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fredag 31 december 2021

CD8+ T solu epitooppien etsintää Sars-2 rakenneproteiineista . M-proteiinista löytyi 6 epitooppia.

 https://jlb.onlinelibrary.wiley.com/doi/10.1002/JLB.4MA0621-020R

Abstract

The outbreak of coronavirus disease 2019 (COVID-19) has now become a pandemic, and the etiologic agent is the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). T cell mediated immune responses play an important role in virus controlling; however, the understanding of the viral protein immunogenicity and the mechanisms of the induced responses are still limited. So, identification of specific epitopes and exploring their immunogenic properties would provide valuable information. In our study, we utilized the Immune Epitope Database and Analysis Resource and NetMHCpan to predict HLA-A2 restricted CD8+ T cell epitopes in structural proteins of SARS-CoV-2, and screened out 23 potential epitopes. Among them, 18 peptides showed strong or moderate binding with HLA-A2 with a T2A2 cell binding model. Next, the mixed peptides induced the increased expression of CD69 and highly expressed levels of IFN-γ and granzyme B in CD8+ T cells, indicating effective activation of specific CD8+ T cells. In addition, the peptide-activated CD8+ T cells showed significantly increased killing to the target cells. Furthermore, tetramer staining revealed that the activated CD8+ T cells mainly recognized seven epitopes. All together, we identified specific CD8+ T cell epitopes in SARS-CoV-2 structural proteins, which could induce the production of specific immune competent CD8+ T cells. Our work contributes to the understanding of specific immune responses and vaccine development for SARS-CoV-2.

 

3.1 Prediction of HLA-A2 restricted CD8+ T cell epitopes in structure proteins of SARS-CoV-2

To broadly screen the epitopes of SARS-CoV-2 and understand the mechanisms of antigen epitope recognition and activation associated with CD8+ T cells, we predicted the HLA-A2 restricted CD8+ T cell epitopes in S, M, N, and E protein of SARS-CoV-2 by using the IEDB and NetMHCpan EL 4.0. Peptides with the predicted binding capability IC50 below 100 nM were selected. Totally, 23 peptides were selected, including 14 in S protein, 3 in E protein, and 6 in M protein (Fig. 1B). The detailed information is shown in Table 2. Next, these potential epitopes were synthesized for further evaluation.


No.HLA subtypes Position Sequence Molecular weight References
n-Sp16 HLA-A2 62-70 VTWFHAIHV 1109.3
n-Sp17 HLA-A2 424-432 KLPDDFTGC 995.12
n-Sp18 HLA-A2 515-524 FELLHAPATV 1097.28
n-Sp19 HLA-A2 721-729 SVTTEILPV 958.12
n-Sp20 HLA-A2 786-794 KQIYKTPPI 1087.33
n-Sp21 HLA-A2 817-826 FIEDLLFNKV 1237.46
n-Sp22 HLA-A2 821-829 LLFNKVTLA 1018.26
n-Sp23 HLA-A2 894-902 LQIPFAMQM 1078.35
n-Sp24 HLA-A2 964-972 KQLSSNFGA 951.05
n-Sp25 HLA-A2 976-984 VLNDILSRL 1042.24 Sekine et al.19, 18
n-Sp26 HLA-A2 983-991 RLDKVEAEV 1058.2
n-Sp27 HLA-A2 1048-1056 HLMSFPQSA 1017.17
n-Sp28 HLA-A2 1062-1070 FLHVTYVPA 1046.23
n-Sp29 HLA-A2 1121-1129 FVSGNCDVV 939.05
n-Ep1 HLA-A2 16-24 SVLLFLAFV 1008.27
n-Ep2 HLA-A2 26-34 FLLVTLAIL 1002.31
n-Ep3 HLA-A2 50-58 SLVKPSFYV 1039.24 Sekine et al.19
n-Mp1 HLA-A2 15-23 KLLEQWNLV 1142.36 Sekine et al.19
n-Mp2 HLA-A2 26-35 FLFLTWICLL 1268.62
n-Mp3 HLA-A2 51-60 LIFLWLLWPV 1299.66
n-Mp4 HLA-A2 61-70 TLACFVLAAV 1007.26  
-Mp5 HLA-A2 65-73 FVLAAVYRI 1051.3
n-Mp6 HLA-A2 89-97 GLMWLSYFI 1129.38

 

Miten herättää vaimennettua luonnollista immuunivastetta ajoissa? SLR-RIG-1 agonistin periaatteesta

 https://rupress.org/jem/article/219/1/e20211818/212765/A-stem-loop-RNA-RIG-I-agonist-protects-against

Löysin tämän artikkelin, kun etsin  jotain Sars-2-antivirusterapiaa, jossa olisi kohdennettu M-proteiiniin  tavalla tai toisella, koska se on nopea sammutamaan  nopeimman  luonnollisen immuniteetin  vasteen ja IFN-1  interferonitien.  

Etsin oikeastaan  kyselymallilla: Miten  solun PRR tunnistus  havaitsee  ( Sars-2)  viruksen   RNA:n duplexrakennetta.   Tässä  on tehty pieni molekyyli, jossa  on   STEM-LOOP- duplexrakennetta ja  RIG-1  mikä  herättää  antivirusvasteen ja IFN-1 muodostuksen rakenteellaan.  Jos tällaista  molekyyliä annetaan aivan infektion alussa,  ehditään herättää  antivirusgeenejä IFN_1:stä riippuvalla tavalla.  Tämä on hiirikoe.  Tämän tapainen  terapia  estäisi myös kroonisen  covidin muodostumista   niissä, joiden immuunivaste on  heikkoa.

Silmäys eri lintulajien alttiuteen sairastua ja kuolla H5N1 lintuinfluenssaan ? Aiemmista tiedoista hyötyä nyt.

 https://go.gale.com/ps/i.do?p=AONE&u=googlescholar&id=GALE|A195522200&v=2.1&it=r&sid=AONE&asid=9f6766c0

Main content

From December 2003 through January 2004, the Phnom Tamao Wildlife Rescue Centre, Cambodia, was affected by the highly pathogenic influenza virus (H5N1). Birds from 26 species died. Influenza virus subtype H5N1 was detected in 6 of 7 species tested. Cats from 5 of 7 species were probably infected; none died.

**********

On January 24, 2004, the first confirmed outbreak of highly pathogenic avian influenza virus (HPAIV) subtype H5N1 in Cambodia was reported to the Office International des Epizooties (1). During the previous month, an unusually high mortality rate had been noted among captive wild birds at the Phnom Tamao Wildlife Rescue Centre (PTWRC) in Takeo Province, 45 km South from Phnom Penh. We report the results of a retrospective investigation of this outbreak.

The Study

During the outbreak period, PTWRC housed 600-1,000 wild animals (70 species of mammals, birds, and reptiles). The center is divided into 3 main sections that cover 37 ha. Birds were kept in sections S1-1, S1-2, and S2, and the cats were in all sections (Figure). The information on bird deaths at PTWRC was systematically recorded by WildAid staff members who were at the Centre at the time of the outbreak. In June 2004, a complete investigation was conducted at PTWRC, and semistructured interviews of key informants were used to identify deaths of domestic poultry in the surrounding villages. Every bird death between December 15, 2003, through January 15, 2004, was defined as a suspected case of HPAIV (H5N1). For S1, the cumulative mortality rate could not be estimated because the exact bird population was not known and the birds were difficult to observe in that section (the semicaptive waterfowl population is able to mix with the wild population and disperse to breed). For S2, information was complete (Table 1). 

 

The first case, in a crested serpent eagle (Spilornis cheela), was reported on December 15, 2003, in S2 (Figure). On December 19, the outbreak had reached every section and continued until January 12; a total of 86 birds, representing 8 taxonomic orders and 12 families, died (Table 1). Of 7 cat species, cats from 5 species were reported sick (16/39 total cats) (Table 2). In $2, 80% of the reported bird deaths were observed from December 15 to 21. Of the 29 wild bird species kept in $2 at the beginning of the outbreak, no birds from 12 species showed signs of disease (Table 1). Mortality rates varied among the orders, 0-100% (Table 1). The only mammals present in the aviaries in $2, slow lorises (Nycticebus sp.), did not become ill. None of the 27 animal keepers, who were 20-50 years of age, were reported to have gotten sick.

Most of the birds died within a few hours without showing any clinical signs of infection. A few birds died 1-2 days after onset of clinical signs (anorexia, extreme lethargy, occasional dark green diarrhea, respiratory distress, and neurologic abnormalities). The cats were sick for 5-7 days and exhibited anorexia and lethargy but no respiratory illness.

Laboratory investigations of the organs from 8 birds sampled in December 2003 were performed (Table 1). For those birds, West Nile virus infection was ruled out by reverse transcription-PCR (RT-PCR), according to the procedure described by Lanciotti et al. (2). All birds sampled, except a parakeet, were positive for influenza subtype H5N1 by RT-PCR (3) (Table 1). Molecular characterizations of hemagglutinin (H)5 and neuraminidase (N)1 were performed from the influenza virus (H5N1) strains from PTWRC as previously described (4). H5 amino acid sequences were identical in the coding region to the sequence of isolates obtained from poultry cases in Cambodia (ill poultry from a flock with high mortality rates) and similar ([greater than or equal to]96.5%) to HPAIV (H5N1) strain H5 sequences from Vietnam and Thailand in 2004 (data not shown). All belonged to the H5 clade 1 (4). Amino acid sequences from N 1 from Cambodia were very close to each other ([greater than or equal to]97.12% identity) and to 2004 Vietnamese and Thai N1 sequences (>96%) (data not shown). The HA and NA sequences of the isolates were deposited in GenBank (accession nos. ISDN186319-ISN186324, ISDN186329, ISDNI86330ISDN 186665, and ISDN242365).

Retrospective investigation of the villages surrounding the PTWRC and Phnom Perth showed that chickens from 2 flocks in which deaths had been reported in mid-December had been provided to the PTWRC, either for the restaurants or for the captive animal feeding. Furthermore, at the time of the outbreak, many wild crows were found dead in the forest surrounding the PTWRC.

The 4 cat serum samples, each from a different species, were positive for HPAIV (H5N1) with serum neutralization test (5); titers ranged from 10 to 40 (Table 2). None of the affected cats died.

Conclusions

The sources of introduction of HPAIV (H5N1) within the PTWRC were probably multiple: virus-infected chicken bought to feed the carnivorous species, infected live chickens brought to restaurants near S2 (i.e., the first place where deaths were detected), and contact between infected wild and captive birds. The introduction through infected chickens is supported by the absence of an outbreak at the PTWRC after the feeding of chickens to carnivorous species was discontinued; however, deaths in domestic poultry continued in the area. In addition, almost all carnivorous bird species in S2 died (93% of Falconiformes and 92% of Strigiformes) as did most species usually fed chicken meat in captivity (herons, storks, crows, great hornbill, pelican). Diet was also the origin of the outbreak among tigers and leopards in Thailand (6,7). The dispersion of the disease between PTWRD sections was probably due to poor biosecurity measures.

The clinical outcome of wild birds with suspected HPAIV (H5N1) infection at PTWRC ranged from severe illness and death to complete absence of clinical signs, as described (8). Several species from the orders Ciconiiformes, Galliformes, Passeriformes, Gruiformes, Coraciiformes, and Pelecaniformes were affected during the outbreak. This observation is consistent with data published earlier, except for Coraciiformes represented by 1 bird in our study (9). Only the carnivorous species (Corvus macrorynchos) among the 5 species of Passeriformes in the aviaries showed clinical signs and later was confirmed by RT-PCR to be positive for HPAIV (H5N1). This outbreak confirms that Falconiformes and Strigiformes are sensitive to HPAIV (H5N1) infection and disease (10-12) and shows that numerous species of these orders can be affected by HPAIV (H5N1) (Table 1). Psittaciformes and Columbiformes were not visibly affected by the outbreak although they were kept in large numbers in S2, where large numbers of deaths occurred. As non-water-bird species, they do not belong to groups in which avian influenza is commonly reported (13). Anseriformes, represented in PTWRC by only 4 birds (Anas poecilorhyncha), did not show any clinical signs. Heterogeneity in the susceptibility of wild ducks to HPAIV (H5N1), including asymptomatic infection, has been demonstrated (14); this species also belongs to the group of wild ducks found asymptomatically infected with HPAIV (H5N1) in the People's Republic of China during the winter of 2005 (15).

 

The serologic evidence of influenza virus (H5N1) infection in 4 species of wild cats is in agreement with previous infection in Thailand (6, 7). The report of illness in the Asiatic golden cat (Catopuma temminckii) and the clouded leopard (Neofelis nebulosa) broadens the host range of the virus among mammals.

This report confirms the great variability of wild bird and mammal responses to HPAIV (H5N1) infection. It also confirms the broadening range of susceptible species that may be specific to this clade 1 virus.

References 

References

(1.) World Organisation for Animal Health. Update on highly pathogenic avian influenza in animals (type H5 and H7) [cited 2008 May 31]. Available from http://www.oie.int/downld/AVIAN%20INFLUENZA/ A2004_AI.php

(2.) Lanciotti RS, Calisher CH, Gubler DJ, Chang GJ, Vance-Vorndam A. Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction. J Clin Microbiol. 1992;30:545-51.

(3.) World Organisation for Animal Health. Recommended laboratory tests to identify influenza A/H5 virus in specimens from patients with an influenza-like illness. 19 February 2004 [cited 2005 Jun 12]. Available from http://www.who.int/csr/disease/avian_influenza/ guidelines/en/avian_labtests1.pdf

(4.) The World Health Organization Global Influenza Program Surveillance Network. Evolution of H5N1 avian influenza viruses in Asia. Emerg Infect Dis. 2005;11:1515-21.

(5.) Choi YK, Nguyen TD, Ozaki H, Webby RJ, Puthavathana P, Buranathal C, et al. Studies of H5NI influenza virus infection of pigs by using viruses isolated in Vietnam and Thailand in 2004. J Virol. 2005;79:10821-5. DOI: 10.1128/JV1.79.16.10821-10825.2005

(6.) Keawcharoen J, Oraveerakul K, Kuiken T, Fouchier RAM, Amonsin A, Payungporn S, et al. Avian influenza H5N1 in tigers and leopards. Emerg Infect Dis. 2004;10:2189-9l. DOI: 10.1007/b100517

(7.) Thanawongnuwech R, Amonsin A, Tantilertcharoen R, Damrongwatanapokin S, Theamboonlers A, Payungporn S, et al. Probable tiger-to-tiger transmission of avian influenza H5N1. Emerg Infect Dis. 2005;11:699-701. DOI: 10.1007/b102143 

8.) Webster RG, Hulse DJ. Microbial adaptation and change: avian influenza. Rev Sci Tech. 2004;23:453-65. DOI: 10.2172/15009826

(9.) Whitworth D, Newman SH, Mundkur T, Harris P, eds. Wild birds and avian influenza: an introduction to applied field research and disease sampling techniques. Rome (Italy): Food and Agriculture Organization, Animal Production and Health; 2007 [cited 2008 Jun 2]. Available from http://www.fao.org/avianflu/en/wildlife/info_res.htm

(10.) World Organisation for Animal Health. Avian influenza in Hong Kong (Special Administrative Region of the People's Republic of China) in a wild bird [in French]. Informations Sanitaires. 2004;17 [cited 2009 Jan 21]. Available from ftp://ftp.oie.int/infos_san_archives/fr/2004/fr_040130v17n05.pdf

(11.) Van Bonn S, Thomas I, Hanquet G, Lambrecht B, Boschmans M, Dupont G, et al. Highly pathogenic H5N1 influenza virus in smuggled Thai eagles, Belgium. Emerg Infect Dis. 2005;11:702-5. DOI: 10.1007/b102143

(12.) Sabirovic M, Wilesmith J, Hall S, Coulson N, Landeg F. Outbreaks of HPAI H5N1 virus in Europe during 2005/2006. DEFRA, 2006 [cited 2009 Jan 21]. Available from http://collections.europarchive.org/ tna/20080107205404/http://defra.gov.uk/ animalh/diseases/monitoring/riskassess.htm

(13.) Olsen B, Munster VJ, Wallensten A, Waldenstrom J, Osterhaus AD, Fouchier RA. Global patterns of influenza A virus in wild birds. Science. 2006;312:384-8. DOI: 10.1126/science. 1122438

(14.) Brown JD, Stallknecht DE, Beck JR, Suarez DL, Swayne DE. Susceptibility of North American ducks and gulls to H5N1 highly pathogenic avian influenza viruses. Emerg Infect Dis. 2006; 12:1663-70.

(15.) Chen H, Smith GJ, Li KS, Wang J, Fan XH, Rayner JM, et al. Establishment of multiple sublineages of H5NI influenza virus in Asia: implications for pandemic control. Proc Natl Acad Sci U S A. 2006;103:2845 50. DOI: 10.1073/pnas.0511120103

Address for correspondence: Stephanie Desvaux, CIRAD, AGIRs, National Institute of Veterinary Research, 86 Truong Chinh, Hanoi, Vietnam; email: stephanie.desvaux@cirad.fr

Author affiliations: Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement, Montpellier, France (S. Desvaux, N. Gaidet); WildAid, Phnom Penh, Cambodia (N. Marx, M. Hunt); Institut Pasteur du Cambodge, Phnom Penh (S. Ong, J.-M. Reynes); Institut Pasteur, Paris, France (J.-C. Manuguerra, S. Van der Werf); National Animal Health and Production Investigation Center, Phnom Penh (S. Sorn); and University of Hong Kong and Queen Marie Hospital, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China (M. Peiris)

DOI: 10.3201/eid1503.081410

Dr Desvaux is a veterinary epidemiologist working at the Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement. Her current research interests focus on HPAIV epidemiology and surveillance in Vietnam.

Table 1. Cumulative deaths during an outbreak of highly pathogenic
avian influenza virus (H5N1), Phnom Tamao Wildlife Rescue
Centre, Cambodia, December 15, 2003-January 13, 2004 *

Order              Family                Species (common name),
                                              no. sampled

Anseriformes       Anatidae               Anas poecilorhyncha
                                          (Indian spot-billed
                                                 duck)
Ciconiiformes      Ardeidae                  Ardea cinerea
                                            (grey  heron),
                                                 n = 2
                                           Ardeola speciosa
                                             (Javan-pond
                                             heron), n = 1
                                          Butorides striatus
                                             (little heron)
                                           Egretta garzetta
                                             (little egret)
                   Ciconidae               Ephippiorhynchus
                                               asiaticus
                                           (black-neck stork)
                                          Leptoptilos dubius
                                           (greater adjutant
                                                 stork)
                                         Leptoptilos javanicus
                                        (lesser adjutant stork)
                                         Mycteria leucocephala
                                            (painted stork)
                                           Ciconia episcopus
                                          (wooly necked stork)
                                          Anastomus oscitans
                                            (Asian openbill
                                                 stork)
Colombiformes      Colombidae             Treron curvirostra
                                             (thick-billed
                                             green pigeon)
                                        Streptopelia chinensis
                                             (spotted dove)
Coraciiformes      Buceritidae              Buceros bicomis
                                            (great hornbill)
Falconiformes      Accipitridae            Gyps bengalensis
                                             (white-rumped
                                                vulture)
                                            Haliastur indus
                                            (Brahminy kite)
                                        Ichthyophaga ichtyaetus
                                           (grey-headed fish
                                                 eagle)
                                         Ictinaetus malayensis
                                             (black eagle)
                                            Milvus migrans
                                              (black kite)
                                            Spilomis cheela
                                           (crested serpent
                                             eagle), n = 1
                                          Spizaetus cirrhatus
                                        (changeable hawk eagle),
                                                  n = 1
Galliformes        Numididae                 Agelastes sp
                                              (guineafowl)
                   Phasianidae               Pavo muticus
                                            (green peafowl)
                                             Gallus gallus
                                           (red jungle fowl)
Gruiformes         Gruidae                   Grus antigone
                                             (Sarus crane)
Passeriformes      Corvidae               Corvus macrorynchos
                                          (large-billed crow),
                                                  n = 1
                   Sturnidae               Gracula religiosa
                                              (hill mynah)
                                         Acridotheres tristis
                                             (common mynah)
                                        Acridotheres javanicus
                                          (white-vented mynah)
                                         Stumus contra (Asian
                                             pied starling)
Pelecaniformes     Anhigindae            Anhinga melanogaster
                                           (oriental darter)
                   Pelecanidae          Pelecanus philippensis
                                         (spot-billed pelican)
Psittaciformes     Psittacidae            Psittacula eupatria
                                        (Alexandrine parakeet),
                                            n = 1 ([dagger])
                                          Psittacula roseate
                                            (blossom-headed
                                               parakeet)
                                         Psittacula alexandri
                                        (red-breasted parakeet)
                                          Psittacula finschii
                                         (grey-headed parakeet)
Strigiformes       Strigidae                Bubo nipalensis
                                             (spot-bellied
                                              eagle owl),
                                                 n = 1
                                             Ketupa ketupu
                                            (buffy fish owl)
                                          Ketupa zeylonensis
                                            (brown fish owl)
                                            Strix seloputo
                                           (spotted wood owl)
                   Tytonidae              Tyto alba (barn owl)
Total
8 sampled
                                                    No. birds
                                   No. dead         not dead
Species (common name),           birds in S1         in S1
no. sampled

Anas poecilorhyncha                   NP               NP
 (Indian spot-billed
 duck)
Ardea cinerea                          4                2
 (grey  heron),
 n = 2
Ardeola speciosa                       7                0
 (Javan-pond
 heron), n = 1
Butorides striatus                    NP               NP
 (little heron)
Egretta garzetta                      NP               NP
 (little egret)
Ephippiorhynchus                       1                3
 asiaticus
 (black-neck stork)
Leptoptilos dubius                     2                1
 (greater adjutant
 stork)
Leptoptilos javanicus                  3               21
 (lesser adjutant stork)
Mycteria leucocephala                  6               20
 (painted stork)
Ciconia episcopus                      0                3
 (wooly necked stork)
Anastomus oscitans                     0                5
 (Asian openbill
 stork)
Treron curvirostra                    NP               NP
 (thick-billed
 green pigeon)
Streptopelia chinensis                NP               NP
 (spotted dove)
Buceros bicomis                       NP               NP
 (great hornbill)
Gyps bengalensis                      NP               NP
 (white-rumped
 vulture)
Haliastur indus                       NP               NP
 (Brahminy kite)
Ichthyophaga ichtyaetus                3                0
 (grey-headed fish
 eagle)
Ictinaetus malayensis                 NP               NP
 (black eagle)
Milvus migrans                         1                0
 (black kite)
Spilomis cheela                        1                0
 (crested serpent
 eagle), n = 1
Spizaetus cirrhatus                    0                0
 (changeable hawk eagle),
 n = 1
Agelastes sp                          NP               NP
 (guineafowl)
Pavo muticus                           0                3
 (green peafowl)
Gallus gallus                         NP               NP
 (red jungle fowl)
Grus antigone                          3                0
 (Sarus crane)
Corvus macrorynchos                    2                0
 (large-billed crow),
 n=1
Gracula religiosa                     NP               NP
 (hill mynah)
Acridotheres tristis                  NP               NP
 (common mynah)
Acridotheres javanicus                NP               NP
 (white-vented mynah)
Stumus contra (Asian                  NP               NP
 pied starling)
Anhinga melanogaster                   0                1
 (oriental darter)
Pelecanus philippensis                 3                2
 (spot-billed pelican)
Psittacula eupatria                    1                0
 (Alexandrine parakeet),
 n = 1 ([dagger])
Psittacula roseate                    NP               NP
 (blossom-headed
 parakeet)
Psittacula alexandri                  NP               NP
 (red-breasted parakeet)
Psittacula finschii                   NP               NP
 (grey-headed parakeet)
Bubo nipalensis                        0                0
 (spot-bellied
 eagle owl),
 n = 1
Ketupa ketupu                         NP               NP
 (buffy fish owl)
Ketupa zeylonensis                    NP               NP
 (brown fish owl)
Strix seloputo                        NP               NP
 (spotted wood owl)
Tyto alba (barn owl)                   5                0
8 sampled                             42               61

                                   Cumulative deaths in S2,
                                    % (dead/total at risk)

Species (common name),           Per species       Per order
no. sampled

Anas poecilorhyncha                0 (0/4)          0 (0/4)
 (Indian spot-billed
 duck)
Ardea cinerea                         NP           47 (9/19)
 (grey  heron),
 n = 2
Ardeola speciosa                  100 (7/7)
 (Javan-pond
 heron), n = 1
Butorides striatus                  0 (0/1)
 (little heron)
Egretta garzetta                   18 (2/11)
 (little egret)
Ephippiorhynchus                      NP
 asiaticus
 (black-neck stork)
Leptoptilos dubius                    NP
 (greater adjutant
 stork)
Leptoptilos javanicus                 NP
 (lesser adjutant stork)
Mycteria leucocephala                 NP
 (painted stork)
Ciconia episcopus                     NP
 (wooly necked stork)
Anastomus oscitans                    NP
 (Asian openbill
 stork)
Treron curvirostra                  0 (0/7           0 (0/17)
 (thick-billed
 green pigeon)
Streptopelia chinensis              0 (0/10)
 (spotted dove)
Buceros bicomis                   100 (1/1)        100 (1/1)
 (great hornbill)
Gyps bengalensis                  100 (1/1)         93 (13/14)
 (white-rumped
 vulture)
Haliastur indus                     0 (0/1)
 (Brahminy kite)
Ichthyophaga ichtyaetus           100 (4/4)
 (grey-headed fish
 eagle)
Ictinaetus malayensis             100 (1/1)
 (black eagle)
Milvus migrans                        NP
 (black kite)
Spilomis cheela                   100 (5/5)
 (crested serpent
 eagle), n = 1
Spizaetus cirrhatus               100 (2/2)
 (changeable hawk eagle),
 n=1
Agelastes sp                      33.3 (1/3)        36 (5/14)
 (guineafowl)
Pavo muticus                       100 (3/3)
 (green peafowl)
Gallus gallus                     12.5 (1/8)
 (red jungle fowl)
Grus antigone                         NP
 (Sarus crane)
Corvus macrorynchos                100 (3/3)        25 (3/12)
 (large-billed crow),
 n = 1
Gracula religiosa                    0 (0/3)
 (hill mynah)
Acridotheres tristis                 0 (0/4)
 (common mynah)
Acridotheres javanicus               0 (0/1)
 (white-vented mynah)
Stumus contra (Asian                 0 (0/1)
 pied starling)
Anhinga melanogaster                  NP
 (oriental darter)
Pelecanus philippensis                NP
 (spot-billed pelican)
Psittacula eupatria                 50 (1/2)         0 (1/146)
 (Alexandrine parakeet),
 n = 1 ([dagger])
Psittacula roseate                   0 (0/20)
 (blossom-headed
 parakeet)
Psittacula alexandri                 0 (0/20)
 (red-breasted parakeet)
Psittacula finschii                  0 (0/104)
 (grey-headed parakeet)
Bubo nipalensis                    100 (1/1)        92 (12/13)
 (spot-bellied
 eagle owl),
 n = 1
Ketupa ketupu                      100 (3/3)
 (buffy fish owl)
Ketupa zeylonensis                  86 (6/7)
 (brown fish owl)
Strix seloputo                     100 (2/2)
 (spotted wood owl)
Tyto alba (barn owl)                  NP
8 sampled                            18.3%          (44/240)

* S1, aviary section in which cumulative mortality rate could not
be estimated because exact bird population was not known and birds
were difficult to observe; S2, aviary section in which captive bird
population was exactly known and number of dead birds was precisely
recorded; NP, species not present in S1 or S2.

([dagger]) Only sample that was negative for highly pathogenic avian
influenza virus (H5N1); all other birds sampled were positive.

Table 2. Morbidity rates for wild cats during outbreak of highly
pathogenic avian influenza virus (H5N1), Phnom Tamao Wildlife Rescue
Centre, Cambodia, December 15, 2003-January 13, 2004

Order       Family      Species (common name)      Cumulative
                                                  morbidity rate,
                                                    % (sick/at
                                                    risk), no.
                                                     sampled

Carnivora   Felidae     Panthera leo (lion)           100 (2/2)
                      Panthera tigris (tiger)    80 (8/10), n= 1 *
                        Catopuma temminckii
                          (Asiatic golden
                                cat)            100 (2/2), n = 1 *
                         Panthera pardus
                            (leopard)           100 (3/3), n = 1 *
                        Neofelis nebulosa
                        (clouded leopard)       100 (1/1), n = 1 *
                          Prionailurus
                          bengalensis
                         (leopard cat)               0 (0/16)
                         Prionailurus
                          viverrinus
                         (fishing cat)               0 (0/5)
Total                                               41 (16/39)

* All serum samples were positive (date of collection: March 4, 2004).

 

OIE-WAHIS uutisia 31.12.2021

 Koska taulokossa mainitaan Suomi, tarkistan mikä lemmikkieläin on saanut ihmiseltä Sars-2 viruksen: Yksi vantaalainen kissa ja asia on hoitunut jo.

Outbreaks
Disease
SARS-CoV-2 in animals (Inf. with)
Start Date
2021-12-10
End Date
2021-12-14
Status
resolved
Total Cases
1
Animal Category
Domestic
Other properties
Total Outbreaks
1
Location
Vantaa
Species
Cats
Is Cluster
No
Latitude
60.2934
Longitude
25.0399
Report Details

 

 https://wahis.oie.int/#/home

 

Most recent notifications

Country/TerritoryDisease-Serotype/genotype/subtypeDate
SloveniaHighly pathogenic influenza A viruses (Inf. with)(non-poultry including wild birds)(2017-)H5N130/12/21
SloveniaHighly pathogenic avian influenza (poultry) H5N128/12/21
FinlandSARS-CoV-2 in animals (Inf. with)27/12/21
RussiaFoot and mouth disease virus (Inf. with) O28/12/21
NigerRift Valley fever virus (Inf. with) 28/12/21
BeninHighly pathogenic avian influenza (poultry) H5N127/12/21
PortugalHighly pathogenic avian influenza (poultry) H5N124/12/21
Chinese TaipeiHighly pathogenic avian influenza (poultry) H5N2 

Suuri kurkikuolema muuttomatkalla Afrikkaan. (Grus grus, GRUIDAE; tranorna, Cranes) Syynä lintuvirus A H5N1.

 https://www.nytimes.com/2021/12/29/world/middleeast/israel-avian-flu.html

JERUSALEM — Israel is acting to contain a severe outbreak of avian flu that has already led to mass culling of infected poultry and has caused the deaths of about 5,000 migratory cranes in a popular nature reserve in the north of the country.

The minister of environmental protection, Tamar Zandberg, described the outbreak, identified as the H5N1 type, as “one of the worst blows to wildlife in Israel’s history” after a visit to the Hula Nature Reserve this week. Hula is a wetland that is a central stop on the winter migration route to Africa.

The reserve, usually bustling with bird watchers at this time of year, is temporarily closed to visitors and the Ministry of Environmental Protection said on Wednesday that Ms. Zandberg was working to suspend the rest of the hunting season in the country, which normally runs until the end of January.

The fear, the ministry said, was that gunshots from bird hunters could cause the wild birds to fly off to other locations, spreading the disease, which it said could also be spread by contaminated car tires on hunters’ vehicles or on the soles of their shoes, or by the dogs retrieving their prey.

Officials have also warned of the danger of the transmission of avian flu from animals to humans, which could be deadly. No such cases have been recorded in Israel.

The first signs of the outbreak came about two months ago, according to the Ministry of Environmental Protection, with infections cropping up in chicken and turkey farms in different areas of the country.

Israel’s minister of agriculture and rural development, Oded Forer, said about 600,000 chickens had been culled. He said that would mean a shortfall of 15 million eggs per month over the next few months and that the department was working to import millions of eggs.

In an interview with Kan Radio, Israel’s public broadcaster, on Tuesday, Mr. Forer blamed the outdated, overcrowded chicken coops that he said were common in Israel for the severity of the outbreak of the virus.

The egg industry had been “neglected for years,” he said, adding that most of the coops in Israel were like those from the 1950s or 60s, and that there was a need to move to more modern coops without cages.


Ihmisen luonnollisen ja adaptatiivisen immuunivasteen kyvyistä selvitä omikron-viruksesta. Tappaja-T-soluepitoopeista tehty tutkimus.

( Tämän tutkimuksen perusteella kannataa  edelleen  noudattaa kaikkia ohjeita ja rokottautua edelleen näillä olevaisilla rokotteilla.ja pitää hyvää yleiskuntoa yllä.  Omasta mielestäni pitäisi  muistuttaa siitä sinkistä ja seleenistä ja D- ja  C-vitamiinista, vihreistä vihanneksista ja tarpeellisesta levosta myös  perusravinnon ja hygienian  ja riittävän ulkoilun ohella.  Alla oleva tutkimus on  niitäpeer- vaiheen artikkeleita ja  mainitaan että niihin ei vielä pitäisi perustaa  mitään erityisempää terapeuttista  suositusta).  

. 2021 Dec 9;2021.12.06.471446.
doi: 10.1101/2021.12.06.471446. Preprint

Minimal cross-over between mutations associated with Omicron variant of SARS-CoV-2 and CD8+ T cell epitopes identified in COVID-19 convalescent individuals

Free PMC article Abstract

There is a growing concern that ongoing evolution of SARS-CoV-2 could lead to variants of concern (VOC) that are capable of avoiding some or all of the multi-faceted immune response generated by both prior infection or vaccination, with the recently described B.1.1.529 (Omicron) VOC being of particular interest. Peripheral blood mononuclear cell samples from PCR-confirmed, recovered COVID-19 convalescent patients (n=30) infected with SARS-CoV-2 in the United States collected in April and May 2020 who possessed at least one or more of six different HLA haplotypes were selected for examination of their anti-SARS-CoV-2 CD8+ T-cell responses using a multiplexed peptide-MHC tetramer staining approach. This analysis examined if the previously identified viral epitopes targeted by CD8+ T-cells in these individuals (n=52 distinct epitopes) are mutated in the newly described Omicron VOC (n=50 mutations). Within this population, only one low-prevalence epitope from the Spike protein restricted to two HLA alleles and found in 2/30 (7%) individuals contained a single amino acid change associated with the Omicron VOC. These data suggest that virtually all individuals with existing anti-SARS-CoV-2 CD8+ T-cell responses should recognize the Omicron VOC, and that SARS-CoV-2 has not evolved extensive T-cell escape mutations at this time.

Importance The newly identified Omicron variant of concern contains more mutations than any of the previous variants described to date. In addition, many of the mutations associated with the Omicron variant are found in areas that are likely bound by neutralizing antibodies, suggesting that the first line of immunological defense against COVID-19 may be compromised. However, both natural infection and vaccination develop T-cell based responses, in addition to antibodies. This study examined if the parts of the virus, or epitopes, targeted by the CD8+ T-cell response in thirty individuals who recovered from COVID-19 in 2020 were mutated in the Omicron variant. Only one of 52 epitopes identified in this population contained an amino acid that was mutated in Omicron. These data suggest that the T-cell immune response in previously infected, and most likely vaccinated individuals, should still be effective against Omicron.

 

Figure 1:

Linkkejä PubMed lähteestä omikron variantista ja covid-rokotuksesta

Investigating the aggressiveness of the COVID-19 Omicron variant and suggestions for possible treatment options.
Mohiuddin M, Kasahara K. Respir Med. 2021 Dec 14;191:106716. doi: 10.1016/j.rmed.2021.106716. Online ahead of print. PMID: 34923286 Free PMC article.
The COVID-19 pandemic has put a strain on all the healthcare systems around the world. ...As a result, it is urgently necessary to explore the most suitable treatments for this variant. The purpose of the study was to investigate the currently available studi …
Minimal cross-over between mutations associated with Omicron variant of SARS-CoV-2 and CD8+ T cell epitopes identified in COVID-19 convalescent individuals.
Redd AD, Nardin A, Kared H, Bloch EM, Abel B, Pekosz A, Laeyendecker O, Fehlings M, Quinn TC, Tobian AA. bioRxiv. 2021 Dec 9:2021.12.06.471446. doi: 10.1101/2021.12.06.471446. Preprint. PMID: 34909772 Free PMC article.
Peripheral blood mononuclear cell samples from PCR-confirmed, recovered COVID-19 convalescent patients (n=30) infected with SARS-CoV-2 in the United States collected in April and May 2020 who possessed at least one or more of six different HLA h …
Omicron SARS-CoV-2 variant: What we know and what we don't.
Ferré VM, Peiffer-Smadja N, Visseaux B, Descamps D, Ghosn J, Charpentier C. Anaesth Crit Care Pain Med. 2021 Dec 10;41(1):100998. doi: 10.1016/j.accpm.2021.100998. Online ahead of print. PMID: 34902630 Free PMC article. No abstract available.
Omicron variant genome evolution and phylogenetics.
Kandeel M, Mohamed MEM, Abd El-Lateef HM, Venugopala KN, El-Beltagi HS. J Med Virol. 2021 Dec 10. doi: 10.1002/jmv.27515. Online ahead of print. PMID: 34888894
Following the discovery of the SARS-CoV-2 Omicron variant (B.1.1.529), the global COVID-19 outbreak has resurfaced after appearing to be relentlessly spreading over the past 2 years. This new variant showed marked deg …
How to translate the knowledge of COVID-19 into the prevention of Omicron variants.
Wang X, Powell CA. Clin Transl Med. 2021 Dec;11(12):e680. doi: 10.1002/ctm2.680. PMID: 34898050 Free PMC article.
Omicron variants are part of the "Coronavirus disease 2019 [COVID-19] Variants of Concerns" and has the potential to spread around the world rapidly and can harm human life. ...There is an urgent need to explore the virology and bi
Emergence of new SARS-CoV-2 Variant of Concern Omicron (B.1.1.529) - highlights Africa's research capabilities, but exposes major knowledge gaps, inequities of vaccine distribution, inadequacies in global COVID-19 response and control efforts.
Petersen E, Ntoumi F, Hui DS, Abubakar A, Kramer LD, Obiero C, Tambyah PA, Blumberg L, Yapi R, Al-Abri S, Pinto TCA, Yeboah-Manu D, Haider N, Asogun D, Velavan TP, Kapata N, Bates M, Ansumana R, Montaldo C, Mucheleng'anga L, Tembo J, Mwaba P, Himwaze CM, Hamid MMA, Mfinanga S, Mboera L, Raj T, Aklillu E, Veas F, Edwards S, Kaleebu P, McHugh TD, Chakaya J, Nyirenda T, Bockarie M, Nyasulu PS, Wejse C, Muyembe-Tamfum JJ, Azhar EI, Maeurer M, Nachega JB, Kock R, Ippolito G, Zumla A. Int J Infect Dis. 2021 Dec 1;114:268-272. doi: 10.1016/j.ijid.2021.11.040. Online ahead of print. PMID: 34863925 Free PMC article. No abstract available.
From SARS to the Omicron variant of COVID-19: China's policy adjustments and changes to prevent and control infectious diseases.
Luo M, Liu Q, Wang J, Gong Z. Biosci Trends. 2021 Dec 18. doi: 10.5582/bst.2021.01535. Online ahead of print. PMID: 34924490 Free article.
The COVID-19 pandemic has been the biggest public health crisis in a century. Since it was initially reported in 2019, the duration and intensity of its impacts are still in serious question around the world, and it is about to enter its third year

 

Omikron variantti ja Covid-rokotussarjat. Pohdintaa alkaneen omicronaallon impaktista ihmiskuntaan.

Identification

DOI: https://doi.org/10.1016/S2213-2600(21)00559-2

 

“It certainly looks like a three-shot vaccination schedule will be needed against omicron”, commented Susanna Dunachie, professor in infectious diseases at the University of Oxford (Oxford, UK). In which case, the term booster might need to be retired. As of Dec 11, 34% of the UK population had received three doses of the COVID-19 vaccine; if this is now regarded as the equivalent of full vaccination, the country is back to where it was in the fourth week of May, 2021.
Pfizer-BioNTech and Moderna, the manufacturers of the two mRNA vaccines that have been approved for COVID-19, have stated that they could produce vaccines specific to omicron within 100 days. “It might be the right time to consider changing the vaccine”, said Hibberd. “The current vaccines are based on the Wuhan strain of SARS-CoV-2, but that is not what the virus looks like anymore.” A vaccine based on omicron would presumably require only two doses. “There are a lot of mutations in omicron that are similar to the other variants of concern that we have seen so far, so there is no reason to think you would not get strong cross-protection from a vaccine based on omicron”, added Hibberd. “The major issue is that we risk creating a two-tier system, with poorer countries stuck with out-of-date vaccines.”
Much will depend on the scale and severity of the breakthrough infections associated with omicron. Currently, researchers are heavily reliant on the sequencing data for omicron, which reveals more than 30 mutations in the spike protein upon which the COVID-19 vaccines are based, and neutralising antibody data, which shows that the variant has partial but not complete resistance to pre-existing immunity. But vaccine effectiveness is also determined by binding antibodies, which prevent SARS-CoV-2 from getting into the cells, and T-cells, which attack infected cells and help with antibody production.
“T-cells respond to the whole of the spike protein, so they are less likely to be bothered by a few mutations”, points out Dunachie. “They probably play a part in preventing severe disease, though we do not yet know how big a part.” When it eventually emerges, the vaccine effectiveness data might indicate that Omicron does not significantly increase the risk of severe disease or death in vaccinated populations. But billions of people around the world are not part of a vaccinated population. Just 7% of Africans have received two jabs with the COVID-19 vaccines. How omicron will interact with populations with low immunity against COVID-19 remains to be seen.
 
 
Omia kommentejani: Omikronvariantti näyttää voittavan alaa jopa  pahimmalta tämänastiselta eli  deltavarianteilta. Voisi ajatella että  niiden välinen kilpailuon kuin  rikkaruohojenkin kesken.  Joskus  voittaa vähemmän paha rikkaruoholaji  hyvin pahan rikkaruoholajin jopa siinä määrin, että ihmiset eivät niin  hätäiel sen voittaneen lajin tuhoamisen kanssa.  saataa olla että omikron on sellainen  siedettävämpi  flunssamainen ilmiö. Muta jos se taas on liian  lyhytikäinen versio viruksesta  sen elämänkaaren aalto tulee kyllä 3 kuukaudessa   vähitellen sammumaan kuten  suurin  osa virusversioista  tähän astikin näyttää tekevän.  Siinä tapauksessa  uuden rokotetteen  valmistaminen veisi  suhteettoman paljon maailman  resursseista joita rokotevalmisut ylipäätänsä tarvitsee kaikenlaisiin  antivirusrokotteisiin jo ennestäänkin.   Positiivisimmin ajatellen omikron saattaisi olla  luonnostaan heikentynyt elävä virus ja luonnon valmistama  rokote  pahinta laatua vastaan (" köyhän miehen rokote"). Millekään virukselle ei ole eduksi tappaa ihmiskuntaa kokonaan ja olla liian letaali parhaimmalle isäntämiljööllensä. Niin letaalit virukset  eliminoituvat itse lopullisesti. Tämä asia selviää kyllä 3 kuukauden sisällä. Sellainen   suuren aallon   läpimittapituus on  aika yleinen  sars-2  alalinjakäyrissä  muhkeimman piikin kohdalla.  Eri maat ovat tosin  eri  vaiheissaan tässä  aallossa ja sellainen  ylläpitää  viiveitä, joiden aikana  sars-2 voi kyteä itselleen  jossain uutta mutanttihahmoa.  Afrikan alue olikin pitkään valkoista kartaa ja sieltä näyttää  tulevan  useampaakin uutta laatua ja viruksella on siellä   runsaita  reservikätköjään. ja rokottamatonta väestöä on  tavattoman paljon.  Toisaalta asennoituminen  rokotuksiin on myös ollut paikoitellen sielläkin   hämmästyttävän   vastahankaista.

måndag 20 december 2021

Sars-2 virukselle tyypillisestä kehyssiirrosta ( frameshift) uusinta tietoa

 https://www.science.org/doi/10.1126/science.abf3546

Tässä on kehyssiirron periaate kuvattu niin hyvin, että  sain myös  minäkin  käsitystä. siitä, miten virus voi  toimittaa  ne 1a ja 1ab polypeptidinsä niin  ajoitetusti muun produktion kanssa, että se pystyy    rubix-hahmonsa niin tehokkaasti   lisäämään koko maailmassa ja samalla sallimaan   välillä   laajempiakin mutaatioryväksiä vaarantamatta elinkykyään liikaa.