scholarly journals Trends and Intensity of Human Rhinovirus Invasions in Kilifi, Coastal Kenya Over a Twelve-Year Period, 2007-2018

2021 ◽  
Author(s):  
John Mwita Morobe ◽  
Everlyn Kamau ◽  
Nickson Murunga ◽  
Winfred Gatua ◽  
Martha Luka ◽  
...  
Keyword(s):  
Common Cold ◽  
High Frequency ◽  
Genomic Region ◽  
Etiologic Agent ◽  
Human Rhinovirus ◽  
Acute Respiratory Disease ◽  
Single Population ◽  
Coastal Kenya ◽  
Time Point

ABSTRACT Background: Human rhinovirus (HRV) is an ubiquitous pathogen and the principal etiologic agent of common cold. Despite the high frequency of HRV infections, data describing its long-term epidemiological patterns in a single population remain limited. Methods: We analysed 1,070 VP4/VP2 genomic region sequences obtained from samples collected between 2007-2018 from hospitalised paediatric patients (< 60 months) with acute respiratory disease in Kilifi County Hospital on the Kenya Coast. Results: Of 7,231 children enrolled, HRV was detected in 1,497 (20.7%) andVP4/VP2 sequences were recovered from 1,070 samples (71.5%). A total of 144 different HRV types were identified (67 HRV-A, 18 HRV-B and 59 HRV-C) and at any time-point, several types co-circulated with alternating predominance. Within types multiple genetically divergent variants were observed. Ongoing HRV infections appeared to be a combination of (i) persistent types (observed up to seven consecutive months), (ii) reintroduced genetically distinct variants and (iii) new invasions (average of 8 new types, annually). Conclusion: Sustained HRV presence in the Kilifi community is mainly due to frequent invasion by new types and variants rather than prolonged circulation of locally established strains.

scholarly journals Trends and Intensity of Rhinovirus Invasions in Kilifi, Coastal Kenya Over a Twelve-Year Period, 2007-2018

2021 ◽  
Author(s):  
John Mwita Morobe ◽  
Everlyn Kamau ◽  
Nickson Murunga ◽  
Winfred Gatua ◽  
Martha M Luka ◽  
...  
Keyword(s):  
Common Cold ◽  
High Frequency ◽  
Respiratory Illness ◽  
Genomic Region ◽  
County Hospital ◽  
Acute Respiratory Illness ◽  
Coastal Kenya ◽  
Etiological Agents ◽  
Rhinovirus C

Abstract Background Rhinoviruses (RVs) are ubiquitous pathogens and the principal etiological agents of common cold. Despite the high frequency of RV infections, data describing their long-term epidemiological patterns in a defined population remain limited. Methods Here, we analysed 1,070 VP4/VP2 genomic region sequences sampled at Kilifi County Hospital on the Kenya Coast. The samples were collected between 2007 and 2018 from hospitalised paediatric patients (&lt; 60 months) with acute respiratory illness. Results Of 7,231 children enrolled, RV was detected in 1,497 (20.7%) and VP4/VP2 sequences were recovered from 1,070 samples (71.5%). A total of 144 different RV types were identified (67 Rhinovirus A, 18 Rhinovirus B and 59 Rhinovirus C) and at any month, several types co-circulated with alternating predominance. Within types multiple genetically divergent variants were observed. Ongoing RV infections through time appeared to be a combination of (i) persistent types (observed up to seven consecutive months), (ii) reintroduced genetically distinct variants and (iii) new invasions (average of eight new types, annually). Conclusion Sustained RV presence in the Kilifi community is mainly due to frequent invasion by new types and variants rather than continuous transmission of locally established types/variants.

scholarly journals Dynamics of mutation accumulation and adaptation during three years of evolution under long-term stationary phase

2020 ◽  
Author(s):  
Sophia Katz ◽  
Sarit Avrani ◽  
Meitar Yavneh ◽  
Sabrin Hilau ◽  
Jonathan Gross ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Bacterial Species ◽  
Mutation Accumulation ◽  
Mutation Rates ◽  
Single Population ◽  
E Coli ◽  
Mutational Spectra ◽  
Resource Exhaustion ◽  
Time Point

AbstractMany bacterial species that cannot sporulate, such as the model bacterium Escherichia coli, can nevertheless survive for years under resource exhaustion, in a state termed long-term stationary phase (LTSP). Here we describe the dynamics of E. coli adaptation during the first three years spent under LTSP. We show that during this time E. coli continuously adapts genetically, through the accumulation of mutations. For non-mutator clones, the majority of mutations accumulated appear to be adaptive under LTSP, reflected in an extremely convergent pattern of mutation accumulation. Despite the rapid and convergent manner in which populations adapt under LTSP, they continue to harbor extensive genetic variation. The dynamics of evolution of mutation rates under LTSP are particularly interesting. The emergence of mutators, affects overall mutation accumulation rates as well as the mutational spectra and the ultimate spectrum of adaptive alleles acquired under LTSP. With time, mutators can evolve even higher mutation rates, through the acquisition of additional mutation-rate enhancing mutations. Different mutator and non-mutator clones within a single population and time point can display extreme variation in their mutation rates, resulting in differences in both the dynamics of adaptation and their associated deleterious burdens. Despite these differences, clones that vary greatly in their mutation rates tend to co-exist within their populations for many years, under LTSP.

Population fragmentation causes inadequate gene flow and increases extinction risk

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Gene Flow ◽  
Extinction Risk ◽  
Random Mating ◽  
Large Population ◽  
Isolated Population ◽  
Population Fragmentation ◽  
Single Population ◽  
Total Size ◽  
Limited Gene Flow

Most species now have fragmented distributions, often with adverse genetic consequences. The genetic impacts of population fragmentation depend critically upon gene flow among fragments and their effective sizes. Fragmentation with cessation of gene flow is highly harmful in the long term, leading to greater inbreeding, increased loss of genetic diversity, decreased likelihood of evolutionary adaptation and elevated extinction risk, when compared to a single population of the same total size. The consequences of fragmentation with limited gene flow typically lie between those for a large population with random mating and isolated population fragments with no gene flow.

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