scholarly journals Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1295
Author(s):  
Karol Serwin ◽  
Andrzej Ossowski ◽  
Maria Szargut ◽  
Sandra Cytacka ◽  
Anna Urbańska ◽  
...  
Keyword(s):  
Pattern Analysis ◽  
Continuous Time Markov Chain ◽  
High Coverage ◽  
Exponential Increase ◽  
Notable Increase ◽  
Mutation Pattern ◽  
Northwestern Poland ◽  
Epidemiological Characteristics ◽  
Second Wave ◽  
Variant Identification

The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolved into a worldwide outbreak, with the first Polish cases in February/March 2020. This study aimed to investigate the molecular epidemiology of the circulating virus lineages between March 2020 and February 2021. We performed variant identification, spike mutation pattern analysis, and phylogenetic and evolutionary analyses for 1106 high-coverage whole-genome sequences, implementing maximum likelihood, multiple continuous-time Markov chain, and Bayesian birth–death skyline models. For time trends, logistic regression was used. In the dataset, virus B.1.221 lineage was predominant (15.37%), followed by B.1.258 (15.01%) and B.1.1.29 (11.48%) strains. Three clades were identified, being responsible for 74.41% of infections over the analyzed period. Expansion in variant diversity was observed since September 2020 with increasing frequency of the number in spike substitutions, mainly H69V70 deletion, P681H, N439K, and S98F. In population dynamics inferences, three periods with exponential increase in infection were observed, beginning in March, July, and September 2020, respectively, and were driven by different virus clades. Additionally, a notable increase in infections caused by the B.1.1.7 lineage since February 2021 was noted. Over time, the virus accumulated mutations related to optimized transmissibility; therefore, faster dissemination is reflected by the second wave of epidemics in Poland.

scholarly journals Stringent containment measures without complete city lockdown to achieve low incidence and mortality across two waves of COVID-19 in Hong Kong

2020 ◽  
Vol 5 (10) ◽  
pp. e003573
Author(s):  
Martin C S Wong ◽  
Rita W Y Ng ◽  
Ka Chun Chong ◽  
Christopher K C Lai ◽  
Junjie Huang ◽  
...  
Keyword(s):  
Hong Kong ◽  
Moving Average ◽  
Linear Regression Analysis ◽  
Leisure Activities ◽  
Multiple Linear Regression Analysis ◽  
Mitigation Strategies ◽  
Incidence And Mortality ◽  
Containment Measures ◽  
Epidemiological Characteristics ◽  
Second Wave

IntroductionAn international city, Hong Kong, in proximity to the first epicentre of COVID- 19, experienced two epidemic waves with different importation pressure. We compared the epidemiological features of patients with COVID-19 in the context of containment policies between the first and second waves.MethodsWe retrieved information on the first 1038 cases detected in Hong Kong (23 January to 25 April 2020) to analyse the epidemiological characteristics including age/gender-specific incidence, clustering, reproduction number (Rt) and containment delay; in relation to the containment measures implemented. Factors associated with containment delay were evaluated by multiple linear regression analysis with age, gender, epidemic wave and infection source as covariates. A time series of 5-day moving average was plotted to examine the changes across the two epidemic waves.ResultsThe incidence and mortality (135.5 and 0.5 per 1 000 000 population) was among the lowest in the world. Aggressive escalation of border control correlated with reductions in Rt from 1.35 to 0.57 and 0.92 to 0.18, and aversions of 450 and 1650 local infections during the first and second waves, respectively. Implementing COVID-19 tests for overseas returners correlated with an upsurge of asymptomatic case detection, and shortened containment delay in the second wave. Medium-sized cluster events in the first wave were family gatherings, whereas those in the second wave were leisure activities among youngsters. Containment delay was associated with older age (adjusted OR (AOR)=1.01, 95% CI 1.00 to 1.02, p=0.040), male gender (AOR=1.41, 95% CI 1.02 to 1.96, p=0.039) and local cases (AOR=11.18, 95% CI 7.43 to 16.83, p<0.001), and with significant improvement in the second wave compared with the first wave (average: 6.8 vs 3.7 days). A higher incidence rate was observed for males, raising possibility of gender predilection in susceptibility of developing symptoms.ConclusionPrompt and stringent all-round containment strategies represent successful measures in pandemic control. These findings could inform formulation and implementation of pandemic mitigation strategies.

scholarly journals EMERGENCE OF SECOND WAVE OF SARS-COV-2 INFECTIONS DURING THE ONGOING COVID-19 PANDEMIC: A MINI REVIEW

2020 ◽  
Vol 8 (Spl-1-SARS-CoV-2) ◽  
pp. S57-S65
Author(s):  
Bhumika Prajapati ◽  
◽  
Kranti Suresh Vora ◽  
Zareena Fathah ◽  
Ranjit Sah ◽  
...  
Keyword(s):  
Epidemic Curve ◽  
Exponential Increase ◽  
Global Pandemic ◽  
The World ◽  
Type 3 ◽  
Second Wave ◽  
Vulnerable Elderly ◽  
Future Plans

The COVID-19 outbreak originated from Wuhan, China has spread over the world, causing a “Global Pandemic”. We analyzed daily confirmed cases and deaths from different countries to understand the progression of the ongoing pandemic in different parts around the world. The data indicated that the pandemic is in different stages in different countries, where they are either at the end of the second wave or middle or early phase of it or still in the middle of the first wave of infection, and they can be divided into four groups. Type 1 countries such as UK, France, Spain, and the Netherlands are currently witnessing the second wave of infection with an exponential increase in daily cases. Countries such as Australia, United States, Japan, and Poland are currently in the declining stage of second-wave, grouped as Type 2 countries. Type 3 countries such as Germany, Italy, Belgium, and Russia are recently seeing the second wave with slowly rising of confirmed cases. Type 4 countries including India, Brazil, Argentina, and Mexico are currently fighting against the first wave of COVID-19. These countries have a chance to learn from the countries which have overcome the second wave successfully. To be ahead of the epidemic curve and preventing it, countries need to make future plans on family, hospital, and community levels. Isolation of the highly vulnerable elderly people and young children, preventing social or public gathering, following the guidelines of COVID-19 prevention including wearing face masks regularly can save countries from devastating effects of the second wave of pandemic COVID-19.

scholarly journals Epidemiological characteristics of tetanus in Vojvodina

2006 ◽  
Vol 59 (11-12) ◽  
pp. 551-555 ◽  
Author(s):  
Vladimir Petrovic ◽  
Zorica Seguljev ◽  
Mladen Petrovic ◽  
Svetlana Ilic
Keyword(s):  
Incidence Rate ◽  
Elderly People ◽  
Case Fatality ◽  
Skin Lesions ◽  
Medical Attention ◽  
Age Group ◽  
High Coverage ◽  
Average Case ◽  
Limb Injuries ◽  
Epidemiological Characteristics

Introduction. Vojvodina is an endemic area for tetanus. Material and Methods. Epidemiological characteristics of tetanus were analyzed based on registered cases of disease and death in the period 1960 - 2004, and epidemiological investigation of 50 registered cases during the last 10 years of this period. Epidemiological characteristics were analyzed chronologically, demographically and topographically. Results and Discussion. During the period of observation, the incidence rate of tetanus declined steadily. Due to immunization and extremely high coverage, tetanus has been practically eliminated in the age group of younger than 29 years. Neonatal tetanus and tetanus in the age group 30-59 years has been reduced to individual cases. Today, tetanus is a problem of the elderly population. Tetanus deaths occur statistically more often among persons older than 66 years. The average case fatality rate during the period of observation was 33.1%. The vaccination history in the majority of investigated cases was unknown (52%) or they have never been vaccinated (28%) because they were mainly elderly people born before introduction of mandatory immunization. Tetanus most often occurs after minor wounds, because of which patients do not seek medical attention. In the majority of cases tetanus occurred after limb injuries. Conclusion. Tetanus in Vojvodina is a problem among immunized elderly people. It mostly occurs after minor injuries or after contamination of chronic skin lesions. Mandatory vaccination of older age groups should contribute to further reduction in the incidence rate of tetanus. .

scholarly journals Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246383
Author(s):  
Ko Ko ◽  
Shintaro Nagashima ◽  
Bunthen E. ◽  
Serge Ouoba ◽  
Tomoyuki Akita ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Characterization ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Asian Strain ◽  
First Case ◽  
Nucleotide Insertion ◽  
Mutation Pattern ◽  
Viral Factor ◽  
Second Wave

Background In this study, we performed molecular characterization of SARS-CoV-2 strains in Hiroshima and its mutation pattern between the first and second waves of the outbreak. Method A total of 55 nasal swab samples from the first wave in Hiroshima and 13 from the second wave were examined quantitatively by RT-qPCR and qualitatively by nested PCR using specific primers. Four samples from each wave underwent next-generation sequencing and phylogenetic tree analysis including controls and all sequences retrieved in Japan from GISAID and GenBank. Subsequently, mutations were examined. Results Viral load ranged 7.85 × 101−1.42 × 108 copies/ml. Of 68 samples, one was Asian type-O, 65 were European type-GR, and 2 were undetectable. Phylogenetic tree analysis indicated that Japan was infected with various Asian strains (L, S, V, O) from January through April. By second week of March, European strains (G, GH, GR) had appeared, and GR strains became predominant after mid-March. The first case in Hiroshima was classified as Asian strain O, and the rest were GR strains. Then, second wave of GR strains appeared independently with 11–15 base mutations. Comparing the first- and second-wave GR strains, mutation rate was 1.17–1.36 × 10−3 base substitutions per site per year; in addition, amino acid changes occurred at S1361P and P3371S in ORF1a, A314V in ORF1b, and P151L in N. All seven GR strains were D614G variants with R202K and G203R mutations in N. A single-nucleotide insertion in ORF8 that causes a defect in ORF8 protein was found in one isolate (S66) from the second wave. Conclusion Our findings reveal the evolutionary hierarchy of SARS-CoV-2 in Japan. The predominant D614G variants and a new form of ORF8 deletion in Hiroshima provide the clue for role of viral factor in local outbreaks of SARS-CoV-2.

scholarly journals Clinical and Epidemiological Characteristics of 1283 Pediatric Patients with Coronavirus Disease 2019 during the First and Second Waves of the Pandemic—Results of the Pediatric Part of a Multicenter Polish Register SARSTer

2021 ◽  
Vol 10 (21) ◽  
pp. 5098
Author(s):  
Maria Pokorska-Śpiewak ◽  
Ewa Talarek ◽  
Anna Mania ◽  
Małgorzata Pawłowska ◽  
Jolanta Popielska ◽  
...  
Keyword(s):  
Pediatric Patients ◽  
Clinical Presentation ◽  
Gastrointestinal Symptoms ◽  
Common Symptom ◽  
Multicenter Cohort Study ◽  
Age Related ◽  
Asymptomatic Patients ◽  
Close Relatives ◽  
Epidemiological Characteristics ◽  
Second Wave

This prospective multicenter cohort study aimed to analyze the epidemiological and clinical characteristics of coronavirus disease 2019 (COVID-19) in children. The study, based on the pediatric part of the Polish SARSTer register, included 1283 children (0 to 18 years) who were diagnosed with COVID-19 between 1 March 2020 and 31 December 2020. Household contact was reported in 56% of cases, more frequently in younger children. Fever was the most common symptom (46%). The youngest children (0–5 years) more frequently presented with fever, rhinitis and diarrhea. Teenagers more often complained of headache, sore throat, anosmia/ageusia and weakness. One fifth of patients were reported to be asymptomatic. Pneumonia was diagnosed in 12% of patients, more frequently in younger children. During the second wave patients were younger than during the first wave (median age 53 vs. 102 months, p < 0.0001) and required longer hospitalization (p < 0.0001). Significantly fewer asymptomatic patients were noted and pneumonia as well as gastrointestinal symptoms were more common. The epidemiological characteristics of pediatric patients and the clinical presentation of COVID-19 are age-related. Younger children were more frequently infected by close relatives, more often suffered from pneumonia and gastrointestinal symptoms and required hospitalization. Clinical courses differed significantly during the first two waves of the pandemic.

scholarly journals Emergence of Novel SARS-CoV-2 variants in India: second wave

2021 ◽  
Vol 15 (11) ◽  
pp. 1578-1583
Author(s):  
Rama Adiga ◽  
Varun Nayak
Keyword(s):  
Indian Subcontinent ◽  
Asian Countries ◽  
Sample Collection ◽  
High Coverage ◽  
Time Period ◽  
Indian State ◽  
Rapid Pace ◽  
Global Initiative ◽  
Second Wave

Introduction: Globally South-East Asia reported 40% of SARS-CoV-2 infected cases in the fourth week of April 2021. It continued to show an increase with India accounting for 50% of cases worldwide and 30% of global deaths. Genomic surveillance should continue at a rapid pace because of the continuously evolving nature of the virus. The time period of sample collection from the Global Initiative on Sharing All Influenza Data database was concurrent with the surge in new cases seen in the Indian subcontinent. Methodology: 7,415 sequences were downloaded from Global Initiative on Sharing All Influenza Data between January and April 2021; out of which 4,411 were high coverage genome sequences and were considered for analysis. Phylogenetic analysis were carried out using Nextstrain. Results: 21A or B.1.617 or delta was the most prevalent lineage in India accounting for 67.7% of the genomes. Next important clades were 20A, 20B and 20I accounting for 23.6%, 11.8% and 12.1% respectively collected between January 2021 and April 2021. The remaining sequences were assigned to clade 20H, 20J, 20D, 20C, 20G,20E,19A and 19B.The spike mutation frequencies of L452R, E484Q and P681R in Indian state of Maharashtra were 62.4%, 66.5% and 61.5% respectively. Two unique N-terminal domain deletion of spike protein were found at position 67 and 68. Conclusions: The phylogenomics of the delta variant or 21A emerged in neighboring Asian countries of Thailand, Bangladesh, Indonesia and Japan. We analyzed the SARS-CoV-2 genomes from India for mutation characterization of the spike glycoprotein and the nucleocapsid protein.

scholarly journals A follow-up study shows no new infections caused by patients with repeat positive of COVID-19 in Wuhan

2020 ◽  
Author(s):  
Xiaomin Wu ◽  
Zengmiao Wang ◽  
Zhenyu He ◽  
Yapin Li ◽  
Yating Wu ◽  
...  
Keyword(s):  
Clinical Features ◽  
Close Contact ◽  
Follow Up Study ◽  
Basic Characteristics ◽  
Epidemiological Characteristics ◽  
Second Wave

AbstractBackgroundIt has been reported that a few recovered COVID-19 patients could suffer repeat positive, testing positive for the SARS-CoV-2 virus again after they were discharged from hospital. Understanding the epidemiological characteristics of patients with repeat positive is vital in preventing a second wave of COVID-19.MethodsIn this study, the epidemiological and clinical features for 20,280 COVID-19 patients from multiple centers between 31 December 2019 and 4 August 2020 in Wuhan were collected and followed. In addition, the RT-qPCR testing results for 4,079 individuals who had close contact with the patients suffering repeat positive were also obtained.Results2,466 (12.16%) of 20,280 patients presented with a repeat positive of SARS-CoV-2 after they were discharged from hospital. 4,079 individuals had close contact with them. The PCR result were negative for the 4,079 individuals.ConclusionsBy a follow-up study in Wuhan, we show the basic characteristics of patients with repeat positive and no new infections caused by patients with repeat positive of COVID-19.

scholarly journals A follow-up study shows that recovered patients with re-positive PCR test in Wuhan may not be infectious

BMC Medicine ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Xiaomin Wu ◽  
Zengmiao Wang ◽  
Zhenyu He ◽  
Yapin Li ◽  
Yating Wu ◽  
...  
Keyword(s):  
Retrospective Study ◽  
Close Contact ◽  
Test Results ◽  
Positive Polymerase Chain Reaction ◽  
Polymerase Chain ◽  
Basic Characteristics ◽  
Epidemiological Characteristics ◽  
Second Wave ◽  
Pcr Test

Abstract Background Previous studies showed that recovered coronavirus disease 2019 (COVID-19) patients can have a subsequent positive polymerase chain reaction (PCR) test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after they are discharged from the hospital. Understanding the epidemiological characteristics of recovered COVID-19 patients who have a re-positive test is vital for preventing a second wave of COVID-19. Methods This retrospective study analyzed the epidemiological and clinical features of 20,280 COVID-19 patients from multiple centers in Wuhan who had a positive PCR test between December 31, 2019, and August 4, 2020. The RT-PCR test results for 4079 individuals who had close contact with the re-positive cases were also obtained. Results In total, 2466 (12.16%) of the 20,280 patients had a re-positive SARS-CoV-2 PCR test after they were discharged from the hospital, and 4079 individuals had close contact with members of this patient group. All of these 4079 individuals had a negative SARS-CoV-2 PCR test. Conclusions This retrospective study in Wuhan analyzed the basic characteristics of recovered COVID-19 patients with re-positive PCR test and found that these cases may not be infectious.

scholarly journals Better strategies for containing COVID-19 pandemic: a study of 25 countries via a vSIADR model

2021 ◽  
Vol 477 (2248) ◽  
Author(s):  
Han Yan ◽  
Yuru Zhu ◽  
Jia Gu ◽  
Yaxuan Huang ◽  
Haoxuan Sun ◽  
...  
Keyword(s):  
Substantial Reduction ◽  
Control Measures ◽  
Linear Mixed Effect Model ◽  
Government Control ◽  
Mixed Effect ◽  
Counter Measures ◽  
Epidemic Size ◽  
The Usa ◽  
Epidemiological Characteristics ◽  
Second Wave

We study epidemiological characteristics of 25 early COVID-19 outbreak countries, which emphasizes on the reproduction of infection and effects of government control measures. The study is based on a vSIADR model which allows asymptomatic and pre-diagnosis infections to reflect COVID-19 clinical realities, and a linear mixed-effect model to analyse the association between each country’s control measures and the effective reproduction number R t . It finds significant effects of higher stringency measures in lowering the reproduction, and a significant shortening effect on the time to the epidemic turning point by applying stronger early counter measures. Epidemic projections under scenarios of the counter measures (China and Korea, the USA and the UK) show substantial reduction in the epidemic size and death by taking earlier and forceful actions. The governments’ response before and after the start of the second wave epidemics were alarmingly weak, which made the average duration of the second wave more than doubled that of the first wave. We identify countries which urgently need to restore to at least the maximum stringency measures implemented so far in the pandemic in order to avoid even higher infection size and death.

scholarly journals Mutation pattern analysis reveals polygenic mini-drivers associated with relapse after surgery in lung adenocarcinoma

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Laura Bennett ◽  
Matthew Howell ◽  
Danish Memon ◽  
Chris Smowton ◽  
Cong Zhou ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Pattern Analysis ◽  
Mutation Pattern
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