Does Avian Coronavirus Co-Circulate with Avian Paramyxovirus and Avian Influenza Virus in Wild Ducks in Siberia?

Avian coronaviruses (ACoV) have been shown to be highly prevalent in wild bird populations. More work on avian coronavirus detection and diversity estimation is needed for the breeding territories of migrating birds, where the high diversity and high prevalence of Orthomyxoviridae and Paramyxoviridae have already been shown in wild birds. In order to detect ACoV RNA, we conducted PCR diagnostics of cloacal swab samples from birds, which we monitored during avian influenza A virus surveillance activities. Samples from two distant Asian regions of Russia (Sakhalin region and Novosibirsk region) were tested. Amplified fragments of the RNA-dependent RNA-polymerase (RdRp) of positive samples were partially sequenced to determine the species of Coronaviridae represented. The study revealed a high presence of ACoV among wild birds in Russia. Moreover, there was a high presence of birds co-infected with avian coronavirus, avian influenza virus, and avian paramyxovirus. We found one case of triple co-infection in a Northern Pintail (Anas acuta). Phylogenetic analysis revealed the circulation of a Gammacoronavirus species. A Deltacoronavirus species was not detected, which supports the data regarding the low prevalence of deltacoronaviruses among surveyed bird species.

An assessment of the current epidemiological and laboratory capacities for influenza-like illnesses and severe acute respiratory infection surveillance, Yemen 2022.

Background and Objectives: We aim to re-activate influenza sentinel surveillance system in Yemen after disruption related to repurposing for COVID-19 pandemic. WHO Country Office (CO) in collaboration with Yemen's Ministry of Public Health and Population (MOPH&P) jointly conducted an assessment mission to assess the current situation of the influenza sentinel surveillance system and assess its capacity to detect influenza epidemics and monitor trends in circulating influenza and other respiratory viruses of epidemic and pandemic potential. This study presents the results of the assessment for three sentinel sites located in Aden, Taiz, and Hadramout/Mukalla. Methodology: A mixed methods approach was used to guide the assessment process and to help achieve the objectives. Data were collected as follows: desk review of the sentinel sites records and data; interviews with stakeholders, including key informants and partners; and direct observation through field visits to the sentinel sites, MOPH&P and the Central Public Health Laboratory (CPHL). Two assessment checklists were used: assessment of sentinel sites for SARI surveillance, and checklist for assessment of availability of SARI sentinel surveillance. Results and Conclusion: COVID-19 has affected health systems and services, and this was demonstrated in this assessment. The influenza sentinel surveillance system in Yemen is not effectively functional; however, there is plenty of room for improvement if investment in the system's restructuring, training, building technical and laboratory capacities, and conducting continuous and regular supervision visits.

Epidemiological investigation of the first locally acquired case of COVID-19 identified by influenza surveillance-Taiwan, February 2020.

BACKGROUND: COVID-19 and influenza have similar clinical presentations that can range from mild to severe disease. The World Health Organization recommends that countries use existing influenza surveillance to monitor COVID-19 transmission in communities. We aim to describe the surveillance and investigation of COVID-19 at the early stage of the pandemic in Taiwan. METHODS: In February 2020, the Taiwan Centers for Disease Control enhanced COVID-19 surveillance through its existing influenza surveillance. We retrospectively tested patients for SARS-CoV-2 who had symptoms of severe complicated influenza but were negative in influenza testing. We conducted an epidemiological investigation and contact tracing for the index patient and secondary cases to prevent virus transmission. RESULTS: We identified the first COVID-19 patient on February 15 through enhanced COVID-19 surveillance. He had no history of traveling abroad and an unclear history of contact with COVID-19 cases. He presented with influenza-like illness on January 27 and was hospitalized from February 3 to 15. We identified 39 close contacts of the index patient, including 11 family members and 28 healthcare workers. In total, four close family contacts of the index patient tested positive for SARS-CoV-2. An additional 84 close contacts of the four secondary cases were identified and traced; none was diagnosed with COVID-19. CONCLUSIONS: We recommend enhancing COVID-19 surveillance by testing patients with influenza-like illness. To prevent the spread of COVID-19, we recommend using appropriate personal protective equipment when in close contact with patients who present with influenza-like illness or when caring for patients with pneumonia of unknown etiology.

High Influenza Vaccine Effectiveness and Absence of Increased Influenza-like-Illness Epidemic Activity in the 2021-2022 Influenza Season in Catalonia (Spain) Based on Surveillance Data Collected by Sentinel Pharmacies.

Influenza surveillance and influenza vaccination are the key activities for preventing and controlling influenza epidemics. The study assessed the influenza surveillance and influenza vaccination data obtained from sentinel pharmacies of Catalonia, Spain, in the 2021-2022 influenza season. The sentinel pharmacies were selected from all community pharmacies to report all influenza-like illness (ILI) cases detected during the 2021-2022 influenza season and collect influenza surveillance and influenza vaccination data. The ILI cases were identified based on European Centre for Disease Control (ECDC) criteria. The moving epidemic method (MEM) was used to assess the ILI epidemic activity. The screening method was used to assess influenza vaccination effectiveness in patients aged 65-or-more years old. The sentinel pharmacies reported 212 ILI cases with a negative COVID-19 test and a total number of 412 ILI cases. An absence of increased ILI epidemic activity was observed in the 2021-2022 influenza season based on two criteria: (1) Number of ILI cases reported per week in the 2021-2022 influenza season significantly lower than the MEM-based epidemic threshold. (2) Mean number of ILI cases reported per week in the 2021-2022 influenza season significantly lower than during the ILI/influenza epidemic periods detected from 2017 to 2020 using the same methodology. Influenza vaccination was effective in preventing ILI among patients aged 65-or-more-years old. The absence of the influenza epidemic during the 2021-2022 influenza season could be explained by influenza vaccination and COVID-19 prevention measures (wearing face masks, social distancing). The sentinel pharmacies provided influenza surveillance data not provided by traditional influenza surveillance systems.

Rapid influenza molecular testing in secondary care and influenza surveillance in England: Any impact?

INTRODUCTION: The use of rapid molecular testing for influenza diagnosis is becoming increasingly popular. Used at the point of care or in a clinical laboratory, these tests detect influenza A and B viruses, though many do not distinguish between influenza A subtypes. The UK Severe Influenza Surveillance System (USISS) collects surveillance data on laboratory-confirmed influenza admissions to secondary care in England. This study set out to understand how rapid influenza molecular testing was being used and how it might influence the availability of subtyping data collected on influenza cases admitted to secondary care in England. METHODS: At the end of the 2017/2018 and 2018/2019 influenza seasons, a questionnaire was sent to all National Health Service Hospital Trusts in England to evaluate the use of rapid influenza testing. Surveillance data collected through USISS was analysed from 2011/2012 to 2020/2021. RESULTS: Of responding trusts, 42% (13/31) in 2017/2018 and 55% (9/17) in 2018/2019 used rapid influenza molecular tests, either alone or in combination with other testing. The majority of rapid tests used did not subtype the influenza A result, and limited follow-up testing occurred. Surveillance data showed significant proportions of influenza A hospital and intensive care unit/high dependency unit admissions without subtyping information, increasing by approximately 35% between 2012/2013 and 2020/2021. CONCLUSIONS: The use of rapid influenza molecular tests is a likely contributing factor to the large proportion of influenza A hospitalisations in England that were unsubtyped. Given their clear clinical advantages, further work must be done to reinforce these data for public health through integrated genomic surveillance.

Global respiratory virus surveillance: strengths, gaps, and way forward.

CURRENT SITUATION: The global influenza surveillance and response system (GISRS), coordinated by the World Health Organization (WHO), is a global framework for surveillance of influenza and other respiratory viruses, data collection, laboratory capacity building, genomic data submission and archival, standardization, and calibration of reagents and vaccine strains, production of seasonal influenza vaccines and creating a facilitatory regulatory environment for the same. GAPS: WHO-designated national influenza centers (NICs) are entrusted with establishing surveillance in their respective countries. National and subnational surveillance remains weak in most parts of the world because of varying capacities of the NICs, lack of funds, poor human and veterinary surveillance mechanisms, lack of intersectoral coordination, and varying commitments of the local government. WAY FORWARD: As influenza viruses have a wide variety of nonhuman hosts, it is critical to strengthen surveillance at local levels for timely detection of untypable or novel strains with potential to cause epidemics or pandemics. In this article, we have proposed possible strategies to strengthen and expand local capacities for respiratory virus surveillance through the designated NICs of the WHO.

Prevalence of COVID-19 and the Continued Citizen-Based Control in Japan.

Since an outbreak of COVID-19 was detected among the crew and passengers of the Diamond Princess cruise ship in early 2020, the total number of cases of SARS-CoV-2 has surpassed 440,000 in Japan. However, that number remains small compared with other countries, such as the United States, a few European countries, and China. Despite the Japanese government not imposing a lockdown or implementing large-scale testing at the municipal level, the country has managed to contain the smaller outbreaks. To avoid infection, it is important to wear a face mask, wash one's hands, and observe social distancing. In addition, we focus on the clinical laboratory testing performed using the latest technology to detect SARS-CoV-2 RNA in a hospital in Yokohama, Japan. Large-scale testing of viral RNA would be useful for detecting asymptomatic virus carriers as is done in other countries, and could be carried out as a future measure for controlling COVID-19.

Accuracy of State-Level Surveillance during Emerging Outbreaks of Respiratory Viruses: A Model-Based Assessment.

It is long perceived that the more data collection, the more knowledge emerges about the real disease progression. During emergencies like the H1N1 and the severe acute respiratory syndrome coronavirus 2 pandemics, public health surveillance requested increased testing to address the exacerbated demand. However, it is currently unknown how accurately surveillance portrays disease progression through incidence and confirmed case trends. State surveillance, unlike commercial testing, can process specimens based on the upcoming demand (e.g., with testing restrictions). Hence, proper assessment of accuracy may lead to improvements for a robust infrastructure. Using the H1N1 pandemic experience, we developed a simulation that models the true unobserved influenza incidence trend in the State of Michigan, as well as trends observed at different data collection points of the surveillance system. We calculated the growth rate, or speed at which each trend increases during the pandemic growth phase, and we performed statistical experiments to assess the biases (or differences) between growth rates of unobserved and observed trends. We highlight the following results: 1) emergency-driven high-risk perception increases reporting, which leads to reduction of biases in the growth rates; 2) the best predicted growth rates are those estimated from the trend of specimens submitted to the surveillance point that receives reports from a variety of health care providers; and 3) under several criteria to queue specimens for viral subtyping with limited capacity, the best-performing criterion was to queue first-come, first-serve restricted to specimens with higher hospitalization risk. Under this criterion, the lab released capacity to subtype specimens for each day in the trend, which reduced the growth rate bias the most compared to other queuing criteria. Future research should investigate additional restrictions to the queue.