Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: a systematic review of the literature

Biggerstaff, Matthew; Cauchemez, Simon; Reed, Carrie; Gambhir, Manoj; Finelli, Lyn

doi:10.1186/1471-2334-14-480

Cited by 534 publications

(450 citation statements)

References 118 publications

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“…Despite distinct phylogenetic histories, PCV3a and PCV3b exhibited similar Re values of 3.08 (PCV3a, 95% HPD: 0.82–7.96) and 1.82 (PCV3b, 95% HPD: 0.63–4.86) (Figure S2, Supporting Information) based on epidemiological modeling in 2016. This suggests the potential to become endemic in pigs, at least if compared to human influenza viruses 37. Considering the limited number of sequences for 2015 and 2017, the Re value of 2016 was considered valid.…”

Section: Resultsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

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Porcine circovirus 3 (PCV3) is a novel virus associated with acute PDNS (porcine dermatitis and nephropathy syndrome)‐like clinical signs identified by metagenomic sequencing from swine. Its high occurrence may pose a potential threat to the swine industry worldwide. The processes resulting in the emergence and spread of PCV3 remain poorly understood. Herein, the possible origin, genotypes, and evolutionary dynamics of PCV3 based on available genomic sequences are determined. The closest ancestor of PCV3 is found to be within the clade 1 bat CVs. Using different phylogenetic methods, two major genotypes are identified, PCV3a and PCV3b. It is found that the effective population size of PCV3 increased rapidly during late 2013 to early 2014 and this is associated with the diversification of PCV3a and PCV3b. A relatively high effective reproductive number (Re) value and higher evolutionary rate were found compared to other single‐stranded DNA viruses, and positive selection on codons 122 and 320 (24 of ORF2) is identified. It is hypothesized that this, together with the prediction of a potential change of an antigenic epitope at position 320, might have allowed PCV3 to escape from the host immune response. Overall, this study has important implications for understanding the ongoing PCV3 cases worldwide and will guide future efforts to develop effective preventive and control measures.

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Section: Resultsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

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“…Additionally, most influenza studies are based on the 1918 and 2009 pandemics (Biggerstaff et al, 2014), so there is still insufficient information on ILI dynamics. Tamerius et al (2011) have reviewed the effect of seasonality, human immunity and virus survival on the spread of respiratory viruses.…”

Section: Recognised Thatmentioning

confidence: 99%

Space-time epidemiology and effect of meteorological parameters on influenza-like illness in Phitsanulok, a northern province in Thailand

Nimbalkar

Tripathi

2016

Geospat Health

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Influenza-like illness (ILI) is an acute respiratory disease that remains a public health concern for its ability to circulate globally affecting any age group and gender causing serious illness with mortality risk. Comprehensive assessment of the spatio-temporal dynamics of ILI is a prerequisite for effective risk assessment and application of control measures. Though meteorological parameters, such as rainfall, average relative humidity and temperature, influence ILI and represent crucial information for control of this disease, the relation between the disease and these variables is not clearly understood in tropical climates. The aim of this study was to analyse the epidemiology of ILI cases using integrated methods (space-time analysis, spatial autocorrelation and other correlation statistics). After 2009s H1N1 influenza pandemic, Phitsanulok Province in northern Thailand was strongly affected by ILI for many years. This study is based on ILI cases in villages in this province from 2005 to 2012. We used highly precise weekly incidence records covering eight years, which allowed accurate estimation of the ILI outbreak. Comprehensive methodology was developed to analyse the global and local patterns of the spread of the disease. Significant space-time clusters were detected over the study region during eight different periods. ILI cases showed seasonal clustered patterns with a peak in 2010 (P>0.05-9.999 iterations). Local indicators of spatial association identified hotspots for each year. Statistically, the weather pattern showed a clear influence on ILI cases and it strongly correlated with humidity at a lag of 1 month, while temperature had a weaker correlation.

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“…Studies have shown that 5-20% of the US population is infected with influenza every year and that 3000-49000 people die due to diseases associated with influenza every year (8 We determined the prevalence of H3N2 pneumonia as 10.1% in all pneumonia patients treated in our clinic. Apisarnthanarak et al (10) examineda total of 145 cases in the study to compare the risk factors of patients with H3N2 and H5N1 pneumonia and reported that the mean age of the patients with H3N2 pneumonia was 72; the proportion of males was 50%; the proportion of females was 50%; the first distinct symptoms of the majority of the cases (90%) were lung symptoms such as cough, phlegm, and shortness of breath; and the concomitant diseases were lung diseases (50%), diabetes mellitus (30%), cardiovascular diseases (20%), and cerebrovascular diseases (10%), and they also reported a close-ratio (7%) to our study in terms of the incidence of H3N2 pneumonia in their study.…”

Section: Discussionmentioning

confidence: 99%

Is H3N2 Pneumonia Different from Other Community-Acquired Pneumonia?

Doğan¹,

Cömert²,

Çağlayan³

et al. 2016

Eurasian J Pulmonol

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Objective: To evaluate the clinical, laboratory, radiological, and demographic data of H3N2 pneumonia cases hospitalized to the Pulmonology Department during H3N2 pandemics and compare them with non-H3N2 community-acquired pneumonia (CAP) cases. Methods:The study population consisted of all CAP cases hospitalized to our Pulmonology Department between December 2013 and February 2014 during the influenza outbreak. The patient files were evaluated for physical findings, laboratory data, radiological findings, and treatment and outcome of cases. H3N2 was diagnosed using polymerase chain reaction (PCR) analysis of throat swabs. The clinical, radiological, and laboratory findings of H3N2 pneumonia cases were compared with those of non-H3N2 pneumonia cases. Mann-Whitney U test, Chi-square test, Fisher's exact test, and logistic regression analysis by the forward step wise method were used for statistical analyses. P value<0.05 was considered significant. Results:During the H3N2 pandemic outbreak, 69 cases were diagnosed with CAP; 62 (89.8%) with non-H3N2 CAP, and 7 (10.2%) with H3N2 pneumonia. The demographic data, CURB-65, pneumonia severity index (PSI) scores, and clinical, radiological, and laboratory findings of the two groups were similar (p>0.05). The rates of treatment failure and/or transport to the intensive care unit with the need of invasive mechanical ventilation and mortality rates were also similar in both groups (p>0.05).Conclusion: H3N2 pneumonia/viral pneumonia is a member of CAP. Although the number of H3N2 cases are extremely small to draw a conclusion, the results of this study highlight that the clinical, radiological, and laboratory findings of H3N2 pneumonia cases are not different from those of non-H3N2 CAP cases.

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Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: a systematic review of the literature

Cited by 534 publications

References 118 publications

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

Space-time epidemiology and effect of meteorological parameters on influenza-like illness in Phitsanulok, a northern province in Thailand

Is H3N2 Pneumonia Different from Other Community-Acquired Pneumonia?

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