MONITORING OF RESPIRATORY VIRUS COINFECTION IN SOUTHERN BRAZIL DURING COVID-19 PANDEMIC (preprint)

Since December 2019, the COVID-19 pandemic caused by SARS-CoV-2 has reached approximately 769 million people, leading to more than 7 million deaths worldwide. Faced with the possible presence of other respiratory pathogens that could co-infect and modify the clinical response of patients detected for SARS-CoV-2, some researchers have explored this line of investigation. The relationship between these co-infections remains unclear, leading to a need to deepen our knowledge about interactions among pathogens, and between pathogens and the host. Thus, the present study employed RT-qPCR to assess the presence of Human Adenovirus (HAdV), Influenza A (Flu A), Influenza B (Flu B), Human Metapneumovirus (HMPV), Respiratory Syncytial Virus (RSV), Human Rhinovirus (HRV), and Parainfluenza Virus (PIV). A total of 187 nasopharyngeal samples from adult patients exhibiting respiratory symptoms were collected between February 2021 and November 2022 at the University Hospital Polydoro Ernani de Sao Thiago in Florianopolis, SC, Brazil. Our findings revealed that 25.16% of samples tested positive for non-SARS-CoV-2 respiratory viruses (29.8% - HRV, 5.3% - PIV, 4.3%-RSV, and 1.1% - HMPV). From the 74.84% of SARS-CoV-2 positive patients, the presence of co-infection was observed in 9,7% of patients, with 7.5% being HRV, 1.1% HAdV and 1.1% Flu A. Since co-infections can potentially alter patient prognoses and impact local epidemiological dynamics, this study highlights the significance of ongoing monitoring and epidemiological assessment through genomic surveillance of other clinically relevant respiratory pathogens.

Direct genome sequencing of respiratory viruses from low viral load clinical specimens using target capture sequencing technology (preprint)

The use of metagenomic next-generation sequencing technology to obtain complete viral genome sequences directly from clinical samples with low viral load remains challenging--especially in the case of respiratory viruses--due to the low copy number of viral versus host genomes. To overcome this limitation, target capture sequencing for the enrichment of specific genomes has been developed and applied for direct genome sequencing of viruses. However, as the efficiency of enrichment varies depending on the probes, the type of clinical sample, etc., validation is essential before target capture sequencing can be applied to clinical diagnostics. Here we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A. We focused on clinical specimens containing low copy numbers of viral genomes. Target capture sequencing yielded approximately 180- and 2000-fold higher read counts of SARS-CoV-2 and influenza A virus, respectively, than metagenomic sequencing when the RNA extracted from specimens contained 59.3 copies/L of SARS-CoV-2 or 544 copies/L of influenza A virus, respectively. In addition, the target capture sequencing identified sequence reads in all SARS-CoV-2- or influenza type A-positive specimens with <26 RNA copies/L, some of which also yielded >70% of the full-length genomes of SARS-CoV-2 or influenza A virus. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with viruses other than SARS-CoV-2, suggesting that this approach will not only detect a wide range of viruses, but also contribute to epidemiological studies.

Molecular epidemiology of invasive Group A Streptococcal infections before and after the COVID-19 pandemic in Switzerland (preprint)

Group A Streptococcus (GAS, aka Streptococcus pyogenes) poses a significant public health concern, causing a diverse spectrum of infections with high mortality rates. Following the COVID-19 pandemic, a resurgence of invasive GAS (iGAS) infections has been documented, necessitating efficient outbreak detection methods. Whole genome sequencing (WGS) serves as the gold standard for GAS molecular typing, albeit constrained by time and costs. This study aimed to characterize the postpandemic increased prevalence of iGAS on the molecular epidemiological level in order to assess whether new, more virulent variants have emerged, as well as to assess the performance of the rapid and cost-effective Fourier-transform infrared (FTIR) spectroscopy as an alternative to WGS for detecting and characterizing GAS transmission routes. A total of 66 iGAS strains isolated from nine Swiss hospitals during the COVID-19 post-pandemic increased GAS prevalence were evaluated and compared to 15 strains collected before and 12 during the COVID-19 pandemic. FT-IR measurements and WGS were conducted for network analysis. Demographic, clinical, and epidemiological data were collected. Skin and soft tissue infection was the most common diagnosis, followed by primary bacteremia and pneumonia. Viral co-infections were found in 25% of cases and were significantly associated with more severe disease requiring intensive care unit admission. WGS analysis did not reveal emerging GAS genetic distinct variants after the COVID-19 pandemic, indicating the absence of a pandemic-induced shift. FT-IR spectroscopy exhibited limitations in differentiating genetically distant GAS strains, yielding poor overlap with WGS-derived clusters. The emm1/ST28 gebotype was predominant in our cohort and was associated with five of the seven deaths recorded, in accordance with the molecular epidemiological data before the pandemic. Additionally, no notable shift in antibiotic susceptibility patterns was observed. Our data suggest that mainly non-pathogen related factors contributed to the recent increased prevalence of iGAS.

Etiological analysis of acute respiratory infections in hospitalized children after the relaxation of COVID-19 non-pharmacological interventions in Quzhou, China (preprint)

Background: Acute respiratory infections (ARIs) can cause morbidity and mortality in children. This study was to determine the characteristics of pathogens in hospitalized children with ARIs after the relaxation of COVID-19 non-pharmacological interventions (NPIs) in Quzhou, China. Methods: Hospitalized children with ARIs were enrolled between May and October 2023, and thirteen common respiratory pathogens were tested by fluorescent quantitative polymerase chain reaction. Mono- and co-infections were assessed, and the association between pathogens and age was explored using restricted cubic spline analysis. Results: A total of 1225 children were included, 820 of them detected one pathogen and 238 of them detected two or more pathogens. Children aged 1-3 years had the highest positive detection rates. The dominant pathogen varied monthly. Mycoplasma pneumoniae (Mp) was the most common pathogen in monoinfection, followed by respiratory syncytial virus (RSV) and human rhinovirus (HRV), while influenza virus was detected at a lower rate. Mp+HRV was the most common combination of coinfections. The detection rates of Mp and HRV were higher in coinfections than in monoinfection, but there was no difference in the detection rate of RSV. In the restricted cubic spline models, a J-shaped association was consistently observed between age and Mp infection, the risk of HRV first increased and then decreased, the risk of RSV was relatively flat until 1.5 years and then decreased raplidly. Conclusion: Our study revealed the epidemiological characteristics of ARIs pathogens after the relaxation of NPIs. There is still a need to enhanced pathogen surveillance, especially for Mp.

Coxsackievirus A7 and Enterovirus A71 Significally Reduce SARS-CoV-2 Infection in Cell and Animal Models (preprint)

In this study, we investigated the features of co-infection with SARS-CoV-2 and nonpathogenic strain LEV8 of coxsackievirus A7 or enterovirus A71 for Vero E6 cells and Syrian hamsters. The investigation of co-infection with SARS-СoV-2 and LEV-8 or EV-A71 in the cell model was shown that a competitive inhibitory effect for these viruses were especially significant against SARS-CoV-2. Pre-infection with enteroviruses in animals caused more than a 100-fold decrease in the levels of SARS-CoV-2 virus replication in the respiratory tracts and more rapid clearance of the lower respiratory tract from infectious SARS-CoV-2. Co-infection with SARS-CoV-2 and LEV-8 or EV-A71 also reduced the severity of clinical manifestations of the SARS-CoV-2 infection for animals. Additionally, the histological data illustrated that co-infection with nonpathogenic coxsackievirus decreased the level of pathological changes by SARS-CoV-2 in the lungs. Research into the chemokine/cytokine profile demonstrated that the studied enteroviruses efficiently triggered this part of antiviral immune response, which can be associated with significant inhibition of SARS-CoV-2 infection. These results demonstrate that there exists a strong viral interference between the studied nonpathogenic strain of coxsackievirus A7 or enteroviruses A71 and SARS-CoV-2 pathogenic for humans in vitro and in vivo.

Exploring the therapeutic potential of defective interfering particles in reducing the replication of SARS-CoV-2 (preprint)

SARS-CoV-2 still presents a global threat to human health due to the continued emergence of new strains and waning immunity amongst vaccinated populations. Therefore, it is still relevant to investigate potential therapeutics, such as therapeutic interfering particles (TIPs). Mathematical and computational modelling are valuable tools to study viral infection dynamics for predictive analysis. Here, we expand on the previous work by Grebennikov et al. (2021) on SARS-CoV-2 intra-cellular replication dynamics to include defective interfering particles (DIPs) as potential therapeutic agents. We formulate a deterministic model that describes the replication of wild-type (WT) SARS-CoV-2 virus in the presence of DIPs. Sensitivity analysis of parameters to several model outputs is employed to inform us on those parameters to be carefully calibrated from experimental data. We then study the effects of co-infection on WT replication and how DIP dose perturbs the release of WT viral particles. Furthermore, we provide a stochastic formulation of the model that is compared to the deterministic one. These models could be further developed into population-level models or used to guide the development and dose of TIPs.

Oro-faecal transmission of SARS-CoV-2: A systematic review of studies employing viral culture from gastrointestinal and other potential sources (preprint)

Background. The extent to which the oro-faecal route contributes to the transmission of SARS-CoV-2 is not established. Methods: We systematically reviewed the evidence on the presence of infectious SARS-CoV-2 in faeces and other gastrointestinal sources by examining studies that used viral culture to investigate the presence of replication-competent virus in these samples. We conducted searches in the WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 using keywords and associated synonyms, with a search date up to 28th of November 2023. Results: We included 13 studies involving 328 COVID-19 subjects - providing 314 faecal or rectal swab SARS-CoV2 positive samples tested also with viral culture. The methods used for viral culture across the studies were heterogeneous. Three studies (2 cohorts and 1 case-series) reported observing replication-competent SARS-CoV-2 confirmed by quantitative RT-PCR (qPCR) and whole genome sequencing, and qPCR including appropriate cycle threshold changes. Overall, six (1.9%) of 314 faecal samples subjected to cell culture showed replication-competent virus. One study found replication competent samples from one immunocompromised patient. No studies were identified demonstrating direct evidence of oro-faecal transmission to humans. Conclusions: Our review found a relatively low frequency of replication-competent SARS-CoV-2 in faecal and other gastrointestinal sources. Although it is biologically plausible, more research is needed, using standardized cell culture methods, control groups, adequate follow-up and robust epidemiologic methods, including whether secondary infections occurred, to determine the role of the oro-faecal route in the transmission of SARS-CoV-2.

Analysis of coinfections in patients with hematologic malignancies and COVID-19 by next-generation sequencing of bronchoalveolar lavage fluid (preprint)

Background Coinfections in patients with coronavirus disease 2019 (COVID-19) affect patient prognosis. Patients with hematologic malignancies (HMs) are usually immunosuppressed and may be at high risk of coinfection, but few related data have been reported. Here, we conducted a retrospective study to explore coinfections in patients with HMs and COVID-19 by next-generation sequencing (NGS) of bronchoalveolar lavage fluid (BALF).Methods The data of hospitalized patients with pneumonia who underwent NGS analysis of BALF were reviewed. COVID-19 patients with HMs were enrolled in the HM group, and those without HMs were enrolled in the non-HM group. The coinfections of the two groups identified by NGS were analyzed.Results Fifteen patients were enrolled in the HM group, and 14 patients were enrolled in the non-HM group. The coinfection rates in the HM group and non-HM group were 80.0% and 85.7%, respectively. The percentage of coinfected bacteria in the HM group was significantly lower than that in the non-HM group (20.0% vs 71.4%, p = 0.005). The coinfection rates of fungi and viruses were 60.0% and 35.7%, respectively, in the HM group and 35.7% and 78.6%, respectively, in the non-HM group, with no significant differences. The most common coexisting pathogen in patients with HMs was Pneumocystis jirovecii (33.3%), and the most common coexisting pathogen in patients without HMs was human gammaherpesvirus 4 (50%). Coinfection with herpesviruses occurred frequently in both groups.Conclusions Our study showed that hospitalized patients with COVID-19 had a high incidence of coinfection. Pneumocystis jiroveci and herpesvirus are commonly coinfected pathogens in patients with HMs. Bacterial coinfection is rare in patients with HMs but is more common in patients without HMs.

Co-infection and clinical characteristics of SARS-CoV-2 and influenza among COVID-19 cases: A-meta analysis (preprint)

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that causes coronavirus disease 2019 (COVID-19) is a public health problem and may have co-infection with other pathogens such as influenza virus.This study aims to assess the co-infection of SARS-CoV-2 with influenza among COVID-19 cases.The all relevant studies were collected from international databases. For improving the quality of the present literature, the all studies were evaluated by two reviewers in order to confirm all of the studies have inclusion criteria. Finally, all articles with sufficient quality scores were included in meta-analysis. Assessment of heterogeneity among the studies of primary studies was performed using the statistic chi‐squared test (Cochran’s Q) and I2 index. In this results, random or fixed effect model were used for determination of heterogeneity test. All statistical analyses were performed using Comprehensive Meta-Analysis (CMA), V.2 software.This meta- analysis included 9 primary studies investigating the co-infection of SARS-CoV-2 with influenza among COVID-19 cases. Pooled prevalence (95% confidence interval) of co-infection is shown that the prevalence of influenza A is higher than influenza B. 2.3(0.5-9.3) vs 0.1 (0.4-3.3). Using the fixed effect model the frequency of fever was (80.6% [95% CI 76.1–84.40, p < 0.153]) and it is shown that fever is the most prevalent symptom in patients.Patients admitted to hospital with COVID-19 also infected with influenza virus. Thus, the current research provides a better understanding about the control and treatment of co-infection with SARS-CoV-2 and the influenza virus.

Comparison of respiratory pathogens in children with lower respiratory tract infections before and during the COVID-19 pandemic in Shanghai, China (preprint)

Objectives: This study aimed to assess the impact of COVID-19 on the prevalence of respiratory pathogens among hospitalized children with lower respiratory tract infections (LTRIs) in Shanghai. Methods: Respiratory specimens were collected from children with LTRIs in Children’s Hospital of Fudan University from February 2019 to January 2021 and common respiratory pathogens were detected using multiplex PCR. The data of 13 respiratory pathogens were analyzed and compared between the year of 2020 (from February 2020 to January 2021) and 2019 (from February 2019 to January 2020). Results: A total of 1049 patients were enrolled, including 417 patients in 2019 and 632 patients in 2020. In 2020, 27.53% of patients were tested positive for at least one pathogens, which was significantly lower than that in 2019 (78.66%). The top three pathogens were Mp, ADV and RV in 2019, whereas RV, RSV and PIV were the predominant ones in 2020. The positive rates of Mp, ADV, RV, PIV, InfB, H3N2 and H1N1 were significantly decreased in 2020. RV was the most detectable respiratory pathogen in 2020, and become the most frequent pathogen in all five age groups. PIV had a high prevalence from October to December 2020 which was even higher than that in 2019. InfA was not detected in 2020. Co-infection was significantly less frequent in 2020. Conclusions: The public health interventions aiming to eliminate COVID-19 have great impact on the prevalence of common respiratory pathogens. The prevalence of RV and PIV reminds us a possible resurgence of some pathogens.

Measles and Influenza A/H3N2 Coinfection in a Measles Suspected Infant from Iran (preprint)

Measles is an acute infectious disease which is highly contagious. This illness is caused by a negative sense, single-stranded RNA virus belonging to the Paramyxoviridae family. In spite of having a highly effective vaccine, measles is still a public health concern. In October 2019, Iran has achieved the status of measles elimination using effective vaccination strategies and surveillance system based on WHO recommendations. However, recent COVID-19 pandemic disrupted impeccable immunization services and altered health-seeking behaviors worldwide. Herein, we report a case of measles and influenza co-infection in a nine month-old infant from Bushehr province of Iran

Association of Socio-demographic Characteristics, Clinical Profile, and Intestinal Parasite Carriage with Disease Severity among COVID-19 Cases at St. Paul Hospital Millennium Medical College, Addis Ababa, Ethiopia (preprint)

This study aimed to investigate the association between disease severity and demographic characteristics, clinical features, and prevalence of intestinal parasite carriage among patients with COVID-19 in Addis Ababa, Ethiopia. A cross-sectional study was conducted at St. Paul's Hospital Millennium Medical College, involving 337 COVID-19 patients. Patient data were collected during hospitalization to assess clinical outcomes, including demographic information, clinical features, and associated factors. Blood and stool samples were collected and analyzed for hematological and biochemical tests, as well as the presence of intestinal parasites. Statistical analysis was performed using the Statistical Packages for Social Sciences v. 26, employing descriptive statistics, chi-square tests, and logistic regression. A p-value of < 0.05 was considered statistically significant. Among the 337 patients with confirmed SARS-CoV-2 infection through PCR testing, 96(28.5%) were found to have co-infections with one or more intestinal parasites. Multivariate analysis revealed that patients aged ≥ 60 years [Adjusted Odds Ratio (AOR) 3.943 (95% CI: 1.792–8.673), p < 0.001], elevated creatinine levels [AOR 2.254 (95% CI: 1.041–4.881), p = 0.039], increased glutamate oxaloacetate transaminase levels [AOR 2.219 (95% CI: 1.234–3.991), p = 0.008], decreased hematocrit levels [AOR 8.839 (95% CI: 4.914–15.900), p < 0.001], and co-infection with intestinal parasites [AOR 2.419 (95% CI: 1.278–4.579), p = 0.007] were significantly associated with increased disease severity in COVID-19 patients. These findings suggest a potential link between co-infection with intestinal parasites and a more severe form of COVID-19, indicating that parasite-induced immunomodulatory responses may hinder the essential immune response against SARS-CoV-2.

Epidemiological characteristics of eleven common respiratory viral infections in children (preprint)

Background Lower respiratory tract infections (LRTIs) are one of the leading causes of hospital admissions among children. In this study, we aimed to describe the epidemiological characteristics of viral pathogens associated with LRTIs in hospitalized children in Yan'an; this has yet to be reported in the literature and may guide public health interventions and resource allocation in this region. Methods Between June 2021 and May 2023, we conducted a retrospective analysis of the results of viral detection using oral pharyngeal swabs from 4565 children with LRTIs in the Inpatient Department of Yan'an University Affiliated Hospital. Eleven respiratory viruses, including influenza A virus (Flu A), influenza A H1N1 virus (H1N1), seasonal influenza A H3N2 virus (H3N2), influenza B virus (Flu B), parainfluenza virus (HPIV), adenovirus (HADV), bocavirus (HBoV), rhinovirus (HRV), metapneumovirus (HNPV), coronavirus (HCoV), and respiratory syncytial virus (HRSV), were confirmed by applying a multiplex real-time polymerase chain reaction (PCR) kit for respiratory viruses. We evaluated the epidemiological features of infections caused by respiratory pathogens, including aging and the seasonal variations of different pathogens, and explored the high-risk factors associated with virus-caused pneumonia. Results At least one virus was detected in all 4565 cases; the positivity rate was 27.95%. We also detected a total of 1,276 cases with mixed infections (with two or more viruses). Of the positive cases, 59.3% were male and 40.7% were female (x2 = 0.41, P = 0.68). The highest positivity rates for respiratory pathogens were observed for HRSV, HRV, and HADV, at 5.98%, 5.67%, and 4.38%, respectively. We also observed variations in the number and positivity rates of respiratory pathogen infections by season and age. HPIV (x2 = 12.05，P < 0.05) and HADV (x2 = 11.73，P < 0.05) were more common in children under 3 years-of-age. Conclusions In conclusion, our analysis revealed that respiratory pathogen infections varied by gender, season, and age in the enrolled population of children.

The picture theory of seven pathways associated with COVID-19 in the real world (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces immune-mediated diseases. Interactions between the host and virus govern induction, resulting in multiorgan impacts. In 2021, as normal life was challenging during the pandemic era, we analyzed SCI journals according to L. Wittgenstein's Tractatus Logi-co-Philosophicus. The pathophysiology of coronavirus disease 2019 (COVID-19) involves the following steps: 1) the angiotensin-converting enzyme (ACE2) and Toll-like receptor (TLR) pathways: 2) the neuropilin (NRP) pathway, with seven papers and continuing with twenty-four: 3) the sterile alpha motif (SAM) and histidine-aspartate domain (HD)-containing protein 1 (SAMHD1) tetramerization pathway, with two papers and continuing with twelve: 4) inflammasome activation pathways, with five papers and continuing with thirteen: 5) the cytosolic DNA sensor cyclic-GMP-AMP synthase (cGAS)/stimulator of interferon genes (STING) (cGAS–STING) signaling pathway, with six papers and successful with eleven: 6) the spike protein pathway, with fourteen and continuing with twenty-three: 7) the immunological memory engram pathway, with thirteen papers and successive with eighteen: 8) the excess acetylcholine pathway, with three papers and successful with nine. We reconfirmed that COVID-19 involves seven (1-7) pathways and a new pathway involving excess acetylcholine. Therefore, it is necessary to therapeutically alleviate and block the pathological course harmoniously with modulating innate lymphoid cells (ILCs) if diverse SARS-CoV-2 variants are subsequently encountered in the future.

Analysing the distribution of SARS-CoV-2 infections in schools: integrating model predictions with real world observations (preprint)

School closures were used as strategies to mitigate transmission in the COVID-19 pandemic. Understanding the nature of SARS-CoV-2 outbreaks and the distribution of infections in classrooms could help inform targeted or precision preventive measures and outbreak management in schools, in response to future pandemics. In this work, we derive an analytical model of Probability Density Function (PDF) of SARS-CoV-2 secondary infections and compare the model with infection data from all public schools in Ontario, Canada between September-December, 2021. The model accounts for major sources of variability in airborne transmission like viral load and dose-response (i.e., the human bodys response to pathogen exposure), air change rate, room dimension, and classroom occupancy. Comparisons between reported cases and the modeled PDF demonstrated the intrinsic overdispersed nature of the real-world and modeled distributions, but uncovered deviations stemming from an assumption of homogeneous spread within a classroom. The inclusion of near-field transmission effects resolved the discrepancy with improved quantitative agreement between the data and modeled distributions. This study provides a practical tool for predicting the size of outbreaks from one index infection, in closed spaces such as schools, and could be applied to inform more focused mitigation measures. Author summaryAt the start of the COVID-19 pandemic, there was huge uncertainty around the risks of SARS-CoV-2 spread in classrooms. In the absence of early predictions surrounding classroom risks, many jurisdictions across countries closed in-person education. There is great interest in adopting a more precision approach to better inform future interventions in the context of airborne virus risks. For this purpose, we need tools that can predict the probability of the size of outbreaks within classrooms along with the impact of interventions including masks, better ventilation, and physical distancing by limiting the number of students per classroom. To this end, we have developed a robust but practical model that yields the probability of secondary infections stemming from index cases occurring within schools on a given day. During model development, the major underlying physical and biological factors that dictate the disease transmission process, both at long-range and close-range, have been accounted for. This enables our model to modify its predictions for different scenarios - and possibly allows its use beyond schools. Finally, the models predictive capability has been verified by comparing its outputs with publicly available data on SARS-CoV-2 diagnoses in Ontario public schools. To our knowledge, this is the first time an analytical model derived from mostly first principles describes real-world infection distributions, satisfactorily. The quantitative match between the theoretical prediction and real-world data offers the proposed model as a possible powerful tool for better-informed precision pandemic mitigation strategies in indoor environments like schools.

Single Infection and Dual Co-infection With Respiratory Viruses Affect Cytokine and Chemokine Expression in Acute Respiratory Illness Negative for SARS-CoV-2 (preprint)

During the COVID-19 pandemic, the circulation of non–SARS-CoV-2 respiratory viruses changed throughout the world. This study aimed to analyze the effect of respiratory syncytial virus (RSV), metapneumovirus (MPV), rhinovirus (RV), and parainfluenza (PIV)-3 single infection, dual co-infection, and viral load on cytokine and chemokine expression in 300 Mexican patients with ARIs negative for SARS-CoV-2. Molecular detection and viral load were performed by RT-qPCR. Cytokine and chemokine expression was determined in samples positive for single RSV, MPV, RV, or PIV-3 infection, and in the most frequent dual co-infections, by a cytokine panel using a magnetic-bead-based multiplex immunoassay. Of the patients positive for viral infection, 91.7% had a single infection and 8.3% had dual co-infections. In this study, RSV was the respiratory virus with the highest prevalence, and the most common dual co-infection was RV+RSV. On the other hand, RV infections had the highest viral loads compared to the other viruses detected. FGF basic, MIP-1α IL-8, IP-10, MCP-1, IFN-γ, and RANTES showed differential expression between single infections and dual co-infections compared to healthy patients. We report, for the first time, the circulation of non-SARS-CoV-2 viruses in the south of Mexico and the cytokine and chemokine profiles associated with these viruses.

Impact of directly acting-antivirals and behavior change due to the COVID 19 pandemic on HCV micro-elimination in MSM in Germany (preprint)

Introduction Directly-acting antivirals (DAA) are the cornerstone to reach HCV elimination. In men who have sex with men (MSM) with HIV coinfection, recently acquired HCV infection (RAHCV) is common. Sexual practices and reinfection rates may hamper micro-elimination despite high treatment rates. Methods The cohort included MSM with RAHCV from 2014 to 2021. The patients’ demographic, clinical, behavioral, and laboratory data were documented, as well as treatment and reinfection outcomes.  Results 237 men with RAHCV were included, 216 (91%) were PLWH. Median age was 46 years (IQR: 39–52), median CD4 count was 660/mm3 (IQR: 527–835). The annual incidence of RAHCV remained between 0.28% and 0.43%, but dropped to 0.02% in 2021 during the onset of the COVID-pandemic almost reaching micro-elimination. The reinfection incidence was 15.5 per 100 patient-years (95%-CI: 12.6-18.8), reinfection was associated with use of crystal methamphetamine (p=0.032) and ketamine (p=0.042). 31.3% had multiple reinfections, four reinfections occurred in PrEP users. Conclusions High treatment and cure rates did not lead to HCV elimination. A change in sexual behavior, potentially imposed by COVID-19 restrictions, led to micro-elimination in the NoCo cohort. As RAHCV is prevalent in HIV-positive and -negative MSM, surveillance is necessary to consolidate elimination goals.

Epidemiological overlaps in COVID-19 and malaria within healthcare and community settings of Southern Ghana (preprint)

Background: COVID-19 disruptions in Africa in 2020-2022 contributed to reductions in malaria control activities including antimalarial surveillance programs. This study investigated the malaria burden and distribution on the background of active transmission of SARS-CoV-2 in Southern Ghana. Specifically, it aimed to identify epidemiological factors that can maximise programmatic control for both diseases, utilising community health education and medical screening (CHEMS). Methods: Between October-December 2022, prospective cross-sectional surveys, with CHEMS were conducted in Greater Accra and Central regions, where 994 participants enrolled either at a hospital or community setting provided demographic and clinical data including history of clinical malaria infection and antimalarial treatment in the past two weeks. Of this study population, 953 provided nasal/throat swabs for COVID-19 RT-PCR testing, with a subset of 136 participants also providing finger-prick blood for malaria RDT testing. Results: The study population comprised of 73.6% adults, with 54.6% COVID-19 vaccination rate. Overall, 18.1% of participants had a history of clinical malaria, which was associated (adjusted odds ratio > 1.50, P-value [≤] 0.022) with COVID-19 symptoms and positivity, study area and hospital setting, suggestive of overlaps in the epidemiological risk for malaria. On a background of widespread SARS-CoV-2 infections (12-37%), malaria parasitaemia was detected in 6%, with 2% being co-infections. Among the malaria positives, 9.5% had a history of antimalarial treatment, which suggested that their infections were recrudescent parasitaemia. Conclusion: The overlaps in the epidemiological risk for malaria and COVID-19 indicate that innovative surveillance programs, with community engagement are needed to maximise control interventions including treatment of asymptomatic malaria infections.

Seasonal Human Coronaviruses OC43, 229E, and NL63 Induce Cell Surface Modulation of Entry Receptors and Display Host Cell-Specific Viral Replication Kinetics (preprint)

The emergence of the COVID-19 pandemic prompted increased interest in seasonal human coronaviruses. 229E, OC43, NL63 and HKU1 are endemic seasonal coronaviruses that cause the common cold and are associated with generally mild respiratory symptoms. In this study, we identified cell lines that exhibited cytopathic effects (CPE) upon infection by three of these coronaviruses and characterized their viral replication kinetics and the effect of infection on host surface receptor expression. We found that NL63 produced CPE in LLC-MK2 cells, while OC43 produced CPE in MRC-5, HCT-8 and WI-38 cell lines, while 229E produced CPE in MRC-5 and WI-38 by day 3 post-infection. We observed a sharp increase in nucleocapsid and spike viral RNA (vRNA) from day 3 to day 5 post-infection for all viruses, however the abundance and the proportion of vRNAs copies measured in the supernatants and cell lysates of infected cells varied considerably depending on the virus-host cell pair. Importantly, we observed modulation of coronavirus entry and attachment receptors upon infection. Infection with 229E and OC43 led to a downregulation of CD13 and GD3, respectively. In contrast, infection with NL63, and also with OC43, lead to an increase in ACE2 expression. Attempts to block entry of NL63 using either soluble ACE2 or anti-ACE2 monoclonal antibodies demonstrated the potential of these strategies to greatly reduce infection. Overall, our results enable a better understanding of seasonal coronaviruses infection kinetics in permissive cell lines, and reveal entry receptor modulation that may have implications in facilitating co-infections with multiple coronaviruses in humans. IMPORTANCESeasonal human coronavirus are an important cause of the common cold associated with generally mild upper respiratory tract infections that can result in respiratory complications for some individuals. There are no vaccines available for these viruses, with only limited antiviral therapeutic options to treat the most severe cases. A better understanding of how these viruses interact with host cells is essential to identify new strategies to prevent infection-related complications. By analyzing viral replication kinetics in different permissive cell lines, we find that cell-dependent host factors influence how viral genes are expressed and virus particles released. We also analyzed entry receptor expression on infected cells and found that these can be up or down modulated depending on the infecting coronavirus. Our findings raise concerns over the possibility of infection enhancement upon co-infection by some coronaviruses, which may facilitate genetic recombination and the emergence of new variants and strains.

RSV-bacterial co-infection is associated with increased illness severity in hospitalized children - Results from a prospective sentinel surveillance study (preprint)

Purpose: During the autumn/winter respiratory syncytial virus (RSV) epidemics, bacterial co-infection is common and affects the severity of the disease. We aimed to understand the relationship between RSV-bacterial co-infections and clinical severity since the change of RSV seasonality after the COVID-19 pandemic. Methods: We conducted a prospective, sentinel surveillance study at 20 sites in Portugal in children under two years old hospitalized with RSV, between April 2021 and January 2023. The effect of co-infection with potentially pathogenic bacteria (PPB) on the length of hospitalization and disease severity (defined by the need for ventilation or admission to an intensive care unit-ICU) was investigated using multivariate linear and log-binomial regression models. Age group (<6 months/≥6 months) and prematurity (yes/no) were included in models as potential confounders. Results: We report two RSV off-season epidemics: June 2021-February 2022 and May-October 2022. Among 678 RSV hospitalizations, 67.4 % occurred in children under 6 months old and 15.3 % in pre-term; 20.4 % tested positive for PPB; median length of hospitalization was five days (IQR: 3-7days); 5.8 % had at least one underlying condition. The most common bacteria were Haemophilus influenzae and Streptococcus pneumoniae. Children co-infected with PPB had a higher rate of ICU admission (29.7 % versus 3.5 %, p<0.001), resulting in more prolonged hospitalizations (median of 7 days versus 5 days, p<0.001) and a 13-fold risk of having severe disease (RR: 13.2, 95 CI: 7.3-23.9). Conclusion: RSV-bacterial co-infection was associated with increased length of hospitalization and severe illness during off-season epidemics. This risk is probably overestimated, as laboratory testing for bacterial infections is usually higher in severely ill-appearing children. Measures to prevent outgrowth of pathogenic bacteria within the respiratory tract should be discussed.