  
Jun Zhang ◽  
Huafeng Fan ◽  
Yongxiang Yi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mutation Process ◽  
Genome Sequences ◽  
Outbreak Period ◽  
Mutant Strains ◽  
Pharmaceutical Interventions

Abstract Within the local outbreak period of SARS-CoV-2 Delta variant in Nanjing and Yangzhou, China, we analyzed the mutation process of the Delta variants in 520 cases, as well as the production, spread and elimination of new mutant strains under the non-pharmaceutical interventions (NPI) strategy. The investigation on distribution of COVID-19 cases and phylogenetic analysis of SARS-CoV-2 genome sequences attributed to tracking the transmission chains, transmission chains were terminated by the isolation of the COVID-19 patients and quarantine of close-contracts, suggesting the importance of NPI in prompting some mutations to disappear and stopping the transmission of new variants. Dynamic zero-Covid strategy has been implemented successfully to against the second-largest local epidemic caused by an imported COVID-19 case in China.

scholarly journals South-east Asian Zika virus strain linked to cluster of cases in Singapore, August 2016

2016 ◽  
Vol 21 (38) ◽  
Author(s):  
Sebastian Maurer-Stroh ◽  
Tze-Minn Mak ◽  
Yi-Kai Ng ◽  
Shiau-Pheng Phuah ◽  
Roland G Huber ◽  
...  
Keyword(s):  
Public Health ◽  
Phylogenetic Analysis ◽  
Virus Strain ◽  
Zika Virus ◽  
East Asian ◽  
Public Health Emergency ◽  
Global Public Health ◽  
Genome Sequences ◽  
First Case ◽  
Large Outbreak

Zika virus (ZIKV) is an ongoing global public health emergency with 70 countries and territories reporting evidence of ZIKV transmission since 2015. On 27 August 2016, Singapore reported its first case of local ZIKV transmission and identified an ongoing cluster. Here, we report the genome sequences of ZIKV strains from two cases and find through phylogenetic analysis that these strains form an earlier branch distinct from the recent large outbreak in the Americas.

scholarly journals Complete Genome Sequences of Two Subgenotype 1b Newcastle Disease Viruses Isolated from Sansui Sheldrake Ducks in Guizhou, China

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Yan Hu ◽  
Zhiqiang Duan ◽  
Xinqin Ji ◽  
Jiafu Zhao ◽  
Houqiang Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Newcastle Disease ◽  
Complete Genome ◽  
Class I ◽  
Guizhou Province ◽  
Genome Sequences

Here, we report the complete genome sequences of two Newcastle disease viruses, Sheldrake duck/China/Guizhou/01/2016 and Sheldrake duck/China/Guizhou/02/2016, isolated from Sansui Sheldrake ducks in Guizhou Province, China. The genome of the isolates is 15,198 nucleotides in length. Phylogenetic analysis revealed that the isolates are clustered into subgenotype 1b in class I.

scholarly journals Draft Genome Sequences of 40 Salmonella enterica Serovar Typhimurium Strains Isolated from Humans and Food in Brazil: TABLE 1 

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Fernanda Almeida ◽  
Marta Inês Cazentini Medeiros ◽  
Dália Prazeres Rodrigues ◽  
Justin Payne ◽  
Ruth E. Timme ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Health Problem ◽  
Salmonella Enterica ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Draft Genome ◽  
Genome Sequences ◽  
Serovar Typhimurium ◽  
Important Health

Salmonellosis is an important health problem worldwide and Salmonella enterica serovar Typhimurium is one of the most common isolated serovars. Here, we reported the draft genomes of 40 S . Typhimurium strains isolated from humans and food in Brazil. These draft genomes will improve phylogenetic analysis and will help enhance our understanding of strains of this serovar isolated in Brazil.

scholarly journals Near-Complete Human Sapovirus Genome Sequences from Kenya

2019 ◽  
Vol 8 (7) ◽  
Author(s):  
Marta Diez-Valcarce ◽  
Anna Montmayeur ◽  
Roman Tatusov ◽  
Jan Vinjé
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Sequences

We report five near-complete sapovirus genome sequences, including GI.3, GII.2, and GII.6 and two novel GII.NA (not assigned) strains. These new sequences expand the collection of human sapoviruses, allowing for a more accurate phylogenetic analysis of circulating strains and for designing broadly reactive primers for their detection and typing.

scholarly journals Cocirculation of Two Distinct Genetic and Antigenic Lineages of Proposed Influenza D Virus in Cattle

2014 ◽  
Vol 89 (2) ◽  
pp. 1036-1042 ◽  
Author(s):  
Emily A. Collin ◽  
Zizhang Sheng ◽  
Yuekun Lang ◽  
Wenjun Ma ◽  
Ben M. Hause ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Influenza Virus ◽  
Respiratory Disease ◽  
New Genus ◽  
Cross Reactivity ◽  
Surface Glycoprotein ◽  
Clinical Samples ◽  
Genome Sequences ◽  
Antigenic Analysis ◽  
Pathogenic Potential

ABSTRACTViruses with approximately 50% homology to human influenza C virus (ICV) have recently been isolated from swine and cattle. The overall low homology to ICV, lack of antibody cross-reactivity to ICV in hemagglutination inhibition (HI) and agar gel immunodiffusion assays, and inability to productively reassort with ICV led to the proposal that these viruses represented a new genus of influenza virus, influenzavirus D (IDV). To further our understanding of the epidemiology of IDV, real-time reverse transcription-PCR was performed on a set of 208 samples from bovines with respiratory disease. Ten samples (4.8%) were positive and six viruses were successfully isolatedin vitro. Phylogenetic analysis of full-genome sequences of these six new viruses and four previously reported viruses revealed two distinct cocirculating lineages represented by D/swine/Oklahoma/1334/2011 (D/OK) and D/bovine/Oklahoma/660/2013 (D/660), which frequently reassorted with one another. Antigenic analysis using the HI assay and lineage-representative D/OK and D/660 antiserum found up to an approximate 10-fold loss in cross-reactivity against heterologous clade antiserum. One isolate, D/bovine/Texas/3-13/2011 (D/3-13), clustered with the D/660 lineage, but also had high HI titers to heterologous (D/OK) clade antiserum. Molecular modeling of the hemagglutinin esterase fusion protein of D/3-13 identified a mutation at position 212 as a possible antigenic determinant responsible for the discrepant HI results. These results suggest that IDV is common in bovines with respiratory disease and that at least two genetic and antigenically distinct clades cocirculate.IMPORTANCEA novel bovine influenza virus was recently identified. Detailed genetic and antigenic studies led to the proposal that this virus represents a new genus of influenza, influenzavirus D (IDV). Here, we show that IDV is common in clinical samples of bovine respiratory disease complex (BRDC), with a prevalence similar to that of other established BRDC etiological agents. These results are in good agreement with the near-ubiquitous seroprevalence of IDV previously found. Phylogenetic analysis of complete genome sequences found evidence for two distinct cocirculating lineages of IDV which freely reassort. Significant antigenic differences, which generally agreed with the surface glycoprotein hemagglutinin esterase phylogeny, were observed between the two lineages. Based on these results, and on the ability of IDV to infect and transmit in multiple mammalian species, additional studies to determine the pathogenic potential of IDV are warranted.

scholarly journals Phylogenetic analysis of complete genome sequences of hepatitis B virus from an Afro-Colombian community: presence of HBV F3/A1 recombinant strain

2012 ◽  
Vol 9 (1) ◽  
Author(s):  
Mónica V Alvarado-Mora ◽  
Camila M Romano ◽  
Michele S Gomes-Gouvêa ◽  
Maria F Gutierrez ◽  
Flair J Carrilho ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Complete Genome ◽  
Recombinant Strain ◽  
Genome Sequences ◽  
B Virus ◽  
Community Presence

scholarly journals Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

2013 ◽  
Vol 94 (9) ◽  
pp. 1995-2004 ◽  
Author(s):  
Rafal Tokarz ◽  
Saddef Haq ◽  
Stephen Sameroff ◽  
Stephen R. C. Howie ◽  
W. Ian Lipkin
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Genomic Analysis ◽  
The Other ◽  
High Rate ◽  
Structural Genes ◽  
Genome Sequences ◽  
Capsid Region ◽  
High Degree ◽  
Degree Of Similarity

Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease.

scholarly journals Characterization of the Xanthomonas translucens Complex Using Draft Genomes, Comparative Genomics, Phylogenetic Analysis, and Diagnostic LAMP Assays

2017 ◽  
Vol 107 (5) ◽  
pp. 519-527 ◽  
Author(s):  
Paul A. Langlois ◽  
Jacob Snelling ◽  
John P. Hamilton ◽  
Claude Bragard ◽  
Ralf Koebnik ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Diagnostic Tools ◽  
Cereal Crops ◽  
Genome Sequences ◽  
Germplasm Exchange ◽  
Geographic Spread ◽  
A Genome ◽  
Xanthomonas Translucens

Prevalence of Xanthomonas translucens, which causes cereal leaf streak (CLS) in cereal crops and bacterial wilt in forage and turfgrass species, has increased in many regions in recent years. Because the pathogen is seedborne in economically important cereals, it is a concern for international and interstate germplasm exchange and, thus, reliable and robust protocols for its detection in seed are needed. However, historical confusion surrounding the taxonomy within the species has complicated the development of accurate and reliable diagnostic tools for X. translucens. Therefore, we sequenced genomes of 15 X. translucens strains representing six different pathovars and compared them with additional publicly available X. translucens genome sequences to obtain a genome-based phylogeny for robust classification of this species. Our results reveal three main clusters: one consisting of pv. cerealis, one consisting of pvs. undulosa and translucens, and a third consisting of pvs. arrhenatheri, graminis, phlei, and poae. Based on genomic differences, diagnostic loop-mediated isothermal amplification (LAMP) primers were developed that clearly distinguish strains that cause disease on cereals, such as pvs. undulosa, translucens, hordei, and secalis, from strains that cause disease on noncereal hosts, such as pvs. arrhenatheri, cerealis, graminis, phlei, and poae. Additional LAMP assays were developed that selectively amplify strains belonging to pvs. cerealis and poae, distinguishing them from other pathovars. These primers will be instrumental in diagnostics when implementing quarantine regulations to limit further geographic spread of X. translucens pathovars.

scholarly journals Occurrence of a novel strain of Moroccan watermelon mosaic virus infecting pumpkins in Kenya

Plant Disease ◽  
2021 ◽  
Author(s):  
Naomi Mumo ◽  
Elijah Miinda Ateka ◽  
Edward Mamati ◽  
Fredah Karambu Rimberia ◽  
George Ochieng' Asudi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Sanger Sequencing ◽  
Cucurbita Pepo ◽  
Citrullus Lanatus ◽  
Watermelon Mosaic Virus ◽  
Cucurbita Moschata ◽  
Genome Sequences ◽  
Mediterranean Regions ◽  
Sequence Identities

The potyvirus Moroccan watermelon mosaic virus (MWMV) naturally infects and severely threatens production of cucurbits and papaya. In this study, we identified and characterized MWMV isolated from pumpkin (Cucurbita moschata) intercropped with MWMV-infected papaya plants through next generation and Sanger sequencing approaches. Complete MWMV genome sequences were obtained from two pumpkin samples through NGS and validated using Sanger sequencing. The isolates share 83.4-83.7 % nucleotide (nt) and 92.3-95.1 % amino acid (aa) sequence identities in the coat protein and 79.5-79.9 % nt and 89.2-89.7 % aa identities in the polyprotein with papaya isolates of MWMV. Phylogenetic analysis using complete polyprotein nt sequences revealed the clustering of both pumpkin isolates of MWMV with corresponding sequences of cucurbit isolates of the virus from other parts of Africa and the Mediterranean regions, distinct from a clade formed by papaya isolates. Through sap inoculation, a pumpkin isolate of MWMV was pathogenic on zucchini (Cucurbita pepo), watermelon (Citrullus lanatus), and cucumber (Cucumis sativus), but not on papaya. Conversely, the papaya isolate of MWMV was non-pathogenic on pumpkin, watermelon, and cucumber, but infected zucchini. The results suggest occurrence of two strains of MWMV in Kenya having different biological characteristics associated with the host specificity.

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