scholarly journals SARS-CoV-2 Delta vaccine breakthrough transmissibility in Alachua, Florida

2021 ◽  
Author(s):  
Brittany Rife Magalis ◽  
Shannan Rich ◽  
Massimiliano S Tagliamonte ◽  
Carla Mavian ◽  
Melanie N. Cash ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Acute Infection ◽  
Patient Characteristics ◽  
Contact Tracing ◽  
Post Vaccination ◽  
Alachua County ◽  
Delta Infection ◽  
June July ◽  
Sterilizing Immunity ◽  
Ongoing Evaluation

Background SARS-CoV-2 Delta variant has caused a dramatic resurgence in infections in the United Sates, raising questions regarding potential transmissibility among vaccinated individuals. Methods Between October 2020 and July 2021, we sequenced 4,439 SARS-CoV-2 full genomes, 23% of all known infections in Alachua County, Florida, including 109 vaccine breakthrough cases. Univariate and multivariate regression analyses were conducted to evaluate associations between viral load (VL) level and patient characteristics. Contact tracing and phylogenetic analysis were used to investigate direct transmissions involving vaccinated individuals. Results The majority of breakthrough sequences with lineage assignment were classified as Delta variants (74.6%) and occurred, on average, about three months (104 +- 57.5 days) after full vaccination, at the same time (June-July 2021) of Delta variant exponential spread within the county. Six Delta variant transmission pairs between fully vaccinated individuals were identified through contact tracing, three of which were confirmed by phylogenetic analysis. Delta breakthroughs exhibited broad VL values during acute infection (IQR 1.2-8.64 Log copies/ml), on average 38% lower than matched unvaccinated patients (3.29-10.81 Log copies/ml, p<0.00001). Nevertheless, 49-50% of all breakthroughs, and 56-60% of Delta-infected breakthroughs exhibited VL above the transmissibility threshold (4 Log copies/ml) irrespective of time post vaccination. Conclusions Delta infection transmissibility and general VL patterns in vaccinated individuals suggest limited levels of sterilizing immunity that need to be considered by public health policies. In particular, ongoing evaluation of vaccine boosters should address whether extra vaccine doses might curb breakthrough contribution to epidemic spread.

scholarly journals Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Calvin P. Sjaarda ◽  
Nazneen Rustom ◽  
Gerald A. Evans ◽  
David Huang ◽  
Santiago Perez-Patrigeon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Surveillance ◽  
Early Stage ◽  
Emerging Diseases ◽  
Contact Tracing ◽  
Travel History ◽  
Infectious Disease Surveillance ◽  
Viral Genomes ◽  
Heterozygous Variant ◽  
Sequencing Platforms

AbstractThe emergence and rapid global spread of SARS-CoV-2 demonstrates the importance of infectious disease surveillance, particularly during the early stages. Viral genomes can provide key insights into transmission chains and pathogenicity. Nasopharyngeal swabs were obtained from thirty-two of the first SARS-CoV-2 positive cases (March 18–30) in Kingston Ontario, Canada. Viral genomes were sequenced using Ion Torrent (n = 24) and MinION (n = 27) sequencing platforms. SARS-CoV-2 genomes carried forty-six polymorphic sites including two missense and three synonymous variants in the spike protein gene. The D614G point mutation was the predominate viral strain in our cohort (92.6%). A heterozygous variant (C9994A) was detected by both sequencing platforms but filtered by the ARTIC network bioinformatic pipeline suggesting that heterozygous variants may be underreported in the SARS-CoV-2 literature. Phylogenetic analysis with 87,738 genomes in the GISAID database identified global origins and transmission events including multiple, international introductions as well as community spread. Reported travel history validated viral introduction and transmission inferred by phylogenetic analysis. Molecular epidemiology and evolutionary phylogenetics may complement contact tracing and help reconstruct transmission chains of emerging diseases. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to limit future pandemics.

Limitations to Contact Tracing And Phylogenetic Analysis in Establishing HIV Type 1 Transmission Networks in Cuba

2007 ◽  
Vol 23 (3) ◽  
pp. 347-356 ◽  
Author(s):  
Sonia Resik ◽  
Philippe Lemey ◽  
Li-Hua Ping ◽  
Vivian Kouri ◽  
Jose Joanes ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Contact Tracing ◽  
Transmission Networks ◽  
Hiv Type 1

scholarly journals COVID-19 Case Investigation and Contact Tracing in Central Washington State, June–July 2020

2021 ◽  
Author(s):  
James S. Miller ◽  
Robert A. Bonacci ◽  
R. Ryan Lash ◽  
Patrick K. Moonan ◽  
Peter Houck ◽  
...  
Keyword(s):  
Washington State ◽  
Contact Tracing ◽  
Case Investigation ◽  
June July

scholarly journals Progress towards rabies elimination from Pemba Island, Southern Tanzania

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Kennedy S. Lushasi ◽  
Sarah Cleaveland ◽  
Joel J. Changalucha ◽  
Daniel Haydon ◽  
Rudovick Kazwala ◽  
...  
Keyword(s):  
Large Scale ◽  
Census Data ◽  
Contact Tracing ◽  
Human Rabies ◽  
Post Vaccination ◽  
Factors Affecting ◽  
Pemba Island ◽  
Routine Surveillance ◽  
Elimination Programme

ObjectiveUsing active surveillance approaches to investigate the transmissiondynamics of rabies on Pemba Island and across Southern Tanzania,whilst a large-scale dog vaccination program was underway1, to gaina greater understanding of the dynamics of infection as the disease isdriven towards elimination.IntroductionRabies is endemic in Tanzania and has circulated on Pemba Islandsince the late 1990s. In 2010, an elimination programme was initiatedin Southern Tanzania to demonstrate that human rabies deathscan be eliminated through mass dog vaccinations. We used activesurveillance approaches2to investigate the dynamics of rabies acrossthe area where this programme was implemented.MethodsGovernment census data and post-vaccination transects were usedto estimate the dog population and coverages achieved by vaccinationcampaigns. Routine surveillance of animal bite injuries using a mobilephone-based surveillance system3and active contact tracing wereused to identify animal rabies cases and human exposures. Epidemictrees were constructed using spatiotemporal distances between casesand used to estimate the effective reproduction number (Re). Weexamined factors affecting rabies incidence and transmission usinggeneralized linear mixed models.ResultsWe estimated a small dog population of 4095 and low dog:humanratio on Pemba (1:105). Overall island-wide vaccination coverageincreased from 16.8% in 2011 to 68.2% in 2014. We found a further48 human exposures (343%), who either were not reported or did notobtain post exposure prophylaxes (PEP). Routine surveillance wasfound to detect less than 10% (~8.75%). There was a rapid declinein cases detected on Pemba, from 42 before mass dog vaccinationswere implemented in 2011, to 2 cases in 2014 (Figures 1). Since May2014, no rabies cases have been detected. Similarly, Redeclined from1.02 to 0 and a significant relationship was found with rabies casesdecreasing with increasing vaccination coverage (p= 0.013, Figure 2).Across seven other districts on the Tanzanian mainland we alsoobserved major declines in rabies cases with very few cases of rabiesin dogs detected in 2016 (Figure 3).ConclusionsWe conclude that rabies has been eliminated from domestic dogpopulations on Pemba over the five years since vaccination campaignshave been implemented. Continued surveillance and investigationsof any bite incidents are therefore needed to ensure any subsequentincursions are controlled and freedom from rabies is maintained.On the Tanzanian mainland, it has taken longer to control rabies,however trajectories look promising with several districts close toeliminating the disease. However, detection of some wildlife casesin the last 12 months in these districts indicates the need to furtherinvestigate remaining foci and the role of wildlife in maintenance.

scholarly journals COVID-19 Contact Tracing in Two Counties — North Carolina, June–July 2020

2020 ◽  
Vol 69 (38) ◽  
pp. 1360-1363 ◽  
Author(s):  
R. Ryan Lash ◽  
Catherine V. Donovan ◽  
Aaron T. Fleischauer ◽  
Zack S. Moore ◽  
Gibbie Harris ◽  
...  
Keyword(s):  
North Carolina ◽  
Contact Tracing ◽  
June July

scholarly journals Are vaccines safe in patients with Long COVID? A prospective observational study

2021 ◽  
Author(s):  
DT Arnold ◽  
A Milne ◽  
E Samms ◽  
L Stadon ◽  
NA Maskell ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Observational Study ◽  
Mental Wellbeing ◽  
Vaccine Hesitancy ◽  
Post Vaccination ◽  
Vector Vaccine ◽  
And Gender ◽  
June July ◽  
The Impact

IntroductionAlthough the efficacy of SARS-CoV-2 vaccination to prevent symptomatic COVID-19 is well established, there are no published studies on the impact on symptoms in patients with Long Covid. Anecdotal reports have suggested both a potential benefit and worsening of symptoms post vaccination with the uncertainty leading to some vaccine hesitancy amongst affected individuals.MethodsPatients initially hospitalised with COVID-19 were prospectively recruited to an observational study with clinical follow-up at 3 months (June-July 2020) and 8 months (Dec 2020-Jan 2021) post-admission. Participants who received the Pfizer-BioNTech (BNT162b2) or Oxford-AstraZeneca (ChAdOx1 nCoV-19) vaccine between January to February 2021 were identified and matched 2:1 (in terms of 8-month symptoms) with participants from the same cohort who were unvaccinated. All were re-assessed at 1 month post vaccination (or matched timepoint for unvaccinated cohort). Validated quality of life (SF-36), mental wellbeing (WEMWBS) and ongoing symptoms were assessed at all timepoints. Formal statistical analysis compared the effect of vaccination on recent quality of life using baseline symptoms, age, and gender in linear regression.ResultsForty-four vaccinated participants were assessed at a median of 32 days (IQR 20-41) post vaccination with 22 matched unvaccinated participants. Most were highly symptomatic of Long Covid at 8 months (82% in both groups had at least 1 persistent symptom), with fatigue (61%), breathlessness (50%) and insomnia (38%) predominating. There was no significant worsening in quality-of-life or mental wellbeing metrics pre versus post vaccination. Nearly two-thirds (n=27) reported transient (<72hr duration) systemic effects (including fever, myalgia and headache).When compared to matched unvaccinated participants from the same cohort, those who had receive a vaccine had a small overall improvement in Long Covid symptoms, with a decrease in worsening symptoms (5.6% vaccinated vs 14.2% unvaccinated) and increase in symptom resolution (23.2% vaccinated vs 15.4% unvaccinated) (p=0.035). No difference in response was identified between Pfizer-BioNTech or Oxford-AstraZeneca vaccines.ConclusionsReceipt of vaccination with either an mRNA or adenoviral vector vaccine was not associated with a worsening of Long Covid symptoms, quality of life, or mental wellbeing. Individuals with prolonged COVID-19 symptoms should receive vaccinations as suggested by national guidance.

scholarly journals ISOLATION AND PHYLOGENETIC ANALYSIS OF FELINE CALICIVIRUS IN SIBERIA

2018 ◽  
Vol 63 (6) ◽  
pp. 268-274
Author(s):  
T. I. Glotova ◽  
O. V. Semenova ◽  
A. A. Nikonova ◽  
A. G. Glotov ◽  
Y. V. Vyatkin ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Acute Infection ◽  
Clinical Signs ◽  
Systemic Infection ◽  
Geographic Region ◽  
Nucleotide Sequences ◽  
Feline Calicivirus ◽  
Group Method ◽  
Reading Frame ◽  
Close Relationship

The results of the study of the distribution of calicivirus infection in a population of domestic cats of different breeds, contained individually or the group method, the virus isolation in the cell culture and a comparative phylogenetic analysis of their nucleotide sequences with published sequences of reference field and vaccine strains of Feline calicivirus (FCV) from other countries: USA, Germany, Japan, China and Korea are presented. Clinical signs of infection were found in 14.3% of the animals examined. After several passages in the primary kidney cells of the kitten embryo, seven cytopathogenic isolates FCV were isolated: 1 - from a cat with an acute infection, 5 - subclinical infection, 1 - systemic infection. They were adapted to continuous FK-81 cells in which they reached a maximum infectious activity of 10.0 ± 1.15 lg TCD 50 / cm3. Based on the sequence analysis of the open reading frame 2 region of the viral genome Eshli strain showed a close relationship with strain KM016908 from China with the identity of the nucleotide sequences between them of 81.0%. The results of the investigations showed that FCV isolates obtained from animals on the territory of Siberia are genetically different from strains included to imported vaccines used to prevent disease in Russian Federation and also among themselves. This causes a decrease in the effectiveness of preventive measures. In nurseries that do not have contacts and connections between themselves but located in the same geographic region FCV populations may have some genetic differences. A close relationship of some field isolates with strains from other countries geographically located so far from the Siberian region has been revealed. Studies on the molecular epizootology of caliciviruses are important in the development of test systems and the monitoring of the spread of strains in Russia.

Seasonal Variation of Suicide in the City of São Paulo, Brazil, 1996–2010

Crisis ◽  
2014 ◽  
Vol 35 (1) ◽  
pp. 5-9 ◽  
Author(s):  
Daniel Hideki Bando ◽  
Fernando Madalena Volpe
Keyword(s):  
Seasonal Pattern ◽  
Total Sample ◽  
Sao Paulo ◽  
Seasonal Patterns ◽  
São Paulo ◽  
Health Statistics ◽  
Males And Females ◽  
June July ◽  
The City ◽  
Over Time

Background: In light of the few reports from intertropical latitudes and their conflicting results, we aimed to replicate and update the investigation of seasonal patterns of suicide occurrences in the city of São Paulo, Brazil. Methods: Data relating to male and female suicides were extracted from the Mortality Information Enhancement Program (PRO-AIM), the official health statistics of the municipality of São Paulo. Seasonality was assessed by studying distribution of suicides over time using cosinor analyses. Results: There were 6,916 registered suicides (76.7% men), with an average of 39.0 ± 7.0 observed suicides per month. For the total sample and for both sexes, cosinor analysis estimated a significant seasonal pattern. For the total sample and for males suicide peaked in November (late spring) with a trough in May–June (late autumn). For females, the estimated peak occurred in January, and the trough in June–July. Conclusions: A seasonal pattern of suicides was found for both males and females, peaking in spring/summer and dipping in fall/winter. The scarcity of reports from intertropical latitudes warrants promoting more studies in this area.

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