Decline of influenza and respiratory syncytial virus detection in facility-based surveillance during the COVID-19 pandemic,South Africa,January to October 2020

BackgroundIn South Africa, COVID-19 control measures to prevent SARS-CoV-2 spread were initiated on 16 March 2020. Such measures may also impact the spread of other pathogens, including influenza virus and respiratory syncytial virus (RSV) with implications for future annual epidemics and expectations for the subsequent northern hemisphere winter.MethodsWe assessed the detection of influenza and RSV through facility-based syndromic surveillance of adults and children with mild or severe respiratory illness in South Africa from January to October 2020, and compared this with surveillance data from 2013 to 2019.ResultsFacility-based surveillance revealed a decline in influenza virus detection during the regular season compared with previous years. This was observed throughout the implementation of COVID-19 control measures. RSV detection decreased soon after the most stringent COVID-19 control measures commenced; however, an increase in RSV detection was observed after the typical season, following the re-opening of schools and the easing of measures.ConclusionCOVID-19 non-pharmaceutical interventions led to reduced circulation of influenza and RSV in South Africa. This has limited the country’s ability to provide influenza virus strains for the selection of the annual influenza vaccine. Delayed increases in RSV case numbers may reflect the easing of COVID-19 control measures. An increase in influenza virus detection was not observed, suggesting that the measures may have impacted the two pathogens differently. The impact that lowered and/or delayed influenza and RSV circulation in 2020 will have on the intensity and severity of subsequent annual epidemics is unknown and warrants close monitoring.     

Dynamics of respiratory viruses other than SARS-CoV-2 during the COVID-19 pandemic in Madrid,Spain

The COVID-19 pandemic and the implemented control measures have impacted the circulation of respiratory-transmitted pathogens. In this report, we present data from a retrospective study that included 17,883 specimens conducted between 2018 and 2022 in our facility, describing the dynamics of circulation of the main respiratory viruses. We observed a significant decrease in all viral detections (other than SARS-CoV-2) starting from March 2020. However, rhinovirus maintained comparable levels to the pre-pandemic period. Additionally, influenza viruses were not detected during the 2020–2021 season, and respiratory syncytial virus (RSV) exhibited a shift in its seasonality, with an epidemic peak occurring in the summer of 2021.     

Transmission of paediatric respiratory syncytial virus and influenza in the wake of the COVID-19 pandemic

The non-pharmaceutical interventions implemented to slow the spread of SARS-CoV-2 have had consequences on the transmission of other respiratory viruses, most notably paediatric respiratory syncytial virus (RSV) and influenza. At the beginning of 2020, lockdown measures in the southern hemisphere led to a winter season with a marked reduction in both infections. Intermittent lockdowns in the northern hemisphere also appeared to interrupt transmission during winter 2020/21. However, a number of southern and northern hemisphere countries have now seen delayed RSV peaks. We examine the implications of these unpredictable disease dynamics for health service delivery in Europe, such as paediatric hospital and intensive care bed space planning, or palivizumab prophylaxis. We discuss the challenges for RSV vaccine trials and influenza immunisation campaigns, and highlight the considerable research opportunities that have arisen with the SARS-CoV-2 pandemic. We argue that the rapid advances in viral whole genome sequencing, phylogenetic analysis, and open data sharing during the pandemic are applicable to the ongoing surveillance of RSV and influenza. Lastly, we outline actions to prepare for forthcoming influenza seasons and for future implementation of RSV vaccines.     

Abrupt termination of the 2019/20 influenza season following preventive measures against COVID-19 in Denmark,Norway and Sweden

BackgroundIn mid-March 2020, a range of public health and social measures (PHSM) against the then new coronavirus disease (COVID-19) were implemented in Denmark, Norway and Sweden.AimWe analysed the development of influenza cases during the implementation of PHSM against SARS-CoV-2 in the Scandinavian countries.MethodBased on the established national laboratory surveillance of influenza, we compared the number of human influenza cases in the weeks immediately before and after the implementation of SARS-CoV-2 PHSM by country. The 2019/20 influenza season was compared with the five previous seasons.ResultsA dramatic reduction in influenza cases was seen in all three countries, with only a 3- to 6-week duration from the peak of weekly influenza cases until the percentage dropped below 1%. In contrast, in the previous nine influenza seasons, the decline from the seasonal peak to below 1% of influenza-positive samples took more than 10 weeks.ConclusionsThe PHSM against SARS-CoV-2 were followed by a dramatic reduction in influenza cases, indicating a wider public health effect of the implemented measures.     

Impact of non-pharmaceutical interventions targeted at COVID-19 pandemic on influenza burden – a systematic review

ObjectivesTo better understand the impact of comprehensive COVID-19 targeted non-pharmaceutical interventions (NPIs) on influenza burden worldwide.MethodsWe conducted a systematic literature search in selected databases (PubMed, WHO COVID-19), preprint servers (medRxiv, bioRxiv) and websites of European Public Health institutes. Documents that compared influenza estimates in the 2019/2020 season with previous seasons were included. Information synthesis was qualitative due to a high heterogeneity in the number and periods of comparative seasons, outcome measures and statistical methods.ResultsWe included 23 records reporting from 15 countries/regions as well as 8 reports from European Public Health agencies. Estimates in the 2019/2020 season based on influenza virus tests (4 out of 7 countries/regions), defined influenza cases (8 out of 9), influenza positivity rate (7 out of 8), and severe complications (1 out of 2) were lower than in former seasons. Results from syndromic indicators, such as influenza-like-illness (ILI), were less clear or even raised (4 out of 7) after the influenza season indicating a misclassification with COVID-19 cases.ConclusionsEvidence synthesis suggests that NPIs targeted at SARS-CoV-2-transmission reduce influenza burden as well. Low threshold NPIs need to be more strongly emphasized in influenza prevention strategies.     

Foodborne and Animal Contact Disease Outbreaks: National influenza mid-season report, 2020–2021

Canada’s national influenza season typically starts in the latter half of November (week 47) and is defined as the week when at least 5% of influenza tests are positive and a minimum of 15 positive tests are observed. As of December 12, 2020 (week 50), the 2020–2021 influenza season had not begun. Only 47 laboratory-confirmed influenza detections were reported from August 23 to December 12, 2020; an unprecedentedly low number, despite higher than usual levels of influenza testing. Of this small number of detections, 64% were influenza A and 36% were influenza B. Influenza activity in Canada was at historically low levels compared with the previous five seasons. Provinces and territories reported no influenza-associated adult hospitalizations. Fewer than five hospitalizations were reported by the paediatric sentinel hospitalization network. With little influenza circulating, the National Microbiology Laboratory had not yet received samples of influenza viruses collected during the 2020–2021 season for strain characterization or antiviral resistance testing. The assessment of influenza vaccine effectiveness, typically available in mid-March, is expected to be similarly limited if low seasonal influenza circulation persists. Nevertheless, Canada’s influenza surveillance system remains robust and has pivoted its syndromic, virologic and severe outcomes system components to support coronavirus disease 2019 (COVID-19) surveillance. Despite the COVID-19 pandemic, the threat of influenza epidemics and pandemics persists. It is imperative 1) to maintain surveillance of influenza, 2) to remain alert to unusual or unexpected events and 3) to be prepared to mitigate influenza epidemics when they resurge.     

Increased influenza severity in children in the wake of SARS-CoV-2

The SARS-CoV-2 pandemic and subsequent interruption of influenza circulation has lowered population immunity to influenza, especially among children with few prepandemic exposures. Using data from a prospective pediatric cohort study based in Managua, Nicaragua, we compared the incidence and severity of influenza A/H3N2 and influenza B/Victoria between 2022 and two prepandemic seasons. We found a higher incidence of A/H3N2 in older children in 2022 compared with pre-2020 and a higher proportion of severe influenza in 2022, primarily among children aged 0–4, suggesting an influence of the SARS-CoV-2 pandemic on influenza incidence and severity in children.     

Effectiveness of newly applied infection control policies to suppress the number of cases with hospital-acquired influenza infection at Iwate Medical University Hospital--comparison of the 2004/5 and 2005/6 seasons

Iwate Medical University Hospital (IMUH) is a general regional hospital with approximately 1,000 beds and emergency facilities. Due to the increased prevalence of cases of hospital-acquired influenza during the 2004/5 epidemic season, measures to systematically and comprehensively prevent the spread of seasonal influenza such as reinforcement of the active surveillance of influenza and adequacy of patient placement and the introduction of a new zoning system based on transmission-based precautions, were implemented. This report compares pre-and post intervention, and analyzes the impact on the prevalence of hospital-acquired influenza patients. Comparison of the prevalence of the 2005/6 season and 2004/5 season, irrespective of the fact that patients with influenza upon admission to the hospital doubled from 9 patients to 18, the number of influenza patients assumed to have secondary infections within the hospital markedly decreased from 48 to 20. In the 2004/5 season, a significant correlation was seen between the increase in the number of community-acquired influenza infections and the number of hospital-acquired ones. In contrast, no significant relationship was seen in the 2005/6 season. To exclude any influence due to seasonal differences in influenza epidemics, the secondary infection rate index one showed a decrease from of 36.8% to 23.7%. Based on the above results, influenza measures at IMUH in the 2005/6 season are considered to have suppresses the number of secondary infections occurring within the hospital.     

Spotlight influenza: The 2019/20 influenza season and the impact of COVID-19 on influenza surveillance in the WHO European Region

BackgroundAnnual seasonal influenza activity in the northern hemisphere causes a high burden of disease during the winter months, peaking in the first weeks of the year.AimWe describe the 2019/20 influenza season and the impact of the COVID-19 pandemic on sentinel surveillance in the World Health Organization (WHO) European Region.MethodsWe analysed weekly epidemiological and virological influenza data from sentinel primary care and hospital sources reported by countries, territories and areas (hereafter countries) in the European Region.ResultsWe observed co-circulation of influenza B/Victoria-lineage, A(H1)pdm09 and A(H3) viruses during the 2019/20 season, with different dominance patterns observed across the Region. A higher proportion of patients with influenza A virus infection than type B were observed. The influenza activity started in week 47/2019, and influenza positivity rate was ≥ 50% for 2 weeks (05–06/2020) rather than 5–8 weeks in the previous five seasons. In many countries a rapid reduction in sentinel reports and the highest influenza activity was observed in weeks 09–13/2020. Reporting was reduced from week 14/2020 across the Region coincident with the onset of widespread circulation of SARS-CoV-2.ConclusionsOverall, influenza type A viruses dominated; however, there were varying patterns across the Region, with dominance of B/Victoria-lineage viruses in a few countries. The COVID-19 pandemic contributed to an earlier end of the influenza season and reduced influenza virus circulation probably owing to restricted healthcare access and public health measures.     

Estimates of mortality attributable to COVID-19: a statistical model for monitoring COVID-19 and seasonal influenza,Denmark, spring 2020

BackgroundTimely monitoring of COVID-19 impact on mortality is critical for rapid risk assessment and public health action.AimBuilding upon well-established models to estimate influenza-related mortality, we propose a new statistical Attributable Mortality Model (AttMOMO), which estimates mortality attributable to one or more pathogens simultaneously (e.g. SARS-CoV-2 and seasonal influenza viruses), while adjusting for seasonality and excess temperatures.MethodsData from Nationwide Danish registers from 2014-week(W)W27 to 2020-W22 were used to exemplify utilities of the model, and to estimate COVID-19 and influenza attributable mortality from 2019-W40 to 2020-W20.ResultsSARS-CoV-2 was registered in Denmark from 2020-W09. Mortality attributable to COVID-19 in Denmark increased steeply, and peaked in 2020-W14. As preventive measures and national lockdown were implemented from 2020-W12, the attributable mortality started declining within a few weeks. Mortality attributable to COVID-19 from 2020-W09 to 2020-W20 was estimated to 16.2 (95% confidence interval (CI): 12.0 to 20.4) per 100,000 person-years. The 2019/20 influenza season was mild with few deaths attributable to influenza, 3.2 (95% CI: 1.1 to 5.4) per 100,000 person-years.ConclusionAttMOMO estimates mortality attributable to several pathogens simultaneously, providing a fuller picture of mortality by COVID-19 during the pandemic in the context of other seasonal diseases and mortality patterns. Using Danish data, we show that the model accurately estimates mortality attributable to COVID-19 and influenza, respectively. We propose using standardised indicators for pathogen circulation in the population, to make estimates comparable between countries and applicable for timely monitoring.     

Influenza Vaccine: Influenza vaccine during the 2019–2020 season and COVID-19 risk: A case-control study in Québec

BackgroundWe carried out a case-control study that examined whether receipt of the inactivated influenza vaccine during the 2019–2020 season impacted on the risk of coronavirus disease 2019 (COVID-19), as there was a concern that the vaccine could be detrimental through viral interference.MethodsA total of 920 cases with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (diagnosed between March and October 2020) and 2,123 uninfected controls were recruited from those who were born in Québec between 1956 and 1976 and who had received diagnostic services at two hospitals (Montréal and Sherbrooke, Québec). After obtaining consent, a questionnaire was administered by phone. Data were analyzed by logistic regression.ResultsAmong healthcare workers, inactivated influenza vaccine received during the previous influenza season was not associated with increased COVID-19 risk (AOR: 0.99, 95% CI: 0.69–1.41). Among participants who were not healthcare workers, influenza vaccination was associated with lower odds of COVID-19 (AOR: 0.73, 95% CI 0.56–0.96).ConclusionWe found no evidence that seasonal influenza vaccine increased the risk of developing COVID-19.     

Successful Management of Subacute Thyroiditis Following SARS-CoV-2 Infection

Subacute thyroiditis (SAT) is a disorder of the thyroid gland and difficult to diagnose. It is probably triggered by a viral infection. Recently, several articles have reported SAT after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, reports describing SAT after SARS-CoV-2 in Japan are lacking. We herein report the first case of SAT after SARS-CoV-2 infection in Japan. After SARS-CoV-2 infection, some patients can develop not only pneumonia but also SAT. Thus, a careful follow-up is recommended for patients after SARS-CoV-2 infection. Furthermore, the effect of SARS-CoV-2 infection on thyroid dysfunction should not be ignored.     

Eleven cases of co-infection with influenza type A and type B suspected by use of a rapid diagnostic kit and confirmed by RT-PCR and virus isolation

In the 2004/05 influenza season there were epidemics of influenza caused by several types of viruses (type B and A (H3) viruses, and type B, A (H3), and A (H1) viruses) in many areas of Japan. In such epidemics a single individual could be co-infected with several influenza viruses. From February to March in 2005, we examined 15 patients who were positive for influenza type A and B viruses when tested with a rapid diagnostic kit. The type A (H3) and B influenza virus genes were successfully amplified by RT-PCR in 10 of the 15 patients, confirming that they were co-infected with type A (H3) and B viruses. The type A (H1) and B virus genes were successfully amplified in another patient, confirming that the patient was co-infected with type A (H1) and B viruses. By contrast, 2 patients were clearly positive for type A and B viruses according to the rapid diagnostic kit, but positive for type B virus alone by RT-PCR. No influenza virus genes were detected by RT-PCR in the remaining 2 patients. To isolate one type from a mixture of two different types of influenza viruses in a specimen, we neutralized one of the types with type-specific antiserum, and isolated the other with MDCK (+) cells. The results obtained by virus isolation were identical to those obtained by RT-PCR. Influenza viruses corresponding to the results of RT-PCR were isolated from 9 of the 11 patients in which isolation was attempted. No viruses were isolated from the 2 patients in whom no virus genes were detectable by RT-PCR. Based on these results we concluded that 11 of 15 patients who were positive for type A and B viruses according to the rapid diagnostic kit were co-infected with type A (H3) or A (H1) and B virus. When several types of influenza viruses are prevalent, as in the 2004/05 influenza season, the possibility of a patient being co-infected with more than one type of influenza virus should be considered.     

The importance of influenza vaccination during the COVID-19 pandemic

The COVID-19 pandemic and the measures taken to mitigate its spread have had a dramatic effect on the circulation patterns of other respiratory viruses, most especially influenza viruses. Since April 2020, the global circulation of influenza has been markedly reduced; however, it is still present in a number of different countries and could pose a renewed threat in the upcoming Northern Hemisphere winter. Influenza vaccination remains the most effective preventive measure that we have at our disposal against influenza infections and should not be ignored for the 2021–2022 season.     

Anti-SARS-CoV-2 antibody testing in IBD healthcare professionals: are we currently able to provide COVID-free IBD clinics?

Abstract

Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spread worldwide triggering a pandemic during the year 2020. The proportion of persons infected with SARS-CoV-2 whose infection remained subclinical is not known. However, such information is important to determine whether the control measures currently employed are sufficient to halt the spread of the virus. Current study has examined the seroprevalence of anti–SARS-CoV-2 antibodies in a population of 92 healthcare professionals working with patients with inflammatory bowel disease (IBD). The enzyme-linked immunosorbent assay (ELISA) test system for SARS-CoV-2 IgG from EUROIMMUN Medizinische Labordiagnostika AG (Germany) was used. Very low herd antibody-mediated immunity was proven, less than 2%, although we have been faced with the COVID-19 pandemic for several months. Anti-SARS-CoV-2 IgG antibody testing is currently unable to provide sufficient information about our anti-infectious immunity.     

Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

Populations of seasonal influenza virus experience strong annual bottlenecks that pose a considerable extinction risk. It has been suggested that an influenza source population located in tropical Southeast or East Asia seeds annual temperate epidemics. Here we investigate the seasonal dynamics and migration patterns of influenza A H3N2 virus by analysis of virus samples obtained from 2003 to 2006 from Australia, Europe, Japan, New York, New Zealand, Southeast Asia, and newly sequenced viruses from Hong Kong. In contrast to annual temperate epidemics, relatively low levels of relative genetic diversity and no seasonal fluctuations characterized virus populations in tropical Southeast Asia and Hong Kong. Bayesian phylogeographic analysis using discrete temporal and spatial characters reveal high rates of viral migration between urban centers tested. Although the virus population that migrated between Southeast Asia and Hong Kong persisted through time, this was dependent on virus input from temperate regions and these tropical regions did not maintain a source for annual H3N2 influenza epidemics. We further show that multiple lineages may seed annual influenza epidemics, and that each region may function as a potential source population. We therefore propose that the global persistence of H3N2 influenza A virus is the result of a migrating metapopulation in which multiple different localities may seed seasonal epidemics in temperate regions in a given year. Such complex global migration dynamics may confound control efforts and contribute to the emergence and spread of antigenic variants and drug-resistant viruses.     

Gastrointestinal manifestations of human immunodeficiency virus and coronavirus disease 2019: Understanding the intersecting regions between the two epidemics

In March 2020, the World Health Organization declared coronavirus disease (COVID-19) a pandemic. As of February 2021, there were 107 million COVID-19 cases worldwide. As a comparison, there are approximately 38 million people living with human immunodeficiency virus (PLHIV) worldwide. The coexistence of both epidemics, and the syndemic effect of both viruses could lead to a delirious impact both at individual and community levels. Many intersecting points were found between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19, and HIV; among which, gastrointestinal (GI) manifestations are the most notable.GI manifestations represent a common clinical presentation in both HIV and SARS-CoV-2. The emergence of GI symptoms as a result of SARS-CoV-2 infection provides a new dynamic to COVID-19 diagnosis, management, and infection control measures, and adds an additional diagnostic challenge in case of coinfection with HIV. The presence of GI manifestations in PLHIV during the COVID-19 pandemic could be referred to HIV enteropathy, presence of opportunistic infection, adverse effect of antiretrovirals, or coinfection with COVID-19. Thus, it is important to exclude SARS-CoV-2 in patients who present with new-onset GI manifestations, especially in PLHIV, to avoid the risk of disease transmission during endoscopic interventions.Structural similarities between both viruses adds a valuable intersecting point, which has mutual benefits in the management of both viruses. These similarities led to the hypothesis that antiretrovirals such as lopinavir/Rironavir have a role in the management of COVID-19, which was the target of our search strategy using the available evidence. These similarities may also facilitate the development of an efficient HIV vaccine in the future using the advances in COVID-19 vaccine development.     

Reducing contacts to stop SARS-CoV-2 transmission during the second pandemic wave in Brussels,Belgium, August to November 2020

To evaluate the effect of physical distancing and school reopening in Brussels between August and November 2020, we monitored changes in the number of reported contacts per SARS-CoV-2 case and associated SARS-CoV-2 transmission. The second COVID-19 pandemic wave in Brussels was the result of increased social contact across all ages following school reopening. Physical distancing measures including closure of bars and restaurants, and limiting close contacts, while primary and secondary schools remained open, reduced social mixing and controlled SARS-CoV-2 transmission.     

Hospital-Acquired SARS-CoV-2 infection among patients admitted to a university hospital

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a public health emergency, as it is a highly contagious disease, health services had to adapt to the high demand for hospitalizations in order to contain hospital outbreaks. We aimed to identify the impact of nosocomial transmission of severe acute respiratory coronavirus virus 2 among inpatients at a university hospital in São Paulo, Brazil. Among 455 inpatients diagnosed with coronavirus disease 2019 in March–May, 2020, nosocomial infection was implicated in 42 (9.2%), of whom 23 (54.7%) died. becoming routine, especially when community transmission occur with high levels of incidence. It was possible to observe with this study that the nosocomial transmission by SARS-CoV-2 was present even with these measures instituted, and some of the damages caused by these infections are intangible.     

Acute bronchiolitis during the COVID-19 pandemic

IntroductionThe autumn and winter bronchiolitis epidemics have virtually disappeared in the first year of the COVID-19 pandemic.Our objectives were characterised bronchiolitis during fourth quarter of 2020 and the role played by SARS-CoV-2.MethodsProspective multi-centre study performed in Madrid (Spain) between October and December 2020 including all children admitted with acute bronchiolitis. Clinical data were collected and multiplex PCR for respiratory viruses were performed.ResultsThirty-three patients were hospitalised with bronchiolitis during the study period: 28 corresponded to rhinovirus (RV), 4 to SARS-CoV-2, and 1 had both types of infection. SAR-CoV-2 bronchiolitis were comparable to RV bronchiolitis except for a shorter hospital stay. A significant decrease in the admission rate for bronchiolitis was found and no RSV was isolated.ConclusionSARS-CoV-2 infection rarely causes acute bronchiolitis and it is not associated with a severe clinical course. During COVID-19 pandemic period there was a marked decrease in bronchiolitis cases.