scholarly journals Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015–16

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Carol A Abidha ◽  
Joyce Nyiro ◽  
Everlyn Kamau ◽  
Osman Abdullahi ◽  
David James Nokes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Control Strategies ◽  
Respiratory Illness ◽  
Respiratory Pathogen ◽  
Human Coronavirus ◽  
Spike Gene ◽  
Low Genetic Diversity ◽  
Coastal Kenya ◽  
Close Phylogenetic Relationship

Abstract Human coronavirus OC43 (HCoV-OC43) is a major contributor to seasonal outbreaks of acute respiratory illness (ARI). The origins of locally circulating HCoV-OC43 strains and characteristics of their genetic diversity are unknown for most settings despite significance to effective HCoV control strategies. Between December 2015 and June 2016, we undertook ARI surveillance in coastal Kenya in nine outpatients and one inpatient health facility (HF). Ninety-two patient samples tested HCoV-OC43 positive and forty (43.5%) were successfully sequenced in spike (S) gene region (2,864 long, ∼70%). Phylogenetic analysis confirmed co-circulation of two distinct HCoV-OC43 clades that closely clustered with genotype G (n = 34, 85%) and genotype H (n = 6, 15%) reference strains. Local viruses within the same clade displayed low genetic diversity yielding identical sequences in multiple HF. Furthermore, the newly sequenced Kenyan viruses showed close phylogenetic relationship to other contemporaneous sampled strains (2015–16) including those originating from distant places (e.g. USA and China). Using a genetic similarity threshold of 99.1 per cent at nucleotide level, the HCoV-OC43 strains sampled globally between 1967 and 2019 fell into nine sequence clusters. Notably, some of these clusters appeared to have become extinct, or occurred only sporadically in a few geographical areas while others persisted globally for multiple years. In conclusion, we found that HCoV-OC43 strains spread rapidly both locally and across the globe with limited genetic evolution in the spike gene. Full-genome sequences that are spatio-temporally representative are required to advance understanding of the transmission pathways of this important human respiratory pathogen.

scholarly journals Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Festus M Nyasimi ◽  
David Collins Owuor ◽  
Joyce M Ngoi ◽  
Alexander G Mwihuri ◽  
Grieven P Otieno ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Control Strategies ◽  
Genomic Analysis ◽  
Respiratory Illness ◽  
Influenza B Virus ◽  
Influenza B ◽  
Genomic Epidemiology ◽  
Coastal Kenya ◽  
B Virus ◽  
N 93

Abstract The genomic epidemiology of influenza B virus (IBV) remains understudied in Africa despite significance to design of effective local and global control strategies. We undertook surveillance throughout 2016 in coastal Kenya, recruiting individuals presenting with acute respiratory illness at nine outpatient health facilities (any age) or admitted to the Kilifi County Hospital (<5 years old). Whole genomes were sequenced for a selected 111 positives; 94 (84.7%) of B/Victoria lineage and 17 (15.3%) of B/Yamagata lineage. Inter-lineage reassortment was detected in ten viruses; nine with B/Yamagata backbone but B/Victoria NA and NP segments and one with a B/Victoria backbone but B/Yamagata PB2, PB1, PA, and MP segments. Five phylogenomic clusters were identified among the sequenced viruses; (i), pure B/Victoria clade 1A (n = 93, 83.8%), (ii), reassortant B/Victoria clade 1A (n = 1, 0.9%), (iii), pure B/Yamagata clade 2 (n = 2, 1.8%), (iv), pure B/Yamagata clade 3 (n = 6, 5.4%), and (v), reassortant B/Yamagata clade 3 (n = 9, 8.1%). Using divergence dates and clustering patterns in the presence of global background sequences, we counted up to twenty-nine independent IBV strain introductions into the study area (∼900 km2) in 2016. Local viruses, including the reassortant B/Yamagata strains, clustered closely with viruses from neighbouring Tanzania and Uganda. Our study demonstrated that genomic analysis provides a clearer picture of locally circulating IBV diversity. The high number of IBV introductions highlights the challenge in controlling local influenza epidemics by targeted approaches, for example, sub-population vaccination or patient quarantine. The finding of divergent IBV strains co-circulating within a single season emphasises why broad immunity vaccines are the most ideal for influenza control in Kenya.

scholarly journals Human metapneumovirus prevalence and patterns of genotype persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007-2016

2019 ◽  
Author(s):  
John W Oketch ◽  
Everlyn Kamau ◽  
Grieven P Otieno ◽  
James R Otieno ◽  
Charles N Agoti ◽  
...  
Keyword(s):  
Local Community ◽  
Hospital Admissions ◽  
Sequence Data ◽  
Current Knowledge ◽  
Respiratory Illness ◽  
Human Metapneumovirus ◽  
Respiratory Pathogen ◽  
Epidemic Season ◽  
Coastal Kenya ◽  
Hmpv Infection

Abstract Background Human metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia. Current knowledge and understanding on its patterns of spread, prevalence and persistence in communities is limited. Methods We present findings of a molecular-epidemiological analysis of nasal samples from children < 5 years of age admitted with syndromic pneumonia between 2007 and 2016 to Kilifi County Hospital, coastal Kenya. HMPV infection was detected using real-time RT-PCR and positives sequenced in the fusion (F) and attachment (G) genes followed by phylogenetic analysis. The association between disease severity and HMPV genotype was assessed using Chi-square test for independence. Results Over 10 years, 274/6756 (4.10%) samples screened were HMPV positive. Annual prevalence fluctuated between years ranging 1.2% to 8.7% and lowest in the recent years (2014-2016). HMPV detections were most frequent between October of one year to April of the following year. Genotyping was successful for 205/274 (74.8%) positives revealing A2b (41.0%), A2c (10.7%), B1 (23.4%) and B2 (24.9%). The dominance patterns were: genotype A2b between 2007-11, B1 between 2012-14, and A2c in more recent epidemics. Genotype B2 viruses were present in all the years. These patterns mirrored the global picture. Temporal phylogenetic clustering within the genotypes for both local and global sequence data was seen. Genotypes occurring in each epidemic season were comprised of multiple variants. Pneumonia severity did not vary by genotype (p=0.264). In both the F and G gene, the sequenced regions were found to be predominantly under purifying selection. Conclusion Genotype and strain patterns from this rural African setting temporally map with global strain distribution, suggesting a well-mixed global virus transmission pool of HMPV. Persistence in the local community is characterized by repeated introductions of HMPV variants from the global pool. The factors underlying the declining prevalence of HMPV in this population should be investigated.

scholarly journals Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya

2018 ◽  
Vol 217 (11) ◽  
pp. 1728-1739 ◽  
Author(s):  
Patience K Kiyuka ◽  
Charles N Agoti ◽  
Patrick K Munywoki ◽  
Regina Njeru ◽  
Anne Bett ◽  
...  
Keyword(s):  
Nucleotide Sequencing ◽  
Human Coronavirus ◽  
Evolutionary Patterns ◽  
Initial Exposure ◽  
Reverse Transcription Pcr ◽  
Paired Samples ◽  
Low Genetic Diversity ◽  
Coastal Kenya ◽  
Hospital Pediatric ◽  
Tract Infections

Abstract Background Human coronavirus NL63 (HCoV-NL63) is a globally endemic pathogen causing mild and severe respiratory tract infections with reinfections occurring repeatedly throughout a lifetime. Methods Nasal samples were collected in coastal Kenya through community-based and hospital-based surveillance. HCoV-NL63 was detected with multiplex real-time reverse transcription PCR, and positive samples were targeted for nucleotide sequencing of the spike (S) protein. Additionally, paired samples from 25 individuals with evidence of repeat HCoV-NL63 infection were selected for whole-genome virus sequencing. Results HCoV-NL63 was detected in 1.3% (75/5573) of child pneumonia admissions. Two HCoV-NL63 genotypes circulated in Kilifi between 2008 and 2014. Full genome sequences formed a monophyletic clade closely related to contemporary HCoV-NL63 from other global locations. An unexpected pattern of repeat infections was observed with some individuals showing higher viral titers during their second infection. Similar patterns for 2 other endemic coronaviruses, HCoV-229E and HCoV-OC43, were observed. Repeat infections by HCoV-NL63 were not accompanied by detectable genotype switching. Conclusions In this coastal Kenya setting, HCoV-NL63 exhibited low prevalence in hospital pediatric pneumonia admissions. Clade persistence with low genetic diversity suggest limited immune selection, and absence of detectable clade switching in reinfections indicates initial exposure was insufficient to elicit a protective immune response.

scholarly journals Human metapneumovirus prevalence and patterns of genotype persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007-2016

2019 ◽  
Author(s):  
John W Oketch ◽  
Everlyn Kamau ◽  
Grieven P Otieno ◽  
James R Otieno ◽  
Charles N Agoti ◽  
...  
Keyword(s):  
Local Community ◽  
Hospital Admissions ◽  
Sequence Data ◽  
Current Knowledge ◽  
Respiratory Illness ◽  
Human Metapneumovirus ◽  
Respiratory Pathogen ◽  
Epidemic Season ◽  
Coastal Kenya ◽  
Hmpv Infection

Abstract Background Human metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia. Current knowledge and understanding on its patterns of spread, prevalence and persistence in communities is limited. Methods We present findings of a molecular-epidemiological analysis of nasal samples from children < 5 years of age admitted with syndromic pneumonia between 2007 and 2016 to Kilifi County Hospital, coastal Kenya. HMPV infection was detected using real-time RT-PCR and positives sequenced in the fusion (F) and attachment (G) genes followed by phylogenetic analysis. The association between disease severity and HMPV genotype was assessed using Chi-square test for independence. Results Over 10 years, 274/6756 (4.10%) samples screened were HMPV positive. Annual prevalence fluctuated between years ranging 1.2% to 8.7% and lowest in the recent years (2014-2016). HMPV detections were most frequent between October of one year to April of the following year. Genotyping was successful for 205/274 (74.8%) positives revealing A2b (41.0%), A2c (10.7%), B1 (23.4%) and B2 (24.9%). The dominance patterns were: genotype A2b between 2007-11, B1 between 2012-14, and A2c in more recent epidemics. Genotype B2 viruses were present in all the years. These patterns mirrored the global picture. Temporal phylogenetic clustering within the genotypes for both local and global sequence data was seen. Genotypes occurring in each epidemic season were comprised of multiple variants. Pneumonia severity did not vary by genotype (p=0.264). In both the F and G gene, the sequenced regions were found to be predominantly under purifying selection. Conclusion Genotype and strain patterns from this rural African setting temporally map with global strain distribution, suggesting a well-mixed global virus transmission pool of HMPV. Persistence in the local community is characterized by repeated introductions of HMPV variants from the global pool. The factors underlying the declining prevalence of HMPV in this population should be investigated.

scholarly journals Human metapneumovirus prevalence and patterns of subgroup persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007-2016

2019 ◽  
Author(s):  
John W Oketch ◽  
Everlyn Kamau ◽  
Grieven P Otieno ◽  
James R Otieno ◽  
Charles N Agoti ◽  
...  
Keyword(s):  
Local Community ◽  
Hospital Admissions ◽  
Sequence Data ◽  
Current Knowledge ◽  
Respiratory Illness ◽  
Human Metapneumovirus ◽  
Respiratory Pathogen ◽  
Epidemic Season ◽  
Coastal Kenya ◽  
Hmpv Infection

Abstract Abstract Background: Human metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia. Current knowledge and understanding on its patterns of spread, prevalence and persistence in communities in low resource settings is limited. Methods: We present findings of a molecular-epidemiological analysis of nasal samples from children < 5 years of age admitted with syndromic pneumonia between 2007 and 2016 to Kilifi County Hospital, coastal Kenya. HMPV infection was detected using real-time RT-PCR and positives sequenced in the fusion (F) and attachment (G) genes followed by phylogenetic analysis. The association between disease severity and HMPV subgroup was assessed using Fisher's exact test. Results: Over 10 years, 274/6756 (4.1%) samples screened were HMPV positive. Annual prevalence fluctuated between years ranging 1.2% to 8.7% and lowest in the recent years (2014-2016). HMPV detections were most frequent between October of one year to April of the following year. Genotyping was successful for 205/274 (74.8%) positives revealing clades A2b (41.0%) and A2c (10.7%), and subgroups B1 (23.4%) and B2 (24.9%). The dominance patterns were: clade A2b between 2007-11, subgroup B1 between 2012-14, and clade A2c in more recent epidemics. Subgroup B2 viruses were present in all the years. Temporal phylogenetic clustering within the subgroups for both local and global sequence data was seen. Subgroups occurring in each epidemic season were comprised of multiple variants. Pneumonia severity did not vary by subgroup ( p=0.264 ). In both the F and G gene, the sequenced regions were found to be predominantly under purifying selection. Conclusion: Subgroup patterns from this rural African setting temporally map with global strain distribution, suggesting a well-mixed global virus transmission pool of HMPV. Persistence in the local community is characterized by repeated introductions of HMPV variants from the global pool. The factors underlying the declining prevalence of HMPV in this population should be investigated. Key words: Human metapneumovirus, prevalence, subgroup, epidemic, temporal.

scholarly journals Human metapneumovirus prevalence and patterns of genotype persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007-2016

2019 ◽  
Author(s):  
John W Oketch ◽  
Everlyn Kamau ◽  
Grieven P Otieno ◽  
James R Otieno ◽  
Charles N Agoti ◽  
...  
Keyword(s):  
Local Community ◽  
Hospital Admissions ◽  
Sequence Data ◽  
Current Knowledge ◽  
Respiratory Illness ◽  
Human Metapneumovirus ◽  
Respiratory Pathogen ◽  
Epidemic Season ◽  
Coastal Kenya ◽  
Hmpv Infection

Abstract Background Human metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia. Current knowledge and understanding on its patterns of spread, prevalence and persistence in communities is limited. Methods We present findings of a molecular-epidemiological analysis of nasal samples from children < 5 years of age admitted with syndromic pneumonia between 2007 and 2016 to Kilifi County Hospital, coastal Kenya. HMPV infection was detected using real-time RT-PCR and positives sequenced in the fusion (F) and attachment (G) genes followed by phylogenetic analysis. The association between disease severity and HMPV genotype was assessed using Chi-square test for independence. Results Over 10 years, 274/6756 (4.10%) samples screened were HMPV positive. Annual prevalence fluctuated between years ranging 1.2% to 8.7% and lowest in the recent years (2014-2016). HMPV detections were most frequent between October of one year to April of the following year. Genotyping was successful for 205/274 (74.8%) positives revealing A2b (41.0%), A2c (10.7%), B1 (23.4%) and B2 (24.9%). The dominance patterns were: genotype A2b between 2007-11, B1 between 2012-14, and A2c in more recent epidemics. Genotype B2 viruses were present in all the years. These patterns mirrored the global picture. Temporal phylogenetic clustering within the genotypes for both local and global sequence data was seen. Genotypes occurring in each epidemic season were comprised of multiple variants. Pneumonia severity did not vary by genotype (p=0.264). In both the F and G gene, the sequenced regions were found to be predominantly under purifying selection. Conclusion Genotype and strain patterns from this rural African setting temporally map with global strain distribution, suggesting a well-mixed global virus transmission pool of HMPV. Persistence in the local community is characterized by repeated introductions of HMPV variants from the global pool. The factors underlying the declining prevalence of HMPV in this population should be investigated.

The Response to Past Climate Perturbations Explains Extremely Low Genetic Diversity in the Genome of an Abundant Ice-Age Remnant, the Alpine Marmot

2018 ◽  
Author(s):  
Toni I. Gossmann​ ◽  
Achchuthan Shanmugasundram​ ◽  
Stefan Börno ◽  
Ludovic Duvaux ◽  
Christophe Lemaire​ ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ice Age ◽  
Past Climate ◽  
Low Genetic Diversity ◽  
Alpine Marmot

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

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