Neutralization of ancestral SARS-CoV-2 and variants Alpha, Beta, Gamma, Delta, Zeta and Omicron by mRNA vaccination and infection-derived immunity through homologous and heterologous variants

Emerging SARS-CoV-2 variants of concern/interest (VOC/VOI) raise questions about effectiveness of neutralizing antibodies derived from infection or vaccination. As the population immunity to SARS-CoV-2 has become more complex due to prior infection and/or vaccination, understanding the antigenic relationship between variants is needed. Here, we have assessed in total 104 blood specimens from convalescent individuals after infection with early-pandemic SARS-CoV-2 (pre-VOC) or with Alpha, Beta, Gamma or Delta, post-vaccination after double-dose mRNA-vaccination and break through infections due to Delta or Omicron. Neutralization against seven authentic SARS-CoV-2 isolates (B.1, Alpha, Beta, Gamma, Delta, Zeta, Omicron) was assessed by plaque-reduction neutralization assay. We found highest neutralization titers against the homologous (previously infecting) variant, with lower neutralization efficiency against heterologous variants. Significant loss of neutralization for Omicron was observed but to a varying degree depending on previously infecting variant (23.0-fold in Beta-convalescence up to 56.1-fold in Alpha-convalescence), suggesting that infection-derived immunity varies, but independent of the infecting variant is only poorly protective against Omicron. Of note, Zeta VOI showed also pronounced escape from neutralization of up to 28.2-fold in Alpha convalescent samples. Antigenic mapping reveals both Zeta and Omicron as separate antigenic clusters. Double dose vaccination showed robust neutralization for Alpha, Beta, Gamma, Delta and Zeta, with fold-change reduction of only 2.8 (for Alpha) up to 6.9 (for Beta). Escape from neutralization for Zeta was largely restored in vaccinated individuals, while Omicron still showed a loss of neutralization of 85.7-fold compared to pre-VOC SARS-CoV-2. Combined immunity from infection followed by vaccination or vaccine breakthrough infection showed highest titers and most robust neutralization for heterologous variants. Breakthrough infection with Delta showed only 12.5-fold reduced neutralization for Omicron, while breakthrough infection with Omicron showed only a 1.5-fold loss for Delta, suggests that infection with antigenically different variants can boost immunity for antigens closer to the vaccine strain. Antigenic cartography showed also a tendency towards broader neutralizing capacity for heterologous variants. We conclude that the complexity of background immunity needs to be taken into account when assessing new VOCs. Development towards separate serotypes such as Zeta was already observed before Omicron emergence, thus other factors than just immune escape must contribute to Omicrons rapid dominance. However, combined infection/vaccination immunity could ultimately lead to broad neutralizing capacity also against non-homologous variants.

Emergence of a Novel Reassortant H5N3 Avian Influenza Virus in Korean Mallard Ducks in 2018

<b><i>Introduction:</i></b> The avian influenza (AI) virus causes a highly contagious disease which is common in wild and domestic birds and sporadic in humans. Mutations and genetic reassortments among the 8 negative-sense RNA segments of the viral genome alter its pathogenic potential, demanding well-targeted, active surveillance for infection control. <b><i>Methods:</i></b> Wild duck fecal samples were collected during the 2018 bird health annual surveillance in South Korea for tracking variations of the AI virus. One low-pathogenic avian influenza H5N3 reassortment virus (A/mallard duck/South Korea/KNU18-91/2018 [H5N3]) was isolated and genomically characterized by phylogenetic and molecular analyses in this study. <b><i>Results:</i></b> It was devoid of polybasic amino acids at the hemagglutinin (HA) cleavage site and exhibited a stalk region without deletion in the neuraminidase (<i>NA</i>) gene and NA inhibitor resistance-linked E/D627K/N and D701N marker mutations in the <i>PB2</i> gene, suggesting its low-pathogenic AI. It showed a potential of a reassortment where only <i>HA</i> originated from the H5N3 poultry virus of China and other genes were derived from Mongolia. In phylogenetic analysis, HA was different from that of the isolate of H5N3 in Korea, 2015. In addition, this novel virus showed adaptation in Madin-Darby canine kidney cells, with 8.05 ± 0.14 log10 50% tissue culture infectious dose (TCID50) /mL at 36 h postinfection. However, it could not replicate in mice well, showing positive growth at 3 days postinfection (dpi) (2.1 ± 0.13 log10 TCID50/mL) but not at 6 dpi. <b><i>Conclusions:</i></b> The HA antigenic relationship of A/mallard duck/South Korea/KNU18-91/2018 (H5N3) showed differences toward one of the old low-pathogenic H5N3 viruses in Korea. These results indicated that a novel reassortment low-pathogenic avian influenza H5N3 subtype virus emerged in South Korea in 2018 via novel multiple reassortments with Eurasian viruses, rather than one of old Korean H5N3 strains.

Comparative study between lumpy skin disease virus and sheep pox virus vaccines against recent field isolate of lumpy skin disease virus

Lumpy Skin Disease (LSD) is a vector born disease of cattle, caused by Lumpy Skin Disease Virus (LSDV), there is antigenic relationship between LSDV, Sheeppox virus (SPPV) and Goat pox virus GTPV within a genus Capripoxvirus, accordingly it can be used homologous or heterologous Capripoxvirus strains for vaccination of cattle against LSD. This study compare the efficacy of live attenuated Neethling LSDV vaccine and live attenuated Romanian SSPV Vaccine against recent circulating LSDV field isolate. The evaluation was done in calves as the main host of LSD, through using three different batches for each vaccine type. Experimental calf groups were vaccinated with vaccines batches, and after 21 days serum samples were collected for evaluation of humoral immune response by using SNT and commercial ELISA technique, then the vaccinated calves were challenged by virulent LSDV field isolate. The results of SNT for vaccinated calves by LSDV vaccines indicated mean neutralizing antibody titer 1.2, 1.6 and1.5 log10 for the batches 1, 2 and 3 respectively, while vaccinated calves by SPPV vaccines indicated 1.05, 1.05 and 1.5 log10 for the batches 1,2 and 3 respectively; the ELISA mean sample to positive (S/P) percentage for the vaccine batches 1, 2 and 3 of LSDV were 40, 45 and 42% respectively and for SPPV vaccine batches 1,2 and 3 were 35, 37 and 40 % respectively, the challenge test indicated mean difference titer for the groups of calves vaccinated with LSDV vaccine were 4.2, 4.5 and 3.8 log10 and for groups vaccinated with SPPV vaccine were 2.6, 2 and 2.65 log10 respectively, it was concluded that potential using of Neethling LSDV vaccine against LSD is superior for combating and prevention of the lumpy skin disease.

Interference at Influenza Hemagglutinin Antigenic-Sites Determines Antibody Levels and Specificities after Repeat Vaccination

Background: It is recommended that children receive a dose of the influenza vaccine at 6 months of age and a second dose the following season. In some years, the second dose will be the same vaccine formulation, in others years it with be re-formulated to include HA proteins derived from antigenically drifted or shifted circulating influenza strains. In addition, natural exposure to influenza can create permanent changes to the memory B cell repertoire and specificities. The effect that the specificity of pre-existing humoral immunity has on antibody levels and specificity after repeat vaccination is an ongoing research area. Methods: We used a computational framework (ssMod.v1) to simulate scenarios that occurred during the 2009 influenza pandemic: children receiving a second dose who have previously exposed to the 2009 influenza HA antigen, children previously exposed to an HA antigen antigenically similar to the 2009 influenza HA antigen, and children previously exposed to an antigenically dissimilar strain. To assess the contribution of pre-existing immunity, two experimental permutations in the sMod.v1 were made: elimination of antibody-mediated antibody clearance of vaccine (HA) antigen by pre-existing antibodies and elimination of the ability of memory B cells to form germinal centers. In the simulation, 30 days after repeat vaccination antibody specificities were examined against 12 antigenically historical vaccine/HA variant influenza strains for each of the five canonical antigenic-sites and the subdominant, conserved, stalk antigenic-site. Results: We found that elimination of antibody-mediated antigen clearance significantly increased antibody levels while elimination of the ability of memory B cells to form germinal center reactions significantly decreased the total antibody levels, but this was dependent on the antigenic relationship between the original vaccine and repeat vaccine and the particular antigenic-site. Moreover, highly-cross-reactive antibody was highest when the antigenic distance between original vaccine HA antigen and repeat vaccine HA antigen was larger and antibody-mediated antigen clearance was eliminated.

Differential Metabolism-associated Gene Expression of Duck Pancreatic Cells in Response to Two Subtypes of Duck Hepatitis A Virus Type 1

Duck hepatitis A virus type 1 (DHAV-1) causes a highly contagious disease in domestic ducklings, which is traditionally characterized by lesions in the liver and rarely in the pancreas. However, several outbreaks of DHAV-1, which were characterized by yellow coloration and hemorrhage in pancreatic tissues, have occurred in China. The causative agent was named as pancreatitis-type DHAV-1. Genomic sequencing indicated variation rates of 3.4-6.5% in the genome of the pancreatitis-type DHAV-1 compared with those of the classical type DHAV-1. The antigenic relationship between the pancreatitis-type DHAV-1 and classical type DHAV-1 indicated large variation. However, the mechanism involved in infection of the pancreatitis-type DHAV-1 is still unclear. Transcriptome analysis of duck pancreas infected with classical type DHAV-1 and pancreatitis-type DHAV-1 was carried out. Following deep sequencing with Illumina-Solexa, a total of 53.9 Gb clean data were obtained from the cDNA library of the pancreas and a total of 29,597 unigenes with an average length of 993.43 bp were generated following de novo sequence assembly. The expression levels of D-3-phosphoglyceratedehydrogenase, phosphoserine aminotransferase, phosphoserine phosphatase, which are involved in glycine, serine and threonine metabolism pathway, were significantly downregulated in the pancreatitis-type DHAV-1-infected group compared with those of the classical type DHAV-1-infected group. These findings provide information regarding differential expression levels of metabolism-associated genes between pancreatitis-type DHAV-1 and classical type DHAV-1, indicating that intensive metabolism disorders may contribute to different subtypes of DHAV-1-infection.

Differential metabolism -associated gene expression of duck pancreatic cells in response to two subtype s of duck hepatitis A virus type 1

Background: Duck hepatitis A virus type 1 (DHAV-1) causes a highly contagious disease in domestic ducklings, which is traditionally characterized by lesions in the liver and rarely in the pancreas. However, several outbreaks of DHAV-1, which were characterized by yellow coloration and hemorrhage in pancreatic tissues, have occurred in China. The causative agent was named as pancreatitis-type DHAV-1. Genomic sequencing indicated variation rates of 3.4-6.5% in the genome of the pancreatitis-type DHAV-1 compared with those of the classical type DHAV-1. The antigenic relationship between the pancreatitis-type DHAV-1 and classical type DHAV-1 indicated large variation. However, the mechanism involved in infection of the pancreatitis-type DHAV-1 is still unclear. Results: In the present study, transcriptome analysis of duck pancreas infected with classical type DHAV-1 and pancreatitis-type DHAV-1 was carried out. Following deep sequencing with Illumina-Solexa, a total of 53.9 Gb clean data were obtained from the cDNA library of the pancreas and a total of 29,597 unigenes with an average length of 993.43 bp were generated following de novo sequence assembly. The expression levels of D-3-phosphoglyceratedehydrogenase, phosphoserine aminotransferase, phosphoserine phosphatase, which are involved in glycine, serine and threonine metabolism pathway, were significantly downregulated in the pancreatitis-type DHAV-1-infected group compared with those of the classical type DHAV-1-infected group.Conclusion: These findings provide information regarding differential expression levels of metabolism-associated genes between pancreatitis-type DHAV-1 and classical type DHAV-1, indicating that intensive metabolism disorders may contribute to different subtypes of DHAV-1-infection.

Differential metabolism-associated gene expression of duck pancreatic cells in response to two subtypes of duck hepatitis A virus type 1

Background: Duck hepatitis A virus type 1 (DHAV-1) causes a highly contagious disease in domestic ducklings, which is traditionally characterized by lesions in the liver and rarely in the pancreas. However, several outbreaks of DHAV-1, which were characterized by yellow coloration and hemorrhage in pancreatic tissues, have occurred in China. The causative agent was named as pancreatitis-type DHAV-1. Genomic sequencing indicated variation rates of 3.4-6.5% in the genome of the pancreatitis-type DHAV-1 compared with those of the classical type DHAV-1. The antigenic relationship between the pancreatitis-type DHAV-1 and classical type DHAV-1 indicated large variation. However, the mechanism involved in infection of the pancreatitis-type DHAV-1 is still unclear. Results: In the present study, transcriptome analysis of duck pancreas infected with classical type DHAV-1 and pancreatitis-type DHAV-1 was carried out. Following deep sequencing with Illumina-Solexa, a total of 53.9 Gb clean data were obtained from the cDNA library of the pancreas and a total of 29,597 unigenes with an average length of 993.43 bp were generated following de novo sequence assembly. The expression levels of D-3-phosphoglyceratedehydrogenase, phosphoserine aminotransferase, phosphoserine phosphatase, which are involved in glycine, serine and threonine metabolism pathway, were significantly downregulated in the pancreatitis-type DHAV-1-infected group compared with those of the classical type DHAV-1-infected group.Conclusion: These findings provide information regarding differential expression levels of metabolism-associated genes between pancreatitis-type DHAV-1 and classical type DHAV-1, indicating that intensive metabolism disorders may contribute to different subtypes of DHAV-1-infection.

Equine herpetic infection: features of pathogenesis and diagnosis

Equine alphaherpesviruses ― causative agents of rhinopneumonitis−viral abortion (EHV-1) and rhinopneumonitis (EHV-4) ― represent the subfamily Alphaherpesvirinae, genus Varicellovirus. EHV-1 causes abortion, respiratory pathology, and neurological disorders in horses of different ages. EHV-4 causes predominantly respiratory disease in foals and sporadic abortions in mares. In the etiopathogenesis of herpesvirus infections EHV-1 and EHV-4, the determining factors are pronounced tropism to epithelial cells, persistence in a non-replicative form, and unpredictable reactivation of a persistent virus with its release into the environment. EHV-1 and EHV-4 have similar antigenic determinants and cross-react in serological reactions. The high level of antigenic relationship between EHV-1 and EHV-4 can make it difficult to interpret serologic results in natural infections. The EHV-1 and EHV-4 strains in active circulation are genetically rather conservative. The exception is the new EHV-1 strains with a mutation in the gene encoding viral DNA polymerase, which caused outbreaks of neuroparalytic disease in some European countries and the United States. In several cases, the neurological syndrome has been reported due to use of some commercial vaccines

Pan-genome analysis of coronaviruses derived from major of canine and feline

Coronaviruses (CoVs) are a well-known cause of severe enteric, respiratory, and systemic disease in a wide range of animals and in humans. To understand the route of disease origin and viral transmission in companion animals, a comparative pan-genomic analysis of coronavirus sequences originating from major felines and canines were conducted. The average nucleotide identity (ANI) is a rapid procedure for assessing the very close antigenic relationship between feline CoV (FCoVs) and canine CoV (CCoVs) and ANI-based phylogenetic tree that clustered CoVs according to their respective host species. While pan-genomic analysis demarcated strains clearly. The distribution of the clinical isolates all across the categories in the hierarchical phylogenetic model enabled the visualization of their original ecological niche rather than their isolation source, as infections are extremely rare events and evolutionary dead-ends. In polymorphism analysis, we found seven accessory gene clusters common to the FCoV/CCoV category clade, including pantropic strains, that perform functions supporting their pathogenicity. In addition, the gene presence/absence among FCoVs and CCoVs would provide very valuable information on species-specific control measures against CoV disease, such as the selection of good markers for differentiating new species from common and/or pantropic isolates. Also, the virulent FCoV strains were grouped with human CoV strains NL63 and 229E confirming hypotheses stating that cats are highly susceptible to HCoVs, while dogs have low susceptibility to the virus. In conclusion, the combined analysis allows for better phylogenetic resolution and the implication of virus origins, recombination, and virus–host interaction, as well as biomarkers.

Zoonotic infection with swine A/H1avN1 influenza virus in a child, Germany, June 2020

A zoonotic A/sw/H1avN1 1C.2.2 influenza virus infection was detected in a German child that presented with influenza-like illness, including high fever. There was a history of close contact with pigs 3 days before symptom onset. The child recovered within 3 days. No other transmissions were observed. Serological investigations of the virus isolate revealed cross-reactions with ferret antisera against influenza A(H1N1)pdm09 virus, indicating a closer antigenic relationship with A(H1N1)pdm09 than with the former seasonal H1N1 viruses.