Influenza seasonality and predominant subtypes of influenza virus in Guangdong, China, 2004-2012

A predictive model of the temperature-dependent inactivation of coronaviruses

The COVID-19 pandemic has stressed healthcare systems and supply lines, forcing medical doctors to risk infection by decontaminating and reusing single-use personal protective equipment. The uncertain future of the pandemic is compounded by limited data on the ability of the responsible virus, SARS-CoV-2, to survive across various climates, preventing epidemiologists from accurately modeling its spread. However, a detailed thermodynamic analysis of experimental data on the inactivation of SARS-CoV-2 and related coronaviruses can enable a fundamental understanding of their thermal degradation that will help model the COVID-19 pandemic and mitigate future outbreaks. This work introduces a thermodynamic model that synthesizes existing data into an analytical framework built on first principles, including the rate law for a first-order reaction and the Arrhenius equation, to accurately predict the temperature-dependent inactivation of coronaviruses. The model provides much-needed thermal decontamination guidelines for personal protective equipment, including masks. For example, at 70 °C, a 3-log (99.9%) reduction in virus concentration can be achieved, on average, in 3 min (under the same conditions, a more conservative decontamination time of 39 min represents the upper limit of a 95% interval) and can be performed in most home ovens without reducing the efficacy of typical N95 masks as shown in recent experimental reports. This model will also allow for epidemiologists to incorporate the lifetime of SARS-CoV-2 as a continuous function of environmental temperature into models forecasting the spread of the pandemic across different climates and seasons.

Characteristics of Seasonal Influenza Virus Activity in a Subtropical City in China, 2013-2019

BACKGROUND

To optimize seasonal influenza vaccination programs in regions with potentially complicated seasonal patterns, the epidemiological characteristics of seasonal influenza activity in a subtropical city of China were explored.

MATERIALS AND METHODS

Influenza virus data of patients with influenza-like illness (ILI) during 2013-2019 were collected from two sentinel hospitals in a subtropical region of China, Yichang city. The influenza virus positive rate among sampled ILI cases served as a proxy to estimate influenza seasonal characteristics, including periodicity, duration, peaks, and predominant subtypes/lineages. Epidemiological features of different years, seasons and age groups were analyzed, and vaccine mismatches were identified.

RESULTS

In total, 8693 ILI cases were included; 1439 (16.6%) were laboratory-confirmed influenza cases. The influenza A positive rate (10.6%) was higher than the influenza B positive rate (5.9%). There were three influenza circulation patterns in Yichang: (1) annual periodicity (in 2013-2014, 2015-2016 and 2018-2019), (2) semiannual periodicity (in 2014-2015), and (3) year-round periodicity (in 2016-2017 and 2017-2018). Summer epidemics existed in two of the six years and were dominated by influenza A/H3N2. Winter and spring epidemics occurred in five of the six years, and A/H1N1, A/H3N2, B/Victoria, and B/Yamagata were codominant. During the study period, the predominant lineages, B/Victoria in 2015-16 and B/Yamagata in 2017-2018, were both mismatched with the influenza B component of the trivalent vaccine. Children 5-14 years old (26.4%) and individuals over 60 years old (16.9%) had the highest influenza positive rates.

CONCLUSIONS

The seasonal epidemic period and the predominant subtype/lineage of influenza viruses in Yichang city are complex. Influenza vaccination timing and strategies need to be optimized according to the local features of influenza virus activity.

Epidemiological features and time-series analysis of influenza incidence in urban and rural areas of Shenyang, China, 2010-2018

In recent years, there have been a significant influenza activity and emerging influenza strains in China, resulting in an increasing number of influenza virus infections and leading to public health concerns. The aims of this study were to identify the epidemiological and aetiological characteristics of influenza and establish seasonal autoregressive integrated moving average (SARIMA) models for forecasting the percentage of visits for influenza-like illness (ILI%) in urban and rural areas of Shenyang. Influenza surveillance data were obtained for ILI cases and influenza virus positivity from 18 sentinel hospitals. The SARIMA models were constructed to predict ILI% for January–December 2019. During 2010–2018, the influenza activity was higher in urban than in rural areas. The age distribution of ILI cases showed the highest rate in young children aged 0–4 years. Seasonal A/H3N2, influenza B virus and pandemic A/H1N1 continuously co-circulated in winter and spring seasons. In addition, the SARIMA (0, 1, 0) (0, 1, 2)₁₂ model for the urban area and the SARIMA (1, 1, 1) (1, 1, 0)₁₂ model for the rural area were appropriate for predicting influenza incidence. Our findings suggested that there were regional and seasonal distinctions of ILI activity in Shenyang. A co-epidemic pattern of influenza strains was evident in terms of seasonal influenza activity. Young children were more susceptible to influenza virus infection than adults. These results provide a reference for future influenza prevention and control strategies in the study area.

Seasonal Activity of Influenza in Iran: Application of Influenza-like Illness Data from Sentinel Sites of Healthcare Centers during 2010 to 2015

This study aimed to predict seasonal influenza activity and detection of influenza outbreaks. Data of all registered cases (n = 53,526) of influenza-like illnesses (ILIs) from sentinel sites of healthcare centers in Iran were obtained from the FluNet web-based tool, World Health Organization (WHO), from 2010 to 2015. The status of the ILI activity was obtained from the FluNet and considered as the gold standard of the seasonal activity of influenza during the study period. The cumulative sum (CUSUM) as an outbreak detection method was used to predict the seasonal activity of influenza. Also, time series similarity between the ILI trend and CUSUM was assessed using the cross-correlogram. Of 7684 (14%) positive cases of influenza, about 71% were type A virus and 28% were type B virus. The majority of the outbreaks occurred in winter and autumn. Results of the cross-correlogram showed that there was a considerable similarity between time series graphs of the ILI cases and CUSUM values. However, the CUSUM algorithm did not have a good performance in the timely detection of influenza activity. Despite a considerable similarity between time series of the ILI cases and CUSUM algorithm in weekly lag, the seasonal activity of influenza in Iran could not be predicted by the CUSUM algorithm.

Temporal patterns of influenza A subtypes and B lineages across age in a subtropical city, during pre-pandemic, pandemic, and post-pandemic seasons

Background

Seasonal patterns of influenza A subtypes and B lineages in tropical/subtropical regions across age have remained to be explored. The impact of the 2009 H1N1 pandemic on seasonal influenza activity have not been well understood.

Methods

Based on a national sentinel hospital-based influenza surveillance system, the epidemiology of influenza virus during 2006/07–2015/16 was characterized in the subtropical city, Chengdu. Chengdu is one of the most populous cities in southwestern China, where the first reported case of A/H1N1pdm09 in mainland China was identified. Wavelet analysis was applied to identify the periodicities of A/H3N2, seasonal A/H1N1, A/H1N1pdm09, Victoria, and Yamagata across age, respectively. The persistence and age distribution patterns were described during the pre-pandemic (2006/07–2008/09), pandemic (2009/10), and post-pandemic (2010/11–2015/16) seasons.

Results

A total of 10,981 respiratory specimens were collected, of which 2516 influenza cases were identified. Periodicity transition from semi-annual cycles to an annual cycle was observed for composite influenza virus as well as A/H3N2 along in Chengdu since the 2009 H1N1 pandemic. Semi-annual cycles of composite influenza virus and A/H3N2 along were observed again during 2014/15–2015/16, coinciding with the emergence and predominance of A/H3N2 significant antigenic drift groups. However, A/H1N1pdm09, Victoria, and Yamagata generally demonstrated an annual winter-spring peak in non-pandemic seasons. Along with periodicity transitions, age groups with higher positive rates shifted from school-aged children and adults to adults and the elderly for A/H1N1pdm09 during 2009/10–2010/11 and for A/H3N2 during 2014/15–2015/16.

Conclusions

Differences in periodicity and age distribution by subtype/lineage and by season highlight the importance of increasing year-round influenza surveillance and developing subtype/lineage- and age-specific prevention and control measures. Changes of periodicity and age shifts should be considered in public health response to influenza pandemics and epidemics. In addition, it is suggested to use quadrivalent influenza vaccines to provide protection against both influenza B lineages.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3689-9) contains supplementary material, which is available to authorized users.

Nonannual seasonality of influenza-like illness in a tropical urban setting

BACKGROUND

In temperate and subtropical climates, respiratory diseases exhibit seasonal peaks in winter. In the tropics, with no winter, peak timings are irregular.

METHODS

To obtain a detailed picture of influenza-like illness (ILI) patterns in the tropics, we established an mHealth study in community clinics in Ho Chi Minh City (HCMC). During 2009-2015, clinics reported daily case numbers via SMS, with a subset performing molecular diagnostics for influenza virus. This real-time epidemiology network absorbs 6000 ILI reports annually, one or two orders of magnitude more than typical surveillance systems. A real-time online ILI indicator was developed to inform clinicians of the daily ILI activity in HCMC.

RESULTS

From August 2009 to December 2015, 63 clinics were enrolled and 36 920 SMS reports were received, covering approximately 1.7M outpatient visits. Approximately 10.6% of outpatients met the ILI case definition. ILI activity in HCMC exhibited strong nonannual dynamics with a dominant periodicity of 206 days. This was confirmed by time series decomposition, stepwise regression, and a forecasting exercise showing that median forecasting errors are 30%-40% lower when using a 206-day cycle. In ILI patients from whom nasopharyngeal swabs were taken, 31.2% were positive for influenza. There was no correlation between the ILI time series and the time series of influenza, influenza A, or influenza B (all P > 0.15).

CONCLUSION

This suggests, for the first time, that a nonannual cycle may be an essential driver of respiratory disease dynamics in the tropics. An immunological interference hypothesis is discussed as a potential underlying mechanism.

Literature review of the epidemiology of influenza B disease in 15 countries in the Asia-Pacific region

Influenza control strategies focus on the use of trivalent influenza vaccines containing two influenza A virus subtypes and one of the two circulating influenza type B lineages (Yamagata or Victoria). Mismatches between the vaccine B lineage and the circulating lineage have been regularly documented in many countries, including those in the Asia‐Pacific region. We conducted a literature review with the aim of understanding the relative circulation of influenza B viruses in Asia‐Pacific countries. PubMed and Western Pacific Region Index Medicus were searched for relevant articles on influenza type B published since 1990 in English language for 15 Asia‐Pacific countries. Gray literature was also accessed. From 4834 articles identified, 121 full‐text articles were analyzed. Influenza was reported as an important cause of morbidity in the Asia‐Pacific region, affecting all age groups. In all 15 countries, influenza B was identified and associated with between 0% and 92% of laboratory‐confirmed influenza cases in any one season/year. Influenza type B appeared to cause more illness in children aged between 1 and 10 years than in other age groups. Epidemiological data for the two circulating influenza type B lineages remain limited in several countries in the Asia‐Pacific, although the co‐circulation of both lineages was seen in countries where strain surveillance data were available. Mismatches between circulating B lineages and vaccine strains were observed in all countries with available data. The data suggest that a shift from trivalent to quadrivalent seasonal influenza vaccines could provide additional benefits by providing broader protection.

Seasonal pattern of influenza activity in a subtropical city, China, 2010-2015

Influenza seasonality study is critical for policy-makers to choose an optimal time for influenza vaccination campaign, especially for subtropical regions where influenza seasonality and periodicity are unclear. In this study, we explored the seasonality and periodicity of influenza in Hefei, China during 2010 to 2015 using five proxies originated from three data sources of clinical surveillance of influenza-like illness (ILI), laboratory surveillance of influenza and death registration of pneumonia and influenza. We combined both wavelets analysis and de-linear-trend regression with Fourier harmonic terms to estimate seasonal characteristics of epidemic phase, peak time, amplitude, ratio of dominant seasonality. We found both annual cycle of influenza epidemics peaking in December-February and semi-annual cycle peaking in December-February and June-July in subtropical city Hefei, China. Compared to proxies developed by ILI and death registration data separately, influenza proxies incorporated laboratory surveillance data performed better seasonality and periodicity, especially in semi-annual periodicity in Hefei. Proxy of ILI consultation rate showed more timeliness peak than other proxies, and could be useful in developing the early warning model for influenza epidemics. Our study suggests to integrate clinical and laboratory surveillance of influenza for future influenza seasonality studies in subtropical regions.

Structure of general-population antibody titer distributions to influenza A virus

Seroepidemiological studies aim to understand population-level exposure and immunity to infectious diseases. Their results are normally presented as binary outcomes describing the presence or absence of pathogen-specific antibody, despite the fact that many assays measure continuous quantities. A population's natural distribution of antibody titers to an endemic infectious disease may include information on multiple serological states - naiveté, recent infection, non-recent infection, childhood infection - depending on the disease in question and the acquisition and waning patterns of immunity. In this study, we investigate 20,152 general-population serum samples from southern Vietnam collected between 2009 and 2013 from which we report antibody titers to the influenza virus HA1 protein using a continuous titer measurement from a protein microarray assay. We describe the distributions of antibody titers to subtypes 2009 H1N1 and H3N2. Using a model selection approach to fit mixture distributions, we show that 2009 H1N1 antibody titers fall into four titer subgroups and that H3N2 titers fall into three subgroups. For H1N1, our interpretation is that the two highest-titer subgroups correspond to recent and historical infection, which is consistent with 2009 pandemic attack rates. Similar interpretations are available for H3N2, but right-censoring of titers makes these interpretations difficult to validate.

An Epidemiological Analysis of Summer Influenza Epidemics in Okinawa

Objective This study evaluates the difference between winter influenza and summer influenza in Okinawa. Methods From January 2007 to June 2014, weekly rapid antigen test (RAT) results performed in four acute care hospitals were collected for the surveillance of regional influenza prevalence in the Naha region of the Okinawa Islands. Results An antigenic data analysis revealed that multiple H1N1 and H3N2 viruses consistently co-circulate in Okinawa, creating synchronized seasonal patterns and a high genetic diversity of influenza A. Additionally, influenza B viruses play a significant role in summer epidemics, almost every year. To further understand influenza epidemics during the summer in Okinawa, we evaluated the full genome sequences of some representative human influenza A and influenza B viruses isolated in Okinawa. Phylogenetic data analysis also revealed that multiple H1N1 and H3N2 viruses consistently co-circulate in Okinawa. Conclusion This surveillance revealed a distinct epidemic pattern of seasonal and pandemic influenza in this subtropical region.

Surveillance for seasonal influenza virus prevalence in hospitalized children with lower respiratory tract infection in Guangzhou, China during the post-pandemic era

Background

Influenza A(H1N1)pdm09, A(H3N2) and B viruses have co-circulated in the human population since the swine-origin human H1N1 pandemic in 2009. While infections of these subtypes generally cause mild illnesses, lower respiratory tract infection (LRTI) occurs in a portion of children and required hospitalization. The aim of our study was to estimate the prevalence of these three subtypes and compare the clinical manifestations in hospitalized children with LRTI in Guangzhou, China during the post-pandemic period.

Methods

Children hospitalized with LRTI from January 2010 to December 2012 were tested for influenza A/B virus infection from their throat swab specimens using real-time PCR and the clinical features of the positive cases were analyzed.

Results

Of 3637 hospitalized children, 216 (5.9%) were identified as influenza A or B positive. Infection of influenza virus peaked around March in Guangzhou each year from 2010 to 2012, and there were distinct epidemics of each subtype. Influenza A(H3N2) infection was more frequently detected than A(H1N1)pdm09 and B, overall. The mean age of children with influenza A virus (H1N1/H3N2) infection was younger than those with influenza B (34.4 months/32.5 months versus 45 months old; p<0.005). Co-infections of influenza A/ B with mycoplasma pneumoniae were found in 44/216 (20.3%) children.

Conclusions

This study contributes the understanding to the prevalence of seasonal influenza viruses in hospitalized children with LRTI in Guangzhou, China during the post pandemic period. High rate of mycoplasma pneumoniae co-infection with influenza viruses might contribute to severe disease in the hospitalized children.

Deep sequencing: becoming a critical tool in clinical virology

Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.