Phylogenetic analysis revealed the central roles of two African countries in the evolution and worldwide spread of Zika virus

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.

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Complete Genome Sequence of a Zika Virus Strain Isolated from the Serum of an Infected Patient in Thailand in 2006

Genome Announcements ◽

10.1128/genomea.00121-18 ◽

2018 ◽

Vol 6 (10) ◽

Cited By ~ 11

Author(s):

Narong Nitatpattana ◽

Kumchol Chaiyo ◽

Supoth Rajakam ◽

Kanya Poolam ◽

Kusuma Chansiprasert ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genome Sequence ◽

Virus Strain ◽

Zika Virus ◽

Complete Genome Sequence ◽

Complete Genome ◽

Infected Patient ◽

Vero Cells ◽

Asian Lineage

ABSTRACT The complete genome of Zika virus (ZIKV) strain CVD_06-274 was isolated from the serum of an infected patient in Thailand in 2006. Phylogenetic analysis showed that this strain belongs to the Asian lineage and also high titers in Vero cells (RCB 10-87). It has potential for development as an inactivated ZIKV vaccine.

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Comparative analysis of chloroplast genomes indicated different origin for Indian Tea (Camellia assamica) cv TV-1 as compared to Chinese tea

10.1101/2020.07.13.199133 ◽

2020 ◽

Author(s):

Hukam C. Rawal ◽

Abhishek Mazumder ◽

Sangeeta Borchetia ◽

Biswajit Bera ◽

S. Soundararajan ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Comparative Analysis ◽

Morphological Characteristics ◽

African Countries ◽

Chloroplast Genomes ◽

Assam Tea ◽

Cp Genome ◽

Indian Tea ◽

Simple Sequence ◽

Different Origin

AbstractTea is an important plantation crop of some Asian and African countries. Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China joining area, yet specific origin of China and Assam tea are not yet clear. In the present study, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus. Cp genome based phylogenetic analysis indicated that Indian Assam Tea, TV-1 formed a different group from that of China tea, indicating that TV-1 might have undergone different domestication and hence owe different origin. The simple sequence repeats (SSRs) analysis and codon usage distribution pattern also supported the clustering order in the cp genome based phylogenetic tree.

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Molecular detection and phylogenetic analysis of Lumpy skin disease virus from outbreaks in Uganda 2017-2018

10.21203/rs.2.14954/v1 ◽

2019 ◽

Author(s):

Sylvester Ochwo ◽

Kimberly Vanderwaal ◽

Christian Ndekezi ◽

Joseph Nkamwesiga ◽

Anna Munsey ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Disease Virus ◽

Skin Disease ◽

Phylogenetic Trees ◽

African Countries ◽

Economic Implications ◽

Lumpy Skin Disease ◽

Lumpy Skin Disease Virus ◽

Gpcr Gene ◽

The Government

Abstract Background Lumpy skin disease (LSD) is an infectious viral disease of cattle caused by a capripox virus. LSD has substantial economic implications, with infection resulting in permanent damage to the skin of affected animals which lowers their commercial value. In Uganda, LSD is endemic and cases of the disease are frequently reported to government authorities. This study was undertaken to molecularly characterize lumpy skin disease virus (LSDV) strains that have been circulating in Uganda between 2017 and 2018. Secondly, the study aimed to determine the phylogenetic relatedness of Ugandan LSDV sequences with published sequences, available in GenBank.Results A total of 7 blood samples and 16 skin nodule biopsies were screened for LSDV using PCR to confirm presence of LSDV nucleic acid. PCR positive samples were then characterised by amplifying the GPCR gene. These amplified genes were sequenced and phylogenetic trees were constructed. Out of the 23 samples analysed, 15 were positive for LSDV by PCR (65.2%). The LSDV GPCR sequences analysed contained the unique signatures of LSDV (A11, T12, T34, S99, and P199) which further confirmed their identity. Sequence comparison with vaccine strains revealed a 12bp deletion unique to Ugandan outbreak strains. Phylogenetic analysis indicated that the LSDV sequences from this study clustered closely with sequences from neighboring East African countries and with LSDV strains from recent outbreaks in Europe. It was noted that the sequence diversity amongst LSDV strains from Africa was higher than diversity from Eurasia.Conclusion The LSDV strains circulating in Uganda were closely related with sequences from neighboring countries. Comparison of GPCR gene showed that vaccine strains were not responsible for outbreaks. This means that vaccination with the currently used vaccine will probably be effective for the control of LSD in Uganda. This information is necessary to understand LSDV molecular epidemiology and to contribute knowledge towards the development of more appropriate control strategies by the Government of Uganda.

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Molecular detection and phylogenetic analysis of Lumpy skin disease virus from outbreaks in Uganda 2017-2018

10.21203/rs.2.14954/v4 ◽

2020 ◽

Author(s):

Sylvester Ochwo ◽

Kimberly VanderWaal ◽

Christian Ndekezi ◽

Joseph Nkamwesiga ◽

Anna Munsey ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Disease Virus ◽

Skin Disease ◽

Phylogenetic Trees ◽

African Countries ◽

Economic Implications ◽

Lumpy Skin Disease ◽

Lumpy Skin Disease Virus ◽

Gpcr Gene ◽

The Government

Abstract Background: Lumpy skin disease (LSD) is an infectious viral disease of cattle caused by a Capripox virus. LSD has substantial economic implications, with infection resulting in permanent damage to the skin of affected animals which lowers their commercial value. In Uganda, LSD is endemic and cases of the disease are frequently reported to government authorities. This study was undertaken to molecularly characterize lumpy skin disease virus (LSDV) strains that have been circulating in Uganda between 2017 and 2018. Secondly, the study aimed to determine the phylogenetic relatedness of Ugandan LSDV sequences with published sequences, available in GenBank. Results: A total of 7 blood samples and 16 skin nodule biopsies were screened for LSDV using PCR to confirm presence of LSDV nucleic acids. PCR positive samples were then characterized by amplifying the GPCR gene. These amplified genes were sequenced and phylogenetic trees were constructed. Out of the 23 samples analyzed, 15 were positive for LSDV by PCR (65.2%). The LSDV GPCR sequences analyzed contained the unique signatures of LSDV (A11, T12, T34, S99, and P199) which further confirmed their identity. Sequence comparison with vaccine strains revealed a 12bp deletion unique to Ugandan outbreak strains. Phylogenetic analysis indicated that the LSDV sequences from this study clustered closely with sequences from neighboring East African countries and with LSDV strains from recent outbreaks in Europe. It was noted that the sequence diversity amongst LSDV strains from Africa was higher than diversity from Eurasia. Conclusion: The LSDV strains circulating in Uganda were closely related with sequences from neighboring African countries and from Eurasia. Comparison of the GPCR gene showed that outbreak strains differed from vaccine strains. This information is necessary to understand LSDV molecular epidemiology and to contribute knowledge towards the development of control strategies by the Government of Uganda.

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Zika Virus Epidemiology in Selected West African Countries between 2007 and 2012

Proceedings ◽

10.3390/proceedings2020050100 ◽

2020 ◽

Vol 50 (1) ◽

pp. 100

Author(s):

Serena Marchi ◽

Simonetta Viviani ◽

Emanuele Montomoli ◽

Yuxiao Tang ◽

Adele Boccuto ◽

...

Keyword(s):

Zika Virus ◽

West African ◽

The Gambia ◽

Reproductive Age ◽

World Health ◽

Enzyme Linked Immunosorbent Assay ◽

Limited Data ◽

Serum Samples ◽

African Countries ◽

Health Organization

Before its recent spread, serological investigations conducted between the 1960s and the 1990s showed the wide presence of Zika virus in Africa. According to the World Health Organization, the entire Africa continent is at risk of Zika outbreak due to the presence of the virus, competent vectors, and the low capacity for surveillance and containment of an epidemic. However, limited data are available on the recent prevalence in the African population. The aim of this study was to evaluate the immunity against Zika virus in samples of a selected cohort from West Africa, in order to investigate the circulation of the virus in the region during the first years of its emergence in the Pacific. Human serum samples were collected in 2007 and between 2011 and 2012 from a cohort of subjects from Mali, Senegal, and The Gambia. The samples were tested using an enzyme-linked immunosorbent assay (ELISA) detection kit and positives were further confirmed by microneutralization test. The results indicate that Zika virus is present and actively circulating in Senegal and The Gambia, with prevalence values of 13.7% and 6.9% in 2012, respectively. Although no significant differences in prevalence were found for the considered time period, seroconversion of some subjects showed the active circulation of Zika virus in the West African area. Analysis by age showed an increase in immunity in relation to increasing age, demonstrating that the population is consistently exposed to the virus throughout life and with a high possibility of being infected during reproductive age. In conclusion, the obtained results allow for better knowledge of the circulation of Zika virus within three different ecological and demographic contexts, and represent an update to the limited data currently available.

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Phylogeography and Evolutionary analysis of African Rotavirus A genotype G12 reveals district genetic diversification within Lineage III

10.1101/591297 ◽

2019 ◽

Author(s):

Babatunde Olanrewaju Motayo ◽

Olukunle Oluwasemowo ◽

Babatunde Adebiyi Olusola ◽

Adewale Victor Opayele ◽

Adedayo Omotayo Faneye

Keyword(s):

South Africa ◽

Genetic Diversity ◽

Phylogenetic Analysis ◽

Evolutionary Rate ◽

Evolutionary Analysis ◽

African Countries ◽

Control Effort ◽

Molecular Surveillance ◽

Rotavirus A ◽

Geographic Boundaries

AbstractRotavirus genotype G12 has become one of the most prevalent genotypes of rotavirus in Africa. To understand the drivers for its genetic diversity we investigated the Bayesian phylogeney, evolution and population demography of the genotype G12 Africa. Rotavirus genotype G12, VP7 sequences were downloaded and aligned from twelve African countries (n=96). Phylogenetic analysis, Evolutionary analysis and Bayesian Phylogeography was carried out, using MEGA Vs 6, BEAST, and SPREAD3. Phylogeny showed that all the African sequences fell into lineage III diversifying into two major clades. The evolutionary rate was 1.678×10-3 (95%HPD, 1.201×10-3 -2.198×10-3) substitutions/ site/ year. The MCC tree topology clustered into three lineages (II, III, IV), African strains diversified into three clusters within lineage III. South Africa was the epicentre of viral dispersal. This study shows the potential for genetic diversification of Rotavirus G12 in Africa, continuous molecular surveillance across Africa is recommended to help control effort.HighlightsOur study revealed that African G12 rotaviruses have diversified into 3 clades within their parental lineage III based on geographic boundaries.Nigeria was identified Nigeria as country of origin, while South Africa served as the epicentre of dispersal of the genotype across Africa.We also discovered that they have a constant demographic profile. Our findings reveal the potential for rapid genetic diversity of Rotavirus G12 and highlight the importance of molecular surveillance in Rotavirus control effort.

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Isolation and molecular characterization of Mycoplasma spp. in sheep and goats in Egypt

Veterinary World ◽

10.14202/vetworld.2019.664-670 ◽

2019 ◽

Vol 12 (5) ◽

pp. 664-670 ◽

Cited By ~ 3

Author(s):

Mounier M. Abdel Halium ◽

Fayez A. Salib ◽

S. A. Marouf ◽

Emil S. Abdel Massieh

Keyword(s):

Phylogenetic Analysis ◽

Small Ruminants ◽

Mycoplasma Species ◽

African Countries ◽

Biochemical Tests ◽

Isolation And Identification ◽

Sheep And Goats ◽

Pcr Product ◽

Nasal Swabs ◽

Bronchial Wash

Background and Aim: Different species of Mycoplasma are associated with many pathological problems in small ruminants including respiratory manifestation, this problem results in significant losses, especially in African countries. This study aimed to (I) study some epidemiological aspects of Mycoplasma species infections in Egyptian sheep and goats at Giza Governorate, (II) diagnosis of Mycoplasma species affections using bacterial isolation and identification, (III) apply the polymerase chain reaction (PCR) for typing of different Mycoplasma species, and (IV) illustrate the phylogenetic tree for the isolated Mycoplasma species and other species from GenBank using the purified PCR product. Materials and Methods: A total of 335 samples were collected from sheep and goats from Giza Governorate in Egypt as 142 nasal swabs from clinically affected animals, 167 pneumonic lungs, 18 samples from tracheal bifurcation, and 8 samples by bronchial wash were cultured on pleuropneumonia-like organisms (PPLOs) media for cultivation of Mycoplasma species. PCR and sequencing and phylogenetic analysis were adopted to identify and classify the isolated Mycoplasma species. Results: A total of 24 Mycoplasma isolates were isolated on PPLO media, identified by biochemical tests, and confirmed and typed by PCR using specific primers. 10 isolates were confirmed as Mycoplasma arginini, four isolates as Mycoplasma ovipneumoniae by PCR, and 10 isolates as undifferentiated Mycoplasma species. A purified isolate of M. arginini and M. ovipneumoniae was sequenced and phylogenetic analysis was illustrated. Conclusion: M. arginini and M. ovipneumoniae are prevalent in Egyptian sheep and goats. Further studies on M. arginini are required due to its high frequency of isolation from pneumonic sheep and goats and also from animals suffer from different respiratory manifestations.

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