Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014

Abstract Background: G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia.Methods: The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains.Results: The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related, irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 x10−3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s.Conclusions: At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.

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Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014

BMC Infectious Diseases ◽

10.1186/s12879-020-05745-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Kebareng G. Rakau ◽

Martin M. Nyaga ◽

Maemu P. Gededzha ◽

Jason M. Mwenda ◽

M. Jeffrey Mphahlele ◽

...

Keyword(s):

Amino Acid ◽

Evolutionary Rate ◽

Time Frame ◽

Amino Acid Sequences ◽

Sub Saharan Africa ◽

Evolutionary Analysis ◽

African Countries ◽

Similar Time ◽

Vaccine Introduction ◽

Rotavirus Vaccination

Abstract Background G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia. Methods The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains. Results The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related, irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 × 10− 3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s. Conclusions At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.

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Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014

10.21203/rs.3.rs-47541/v3 ◽

2020 ◽

Author(s):

Kebareng G. Rakau ◽

Martin M. Nyaga ◽

Maemu P. Gededzha ◽

Jason M. Mwenda ◽

M. Jeffrey Mphahlele ◽

...

Keyword(s):

Amino Acid ◽

Evolutionary Rate ◽

Time Frame ◽

Amino Acid Sequences ◽

Sub Saharan Africa ◽

Evolutionary Analysis ◽

African Countries ◽

Similar Time ◽

Vaccine Introduction ◽

Rotavirus Vaccination

Abstract Background: G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia. Methods: The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains.Results: The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related , irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 x10−3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s.Conclusions: At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.

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Genetic characterization of G12P[6] and G12P[8] rotavirus strains in six African countries

10.21203/rs.3.rs-47541/v1 ◽

2020 ◽

Author(s):

Kebareng G. Rakau ◽

Martin M. Nyaga ◽

Maemu P. Gededzha ◽

Jason M. Mwenda ◽

M. Jeffrey Mphahlele ◽

...

Keyword(s):

Amino Acid Level ◽

Sub Saharan Africa ◽

African Countries ◽

Vaccine Introduction ◽

Rotavirus Vaccination ◽

Human Rotavirus ◽

Sub Saharan ◽

The Stability ◽

Long Term Impact

Abstract Background: G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia.Methods: The investigation was carried out by comparing VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and mapping the recognized neutralization epitopes of these strains.Results: The findings suggested that the VP7 and VP4 genes of the G12 strains circulating in African countries are homologous at the nucleotide and amino acid level, irrespective of country of origin and year of detection, although there was a unique clustering of the Ethiopian strains. The study strains shared a common ancestry with G12 strains circulating globally. Neutralization epitope mapping revealed that rotavirus VP4 P[8] genes associated with G12 had amino acids similar to those reported globally including the vaccines RotaTeq® P[8] and Rotarix®.Conclusions: It is unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Furthermore, it is too early post vaccine introduction to indicate any effect of vaccine-induced pressure on maintaining the stability of these strains in circulation. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.

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Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014

10.21203/rs.3.rs-47541/v2 ◽

2020 ◽

Author(s):

Kebareng G. Rakau ◽

Martin M. Nyaga ◽

Maemu P. Gededzha ◽

Jason M. Mwenda ◽

M. Jeffrey Mphahlele ◽

...

Keyword(s):

Amino Acid Level ◽

Sub Saharan Africa ◽

African Countries ◽

Vaccine Introduction ◽

Rotavirus Vaccination ◽

Human Rotavirus ◽

Sub Saharan ◽

Long Term Impact

Abstract Background: G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia. Methods: The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Results: The findings suggested that the VP7 and VP4 genes of the G12 strains circulating in African countries are closely related at the nucleotide and amino acid level, irrespective of country of origin and year of detection, although there was a unique clustering of the Ethiopian strains. Neutralization epitope screening revealed that rotavirus VP4 P[8] genes associated with G12 had amino acids similar to those reported globally including the vaccines RotaTeq and Rotarix. Conclusions: At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.

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A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya

PeerJ ◽

10.7717/peerj.6465 ◽

2019 ◽

Vol 7 ◽

pp. e6465 ◽

Cited By ~ 3

Author(s):

James M. Wainaina ◽

Elijah Ateka ◽

Timothy Makori ◽

Monica A. Kehoe ◽

Laura M. Boykin

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Common Bean ◽

Virus Detection ◽

Primary Source ◽

Amino Acid Sequences ◽

Sub Saharan Africa ◽

Viral Metagenomics ◽

Diagnostic Tools ◽

Bayesian Phylogenetic Analysis

Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I–III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.

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Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi

Journal of Virology ◽

10.1128/jvi.01246-17 ◽

2017 ◽

Vol 92 (3) ◽

Cited By ~ 15

Author(s):

Khuzwayo C. Jere ◽

Chrispin Chaguza ◽

Naor Bar-Zeev ◽

Jenna Lowe ◽

Chikondi Peno ◽

...

Keyword(s):

Amino Acid ◽

Vaccine Effectiveness ◽

Recent Common Ancestor ◽

Rotavirus Vaccine ◽

Careful Evaluation ◽

African Countries ◽

Vaccine Introduction ◽

Rotavirus Gastroenteritis ◽

Structural Conformation ◽

Rotavirus Vaccines

ABSTRACT To combat the high burden of rotavirus gastroenteritis, multiple African countries have introduced rotavirus vaccines into their childhood immunization programs. Malawi incorporated a G1P[8] rotavirus vaccine (Rotarix) into its immunization schedule in 2012. Utilizing a surveillance platform of hospitalized rotavirus gastroenteritis cases, we examined the phylodynamics of G1P[8] rotavirus strains that circulated in Malawi before (1998 to 2012) and after (2013 to 2014) vaccine introduction. Analysis of whole genomes obtained through next-generation sequencing revealed that all randomly selected prevaccine G1P[8] strains sequenced ( n = 32) possessed a Wa-like genetic constellation, whereas postvaccine G1P[8] strains ( n = 18) had a DS-1-like constellation. Phylodynamic analyses indicated that postvaccine G1P[8] strains emerged through reassortment events between human Wa- and DS-1-like rotaviruses that circulated in Malawi from the 1990s and hence were classified as atypical DS-1-like reassortants. The time to the most recent common ancestor for G1P[8] strains was from 1981 to 1994; their evolutionary rates ranged from 9.7 × 10 −4 to 4.1 × 10 −3 nucleotide substitutions/site/year. Three distinct G1P[8] lineages chronologically replaced each other between 1998 and 2014. Genetic drift was the likely driver for lineage turnover in 2005, whereas replacement in 2013 was due to reassortment. Amino acid substitution within the outer glycoprotein VP7 of G1P[8] strains had no impact on the structural conformation of the antigenic regions, suggesting that it is unlikely that they would affect recognition by vaccine-induced neutralizing antibodies. While the emergence of DS-1-like G1P[8] rotavirus reassortants in Malawi was therefore likely due to natural genotype variation, vaccine effectiveness against such strains needs careful evaluation. IMPORTANCE The error-prone RNA-dependent RNA polymerase and the segmented RNA genome predispose rotaviruses to genetic mutation and genome reassortment, respectively. These evolutionary mechanisms generate novel strains and have the potential to lead to the emergence of vaccine escape mutants. While multiple African countries have introduced a rotavirus vaccine, there are few data describing the evolution of rotaviruses that circulated before and after vaccine introduction. We report the emergence of atypical DS-1-like G1P[8] strains during the postvaccine era in Malawi. Three distinct G1P[8] lineages circulated chronologically from 1998 to 2014; mutation and reassortment drove lineage turnover in 2005 and 2013, respectively. Amino acid substitutions within the outer capsid VP7 glycoprotein did not affect the structural conformation of mapped antigenic sites, suggesting a limited effect on the recognition of G1-specific vaccine-derived antibodies. The genes that constitute the remaining genetic backbone may play important roles in immune evasion, and vaccine effectiveness against such atypical strains needs careful evaluation.

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Genetic variability of the M genome segment of clinical and environmental Toscana virus strains

Journal of General Virology ◽

10.1099/vir.0.82330-0 ◽

2007 ◽

Vol 88 (4) ◽

pp. 1288-1294 ◽

Cited By ~ 12

Author(s):

Giulietta Venturi ◽

Massimo Ciccozzi ◽

Stefania Montieri ◽

Alessandro Bartoloni ◽

Daniela Francisci ◽

...

Keyword(s):

Amino Acid ◽

Sequence Data ◽

Amino Acid Level ◽

Amino Acid Sequences ◽

Evolutionary Analysis ◽

Coding Region ◽

Toscana Virus ◽

Time Period ◽

M Genome ◽

Viral Isolates

Twenty-seven strains of Toscana virus, collected over a period of 23 years and isolated from several localities and from different hosts (humans, arthropods and a bat), were investigated by sequencing of a portion of the M genomic segment comprising the GN glycoprotein coding region. Sequence data indicated that the divergence among isolates ranged from 0 to 5.7 % at the nucleotide level and from 0 to 3.4 % at the amino acid level. Phylogenetic analysis revealed four main clusters. A close correspondence between viral strains and area/year of isolation could not be demonstrated, whilst co-circulation of different viral strains in the same area and in the same time period was observed for both patients and environmental viral isolates. Alignment of the deduced amino acid sequences and evolutionary analysis indicated that most of the sites along the gene may be invariable because of purifying and/or neutral selection.

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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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Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus

10.26434/chemrxiv.12424958 ◽

2020 ◽

Author(s):

CHITTARANJAN BARUAH ◽

PAPARI DEVI ◽

DHIRENDRA K SHARMA

Keyword(s):

Functional Analysis ◽

Amino Acid ◽

Sequence Analysis ◽

Structure Prediction ◽

Functional Characterization ◽

Amino Acid Sequences ◽

Accessory Proteins ◽

Evolutionary Analysis ◽

Bat Coronavirus ◽

Close Relatedness

This paper has attempted into the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and ab-initio modeling. The evolutionary analysis of both the proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus.

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Multiple DNA viruses identified in multimammate mouse (Mastomys natalensis) populations from across regions of sub-Saharan Africa

Archives of Virology ◽

10.1007/s00705-020-04738-9 ◽

2020 ◽

Vol 165 (10) ◽

pp. 2291-2299

Author(s):

Sébastien Calvignac-Spencer ◽

Léonce Kouadio ◽

Emmanuel Couacy-Hymann ◽

Nafomon Sogoba ◽

Kyle Rosenke ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Host Species ◽

T Antigen ◽

Amino Acid Sequences ◽

Sub Saharan Africa ◽

Mammalian Host ◽

Mastomys Natalensis ◽

Dna Viruses ◽

Zoonotic Risk

Abstract The multimammate mouse (Mastomys natalensis; M. natalensis) serves as the main reservoir for the zoonotic arenavirus Lassa virus (LASV), and this has led to considerable investigation into the distribution of LASV and other related arenaviruses in this host species. In contrast to the situation with arenaviruses, the presence of other viruses in M. natalensis remains largely unexplored. In this study, herpesviruses and polyomaviruses were identified and partially characterized by PCR methods, sequencing, and phylogenetic analysis. In tissues sampled from M. natalensis populations in Côte d'Ivoire and Mali, six new DNA viruses (four betaherpesviruses, one gammaherpesvirus and one polyomavirus) were identified. Phylogenetic analysis based on glycoprotein B amino acid sequences showed that the herpesviruses clustered with cytomegaloviruses and rhadinoviruses of multiple rodent species. The complete circular genome of the newly identified polyomavirus was amplified by PCR. Amino acid sequence analysis of the large T antigen or VP1 showed that this virus clustered with a known polyomavirus from a house mouse (species Mus musculus polyomavirus 1). These two polyomaviruses form a clade with other rodent polyomaviruses, and the newly identified virus represents the third known polyomavirus of M. natalensis. This study represents the first identification of herpesviruses and the discovery of a novel polyomavirus in M. natalensis. In contrast to arenaviruses, we anticipate that these newly identified viruses represent a low zoonotic risk due to the normally highly restricted specificity of members of these two DNA virus families to their individual mammalian host species.

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