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11 results on '"Anthony SJ"'

1. Predicting the potential for zoonotic transmission and host associations for novel viruses

Author

Pandit, PS, Anthony, SJ, Goldstein, T, Olival, KJ, Doyle, MM, Gardner, NR, Bird, B, Smith, WA, Wolking, D, Gilardi, K, Monagin, C, Kelly, T, Uhart, M, Epstein, JH, Machalaba, C, Rostal, MK, Dawson, P, Hagan, E, Sullivan, A, Li, H, Chmura, AA, Latinne, A, Lange, C, O'Rourke, T, Olson, SH, Keatts, L, Mendoza, AP, Perez, A, de Paula, CD, Zimmerman, D, Valitutto, M, LeBreton, M, McIver, D, Islam, A, Duong, V, Mouiche, M, Shi, Z, Mulembakani, P, Kumakamba, C, Ali, M, Kebede, N, Tamoufe, U, Bel-Nono, S, Camara, A, Pamungkas, J, Coulibaly, K, Abu-Basha, E, Kamau, J, Silithammavong, S, Desmond, J, Hughes, T, Shiilegdamba, E, Aung, O, Karmacharya, D, Nziza, J, Ndiaye, D, Gbakima, A, Sijali, Z, Wacharapluesadee, S, Robles, EA, Ssebide, B, Suzan, G, Aguirre, LF, Solorio, MR, Dhole, TN, Nga, NTT, Hitchens, PL, Joly, DO, Saylors, K, Fine, A, Murray, S, Karesh, W, Daszak, P, Mazet, JAK, Johnson, CK, Pandit, PS, Anthony, SJ, Goldstein, T, Olival, KJ, Doyle, MM, Gardner, NR, Bird, B, Smith, WA, Wolking, D, Gilardi, K, Monagin, C, Kelly, T, Uhart, M, Epstein, JH, Machalaba, C, Rostal, MK, Dawson, P, Hagan, E, Sullivan, A, Li, H, Chmura, AA, Latinne, A, Lange, C, O'Rourke, T, Olson, SH, Keatts, L, Mendoza, AP, Perez, A, de Paula, CD, Zimmerman, D, Valitutto, M, LeBreton, M, McIver, D, Islam, A, Duong, V, Mouiche, M, Shi, Z, Mulembakani, P, Kumakamba, C, Ali, M, Kebede, N, Tamoufe, U, Bel-Nono, S, Camara, A, Pamungkas, J, Coulibaly, K, Abu-Basha, E, Kamau, J, Silithammavong, S, Desmond, J, Hughes, T, Shiilegdamba, E, Aung, O, Karmacharya, D, Nziza, J, Ndiaye, D, Gbakima, A, Sijali, Z, Wacharapluesadee, S, Robles, EA, Ssebide, B, Suzan, G, Aguirre, LF, Solorio, MR, Dhole, TN, Nga, NTT, Hitchens, PL, Joly, DO, Saylors, K, Fine, A, Murray, S, Karesh, W, Daszak, P, Mazet, JAK, and Johnson, CK

Abstract

Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host-range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as hosts for 513 newly discovered viruses detected by large-scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.

Published
2022

2. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus.

Author

Wells, HL, Wells, HL, Letko, M, Lasso, G, Ssebide, B, Nziza, J, Byarugaba, DK, Navarrete-Macias, I, Liang, E, Cranfield, M, Han, BA, Tingley, MW, Diuk-Wasser, M, Goldstein, T, Johnson, CK, Mazet, JAK, Chandran, K, Munster, VJ, Gilardi, K, Anthony, SJ, Wells, HL, Wells, HL, Letko, M, Lasso, G, Ssebide, B, Nziza, J, Byarugaba, DK, Navarrete-Macias, I, Liang, E, Cranfield, M, Han, BA, Tingley, MW, Diuk-Wasser, M, Goldstein, T, Johnson, CK, Mazet, JAK, Chandran, K, Munster, VJ, Gilardi, K, and Anthony, SJ

Abstract

Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 are not phylogenetically closely related; however, both use the angiotensin-converting enzyme 2 (ACE2) receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario, and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2 and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.

Published
2021

3. The origins of SARS-CoV-2: A critical review

Author

Holmes, EC, Goldstein, SA, Rasmussen, AL, Robertson, DL, Crits-Christoph, A, Wertheim, JO, Anthony, SJ, Barclay, WS, Boni, MF, Doherty, PC, Farrar, J, Geoghegan, JL, Jiang, X, Leibowitz, JL, Neil, SJD, Skern, T, Weiss, SR, Worobey, M, Andersen, KG, Garry, RF, Rambaut, A, Holmes, EC, Goldstein, SA, Rasmussen, AL, Robertson, DL, Crits-Christoph, A, Wertheim, JO, Anthony, SJ, Barclay, WS, Boni, MF, Doherty, PC, Farrar, J, Geoghegan, JL, Jiang, X, Leibowitz, JL, Neil, SJD, Skern, T, Weiss, SR, Worobey, M, Andersen, KG, Garry, RF, and Rambaut, A

Abstract

Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.

Published
2021

4. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus.

Author

Wells, HL, Wells, HL, Letko, M, Lasso, G, Ssebide, B, Nziza, J, Byarugaba, DK, Navarrete-Macias, I, Liang, E, Cranfield, M, Han, BA, Tingley, MW, Diuk-Wasser, M, Goldstein, T, Johnson, CK, Mazet, JAK, Chandran, K, Munster, VJ, Gilardi, K, Anthony, SJ, Wells, HL, Wells, HL, Letko, M, Lasso, G, Ssebide, B, Nziza, J, Byarugaba, DK, Navarrete-Macias, I, Liang, E, Cranfield, M, Han, BA, Tingley, MW, Diuk-Wasser, M, Goldstein, T, Johnson, CK, Mazet, JAK, Chandran, K, Munster, VJ, Gilardi, K, and Anthony, SJ

Abstract

Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 are not phylogenetically closely related; however, both use the angiotensin-converting enzyme 2 (ACE2) receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario, and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2 and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.

Published
2021

5. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, J, Adkins, S, Alioto, D, Alkhovsky, S, Amarasinghe, G, Anthony, S, Avsic-Aupanc, T, Ayllon, M, Bahl, J, Balkema-Buschmann, A, Ballinger, M, Bartonicka, T, Basler, C, Bavari, S, Beer, M, Bente, D, Bergeron, E, Bird, B, Blair, C, Blasdell, K, Bradfute, S, Breyta, R, Briese, T, Brown, P, Buchholz, U, Buchmeier, M, Bukreyev, A, Burt, F, Buzkan, N, Calisher, C, Cao, M, Casas, I, Chamberlain, J, Chandran, K, Charrel, R, Chen, B, Chiumenti, M, Choi, I, Clegg, J, Crozier, I, da Graca, J, Dal Bo, E, Davila, A, de la Torre, J, de Lamballerie, X, de Swart, R, Di Bello, P, Di Paola, N, Di Serio, F, Dietzgen, R, Digiaro, M, Dolja, V, Dolnik, O, Drebot, M, Drexler, J, Durrwald, R, Dufkova, L, Dundon, W, Duprex, W, Dye, J, Easton, A, Ebihara, H, Elbeaino, T, Ergunay, K, Fernandes, J, Fooks, A, Formenty, P, Forth, L, Fouchier, R, Freitas-Astua, J, Gago-Zachert, S, Gao, G, Garcia, M, Garcia-Sastre, A, Garrison, A, Gbakima, A, Goldstein, T, Gonzalez, J, Griffiths, A, Groschup, M, Gunther, S, Guterres, A, Hall, R, Hammond, J, Hassan, M, Hepojoki, J, Hepojoki, S, Hetzel, U, Hewson, R, Hoffmann, B, Hongo, S, Hoper, D, Horie, M, Hughes, H, Hyndman, T, Jambai, A, Jardim, R, Jiang, D, Jin, Q, Jonson, G, Junglen, S, Karadag, S, Keller, K, Klempa, B, Klingstrom, J, Kobinger, G, Kondo, H, Koonin, E, Krupovic, M, Kurath, G, Kuzmin, I, Laenen, L, Lamb, R, Lambert, A, Langevin, S, Lee, B, Lemos, E, Leroy, E, Li, D, Li, J, Liang, M, Liu, W, Liu, Y, Lukashevich, I, Maes, P, de Souza, W, Marklewitz, M, Marshall, S, Martelli, G, Martin, R, Marzano, S, Massart, S, Mccauley, J, Mielke-Ehret, N, Minafra, A, Minutolo, M, Mirazimi, A, Muhlbach, H, Muhlberger, E, Naidu, R, Natsuaki, T, Navarro, B, Navarro, J, Netesov, S, Neumann, G, Nowotny, N, Nunes, M, Nylund, A, Okland, A, Oliveira, R, Palacios, G, Pallas, V, Palyi, B, Papa, A, Parrish, C, Pauvolid-Correa, A, Paweska, J, Payne, S, Perez, D, Pfaff, F, Radoshitzky, S, Aziz-ul, R, Ramos-Gonzalez, P, Resende, R, Reyes, C, Rima, B, Romanowski, V, Luna, G, Rota, P, Rubbenstroth, D, Runstadler, J, Ruzek, D, Sabanadzovic, S, Salat, J, Sall, A, Salvato, M, Sarpkaya, K, Sasaya, T, Schwemmle, M, Shabbir, M, Shi, X, Shi, Z, Shirako, Y, Simmonds, P, Sirmarovaa, J, Sironi, M, Smither, S, Smura, T, Song, J, Spann, K, Spengler, J, Stenglein, M, Stone, D, Strakova, P, Takada, A, Tesh, R, Thornburg, N, Tomonaga, K, Tordo, N, Towner, J, Turina, M, Tzanetakis, I, Ulrich, R, Vaira, A, van den Hoogen, B, Varsani, A, Vasilakis, N, Verbeek, M, Wahl, V, Walker, P, Wang, H, Wang, J, Wang, X, Wang, L, Wei, T, Wells, H, Whitfield, A, Williams, J, Wolf, Y, Wu, Z, Yang, X, Yu, X, Yutin, N, Zerbini, F, Zhang, T, Zhang, Y, Zhou, G, Zhou, X, Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avsic-Aupanc T, Ayllon MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonicka T, Basler C, Bavari S, Beer M, Bente DA, Bergeron E, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao MJ, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi I, Clegg JCS, Crozier I, da Graca JV, Dal Bo E, Davila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Durrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergunay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astua J, Gago-Zachert S, Gao GF, Garcia ML, Garcia-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JPJ, Griffiths A, Groschup MH, Gunther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Hoper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiang DH, Jin Q, Jonson GB, Junglen S, Karadag S, Keller KE, Klempa B, Klingstrom J, Kobinger G, Kondo H, Koonin EV, Krupovic M, Kurath G, Kuzmin IV, Laenen L, Lamb RA, Lambert AJ, Langevin SL, Lee BH, Lemos ERS, Leroy EM, Li DX, Li JR, Liang MF, Liu WW, Liu Y, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Martelli GP, Martin RR, Marzano SYL, Massart S, McCauley JW, Mielke-Ehret N, Minafra A, Minutolo M, Mirazimi A, Muhlbach HP, Muhlberger E, Naidu R, Natsuaki T, Navarro B, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Nylund A, Okland AL, Oliveira RC, Palacios G, Pallas V, Palyi B, Papa A, Parrish CR, Pauvolid-Correa A, Paweska JT, Payne S, Perez DR, Pfaff F, Radoshitzky SR, Aziz-ul Rahman, Ramos-Gonzalez PL, Resende RO, Reyes CA, Rima BK, Romanowski V, Luna GR, Rota P, Rubbenstroth D, Runstadler JA, Ruzek D, Sabanadzovic S, Salat J, Sall AA, Salvato MS, Sarpkaya K, Sasaya T, Schwemmle M, Shabbir MZ, Shi XH, Shi ZL, Shirako Y, Simmonds P, Sirmarovaa J, Sironi M, Smither S, Smura T, Song JW, Spann KM, Spengler JR, Stenglein MD, Stone DM, Strakova P, Takada A, Tesh RB, Thornburg NJ, Tomonaga K, Tordo N, Towner JS, Turina M, Tzanetakis I, Ulrich RG, Vaira AM, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, Wahl V, Walker PJ, Wang H, Wang JW, Wang XF, Wang LF, Wei TY, Wells H, Whitfield AE, Williams JV, Wolf YI, Wu ZQ, Yang X, Yu XJ, Yutin N, Zerbini FM, Zhang T, Zhang YZ, Zhou GH, Zhou XP, Kuhn, J, Adkins, S, Alioto, D, Alkhovsky, S, Amarasinghe, G, Anthony, S, Avsic-Aupanc, T, Ayllon, M, Bahl, J, Balkema-Buschmann, A, Ballinger, M, Bartonicka, T, Basler, C, Bavari, S, Beer, M, Bente, D, Bergeron, E, Bird, B, Blair, C, Blasdell, K, Bradfute, S, Breyta, R, Briese, T, Brown, P, Buchholz, U, Buchmeier, M, Bukreyev, A, Burt, F, Buzkan, N, Calisher, C, Cao, M, Casas, I, Chamberlain, J, Chandran, K, Charrel, R, Chen, B, Chiumenti, M, Choi, I, Clegg, J, Crozier, I, da Graca, J, Dal Bo, E, Davila, A, de la Torre, J, de Lamballerie, X, de Swart, R, Di Bello, P, Di Paola, N, Di Serio, F, Dietzgen, R, Digiaro, M, Dolja, V, Dolnik, O, Drebot, M, Drexler, J, Durrwald, R, Dufkova, L, Dundon, W, Duprex, W, Dye, J, Easton, A, Ebihara, H, Elbeaino, T, Ergunay, K, Fernandes, J, Fooks, A, Formenty, P, Forth, L, Fouchier, R, Freitas-Astua, J, Gago-Zachert, S, Gao, G, Garcia, M, Garcia-Sastre, A, Garrison, A, Gbakima, A, Goldstein, T, Gonzalez, J, Griffiths, A, Groschup, M, Gunther, S, Guterres, A, Hall, R, Hammond, J, Hassan, M, Hepojoki, J, Hepojoki, S, Hetzel, U, Hewson, R, Hoffmann, B, Hongo, S, Hoper, D, Horie, M, Hughes, H, Hyndman, T, Jambai, A, Jardim, R, Jiang, D, Jin, Q, Jonson, G, Junglen, S, Karadag, S, Keller, K, Klempa, B, Klingstrom, J, Kobinger, G, Kondo, H, Koonin, E, Krupovic, M, Kurath, G, Kuzmin, I, Laenen, L, Lamb, R, Lambert, A, Langevin, S, Lee, B, Lemos, E, Leroy, E, Li, D, Li, J, Liang, M, Liu, W, Liu, Y, Lukashevich, I, Maes, P, de Souza, W, Marklewitz, M, Marshall, S, Martelli, G, Martin, R, Marzano, S, Massart, S, Mccauley, J, Mielke-Ehret, N, Minafra, A, Minutolo, M, Mirazimi, A, Muhlbach, H, Muhlberger, E, Naidu, R, Natsuaki, T, Navarro, B, Navarro, J, Netesov, S, Neumann, G, Nowotny, N, Nunes, M, Nylund, A, Okland, A, Oliveira, R, Palacios, G, Pallas, V, Palyi, B, Papa, A, Parrish, C, Pauvolid-Correa, A, Paweska, J, Payne, S, Perez, D, Pfaff, F, Radoshitzky, S, Aziz-ul, R, Ramos-Gonzalez, P, Resende, R, Reyes, C, Rima, B, Romanowski, V, Luna, G, Rota, P, Rubbenstroth, D, Runstadler, J, Ruzek, D, Sabanadzovic, S, Salat, J, Sall, A, Salvato, M, Sarpkaya, K, Sasaya, T, Schwemmle, M, Shabbir, M, Shi, X, Shi, Z, Shirako, Y, Simmonds, P, Sirmarovaa, J, Sironi, M, Smither, S, Smura, T, Song, J, Spann, K, Spengler, J, Stenglein, M, Stone, D, Strakova, P, Takada, A, Tesh, R, Thornburg, N, Tomonaga, K, Tordo, N, Towner, J, Turina, M, Tzanetakis, I, Ulrich, R, Vaira, A, van den Hoogen, B, Varsani, A, Vasilakis, N, Verbeek, M, Wahl, V, Walker, P, Wang, H, Wang, J, Wang, X, Wang, L, Wei, T, Wells, H, Whitfield, A, Williams, J, Wolf, Y, Wu, Z, Yang, X, Yu, X, Yutin, N, Zerbini, F, Zhang, T, Zhang, Y, Zhou, G, Zhou, X, Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avsic-Aupanc T, Ayllon MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonicka T, Basler C, Bavari S, Beer M, Bente DA, Bergeron E, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao MJ, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi I, Clegg JCS, Crozier I, da Graca JV, Dal Bo E, Davila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Durrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergunay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astua J, Gago-Zachert S, Gao GF, Garcia ML, Garcia-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JPJ, Griffiths A, Groschup MH, Gunther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Hoper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiang DH, Jin Q, Jonson GB, Junglen S, Karadag S, Keller KE, Klempa B, Klingstrom J, Kobinger G, Kondo H, Koonin EV, Krupovic M, Kurath G, Kuzmin IV, Laenen L, Lamb RA, Lambert AJ, Langevin SL, Lee BH, Lemos ERS, Leroy EM, Li DX, Li JR, Liang MF, Liu WW, Liu Y, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Martelli GP, Martin RR, Marzano SYL, Massart S, McCauley JW, Mielke-Ehret N, Minafra A, Minutolo M, Mirazimi A, Muhlbach HP, Muhlberger E, Naidu R, Natsuaki T, Navarro B, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Nylund A, Okland AL, Oliveira RC, Palacios G, Pallas V, Palyi B, Papa A, Parrish CR, Pauvolid-Correa A, Paweska JT, Payne S, Perez DR, Pfaff F, Radoshitzky SR, Aziz-ul Rahman, Ramos-Gonzalez PL, Resende RO, Reyes CA, Rima BK, Romanowski V, Luna GR, Rota P, Rubbenstroth D, Runstadler JA, Ruzek D, Sabanadzovic S, Salat J, Sall AA, Salvato MS, Sarpkaya K, Sasaya T, Schwemmle M, Shabbir MZ, Shi XH, Shi ZL, Shirako Y, Simmonds P, Sirmarovaa J, Sironi M, Smither S, Smura T, Song JW, Spann KM, Spengler JR, Stenglein MD, Stone DM, Strakova P, Takada A, Tesh RB, Thornburg NJ, Tomonaga K, Tordo N, Towner JS, Turina M, Tzanetakis I, Ulrich RG, Vaira AM, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, Wahl V, Walker PJ, Wang H, Wang JW, Wang XF, Wang LF, Wei TY, Wells H, Whitfield AE, Williams JV, Wolf YI, Wu ZQ, Yang X, Yu XJ, Yutin N, Zerbini FM, Zhang T, Zhang YZ, Zhou GH, and Zhou XP

Abstract

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Published
2020

6. Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus.

Author

Anthony, SJ, Anthony, SJ, Gilardi, K, Menachery, VD, Goldstein, T, Ssebide, B, Mbabazi, R, Navarrete-Macias, I, Liang, E, Wells, H, Hicks, A, Petrosov, A, Byarugaba, DK, Debbink, K, Dinnon, KH, Scobey, T, Randell, SH, Yount, BL, Cranfield, M, Johnson, CK, Baric, RS, Lipkin, WI, Mazet, JAK, Anthony, SJ, Anthony, SJ, Gilardi, K, Menachery, VD, Goldstein, T, Ssebide, B, Mbabazi, R, Navarrete-Macias, I, Liang, E, Wells, H, Hicks, A, Petrosov, A, Byarugaba, DK, Debbink, K, Dinnon, KH, Scobey, T, Randell, SH, Yount, BL, Cranfield, M, Johnson, CK, Baric, RS, Lipkin, WI, and Mazet, JAK

Abstract

The evolutionary origins of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) are unknown. Current evidence suggests that insectivorous bats are likely to be the original source, as several 2c CoVs have been described from various species in the family Vespertilionidae Here, we describe a MERS-like CoV identified from a Pipistrellus cf. hesperidus bat sampled in Uganda (strain PREDICT/PDF-2180), further supporting the hypothesis that bats are the evolutionary source of MERS-CoV. Phylogenetic analysis showed that PREDICT/PDF-2180 is closely related to MERS-CoV across much of its genome, consistent with a common ancestry; however, the spike protein was highly divergent (46% amino acid identity), suggesting that the two viruses may have different receptor binding properties. Indeed, several amino acid substitutions were identified in key binding residues that were predicted to block PREDICT/PDF-2180 from attaching to the MERS-CoV DPP4 receptor. To experimentally test this hypothesis, an infectious MERS-CoV clone expressing the PREDICT/PDF-2180 spike protein was generated. Recombinant viruses derived from the clone were replication competent but unable to spread and establish new infections in Vero cells or primary human airway epithelial cells. Our findings suggest that PREDICT/PDF-2180 is unlikely to pose a zoonotic threat. Recombination in the S1 subunit of the spike gene was identified as the primary mechanism driving variation in the spike phenotype and was likely one of the critical steps in the evolution and emergence of MERS-CoV in humans.IMPORTANCE Global surveillance efforts for undiscovered viruses are an important component of pandemic prevention initiatives. These surveys can be useful for finding novel viruses and for gaining insights into the ecological and evolutionary factors driving viral diversity; however, finding a viral sequence is not sufficient to determine whether it can infect people (i.e., poses a zoonotic threat). Here, we invest

Published
2017

7. Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus.

Author

Anthony, SJ, Schultz-Cherry, Stacey1, Anthony, SJ, Gilardi, K, Menachery, VD, Goldstein, T, Ssebide, B, Mbabazi, R, Navarrete-Macias, I, Liang, E, Wells, H, Hicks, A, Petrosov, A, Byarugaba, DK, Debbink, K, Dinnon, KH, Scobey, T, Randell, SH, Yount, BL, Cranfield, M, Johnson, CK, Baric, RS, Lipkin, WI, Mazet, JAK, Anthony, SJ, Schultz-Cherry, Stacey1, Anthony, SJ, Gilardi, K, Menachery, VD, Goldstein, T, Ssebide, B, Mbabazi, R, Navarrete-Macias, I, Liang, E, Wells, H, Hicks, A, Petrosov, A, Byarugaba, DK, Debbink, K, Dinnon, KH, Scobey, T, Randell, SH, Yount, BL, Cranfield, M, Johnson, CK, Baric, RS, Lipkin, WI, and Mazet, JAK

Abstract

The evolutionary origins of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) are unknown. Current evidence suggests that insectivorous bats are likely to be the original source, as several 2c CoVs have been described from various species in the family Vespertilionidae Here, we describe a MERS-like CoV identified from a Pipistrellus cf. hesperidus bat sampled in Uganda (strain PREDICT/PDF-2180), further supporting the hypothesis that bats are the evolutionary source of MERS-CoV. Phylogenetic analysis showed that PREDICT/PDF-2180 is closely related to MERS-CoV across much of its genome, consistent with a common ancestry; however, the spike protein was highly divergent (46% amino acid identity), suggesting that the two viruses may have different receptor binding properties. Indeed, several amino acid substitutions were identified in key binding residues that were predicted to block PREDICT/PDF-2180 from attaching to the MERS-CoV DPP4 receptor. To experimentally test this hypothesis, an infectious MERS-CoV clone expressing the PREDICT/PDF-2180 spike protein was generated. Recombinant viruses derived from the clone were replication competent but unable to spread and establish new infections in Vero cells or primary human airway epithelial cells. Our findings suggest that PREDICT/PDF-2180 is unlikely to pose a zoonotic threat. Recombination in the S1 subunit of the spike gene was identified as the primary mechanism driving variation in the spike phenotype and was likely one of the critical steps in the evolution and emergence of MERS-CoV in humans.IMPORTANCE Global surveillance efforts for undiscovered viruses are an important component of pandemic prevention initiatives. These surveys can be useful for finding novel viruses and for gaining insights into the ecological and evolutionary factors driving viral diversity; however, finding a viral sequence is not sufficient to determine whether it can infect people (i.e., poses a zoonotic threat). Here, we invest

Published
2017

8. Nipah virus ecology and infection dynamics in its bat reservoir, Pteropus medius, in Bangladesh

Author

Epstein, JH, Anthony, SJ, Islam, A, Kilpatrick, AM, Khan, SA, Ross, N, Smith, I, Barr, J, Zambrana-Torrelio, C, Tao, Y, Islam, Ariful, Quan, PL, Olival, K, Gurley, E, Hossain, MJ, Field, HE, Fielder, M, Briese, T, Rahman, M, Crameri, G, Wang, L-F, Luby, S, Lipkin, WI, Daszak, P, Epstein, JH, Anthony, SJ, Islam, A, Kilpatrick, AM, Khan, SA, Ross, N, Smith, I, Barr, J, Zambrana-Torrelio, C, Tao, Y, Islam, Ariful, Quan, PL, Olival, K, Gurley, E, Hossain, MJ, Field, HE, Fielder, M, Briese, T, Rahman, M, Crameri, G, Wang, L-F, Luby, S, Lipkin, WI, and Daszak, P

Published
2016

9. Non-random patterns in viral diversity

Author

Anthony, SJ, Islam, A, Johnson, C, Navarrete-Macias, I, Liang, E, Jain, K, Hitchens, PL, Che, X, Soloyvov, A, Hicks, AL, Ojeda-Flores, R, Zambrana-Torrelio, C, Ulrich, W, Rostal, MK, Petrosov, A, Garcia, J, Haider, N, Wolfe, N, Goldstein, T, Morse, SS, Rahman, M, Epstein, JH, Mazet, JK, Daszak, P, Lipkin, WI, Anthony, SJ, Islam, A, Johnson, C, Navarrete-Macias, I, Liang, E, Jain, K, Hitchens, PL, Che, X, Soloyvov, A, Hicks, AL, Ojeda-Flores, R, Zambrana-Torrelio, C, Ulrich, W, Rostal, MK, Petrosov, A, Garcia, J, Haider, N, Wolfe, N, Goldstein, T, Morse, SS, Rahman, M, Epstein, JH, Mazet, JK, Daszak, P, and Lipkin, WI

Abstract

It is currently unclear whether changes in viral communities will ever be predictable. Here we investigate whether viral communities in wildlife are inherently structured (inferring predictability) by looking at whether communities are assembled through deterministic (often predictable) or stochastic (not predictable) processes. We sample macaque faeces across nine sites in Bangladesh and use consensus PCR and sequencing to discover 184 viruses from 14 viral families. We then use network modelling and statistical null-hypothesis testing to show the presence of non-random deterministic patterns at different scales, between sites and within individuals. We show that the effects of determinism are not absolute however, as stochastic patterns are also observed. In showing that determinism is an important process in viral community assembly we conclude that it should be possible to forecast changes to some portion of a viral community, however there will always be some portion for which prediction will be unlikely.

Published
2015

10. A strategy to estimate unknown viral diversity in mammals

Author

Anthony, SJ, Epstein, JH, Murray, KA, Navarrete-Macias, I, Zambrana-Torrelio, CM, Solovyov, A, Ojeda-Flores, R, Arrigo, NC, Islam, Ariful, Khan, SA, Hosseini, P, Bogich, TL, Olival, KJ, Sanchez-Leon, MD, Karesh, WB, Goldstein, T, Luby, SP, Morse, SS, Mazet, JAK, Daszak, P, Lipkin, WI, Anthony, SJ, Epstein, JH, Murray, KA, Navarrete-Macias, I, Zambrana-Torrelio, CM, Solovyov, A, Ojeda-Flores, R, Arrigo, NC, Islam, Ariful, Khan, SA, Hosseini, P, Bogich, TL, Olival, KJ, Sanchez-Leon, MD, Karesh, WB, Goldstein, T, Luby, SP, Morse, SS, Mazet, JAK, Daszak, P, and Lipkin, WI

Abstract

ABSTRACT The majority of emerging zoonoses originate in wildlife, and many are caused by viruses. However, there are no rigorous estimates of total viral diversity (here termed “virodiversity”) for any wildlife species, despite the utility of this to future surveillance and control of emerging zoonoses. In this case study, we repeatedly sampled a mammalian wildlife host known to harbor emerging zoonotic pathogens (the Indian Flying Fox, Pteropus giganteus ) and used PCR with degenerate viral family-level primers to discover and analyze the occurrence patterns of 55 viruses from nine viral families. We then adapted statistical techniques used to estimate biodiversity in vertebrates and plants and estimated the total viral richness of these nine families in P. giganteus to be 58 viruses. Our analyses demonstrate proof-of-concept of a strategy for estimating viral richness and provide the first statistically supported estimate of the number of undiscovered viruses in a mammalian host. We used a simple extrapolation to estimate that there are a minimum of 320,000 mammalian viruses awaiting discovery within these nine families, assuming all species harbor a similar number of viruses, with minimal turnover between host species. We estimate the cost of discovering these viruses to be ~$6.3 billion (or ~$1.4 billion for 85% of the total diversity), which if annualized over a 10-year study time frame would represent a small fraction of the cost of many pandemic zoonoses. IMPORTANCE Recent years have seen a dramatic increase in viral discovery efforts. However, most lack rigorous systematic design, which limits our ability to understand viral diversity and its ecological drivers and reduces their value to public health intervention. Here, we present a new framework for the discovery of novel viruses in wildlife and use it to make the first-ever est

Published
2013

11. Ebola virus antibodies in fruit bats, bangladesh.

Author

Olival, KJ, Islam, Ariful, Yu, M, Anthony, SJ, Epstein, JH, Khan, SA, Khan, SU, Crameri, G, Wang, LF, Lipkin, WI, Luby, SP, Daszak, P, Olival, KJ, Islam, Ariful, Yu, M, Anthony, SJ, Epstein, JH, Khan, SA, Khan, SU, Crameri, G, Wang, LF, Lipkin, WI, Luby, SP, and Daszak, P

Published
2013

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