The pitfalls of inferring virus–virus interactions from co-detection prevalence data: application to influenza and SARS-CoV-2

There is growing experimental evidence that many respiratory viruses—including influenza and SARS-CoV-2—can interact, such that their epidemiological dynamics may not be independent. To assess these interactions, standard statistical tests of independence suggest that the prevalence ratio—defined as the ratio of co-infection prevalence to the product of single-infection prevalences—should equal unity for non-interacting pathogens. As a result, earlier epidemiological studies aimed to estimate the prevalence ratio from co-detection prevalence data, under the assumption that deviations from unity implied interaction. To examine the validity of this assumption, we designed a simulation study that built on a broadly applicable epidemiological model of co-circulation of two emerging or seasonal respiratory viruses. By focusing on the pair influenza–SARS-CoV-2, we first demonstrate that the prevalence ratio systematically underestimates the strength of interaction, and can even misclassify antagonistic or synergistic interactions that persist after clearance of infection. In a global sensitivity analysis, we further identify properties of viral infection—such as a high reproduction number or a short infectious period—that blur the interaction inferred from the prevalence ratio. Altogether, our results suggest that ecological or epidemiological studies based on co-detection prevalence data provide a poor guide to assess interactions among respiratory viruses.

Roles of extended human papillomavirus genotyping and multiple infections in early detection of cervical precancer and cancer and HPV vaccination

Background The aim of the study was to investigate the risk of human papillomavirus (HPV) genotyping particularly vaccine genotypes and multiple infections for cervical precancer and cancer, which might contribute to developing genotype-specific screening strategy and assessing potential effects of HPV vaccine. Methods The HPV genotypes were identified using the Seq HPV assay on self-collected samples. Hierarchical ranking of each genotype was performed according to positive predictive value (PPV) for cervical intraepithelial neoplasia 2/3 or worse (CIN2+/CIN3+). Multivariate logistic regression model was used to estimate the odds ratios (ORs) with 95% confidence interval (CI) of CIN2+ according to multiplicity of types and vaccine types. Results A total of 2811 HPV-positive women were analyzed. The five dominant HPV genotypes in high-grade lesions were 16/58/52/33/18. The overall ranking orders were HPV16/33/35/58/31/68/18/ 56/52/66/51/59/45/39 for CIN2+ and HPV16/33/31/58/45/66/52/18/35/56/51/68/59/39 for CIN3+. The risks of single infection versus co-infections with other types lower in the hierarchy having CIN2+ were not statistically significant for HPV16 (multiple infection vs. single infection: OR = 0.8, 95%CI = 0.6-1.1, P = 0.144) or other genotypes (P > 0.0036) after conservative Bonferroni correction. Whether HPV16 was present or not, the risks of single infection versus multiple infection with any number (2, ≥2, or ≥ 3) of types for CIN2+ were not significantly different. In addition, HPV31/33/45/52/58 covered by nonavalent vaccine added 27.5% of CIN2, 23.0% of CIN3, and 12.5% of cancer to the HPV16/18 genotyping. These genotype-groups were at significantly higher risks than genotypes not covered by nonavalent vaccine. Moreover, genotypes covered by nonavalent vaccine contributed to 85.2% of CIN2 lesions, 97.9% of CIN3 and 93.8% of cancers. Conclusions Partial extended genotyping such as HPV33/31/58 but not multiplicity of HPV infections could serve as a promising triage for HPV-positive self-samples. Moreover, incidence rates of cervical cancer and precancer were substantial attributable to HPV genotypes covered by current nonavalent vaccination.

Transcriptome Analysis of Atlantic Salmon (Salmo salar) Skin in Response to Sea Lice and Infectious Salmon Anemia Virus Co-Infection Under Different Experimental Functional Diets

Sea lice (Lepeophtheirus salmonis) are ectoparasitic copepods that cause significant economic loss in marine salmoniculture. In commercial salmon farms, infestation with sea lice can enhance susceptibility to other significant pathogens, such as the highly contagious infectious salmon anemia virus (ISAv). In this study, transcriptomic analysis was used to evaluate the impact of four experimental functional feeds (i.e. 0.3% EPA/DHA+high-ω6, 0.3% EPA/DHA+high-ω6+immunostimulant (IS), 1% EPA/DHA+high-ω6, and 1% EPA/DHA+high-ω3) on Atlantic salmon (Salmo salar) during a single infection with sea lice (L. salmonis) and a co-infection with sea lice and ISAv. The overall objectives were to compare the transcriptomic profiles of skin between lice infection alone with co-infection groups and assess differences in gene expression response among animals with different experimental diets. Atlantic salmon smolts were challenged with L. salmonis following a 28-day feeding trial. Fish were then challenged with ISAv at 18 days post-sea lice infection (dpi), and maintained on individual diets, to establish a co-infection model. Skin tissues sampled at 33 dpi were subjected to RNA-seq analysis. The co-infection’s overall survival rates were between 37%-50%, while no mortality was observed in the single infection with lice. With regard to the infection status, 756 and 1303 consensus differentially expressed genes (DEGs) among the four diets were identified in “lice infection vs. pre-infection” and “co-infection vs. pre-infection” groups, respectively, that were shared between the four experimental diets. The co-infection groups (co-infection vs. pre-infection) included up-regulated genes associated with glycolysis, the interferon pathway, complement cascade activity, and heat shock protein family, while the down-regulated genes were related to antigen presentation and processing, T-cell activation, collagen formation, and extracellular matrix. Pathway enrichment analysis conducted between infected groups (lice infection vs. co-infection) resulted in several immune-related significant GO terms and pathways unique to this group, such as “autophagosome”, “cytosolic DNA-sensing pathway” and “response to type I interferons”. Understanding how experimental functional feeds can impact the host response and the trajectory of co-infections will be an essential step in identifying efficacious intervention strategies that account for the complexities of disease in open cage culture.

Prevalence of cestodes infection among school children of urban parts of Lower Dir district, Pakistan

Tapeworms of zoonotic importance have been described as a leading public health problem. Current research was aim to assess the prevalence of tapeworms among 5-12years school children residing in district Lower Dir, Pakistan from January 2019-December 2019. The wet mount preparation in saline/iodine/methods were used for stool examination. Data was analyzed using appropriate descriptive, static methods. Of the 400 children studied 71.7% were infected with one or more species of intestinal parasites. Single infection of cestode species was found in 69 individuals with 17.2% prevalence and multiple parasitic infections were identified in 19.7% (n=79/400) individuals. The multiple infection were comprised as 10% (n=40) double, 6.75% (n=27) triple and 3% (n=12) quadruple. A total of 9 species of helminths and one species of protozoan infection. Among the helminths Ascaris lumbricoides was the most prevalent 33.1% (n=95), Taenia saginata 22.6% (n=65), hookworm 19.8% (n=57), Hymenolepis nana 18.8% (n=54), Enterobius vermicularis and Hymenolepis diminuta 1.39% (n=4each), Trichuris trichura 1.04% (n=3), Toxocara spp 0.69% (n=2) and Schistosoma japonicum 0.34% (n=1) were reported. One protozoan species was Cryptosporidium spp 0.69% (n=2) in current study. In case of A.lumbricoides, hookworm, E.vermicularis, T.trichura, T.saginata, H.nana and H.diminuta the male children of below 8 years of age were highly infected. Other infections are reported in the same prevalence with slight difference if any. We conclude that there is a need for mass scale campaigns to create awareness regarding health and hygiene in children and the need for development of effective poverty control programs because deworming alone is not adequate to control parasitic infections.

Identification and Molecular Characterization of Novel Mycoviruses in Saccharomyces and Non-Saccharomyces Yeasts of Oenological Interest

Wine yeasts can be natural hosts for dsRNA, ssRNA viruses and retrotransposon elements. In this study, high-throughput RNA sequencing combined with bioinformatic analyses unveiled the virome associated to 16 Saccharomyces cerevisiae and 8 non-Saccharomyces strains of oenological interest. Results showed the presence of six viruses and two satellite dsRNAs from four different families, two of which—Partitiviridae and Mitoviridae—were not reported before in yeasts, as well as two ORFan contigs of viral origin. According to phylogenetic analysis, four new putative mycoviruses distributed in Totivirus, Cryspovirus, and Mitovirus genera were identified. The majority of commercial S. cerevisiae strains were confirmed to be the host for helper L-A type totiviruses and satellite M dsRNAs associated with the killer phenotype, both in single and mixed infections with L-BC totiviruses, and two viral sequences belonging to a new cryspovirus putative species discovered here for the first time. Moreover, single infection by a narnavirus 20S-related sequence was also found in one S. cerevisiae strain. Considering the non-Saccharomyces yeasts, Starmerella bacillaris hosted four RNAs of viral origin—two clustering in Totivirus and Mitovirus genera, and two ORFans with putative satellite behavior. This study confirmed the infection of wine yeasts by viruses associated with useful technological characteristics and demonstrated the presence of complex mixed infections with unpredictable biological effects.

SARS-CoV-2 and Influenza A virus Co-infections in Ferrets

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and seasonal influenza viruses are co-circulating in the human population. However, only a few cases of viral co-infection with these two viruses have been documented in humans with some people having severe disease and others mild disease. In order to examine this phenomenon, ferrets were co-infected with SARS-CoV-2 and human seasonal influenza A viruses (IAVs) (H1N1 or H3N2) and were compared to animals that received each virus alone. Ferrets were either immunologically naïve to both viruses or vaccinated with the 2019-2020 split-inactivated influenza virus vaccine. Co-infected naive ferrets lost significantly more body weight than ferrets infected with each virus alone and induced more severe inflammation in both the nose and lungs than ferrets single-infected with each virus. Co-infected naïve animals had predominantly higher IAV titers than SARS-CoV-2 titers, and IAVs efficiently transmitted to the co-housed ferrets by direct contact. Comparatively, SARS-CoV-2 failed to transmit to the ferrets that co-housed with co-infected ferrets by direct contact. Moreover, vaccination significantly reduced IAVs virus titers and shortened the viral shedding, but did not completely block influenza virus direct contact transmission. Notably, vaccination significantly ameliorated the influenza associated disease by protecting vaccinated animals from severe morbidity after IAV single infection or IAV and SARS-CoV-2 co-infection, suggesting that seasonal influenza virus vaccination is pivotal to prevent severe disease induced by IAVs and SARS-CoV-2 co-infection during the COVID-19 pandemic. Importance Influenza A viruses cause severe morbidity and mortality during each influenza virus season. The emergence of SARS-CoV-2 infection in the human population offers the opportunity to potential co-infections of both viruses. The development of useful animal models to asses pathogenesis, transmission, and viral evolution of these viruses as the co-infect a host is of critical importance for the development of vaccines and therapeutics. The ability to prevent the most severe effects of viral co-infections can be studied using effect co-infection ferret models described in this report.

Helminth Infections in Cattle and Goats in Kanchanaburi, Thailand, with Focus on Strongyle Nematode Infections

Gastrointestinal helminths are major enteric parasites affecting the health of important livestock ruminants, such as cattle and goats. It is important to routinely survey these animals for helminth infections to allow effective management and control programs to be implemented. A cross-sectional helminth survey carried out in Kanchanaburi Province, Thailand, revealed the infection rate of gastrointestinal helminths in cattle (n = 157) and goats (n = 117) to be 35.7% and 88%, respectively, by microscopic fecal examination, and a 100% herd prevalence was observed in goats. Eggs of strongyle nematodes, Strongyloides spp., Trichuris spp., Capillaria spp., Paramphistomum spp., and Moniezia spp. were detected, with a relatively high rate of strongyle nematode infection in both cattle (28.7%) and goats (86.3%). Mixed infections were observed in 14.3% and 35.9% of egg-positive samples from cattle and goats, respectively. Risk factor analysis showed that dairy cattle were 5.1 times more likely to be infected with strongyles than meat cattle. In contrast, meat goats were 9.3 times more likely to be infected with strongyles than dairy goats. The inverse findings in cattle and goats are discussed. Female gender was associated with a higher risk of strongyle infection in goats. DNA sequencing and in-house semi-nested PCR with primers specific to a region in the internal transcribed spacer 2 (ITS2) were successfully used to identify strongyle genera in randomly selected egg-positive cattle (n = 24) and goat (n = 24) samples. Four strongyle genera, i.e., Cooperia spp., Haemonchus spp., Oesophagostomum spp., and Trichostrongylus spp. were identified by DNA sequencing. By semi-nested PCR, Cooperia spp. were detected as a major parasite of cattle (70.8%), whereas Haemonchus spp. were abundant in goats (100%). The majority of samples from cattle (58.3%) and goats (95.8%) were found to coinfect with at least two strongyle genera, suggesting that coinfection with multiple strongyle genera was more common than single infection in these animals.

Impact of Coinfection With SARS-CoV-2 and Influenza on Disease Severity: A Systematic Review and Meta-Analysis

Background: Although coinfection with influenza in COVID-19 patients has drawn considerable attention, it is still not completely understood whether simultaneously infected with these two viruses influences disease severity. We therefore aimed to estimate the impact of coinfected with SARS-CoV-2 and influenza on the disease outcomes compared with the single infection of SARS-CoV-2.Materials and Methods: We searched the PubMed, Web of Science, Embase, Cochrane Library, China National Knowledge Infrastructure Database (CNKI) to identify relevant articles up to July 9, 2021. Studies that assessed the effect of SARS-CoV-2 and influenza coinfection on disease outcomes or those with sufficient data to calculate risk factors were included. Risk effects were pooled using fixed or random effects model.Results: We ultimately identified 12 studies with 9,498 patients to evaluate the risk effects of SARS-CoV-2 and influenza coinfection on disease severity. Results indicated that coinfection was not significantly associated with mortality (OR = 0.85, 95%CI: 0.51, 1.43; p = 0.55, I2 = 76.00%). However, mortality was found significantly decreased in the studies from China (OR = 0.51, 95%CI: 0.39, 0.68; I2 = 26.50%), while significantly increased outside China (OR = 1.56, 95%CI: 1.12, 2.19; I2 = 1.00%). Moreover, a lower risk for critical outcomes was detected among coinfection patients (OR = 0.64, 95%CI: 0.43, 0.97; p = 0.04, I2 = 0.00%). Additionally, coinfection patients presented different laboratory indexes compared with the single SARS-CoV-2 infection, including lymphocyte counts and APTT.Conclusion: Our study revealed that coinfection with SARS-CoV-2 and influenza had no effect on overall mortality. However, risk for critical outcomes was lower in coinfection patients and different associations were detected in the studies from different regions and specific laboratory indexes. Further studies on influenza strains and the order of infection were warranted. Systematic testing for influenza coinfection in COVID-19 patients and influenza vaccination should be recommended.

Malaria Co – Infection with Urinary Schistosomiasis, Typhoid Fever, Hepatitis B Virus, and Human Immunodeficiency (HIV) Virus among Students in Three Local Government Areas of Ekiti State, South Western Nigeria

Introduction: Malaria, Typhoid fever, urinary schistosomiasis, AIDS and hepatitis B virus disease are major public health problems in the tropical and subtropical countries; they exert a huge burden of morbidity, mortality and economic loss on the populace. Aims: The study investigates the prevalence of co–infection of malaria, typhoid fever, urinary schistosomiasis, hepatitis B virus and HIV virus among 306 students between the ages of 10- 21 years in three local government areas of Ekiti – state Nigeria. Methodology: Blood samples were randomly collected for the examination of malaria parasites, typhoid fever, hepatitis B virus and HIV virus while urine examination was done for urinary schistosomiasis by random sampling and survey for a period one week. Results: The results show that the overall prevalence of malaria, typhoid fever, urinary schistosomiasis and hepatitis B virus were 42.2%, 2.9%, 2.9% and 2.9% respectively. The female students had the highest prevalence of single infection with malaria fever having the highest figure (42.2%). Malaria and Urinary schistosomiasis had the highest prevalence of double infection of 2.3 %, while schistosomiasis and hepatitis B had the lowest prevalence of 0.3%. Also, male students had the highest prevalence of double and triple infections. The co-infection rate of malaria, urinary Schistosomiasis and hepatitis B was 0.3% and this occurred in male between the ages of 19-21 years, none of the students tested positive for HIV virus and therefore no students was found in the quaternaries. Conclusion: Co-infections is prevalent in this study area, therefore there should be integrated control approach directed against these diseases.