Большой потенциал
Apr. 13th, 2022 08:36 pm![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
chuka_lisИсследователи из Китая оценили, на сколько мутации в шипике (уже известные по циркулирующим штаммам) и некоторые их комбинации позволяют коронавирусу расширять свои горизонты, перескакивая между видами. Для этого они создали псевдовирусные частицы, шипики которых содержали эти определенные мутации- либо 1, либо комбинацию, всего 27 вариантов, и проверяли, как эти псевдовирусы заражают клеточные культуры (20 линий), которые экспрессировали АСЕ2 рецепторы разных видов животных. Включая приматов, домашних питомцев и кур.
Оказалось, что часть из мутаций, присущих разным вариантам САРС2, дают им преимущество и в заражении других животных. Например, омикроновые, облегчают заражение грызунов. А если к мутациям омикрона 2 добавить еще одну (из уже имеющихся в другом штамме коронавируса), то вариант с такой комбинацией уже сможет заражать и кур. Что откроет большую перспективу для вируса, ведь птицы- это новая ниша обитания, к тому же мобильная, да и людям от этого не очень- чего стоит птичий грипп, а и просто грипп, который тоже переносится птицами. К тому же, вирус всегда может перескакивать обратно. И иметь при этом, в общем-то, любую патогенность (она может быть как ниже, после такого похода "налево", так и выше).
Другая группа ученых, исследуя структурные особенности шипиков омикронов1 и 2, и их способности к эффективному взаимодействию с человеческими АСЕ2, сравнивая со взаимодействием в другими типами АСЕ2, пришла к выводу, что штаммы омикронов 1 и 2 получились после того, как коронавирус пересокчил от людей к кошкам, от них к мышкам, и потом назад - к людям.
Контролировать вирус, который обладает такой "гибкостью" и зоонозной всеядностью, сложно.
Increasing evidence supports inter-species transmission of SARS-CoV-2 variants from human to domestic or wild animals during the ongoing COVID-19 pandemic, which is posing great challenges to epidemic control. Clarifying the host range of emerging SARS-CoV-2 variants will provide instructive information for the containment of viral spillover. The spike protein (S) of SARS-CoV-2 is the key determinant of receptor utilization, and therefore amino acid mutations on S will probably alter viral host range. Here, in order to evaluate the impact of S mutations, we constructed 20 Hela cell lines stably expressing ACE2 orthologs from different animals, and prepared 27 pseudotyped SARS-CoV-2 carrying different spike mutants, among which 20 bear single mutation and the other 7 were cloned from emerging SARS-CoV-2 variants, including D614G, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.135), Lambda (B.1.429) and Mu (B.1.525). Using pseudoviral reporter assay, we identified that the substitutions of T478I and N501Y enabled the pseudovirus to utilize chicken ACE2, indicating potential infectivity to avian species. Furthermore, the S mutants of real SARS-CoV-2 variants comprising N501Y showed significantly acquired abilities to infect cells expressing mouse ACE2, indicating a critical role of N501Y in expanding SARS-CoV-2 host range. In addition, A262S and T478I significantly enhanced the utilization of various mammals ACE2. In summary, our results indicated that T478I and N501Y substitutions were two S mutations important for receptor adaption of SARS-CoV-2, potentially contributing to spillover of the virus to many other animal hosts. Therefore, more attention should be paid to SARS-CoV-2 variants with these two mutations.The persistent emergence of diverse SARS-CoV-2 variants which are mainly defined by S mutations has been posing great challenges to the control of the current COVID-19 pandemic. Viral spillover from animals to humans and further spillback to other animals were believed to be a key factor for the frequent emergence of SARS-CoV-2 variants [14, 33]. The host range of SARS-CoV-2 is mainly determined by the recognition between S protein and its cellular receptor ACE2 orthologs. Genetic changes in the S usually switch viral host range and alter viral infectivity [26, 38]. Predicting and monitoring the interaction among different S mutants and ACE2 orthologs are critical to identified animal reservoirs and intermediate hosts of SARS-CoV-2, which will help to prevent the spread and circulation of SARS-CoV-2.Birds are important reservoirs of a variety of viruses, including some coronavirus and influenza virus[39]. However, the original strain of SARS-CoV-2 was unable to utilize avian ACE2 and replicate poorly in poultry [2]. In our study, we assessed the interaction of 27 S mutants to 20 ACE2 orthologs using pseudovirus. Interestingly, T478I and N501Y mutations on S enabled the pseudovirus to utilize chicken ACE2, indicating potential expansion of SARS-CoV-2 host range to avian species. This result accorded with the latest report that Omicron variant which carrying N501Y mutation was capable of infecting cells expressing avian ACE2 [10]. Notably, N501Y mutation is widely exist in other VOC and VOI variants, such as Alpha, Beta, Gamma and Lambda [6, 36]. T478I showed an even higher frequency in our dataset which was carried by more than two million variants and about 2-fold of N501Y, and the VOC of Delta and Omicron carry T478K which may be similar to T478I in altering ACE2 utilization (S2 Table). These results suggested that 478th and 501th could be potentially key site for interspecies transmission of SARS-CoV-2 and raised the concern about the neglecting of circulation of SARS-CoV-2 in poultry and wild birds.The change of ACE2 utilization caused by N501Y and T478I mutations may be explained from the view of protein structure. Previous analysis of the S-human-ACE2 complex revealed that N501Y probably introduced additional π-π and π-cation interactions between S RBD and an interface of human ACE2, increasing the binding affinity [40, 41]. According to the structure stimulation of S-chicken-ACE2 complex, this interface showed a similar structure to that of human ACE2, providing the structural basis for cross-species interaction of SARS-CoV-2 variants. However, in chicken ACE2, position 354 is an Asn not a Gly, and D354 in chicken ACE2 does not fit into RBD as tightly as G354 of hACE2. Therefore, more verification is required to confirm the utilization of chicken ACE2 by N501Y S. T478 is located at the RBD-ACE2 binding interface close to the N-terminal T20 of human ACE2[42]. T478I substitution brought a slightly larger side chain and changed S protein conformation, which might allow interaction to V20 of chicken ACE2 and enhanced the stabilization of the RBD-ACE2 complex. Considering chicken is an important agricultural animal widely kept in human communities, the detection of SARS-CoV-2 in farmed chickens may be needed for epidemic control [43].
Old world monkeys were used as experimental animal models for SARS-CoV-2 infection due to their similarity to human in ACE2 sequences [44]. However, our study demonstrated that P26L, A522S/V and Q677H significantly reduced the utilization of human ACE2, but showed no change for monkey ACE2 (Macaca nemestrina), regardless of the high identity of monkey ACE2 and human ACE2. This indicated that sequence identity did not necessarily correlate the ability of efficiency of receptor utilization by SARS-CoV-2. This speculation is supported by a previous study showing that three new world monkey species did not support SARS-CoV-2 entry due to two specific residues (H41 and E42) within their ACE2[12].Domestic animals (pets and livestock) frequently contact with humans which may be intermediate hosts of SARS-CoV-2. Several studies demonstrated that SARS-CoV-2 has been detected in cats and dogs, and laboratory experiments revealed that SARS-CoV-2 replicated efficiently in cats[45–48]. Our results showed that L18F, A222V, A262S, T478I and V1176F increased S utilization of dog and cat ACE2s. Thus, the variants carrying these mutations may spread among pet animals, which should be paid special attention in the epidemic control.Natural SARS-CoV-2 infections in wild animals have been reported in tiger, lions, and white-tailed deer [16, 49]. Especially, pangolins carrying the SARS-CoV-2-like CoVs manifested clinical symptoms and histological pathogenicity [50]. However, most S mutations, including N439K, G446V, S477N, A522V and Q677H, significantly reduced ACE2 utilization efficiency for various wild animals such as pangolin, mustela and lynx. Similar results were also found in our study for bat ACE2s. Bats are highly diverse with the second largest number of species in mammals, carrying a wide variety of coronaviruses [51]. Bats might be potential hosts of ancestral SARS-CoV and SARS-CoV-2[1, 52]. Several studies showed that Rhinolophus sinicus could support SARS-CoV-2 entry, whereas its congeneric relatives Rhinolophus ferrumequinum and Rhinolophus pearsonii could not [53].As shown in our study, ACE2 mutants containing P26L, T323I, N439K and G446V dramatically decreased the utilization of flying fox (Pteropus Alecto) ACE2, but had no obvious effects on bat (Rhinolophus sinicus) ACE2. Furthermore, S477N, A522S/V and Q677H decreased the utilization of bat ACE2, whereas had no obvious effects in flying fox ACE2. Overall, these results suggest that the viral has altered its adaptation to human communities during the epidemic and wild animals can hardly serve as intermediate hosts during the viral spread in human communities.Recent studies reported that Omicron variants infected mice, accumulated mutations when circulating in mice, and then re-infected humans [54]. Therefore, rodents may be important intermediate hosts for the transmission of SARS-CoV-2 currently [18]. According our results, N501Y S mutant could utilize mouse ACE2, consistent with previous reports [24, 55, 56]. L18F, A222V, A262S, T478I and V1176F could promote the utilization of rabbit ACE2 (Fig 3). Notably, these mutations are widely carried by VOC and VOI variants. For instance, L18F, P26L and V1176F mutations are carried by Gamma variant; D80Y is present in Beta and Delta; and T478K is carried by Omicron variant; N501Y mutation widely exists in current pandemic variants N501Y mutation is widely exist in VOC and VOI variants, such as Alpha, Beta, Gamma, Omicron and Lambda (S3 Fig). Therefore, in addition to poultry and pets, rodents in the communities may also be important intermediate for the spreading and reservoirs for the mutations of SARS-CoV-2
The Omicron BA.2 variant has become a dominant infective strain worldwide. Receptor binding studies reveal that the BA.2 spike trimer have 11-fold and 2-fold higher potency to human ACE2 than the spike trimer from the wildtype and Omicron BA.1 strains. The structure of the BA.2 spike timer reveals that all three receptor-binding domains (RBD) in the spike trimer are in open conformation, ready for high affinity binding to human ACE2, providing the basis for the increased infectivity of the BA.2 strain. JMB2002, a therapeutic antibody that was shown to have efficient inhibition of Omicron BA.1, also shows potent neutralization activities against Omicron BA.2. In addition, both BA.1 and BA.2 spike trimers are able to bind to the mouse ACE2 with high potency. In contrast, the wildtype spike trimer binds well to cat ACE2 but not to mouse ACE2. The structures of both BA.1 and BA.2 spike trimer bound to mouse ACE2 reveal the basis for their high affinity interactions. Together, these results suggest a possible evolution pathway for Omicron BA.1 and BA.2 variants from human-cat-mouse-human circle, which could have important implications in establishing an effective strategy in combating viral infection.
Оказалось, что часть из мутаций, присущих разным вариантам САРС2, дают им преимущество и в заражении других животных. Например, омикроновые, облегчают заражение грызунов. А если к мутациям омикрона 2 добавить еще одну (из уже имеющихся в другом штамме коронавируса), то вариант с такой комбинацией уже сможет заражать и кур. Что откроет большую перспективу для вируса, ведь птицы- это новая ниша обитания, к тому же мобильная, да и людям от этого не очень- чего стоит птичий грипп, а и просто грипп, который тоже переносится птицами. К тому же, вирус всегда может перескакивать обратно. И иметь при этом, в общем-то, любую патогенность (она может быть как ниже, после такого похода "налево", так и выше).
Другая группа ученых, исследуя структурные особенности шипиков омикронов1 и 2, и их способности к эффективному взаимодействию с человеческими АСЕ2, сравнивая со взаимодействием в другими типами АСЕ2, пришла к выводу, что штаммы омикронов 1 и 2 получились после того, как коронавирус пересокчил от людей к кошкам, от них к мышкам, и потом назад - к людям.
Контролировать вирус, который обладает такой "гибкостью" и зоонозной всеядностью, сложно.
Increasing evidence supports inter-species transmission of SARS-CoV-2 variants from human to domestic or wild animals during the ongoing COVID-19 pandemic, which is posing great challenges to epidemic control. Clarifying the host range of emerging SARS-CoV-2 variants will provide instructive information for the containment of viral spillover. The spike protein (S) of SARS-CoV-2 is the key determinant of receptor utilization, and therefore amino acid mutations on S will probably alter viral host range. Here, in order to evaluate the impact of S mutations, we constructed 20 Hela cell lines stably expressing ACE2 orthologs from different animals, and prepared 27 pseudotyped SARS-CoV-2 carrying different spike mutants, among which 20 bear single mutation and the other 7 were cloned from emerging SARS-CoV-2 variants, including D614G, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.135), Lambda (B.1.429) and Mu (B.1.525). Using pseudoviral reporter assay, we identified that the substitutions of T478I and N501Y enabled the pseudovirus to utilize chicken ACE2, indicating potential infectivity to avian species. Furthermore, the S mutants of real SARS-CoV-2 variants comprising N501Y showed significantly acquired abilities to infect cells expressing mouse ACE2, indicating a critical role of N501Y in expanding SARS-CoV-2 host range. In addition, A262S and T478I significantly enhanced the utilization of various mammals ACE2. In summary, our results indicated that T478I and N501Y substitutions were two S mutations important for receptor adaption of SARS-CoV-2, potentially contributing to spillover of the virus to many other animal hosts. Therefore, more attention should be paid to SARS-CoV-2 variants with these two mutations.The persistent emergence of diverse SARS-CoV-2 variants which are mainly defined by S mutations has been posing great challenges to the control of the current COVID-19 pandemic. Viral spillover from animals to humans and further spillback to other animals were believed to be a key factor for the frequent emergence of SARS-CoV-2 variants [14, 33]. The host range of SARS-CoV-2 is mainly determined by the recognition between S protein and its cellular receptor ACE2 orthologs. Genetic changes in the S usually switch viral host range and alter viral infectivity [26, 38]. Predicting and monitoring the interaction among different S mutants and ACE2 orthologs are critical to identified animal reservoirs and intermediate hosts of SARS-CoV-2, which will help to prevent the spread and circulation of SARS-CoV-2.Birds are important reservoirs of a variety of viruses, including some coronavirus and influenza virus[39]. However, the original strain of SARS-CoV-2 was unable to utilize avian ACE2 and replicate poorly in poultry [2]. In our study, we assessed the interaction of 27 S mutants to 20 ACE2 orthologs using pseudovirus. Interestingly, T478I and N501Y mutations on S enabled the pseudovirus to utilize chicken ACE2, indicating potential expansion of SARS-CoV-2 host range to avian species. This result accorded with the latest report that Omicron variant which carrying N501Y mutation was capable of infecting cells expressing avian ACE2 [10]. Notably, N501Y mutation is widely exist in other VOC and VOI variants, such as Alpha, Beta, Gamma and Lambda [6, 36]. T478I showed an even higher frequency in our dataset which was carried by more than two million variants and about 2-fold of N501Y, and the VOC of Delta and Omicron carry T478K which may be similar to T478I in altering ACE2 utilization (S2 Table). These results suggested that 478th and 501th could be potentially key site for interspecies transmission of SARS-CoV-2 and raised the concern about the neglecting of circulation of SARS-CoV-2 in poultry and wild birds.The change of ACE2 utilization caused by N501Y and T478I mutations may be explained from the view of protein structure. Previous analysis of the S-human-ACE2 complex revealed that N501Y probably introduced additional π-π and π-cation interactions between S RBD and an interface of human ACE2, increasing the binding affinity [40, 41]. According to the structure stimulation of S-chicken-ACE2 complex, this interface showed a similar structure to that of human ACE2, providing the structural basis for cross-species interaction of SARS-CoV-2 variants. However, in chicken ACE2, position 354 is an Asn not a Gly, and D354 in chicken ACE2 does not fit into RBD as tightly as G354 of hACE2. Therefore, more verification is required to confirm the utilization of chicken ACE2 by N501Y S. T478 is located at the RBD-ACE2 binding interface close to the N-terminal T20 of human ACE2[42]. T478I substitution brought a slightly larger side chain and changed S protein conformation, which might allow interaction to V20 of chicken ACE2 and enhanced the stabilization of the RBD-ACE2 complex. Considering chicken is an important agricultural animal widely kept in human communities, the detection of SARS-CoV-2 in farmed chickens may be needed for epidemic control [43].
Old world monkeys were used as experimental animal models for SARS-CoV-2 infection due to their similarity to human in ACE2 sequences [44]. However, our study demonstrated that P26L, A522S/V and Q677H significantly reduced the utilization of human ACE2, but showed no change for monkey ACE2 (Macaca nemestrina), regardless of the high identity of monkey ACE2 and human ACE2. This indicated that sequence identity did not necessarily correlate the ability of efficiency of receptor utilization by SARS-CoV-2. This speculation is supported by a previous study showing that three new world monkey species did not support SARS-CoV-2 entry due to two specific residues (H41 and E42) within their ACE2[12].Domestic animals (pets and livestock) frequently contact with humans which may be intermediate hosts of SARS-CoV-2. Several studies demonstrated that SARS-CoV-2 has been detected in cats and dogs, and laboratory experiments revealed that SARS-CoV-2 replicated efficiently in cats[45–48]. Our results showed that L18F, A222V, A262S, T478I and V1176F increased S utilization of dog and cat ACE2s. Thus, the variants carrying these mutations may spread among pet animals, which should be paid special attention in the epidemic control.Natural SARS-CoV-2 infections in wild animals have been reported in tiger, lions, and white-tailed deer [16, 49]. Especially, pangolins carrying the SARS-CoV-2-like CoVs manifested clinical symptoms and histological pathogenicity [50]. However, most S mutations, including N439K, G446V, S477N, A522V and Q677H, significantly reduced ACE2 utilization efficiency for various wild animals such as pangolin, mustela and lynx. Similar results were also found in our study for bat ACE2s. Bats are highly diverse with the second largest number of species in mammals, carrying a wide variety of coronaviruses [51]. Bats might be potential hosts of ancestral SARS-CoV and SARS-CoV-2[1, 52]. Several studies showed that Rhinolophus sinicus could support SARS-CoV-2 entry, whereas its congeneric relatives Rhinolophus ferrumequinum and Rhinolophus pearsonii could not [53].As shown in our study, ACE2 mutants containing P26L, T323I, N439K and G446V dramatically decreased the utilization of flying fox (Pteropus Alecto) ACE2, but had no obvious effects on bat (Rhinolophus sinicus) ACE2. Furthermore, S477N, A522S/V and Q677H decreased the utilization of bat ACE2, whereas had no obvious effects in flying fox ACE2. Overall, these results suggest that the viral has altered its adaptation to human communities during the epidemic and wild animals can hardly serve as intermediate hosts during the viral spread in human communities.Recent studies reported that Omicron variants infected mice, accumulated mutations when circulating in mice, and then re-infected humans [54]. Therefore, rodents may be important intermediate hosts for the transmission of SARS-CoV-2 currently [18]. According our results, N501Y S mutant could utilize mouse ACE2, consistent with previous reports [24, 55, 56]. L18F, A222V, A262S, T478I and V1176F could promote the utilization of rabbit ACE2 (Fig 3). Notably, these mutations are widely carried by VOC and VOI variants. For instance, L18F, P26L and V1176F mutations are carried by Gamma variant; D80Y is present in Beta and Delta; and T478K is carried by Omicron variant; N501Y mutation widely exists in current pandemic variants N501Y mutation is widely exist in VOC and VOI variants, such as Alpha, Beta, Gamma, Omicron and Lambda (S3 Fig). Therefore, in addition to poultry and pets, rodents in the communities may also be important intermediate for the spreading and reservoirs for the mutations of SARS-CoV-2
The Omicron BA.2 variant has become a dominant infective strain worldwide. Receptor binding studies reveal that the BA.2 spike trimer have 11-fold and 2-fold higher potency to human ACE2 than the spike trimer from the wildtype and Omicron BA.1 strains. The structure of the BA.2 spike timer reveals that all three receptor-binding domains (RBD) in the spike trimer are in open conformation, ready for high affinity binding to human ACE2, providing the basis for the increased infectivity of the BA.2 strain. JMB2002, a therapeutic antibody that was shown to have efficient inhibition of Omicron BA.1, also shows potent neutralization activities against Omicron BA.2. In addition, both BA.1 and BA.2 spike trimers are able to bind to the mouse ACE2 with high potency. In contrast, the wildtype spike trimer binds well to cat ACE2 but not to mouse ACE2. The structures of both BA.1 and BA.2 spike trimer bound to mouse ACE2 reveal the basis for their high affinity interactions. Together, these results suggest a possible evolution pathway for Omicron BA.1 and BA.2 variants from human-cat-mouse-human circle, which could have important implications in establishing an effective strategy in combating viral infection.
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