scholarly journals Genomic and epidemiological analysis of SARS-CoV-2 viruses in Sri Lanka

2021 ◽  
Author(s):  
Chandima Jeewandara ◽  
Deshni Jayathilaka ◽  
Diyanath Ranasinghe ◽  
Nienyun Sharon Hsu ◽  
Dinuka Ariyaratne ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Epidemiological Data ◽  
Recent Common Ancestor ◽  
Sri Lankan ◽  
Lower And Upper Bounds ◽  
Epidemiological Analysis ◽  
Most Recent Common Ancestor ◽  
Returning Travellers ◽  
Small Clusters ◽  
Roll Out

Since identification of the first Sri Lankan individual with the SARS-CoV-2 in early March 2020, small clusters that occurred were largely contained until the current extensive outbreak that started in early October 2020. In order to understand the molecular epidemiology of SARS-CoV-2 in Sri Lanka, we carried out genomic sequencing overlaid on available epidemiological data. The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country. The estimated time of the most recent common ancestor of this lineage was 10th August 2020 (95% lower and upper bounds 6th July to 7th September), suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258 , as well as the more transmissible B.1.1.7 lineage. Ongoing genomic surveillance in Sri Lanka is vital as vaccine roll-out increases.

scholarly journals Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka

2021 ◽  
Vol 12 ◽  
Author(s):  
Chandima Jeewandara ◽  
Deshni Jayathilaka ◽  
Diyanath Ranasinghe ◽  
Nienyun Sharon Hsu ◽  
Dinuka Ariyaratne ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Common Ancestor ◽  
Epidemiological Data ◽  
Upper Bounds ◽  
Recent Common Ancestor ◽  
Lower And Upper Bounds ◽  
Epidemiological Analysis ◽  
Most Recent Common Ancestor ◽  
Large Outbreak ◽  
Returning Travellers

Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021.Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages.Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country.Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage.

scholarly journals Early origin and global colonisation of foot-and-mouth disease virus

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pakorn Aiewsakun ◽  
Nakarin Pamornchainavakul ◽  
Chaidate Inchaisri
Keyword(s):  
Disease Virus ◽  
Foot And Mouth Disease ◽  
Epidemiological Data ◽  
Mouth Disease ◽  
Recent Common Ancestor ◽  
Structural Protein ◽  
Most Recent Common Ancestor ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Early Origin

Abstract In this study, we compiled 84-year worth (1934–2017) of genomic and epidemiological data of foot-and-mouth disease virus (FMDV), and performed comprehensive analyses to determine its early origin and transmission route. We found that recombination is a key feature of FMDV, and that the genomic regions coding for structural and non-structural proteins have markedly different evolutionary histories, and evolve at different rates. Despite all of these differences, analyses of both structural and non-structural protein coding regions consistently suggested that the most recent common ancestor of FMDV could be dated back to the Middle Age, ~ 200 to 300 years earlier than previously thought. The ancestors of the Euro-Asiatic and SAT strains could be dated back to the mid-seventeenth century, and to the mid-fifteenth to mid-sixteenth century, respectively. Our results implicated Mediterranean counties as an early geographical origin of FMDV before spreading to Europe and subsequently to Asia and South America.

scholarly journals Study of a SARS-CoV-2 Outbreak in a Belgian Military Education and Training Center in Maradi, Niger

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 949 ◽  
Author(s):  
Jean-Paul Pirnay ◽  
Philippe Selhorst ◽  
Christel Cochez ◽  
Mauro Petrillo ◽  
Vincent Claes ◽  
...  
Keyword(s):  
Viral Load ◽  
Military Service ◽  
Epidemiological Data ◽  
Education And Training ◽  
Military Education ◽  
Recent Common Ancestor ◽  
Training Center ◽  
Most Recent Common Ancestor ◽  
Military Command ◽  
And Training

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compromises the ability of military forces to fulfill missions. At the beginning of May 2020, 22 out of 70 Belgian soldiers deployed to a military education and training center in Maradi, Niger, developed mild COVID-19 compatible symptoms. Immediately upon their return to Belgium, and two weeks later, all seventy soldiers were tested for SARS-CoV-2 RNA (RT-qPCR) and antibodies (two immunoassays). Nine soldiers had at least one positive COVID-19 diagnostic test result. Five of them exhibited COVID-19 symptoms (mainly anosmia, ageusia, and fever), while four were asymptomatic. In four soldiers, SARS-CoV-2 viral load was detected and the genomes were sequenced. Conventional and genomic epidemiological data suggest that these genomes have an African most recent common ancestor and that the Belgian military service men were infected through contact with locals. The medical military command implemented testing of all Belgian soldiers for SARS-CoV-2 viral load and antibodies, two to three days before their departure on a mission abroad or on the high seas, and for specific missions immediately upon their return in Belgium. Some military operational settings (e.g., training camps in austere environments and ships) were also equipped with mobile infectious disease (COVID-19) testing capacity.

scholarly journals A territory-wide study of early COVID-19 outbreak in Hong Kong community: A clinical, epidemiological and phylogenomic investigation

2020 ◽  
Author(s):  
Kenneth Siu-Sing Leung ◽  
Timothy Ting-Leung Ng ◽  
Alan Ka-Lun Wu ◽  
Miranda Chong-Yee Yau ◽  
Hiu-Yin Lao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hong Kong ◽  
Local Community ◽  
Common Ancestor ◽  
Evolutionary Rate ◽  
Reproduction Number ◽  
Epidemiological Data ◽  
Recent Common Ancestor ◽  
Common Mutation ◽  
Most Recent Common Ancestor

AbstractInitial cases of COVID-19 reported in Hong Kong were mostly imported from China. However, most cases reported in February 2020 were locally-acquired infections, indicating local community transmissions. We extracted the demographic, clinical and epidemiological data from 50 COVID-19 patients, who accounted for 53.8% of the cases in Hong Kong by February 2020. Whole-genome sequencing of the SARS-CoV-2 were conducted to determine the phylogenetic relatedness and transmission dynamics. Only three (6.0%) patients required ICU admission. Phylogenetic analysis identified six transmission clusters. All locally-acquired cases harboured a common mutation Orf3a G251V and were clustered in two subclades in global phylogeny of SARS-CoV-2. The estimated time to the most recent common ancestor of local COVID-2019 outbreak was December 24, 2019 with an evolutionary rate of 3.04×10−3 substitutions per site per year. The reproduction number value was 1.84. Social distancing and vigilant epidemiological control are crucial to the containment of COVID-19 transmission.Article summary linesA combined epidemiological and phylogenetic analysis of early COVID-19 outbreak in Hong Kong revealed that a SARS-CoV-2 variant with ORF3a G251V mutation accounted for all locally acquired cases, and that asymptomatic carriers could be a huge public health risk for COVID-19 control.

The Role of Music and Allied Arts in Public Writings on Cultural Diversity: “People of Sri Lanka”

2020 ◽  
Vol 6 ◽  
pp. 93-100
Author(s):  
Gisa Jähnichen
Keyword(s):  
Sri Lanka ◽  
Cultural Diversity ◽  
South Asia ◽  
Case Studies ◽  
Sri Lankan ◽  
Culturally Different ◽  
The World ◽  
Official Languages ◽  
The Way

The Sri Lankan Ministry of National Coexistence, Dialogue, and Official Languages published the work “People of Sri Lanka” in 2017. In this comprehensive publication, 21 invited Sri Lankan scholars introduced 19 different people’s groups to public readers in English, mainly targeted at a growing number of foreign visitors in need of understanding the cultural diversity Sri Lanka has to offer. This paper will observe the presentation of these different groups of people, the role music and allied arts play in this context. Considering the non-scholarly design of the publication, a discussion of the role of music and allied arts has to be supplemented through additional analyses based on sources mentioned by the 21 participating scholars and their fragmented application of available knowledge. In result, this paper might help improve the way facts about groups of people, the way of grouping people, and the way of presenting these groupings are displayed to the world beyond South Asia. This fieldwork and literature guided investigation should also lead to suggestions for ethical principles in teaching and presenting of culturally different music practices within Sri Lanka, thus adding an example for other case studies.

Blood Pressure values of Sri Lankan Tamils in Jaffna District, Sri Lanka

2015 ◽  
Vol 2 (3) ◽  
pp. 66-71
Author(s):  
Balasubramaniam M ◽  
◽  
Sivapalan K ◽  
Tharsha J ◽  
Sivatharushan V ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Sri Lanka ◽  
Sri Lankan ◽  
Sri Lankan Tamils

scholarly journals Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants

Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 1187-1198 ◽  
Author(s):  
Mikkel H Schierup ◽  
Xavier Vekemans ◽  
Freddy B Christiansen
Keyword(s):  
Dominance Hierarchy ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Self Incompatibility ◽  
Most Recent Common Ancestor ◽  
Dominance Interactions ◽  
Turnover Process ◽  
Neutral Gene ◽  
Interspecific Comparisons ◽  
Coalescence Times

Abstract Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

scholarly journals Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018

2021 ◽  
Author(s):  
Wenjun Cheng ◽  
Tianjiao Ji ◽  
Shuaifeng Zhou ◽  
Yong Shi ◽  
Lili Jiang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Mainland China ◽  
Recent Common Ancestor ◽  
Genetic Characteristics ◽  
Most Recent Common Ancestor ◽  
Significant Difference ◽  
Echovirus 6 ◽  
Epidemiological Characteristics ◽  
Highest Posterior Density ◽  
Genotype F

AbstractEchovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.

scholarly journals Molecular epidemiology of coxsackievirus A16 circulating in children in Beijing, China from 2010 to 2019

2021 ◽  
Author(s):  
Ya-Fang Hu ◽  
Li-Ping Jia ◽  
Fang-Yuan Yu ◽  
Li-Ying Liu ◽  
Qin-Wei Song ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Evolutionary Rate ◽  
Foot And Mouth Disease ◽  
Recent Common Ancestor ◽  
Rt Pcr ◽  
Coxsackievirus A16 ◽  
Most Recent Common Ancestor ◽  
Etiological Agents ◽  
High Level ◽  
And Control

Abstract Background Coxsackievirus A16 (CVA16) is one of the major etiological agents of hand, foot and mouth disease (HFMD). This study aimed to investigate the molecular epidemiology and evolutionary characteristics of CVA16. Methods Throat swabs were collected from children with HFMD and suspected HFMD during 2010–2019. Enteroviruses (EVs) were detected and typed by real-time reverse transcription-polymerase chain reaction (RT-PCR) and RT-PCR. The genotype, evolutionary rate, the most recent common ancestor, population dynamics and selection pressure of CVA16 were analyzed based on viral protein gene (VP1) by bioinformatics software. Results A total of 4709 throat swabs were screened. EVs were detected in 3180 samples and 814 were CVA16 positive. More than 81% of CVA16-positive children were under 5 years old. The prevalence of CVA16 showed obvious periodic fluctuations with a high level during 2010–2012 followed by an apparent decline during 2013–2017. However, the activities of CVA16 increased gradually during 2018–2019. All the Beijing CVA16 strains belonged to sub-genotype B1, and B1b was the dominant strain. One B1c strain was detected in Beijing for the first time in 2016. The estimated mean evolutionary rate of VP1 gene was 4.49 × 10–3 substitution/site/year. Methionine gradually fixed at site-23 of VP1 since 2012. Two sites were detected under episodic positive selection, one of which (site-223) located in neutralizing linear epitope PEP71. Conclusions The dominant strains of CVA16 belonged to clade B1b and evolved in a fast evolutionary rate during 2010–2019 in Beijing. To provide more favorable data for HFMD prevention and control, it is necessary to keep attention on molecular epidemiological and evolutionary characteristics of CVA16.

scholarly journals The Ancestry of a Sample of Sequences Subject to Recombination

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1217-1228 ◽  
Author(s):  
Carsten Wiuf ◽  
Jotun Hein
Keyword(s):  
Genetic Distance ◽  
Population Size ◽  
Upper Bound ◽  
Recombination Rate ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Sequence Length ◽  
Most Recent Common Ancestor ◽  
The Mean ◽  
Mean Time

Abstract In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.

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