Phylogenetic and Ecologic Perspectives of a Monkeypox Outbreak, Southern Sudan, 2005

Yoshinori Nakazawa

, Ginny L. Emerson, Darin S. Carroll, Hui Zhao, Yu Li, Mary G. Reynolds, Kevin L. Karem, Victoria A. Olson, R. Ryan Lash, Whitni B. Davidson, Scott K. Smith, Rebecca S. Levine, Russell L. Regnery, Scott A. Sammons, Michael A. Frace, Elmangory M. Mutasim, Mubarak E. M. Karsani, Mohammed O. Muntasir, Alimagboul A. Babiker, Langova Opoka, Vipul Chowdhary, and Inger K. Damon

Author affiliations: Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (Y. Nakazawa, G. L. Emerson, D.S. Carroll, H. Zhao, Y. Li, M.G. Reynolds, K. L. Karem, V. A. Olson, R. R. Lash, W. B. Davidson, S. K. Smith, R. S. Levine, R. L. Regnery, S. A. Sammons, M.A. Frace, I.K. Damon); National Public Health Laboratory, Khartoum, Sudan (E.M. Mutasim, M.E.M. Karsani); Federal Ministry of Health, Khartoum (M.O. Muntasir, A.A. Babiker); World Health Organization Regional Office for the Eastern Mediterranean, Cairo, Egypt (M.L. Opoka); Médecins Sans Frontières, Khartoum (V. Chowdhary)

Abstract

Identification of human monkeypox cases during 2005 in southern Sudan (now South Sudan) raised several questions about the natural history of monkeypox virus (MPXV) in Africa. The outbreak area, characterized by seasonally dry riverine grasslands, is not identified as environmentally suitable for MPXV transmission. We examined possible origins of this outbreak by performing phylogenetic analysis of genome sequences of MPXV isolates from the outbreak in Sudan and from differing localities. We also compared the environmental suitability of study localities for monkeypox transmission. Phylogenetically, the viruses isolated from Sudan outbreak specimens belong to a clade identified in the Congo Basin. This finding, added to the political instability of the area during the time of the outbreak, supports the hypothesis of importation by infected animals or humans entering Sudan from the Congo Basin, and person-to-person transmission of virus, rather than transmission of indigenous virus from infected animals to humans.

Monkeypox is caused by a member of the genus Orthopoxvirus, first identified as the cause of disease in captive cynomolgus monkeys in 1959 (1). Twelve years later, the virus was identified as the cause of smallpox-like disease in humans (2). Although monkeypox virus (MPXV) can infect a wide variety of animal species when experimentally introduced, it is currently unknown which species are directly involved in its natural transmission cycle and whether >1 species are responsible for MPXV perpetuation in nature (3). Multiple events of human-to-human transmission have been reported, but sustained MPXV infection cycles among humans have not been documented (4–6). Likos et al. (7) investigated phylogenetic relationships between MPXV isolates by examining 5 whole-genome sequences. That analysis confirmed the existence of 2 distinct groups suggested by previous studies (8–10): the first group contained isolates from the Congo Basin (Congo Basin clade), and the second group included isolates from countries in western Africa. Differences in epidemiologic and clinical features between MPXV isolates (e.g., higher rates of illness and death of the Congo Basin clade) support the differentiation between these 2 clades.
In 2005, an outbreak of monkeypox among humans was reported from Unity State, Sudan (now South Sudan) (4); 19 cases were identified (5). Monkeypox cases among humans derived from contact with native animals have been reported in central and western Africa only; thus, this outbreak in Sudan could represent, if zoonotic transmission is confirmed, endemic transmission of monkeypox outside the recognized geographic range of the disease (7,11). Preliminary genetic and serologic analyses and epidemiologic investigations of the 2005 outbreak in Sudan showed ecological and genetic differences between the causative agent of this outbreak and of those that caused central and western African monkeypox outbreaks, and suggested that it could potentially be a novel virus (5). However, evidence indicating that the outbreak resulted from local virus transmission from wildlife to humans has not been presented.
Ecological niche modeling (ENM) has been used in the study of the ecological characteristics and distribution of a variety of diseases, such as dengue fever (12), leishmaniasis (13), plague (14,15), tularemia (14,16), West Nile virus infection (17), avian influenza (18,19), filovirus infections (20,21), and monkeypox (22–24). ENM is used as a tool for analyzing and identifying ecological requirements for the transmission of diseases and for localizing the geographic areas in which these requirements are met. When applied to human cases of monkeypox, ENM has enabled detection of an environmental signal common to all reported cases, which successfully predicts the range of the 2 recognized clades of monkeypox throughout the humid lowland forest regions of Africa (23). The area where the 2005 outbreak occurred represents a drier climate, and the dominant vegetation is substantially different from that in areas where monkeypox viruses from either of the 2 clades have been reported. Furthermore, Sudan has not been recognized as an area of potential favorability for MPXV transmission by previous ENM analyses.
To examine 2 hypotheses about the origin of the virus that caused the outbreak in Sudan, we explored genetic and ecological evidence from the 2005 Sudan outbreak and compared this evidence with what is currently understood about viruses in the 2 recognized clades of MPXV. The first hypothesis is that there was a previously unrecognized MPXV strain circulating naturally in the area of the outbreak; the second hypothesis is that the virus was imported into the area from a place where monkeypox is endemic. We used 2 independent lines of investigation: 1) the genetic characterization of the virus isolates from Sudan (Sudan isolates 1 and 2) and their comparison with previous isolates of MPXV from various regions of Africa by using phylogenetic analysis and 2) the generation of ecological niche models and characterization of ecological factors associated with monkeypox virus transmission on the basis of reported human cases in central and western Africa, including the assessment of environmental suitability for MPXV transmission among the Sudan localities.