87. Ren, H.; Jin, Y.; Hu, M.; Zhou, J.; Song, T.; Huang, Z.; Li, B.; Li, K.; Zhou, W.; Dai, H.; et al. Ecological dynamics of influenza A viruses: Cross-species transmission and global migration. *Sci. Rep.* **2016**, *6*, 36839. [CrossRef]

88. Wohl, S.; Schaffner, S.F.; Sabeti, P.C. Genomic analysis of viral outbreaks. *Annu. Rev. Virol.* **2016**, *3*, 173–195. [CrossRef]

89. Xu, W.; Berhane, Y.; Dubé, C.; Liang, B.; Pasick, J.; van Domselaar, G.; Alexandersen, S. Epidemiological and evolutionary inference of the transmission network of the 2014 highly pathogenic avian influenza H5N2 outbreak in British Columbia, Canada. *Sci. Rep.* **2016**, *6*, 30858. [CrossRef]

90. Agoti, C.N.; Munywoki, P.K.; Phan, M.V.T.; Otieno, J.R.; Kamau, E.; Bett, A.; Kombe, I.; Githinji, G.; Medley, G.F.; Cane, P.A.; et al. Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis. *Virus Evol.* **2017**, *3*, vex006. [CrossRef]

91. Baele, G.; Suchard, M.A.; Rambaut, A.; Lemey, P. Emerging concepts of data integration in pathogen phylodynamics. *Syst. Biol.* **2016**, *66*, e47–e65. [CrossRef]

92. Glebova, O.; Knyazev, S.; Melnyk, A.; Artyomenko, A.; Khudyakov, Y.; Zelikovsky, A.; Skums, P. Inference of genetic relatedness between viral quasispecies from sequencing data. *BMC Genom.* **2017**, *18*, 918. [CrossRef]

93. Snitkin, E.S.; Won, S.; Pirani, A.; Lapp, Z.; Weinstein, R.A.; Lolans, K.; Hayden, M.K. Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant *Klebsiella pneumoniae* in a regional outbreak. *Sci. Transl. Med.* **2017**, *9*, eaan0093. [CrossRef]

94. Worby, C.J.; Lipsitch, M.; Hanage, W.P. Shared genomic variants: Identification of transmission routes using pathogen deep-sequence data. *Am. J. Epidemiol.* **2017**, *186*, 1209–1216. [CrossRef] [PubMed]

95. Campbell, F.; Didelot, X.; Fitzjohn, R.; Ferguson, N.; Cori, A.; Jombart, T. Outbreaker2: A modular platform for outbreak reconstruction. *BMC Bioinform.* **2018**, *19*, 17–24. [CrossRef]

96. Choi, S.C. Genomic epidemiology for microbial evolutionary studies and the use of Oxford Nanopore sequencing technology. *Korean J. Microbiol.* **2018**, *54*, 188–199. [CrossRef]

97. Ezeoke, I.; Galac, M.R.; Lin, Y.; Liem, A.T.; Roth, P.A.; Kilianski, A.; Gibbons, H.S.; Bloch, D.; Kornblum, J.; del Rosso, P.; et al. Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks. *PLoS ONE* **2018**, *13*, e0202615. [CrossRef] [PubMed]

98. Gotoh, Y.; Taniguchi, T.; Yoshimura, D.; Katsura, K.; Saeki, Y.; Hirabara, Y.; Fukuda, M.; Takajo, I.; Tomida, J.; Kawamura, Y.; et al. Multi-step genomic dissection of a suspected intra-hospital *Helicobacter cinaedi* outbreak. *Microb. Genom.* **2019**, *5*, 1–11. [CrossRef]

99. Kendall, M.; Ayabina, D.; Xu, Y.; Stimson, J.; Colijn, C. Estimating transmission from genetic and epidemiological data: A metric to compare transmission trees. *Stat. Sci.* **2018**, *33*, 70–85. [CrossRef]

100. Leitner, T.; Romero-Severson, E. Phylogenetic patterns recover known HIV epidemiological relationships and reveal common transmission of multiple variants. *Nat. Microbiol.* **2018**, *3*, 983–988. [CrossRef]

101. Meehan, C.J.; Moris, P.; Kohl, T.A.; Pečerska, J.; Akter, S.; Merker, M.; Utpatel, C.; Beckert, P.; Gehre, F.; Lempens, P.; et al. The relationship between transmission time and clustering methods in *Mycobacterium tuberculosis* epidemiology. *EBioMedicine* **2018**, *37*, 410–416. [CrossRef]

102. Payne, D.C.; Biggs, H.M.; Al-Abdallat, M.M.; Alqasrawi, S.; Lu, X.; Abedi, G.R.; Haddadin, A.; Iblan, I.; Alsanouri, T.; Al Nsour, M.; et al. Multihospital outbreak of a middle east respiratory syndrome coronavirus deletion variant, Jordan: A molecular, serologic, and epidemiologic investigation. *Open Forum Infect. Dis.* **2018**, *5*, ofy095. [CrossRef] [PubMed]

103. Blackburn, R.M.; Frampton, D.; Smith, C.M.; Fragaszy, E.B.; Watson, S.J.; Ferns, R.B.; Binter, S.; Coen, P.G.; Grant, P.; Shallcross, L.; et al. Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012–2014). *Influenza Other Respir. Viruses* **2019**, *13*, 556–563. [CrossRef]

104. DeSilva, M.B.; Styles, T.; Basler, C.; Moses, F.L.; Husain, F.; Reichler, M.; Whitmer, S.; McAuley, J.; Belay, E.; Friedman, M.; et al. Introduction of Ebola virus into a remote border district of Sierra Leone, 2014: Use of field epidemiology and RNA sequencing to describe chains of transmission. *Epidemiol. Infect.* **2019**, *147*, e88. [CrossRef] [PubMed]

105. Firestone, S.M.; Hayama, Y.; Bradhurst, R.; Yamamoto, T.; Tsutsui, T.; Stevenson, M.A. Reconstructing foot-and-mouth disease outbreaks: A methods comparison of transmission network models. *Sci. Rep.* **2019**, *9*, 2074–2086. [CrossRef] [PubMed]

106. Guthrie, J.L.; Strudwick, L.; Roberts, B.; Allen, M.; McFadzen, J.; Roth, D.; Jorgensen, D.; Rodrigues, M.; Tang, P.; Hanley, B.; et al. Whole genome sequencing for improved understanding of *Mycobacterium tuberculosis* transmission in a remote circumpolar region. *Epidemiol. Infect.* **2019**, *147*, e188. [CrossRef]

107. Hall, M.D.; Colijn, C. Transmission trees on a known pathogen phylogeny: Enumeration and sampling. *Mol. Biol. Evol.* **2019**, *36*, 1333–1343. [CrossRef]

108. Hall, M.D.; Holden, M.T.; Srisomang, P.; Mahavanakul, W.; Wuthiekanun, V.; Limmathurotsakul, D.; Fountain, K.; Parkhill, J.; Nickerson, E.K.; Peacock, S.J.; et al. Improved characterisation of MRSA transmission using within-host bacterial sequence diversity. *Life* **2019**, *8*, e46402. [CrossRef]

109. Ratmann, O.; PANGEA Consortium and Rakai Health Sciences Program; Grabowski, M.K.; Hall, M.; Golubchik, T.; Wymant, C.; Abeler-Dörner, L.; Bonsall, D.; Hoppe, A.; Brown, A.L.; et al. Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis. *Nat. Commun.* **2019**, *10*, 1–13. [CrossRef]

110. Sashittal, P.; El-Kebir, M. SharpTNI: Counting and Sampling Parsimonious Transmission Networks under a Weak Bottleneck. Article Number (bioRxiv: 842237). Available online: https://www.biorxiv.org/content/10.1101/842237v1 (accessed on 4 February 2022).
111. Van Beek, J.; Räisänen, K.; Broas, M.; Kauranen, J.; Kähkölä, A.; Laine, J.; Mustonen, E.; Nurkkala, T.; Puhto, T.; Sinkkonen, J.; et al. Tracing local and regional clusters of carbapenemase-producing Klebsiella pneumoniae ST512 with whole genome sequencing, Finland, 2013 to 2018. *Eurosurveillance* **2019**, *24*, 1800522. [CrossRef]

112. Vaughan, T.G.; Leventhal, G.E.; Rasmussen, D.A.; Drummond, A.J.; Welch, D.; Stadler, T. Estimating epidemic incidence and prevalence from genomic data. *Mol. Biol. Evol.* **2019**, *36*, 1804–1816. [CrossRef]

113. Bbosa, N.; Ssemwanga, D.; Ssekagiri, A.; Xi, X.; Mayanja, Y.; Bahemuka, U.; Seeley, J.; Pillay, D.; Abeler-Dörner, L.; Golubchik, T.; et al. Phylogenetic and demographic characterization of directed HIV-1 transmission using deep sequences from high-risk and general population cohorts/groups in Uganda. *Viruses* **2020**, *12*, 331. [CrossRef] [PubMed]

114. Schneider, A.D.B.; Ford, C.T.; Hostager, R.; Williams, J.; Cioce, M.; Çatalyürek, Ü.V.; Wertheim, J.O.; Janies, D. StrainHub: A phylogenetic tool to construct pathogen transmission networks. *Bioinformatics* **2020**, *36*, 945–947. [CrossRef] [PubMed]

115. Dhar, S.; Zhang, C.; Mandoiu, I.I.; Bansal, M.S. TNet: Transmission network inference using within-host strain diversity and its application to geographical tracking of COVID-19 spread. *IEEE ACM Trans. Comput. Biol. Bioinform.* **2022**, *19*, 230–242. [CrossRef]

116. Nelson, K.N.; Gandhi, N.R.; Mathema, B.; Lopman, B.A.; Brust, J.C.M.; Auld, S.C.; Ismail, N.; Omar, S.V.; Brown, T.S.; Allana, S.; et al. Modeling missing cases and transmission links in networks of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa. *Am. J. Epidemiol.* **2020**, *189*, 735–745. [CrossRef] [PubMed]

117. Nelson, K.N.; Jenness, S.M.; Mathema, B.; Lopman, B.A.; Auld, S.C.; Shah, N.S.; Brust, J.C.M.; Ismail, N.; Omar, S.V.; Brown, T.S.; et al. Social mixing and clinical features linked with transmission in a network of extensively drug-resistant tuberculosis cases in KwaZulu-Natal, South Africa. *Clin. Infect. Dis.* **2019**, *70*, 2396–2402. [CrossRef] [PubMed]

118. Wang, X.; Zhou, Q.; He, Y.; Liu, L.; Ma, X.; Wei, X.; Jiang, N.; Liang, L.; Zheng, Y.; Ma, L.; et al. Nosocomial outbreak of COVID-19 pneumonia in Wuhan, China. *Eur. Respir. J.* **2020**, *55*, 2000544. [CrossRef] [PubMed]

119. Worobey, M.; Pekar, J.; Larsen, B.B.; Nelson, M.I.; Hill, V.; Joy, J.B.; Rambaut, A.; Suchard, M.A.; Wertheim, J.O.; Lemey, P. The emergence of SARS-CoV-2 in Europe and North America. *Science* **2020**, *370*, 564–570. [CrossRef]

120. Bataille, A.; van der Meer, F.; Stegeman, A.; Koch, G. Evolutionary analysis of inter-farm transmission dynamics in a highly pathogenic avian influenza epidemic. *PLoS Pathog.* **2011**, *7*, e1002094. [CrossRef]

121. Smith, G.J.D.; Vijaykrishna, D.; Bahl, J.; Lycett, S.J.; Worobey, M.; Pybus, O.G.; Ma, S.K.; Cheung, C.L.; Raghwani, J.; Bhatt, S.; et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. *Nature* **2009**, *459*, 1122–1125. [CrossRef]

122. Briand, F.-X.; Niqueux, E.; Schmitz, A.; Martenot, C.; Cherbonnel, M.; Massin, P.; Kerbrat, F.; Chatel, M.; Guillemoto, C.; Guillou-Cloarec, C.; et al. Highly pathogenic avian influenza A(H5N8) virus spread by short- and long-range transmission, France, 2016–17. *Emerg. Infect. Dis.* **2021**, *27*, 508–516. [CrossRef]

123. Murcia, P.R.; Wood, J.L.N.; Holmes, E. Genome-scale evolution and phylodynamics of equine H3N8 influenza A virus. *J. Virol.* **2011**, *85*, 5312–5322. [CrossRef] [PubMed]

124. Biek, R.; Henderson, J.C.; Waller, L.A.; Rupprecht, C.E.; Real, L.A. A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus. *Proc. Natl. Acad. Sci. USA* **2007**, *104*, 7993–7998. [CrossRef] [PubMed]

125. Vega, V.B.; Ruan, Y.; Liu, J.; Lee, W.H.; Wei, C.L.; Se-Thoe, S.Y.; Tang, K.F.; Zhang, T.; Kolatkar, P.R.; Ooi, E.E.; et al. Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003. *BMC Infect. Dis.* **2004**, *4*, 32. [CrossRef] [PubMed]

126. Nie, Q.; Li, X.; Chen, W.; Liu, D.; Chen, Y.; Li, H.; Li, D.; Tian, M.; Tan, W.; Zai, J. Phylogenetic and phylodynamic analyses of SARS-CoV-2. *Virus Res.* **2020**, *287*, 198098. [CrossRef]

127. Vrancken, B.; Rambaut, A.; Suchard, M.A.; Drummond, A.; Baele, G.; Derdelinckx, I.; van Wijngaerden, E.; Vandamme, A.-M.; van Laethem, K.; Lemey, P. The genealogical population dynamics of HIV-1 in a large transmission chain: Bridging within and among host evolutionary rates. *PLoS Comput. Biol.* **2014**, *10*, e1003505. [CrossRef]

128. Gire, S.K.; Goba, A.; Andersen, K.G.; Sealfon, R.S.G.; Park, D.J.; Kanneh, L.; Jalloh, S.; Momoh, M.; Fullah, M.; Dudas, G.; et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. *Science* **2014**, *345*, 1369–1372. [CrossRef]

129. Burns, C.C.; Shaw, J.; Jorba, J.; Bukbuk, D.N.; Adu, F.; Gumede, N.; Pate, M.A.; Abanida, E.A.; Gasasira, A.; Iber, J.; et al. Multiple independent emergences of type 2 vaccine-derived polioviruses during a large outbreak in Northern Nigeria. *J. Virol.* **2013**, *87*, 4907–4922. [CrossRef]

130. Devold, M.; Karlsen, M.; Nylund, A. Sequence analysis of the fusion protein gene from infectious salmon anemia virus isolates: Evidence of recombination and reassortment. *J. Gen. Virol.* **2006**, *87*, 2031–2040. [CrossRef]

131. Kibenge, F.S.B.; Kibenge, M.J.T.; Wang, Y.; Qian, B.; Hariharan, S.; McGeachy, S. Mapping of putative virulence motifs on infectious salmon anemia virus surface glycoprotein genes. *J. Gen. Virol.* **2007**, *88*, 3100–3111. [CrossRef]

132. Karami-Zarandi, M.; Douraghi, M.; Vaziri, B.; Adibhesami, H.; Rahbar, M.; Yaseri, M. Variable spontaneous mutation rate in clinical strains of multidrug-resistant *Acinetobacter baumannii* and differentially expressed proteins in a hypermutator strain. *Mutat. Res. Mol. Mech. Mutagen.* **2017**, *800-802*, 37–45. [CrossRef]

133. Harris, S.R.; Feil, E.J.; Holden, M.T.G.; Quail, M.A.; Nickerson, E.K.; Chantratita, N.; Gardete, S.; Tavares, A.; Day, N.; Lindsay, J.A.; et al. Evolution of MRSA during hospital transmission and intercontinental spread. *Science* **2010**, *327*, 469–474. [CrossRef] [PubMed]

134. Romero-Severson, E.; Nasir, A.; Leitner, T. What should health departments do with HIV sequence data? *Viruses* **2020**, *12*, 1018. [CrossRef] [PubMed]
111. Van Beek, J.; Räisänen, K.; Broas, M.; Kauranen, J.; Kähkölä, A.; Laine, J.; Mustonen, E.; Nurkkala, T.; Puhto, T.; Sinkkonen, J.; et al. Tracing local and regional clusters of carbapenemase-producing Klebsiella pneumoniae ST512 with whole genome sequencing, Finland, 2013 to 2018. *Eurosurveillance* **2019**, *24*, 1800522. [CrossRef]

112. Vaughan, T.G.; Leventhal, G.E.; Rasmussen, D.A.; Drummond, A.J.; Welch, D.; Stadler, T. Estimating epidemic incidence and prevalence from genomic data. *Mol. Biol. Evol.* **2019**, *36*, 1804–1816. [CrossRef]

113. Bbosa, N.; Ssemwanga, D.; Ssekagiri, A.; Xi, X.; Mayanja, Y.; Bahemuka, U.; Seeley, J.; Pillay, D.; Abeler-Dörner, L.; Golubchik, T.; et al. Phylogenetic and demographic characterization of directed HIV-1 transmission using deep sequences from high-risk and general population cohorts/groups in Uganda. *Viruses* **2020**, *12*, 331. [CrossRef] [PubMed]

114. Schneider, A.D.B.; Ford, C.T.; Hostager, R.; Williams, J.; Cioce, M.; Çatalyürek, Ü.V.; Wertheim, J.O.; Janies, D. StrainHub: A phylogenetic tool to construct pathogen transmission networks. *Bioinformatics* **2020**, *36*, 945–947. [CrossRef] [PubMed]

115. Dhar, S.; Zhang, C.; Mandoiu, I.I.; Bansal, M.S. TNet: Transmission network inference using within-host strain diversity and its application to geographical tracking of COVID-19 spread. *IEEE ACM Trans. Comput. Biol. Bioinform.* **2022**, *19*, 230–242. [CrossRef]

116. Nelson, K.N.; Gandhi, N.R.; Mathema, B.; Lopman, B.A.; Brust, J.C.M.; Auld, S.C.; Ismail, N.; Omar, S.V.; Brown, T.S.; Allana, S.; et al. Modeling missing cases and transmission links in networks of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa. *Am. J. Epidemiol.* **2020**, *189*, 735–745. [CrossRef] [PubMed]

117. Nelson, K.N.; Jenness, S.M.; Mathema, B.; Lopman, B.A.; Auld, S.C.; Shah, N.S.; Brust, J.C.M.; Ismail, N.; Omar, S.V.; Brown, T.S.; et al. Social mixing and clinical features linked with transmission in a network of extensively drug-resistant tuberculosis cases in KwaZulu-Natal, South Africa. *Clin. Infect. Dis.* **2019**, *70*, 2396–2402. [CrossRef] [PubMed]

118. Wang, X.; Zhou, Q.; He, Y.; Liu, L.; Ma, X.; Wei, X.; Jiang, N.; Liang, L.; Zheng, Y.; Ma, L.; et al. Nosocomial outbreak of COVID-19 pneumonia in Wuhan, China. *Eur. Respir. J.* **2020**, *55*, 2000544. [CrossRef] [PubMed]

119. Worobey, M.; Pekar, J.; Larsen, B.B.; Nelson, M.I.; Hill, V.; Joy, J.B.; Rambaut, A.; Suchard, M.A.; Wertheim, J.O.; Lemey, P. The emergence of SARS-CoV-2 in Europe and North America. *Science* **2020**, *370*, 564–570. [CrossRef]

120. Bataille, A.; van der Meer, F.; Stegeman, A.; Koch, G. Evolutionary analysis of inter-farm transmission dynamics in a highly pathogenic avian influenza epidemic. *PLoS Pathog.* **2011**, *7*, e1002094. [CrossRef]

121. Smith, G.J.D.; Vijaykrishna, D.; Bahl, J.; Lycett, S.J.; Worobey, M.; Pybus, O.G.; Ma, S.K.; Cheung, C.L.; Raghwani, J.; Bhatt, S.; et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. *Nature* **2009**, *459*, 1122–1125. [CrossRef]

122. Briand, F.-X.; Niqueux, E.; Schmitz, A.; Martenot, C.; Cherbonnel, M.; Massin, P.; Kerbrat, F.; Chatel, M.; Guillemoto, C.; Guillou-Cloarec, C.; et al. Highly pathogenic avian influenza A(H5N8) virus spread by short- and long-range transmission, France, 2016–17. *Emerg. Infect. Dis.* **2021**, *27*, 508–516. [CrossRef]

123. Murcia, P.R.; Wood, J.L.N.; Holmes, E. Genome-scale evolution and phylodynamics of equine H3N8 influenza A virus. *J. Virol.* **2011**, *85*, 5312–5322. [CrossRef] [PubMed]

124. Biek, R.; Henderson, J.C.; Waller, L.A.; Rupprecht, C.E.; Real, L.A. A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus. *Proc. Natl. Acad. Sci. USA* **2007**, *104*, 7993–7998. [CrossRef] [PubMed]

125. Vega, V.B.; Ruan, Y.; Liu, J.; Lee, W.H.; Wei, C.L.; Se-Thoe, S.Y.; Tang, K.F.; Zhang, T.; Kolatkar, P.R.; Ooi, E.E.; et al. Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003. *BMC Infect. Dis.* **2004**, *4*, 32. [CrossRef] [PubMed]

126. Nie, Q.; Li, X.; Chen, W.; Liu, D.; Chen, Y.; Li, H.; Li, D.; Tian, M.; Tan, W.; Zai, J. Phylogenetic and phylodynamic analyses of SARS-CoV-2. *Virus Res.* **2020**, *287*, 198098. [CrossRef]

127. Vrancken, B.; Rambaut, A.; Suchard, M.A.; Drummond, A.; Baele, G.; Derdelinckx, I.; van Wijngaerden, E.; Vandamme, A.-M.; van Laethem, K.; Lemey, P. The genealogical population dynamics of HIV-1 in a large transmission chain: Bridging within and among host evolutionary rates. *PLoS Comput. Biol.* **2014**, *10*, e1003505. [CrossRef]

128. Gire, S.K.; Goba, A.; Andersen, K.G.; Sealfon, R.S.G.; Park, D.J.; Kanneh, L.; Jalloh, S.; Momoh, M.; Fullah, M.; Dudas, G.; et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. *Science* **2014**, *345*, 1369–1372. [CrossRef]

129. Burns, C.C.; Shaw, J.; Jorba, J.; Bukbuk, D.N.; Adu, F.; Gumede, N.; Pate, M.A.; Abanida, E.A.; Gasasira, A.; Iber, J.; et al. Multiple independent emergences of type 2 vaccine-derived polioviruses during a large outbreak in Northern Nigeria. *J. Virol.* **2013**, *87*, 4907–4922. [CrossRef]

130. Devold, M.; Karlsen, M.; Nylund, A. Sequence analysis of the fusion protein gene from infectious salmon anemia virus isolates: Evidence of recombination and reassortment. *J. Gen. Virol.* **2006**, *87*, 2031–2040. [CrossRef]

131. Kibenge, F.S.B.; Kibenge, M.J.T.; Wang, Y.; Qian, B.; Hariharan, S.; McGeachy, S. Mapping of putative virulence motifs on infectious salmon anemia virus surface glycoprotein genes. *J. Gen. Virol.* **2007**, *88*, 3100–3111. [CrossRef]

132. Karami-Zarandi, M.; Douraghi, M.; Vaziri, B.; Adibhesami, H.; Rahbar, M.; Yaseri, M. Variable spontaneous mutation rate in clinical strains of multidrug-resistant *Acinetobacter baumannii* and differentially expressed proteins in a hypermutator strain. *Mutat. Res. Mol. Mech. Mutagen.* **2017**, *800-802*, 37–45. [CrossRef]

133. Harris, S.R.; Feil, E.J.; Holden, M.T.G.; Quail, M.A.; Nickerson, E.K.; Chantratita, N.; Gardete, S.; Tavares, A.; Day, N.; Lindsay, J.A.; et al. Evolution of MRSA during hospital transmission and intercontinental spread. *Science* **2010**, *327*, 469–474. [CrossRef] [PubMed]

134. Romero-Severson, E.; Nasir, A.; Leitner, T. What should health departments do with HIV sequence data? *Viruses* **2020**, *12*, 1018. [CrossRef] [PubMed]