Robbins Schug's research shows that leprosy appeared at Harappa during the urban phase of the Indus Civilization, and its prevalence significantly increased through time. New diseases, such as tuberculosis, also appear in the Late Harappan or post-urban phase burials. Violent injury such as cranial trauma also increases through time, a finding that is remarkable, she said, given that evidence for violence is very rare in prehistoric South Asian sites generally.
"As the environment changed, the exchange network became increasingly incoherent. When you combine that with social changes and this particular cultural context, it all worked together to create a situation that became untenable," she said.
The results of the study are striking, according to Robbins Schug, because violence and disease increased through time, with the highest rates found as the human population was abandoning the cities. However, an even more interesting result is that individuals who were excluded from the city's formal cemeteries had the highest rates of violence and disease. In a small ossuary southeast of the city, men, women, and children were interred in a small pit. The rate of violence in this sample was 50 percent for the 10 crania preserved, and more than 20 percent of these individuals demonstrated evidence of infection with leprosy.Evidence of class divides and violent deaths are in strong contrast to relatively egalitarian and peaceful earlier periods of the Indus River Valley civilization, suggesting that its high culture's desirable features were unable to sustain themselves in the face of the pressures created by a prolonged and severe drought.
The study also notes that the expanding scope of Harappan trade brought more infectious agents in touch with its urban areas.
The underlying article which is the source for the brief review above has a very rich and generally well supported context for the finds such as the following (citations omitted):
The Harappan Civilization developed in the context of a semi-arid climate that was pervasive in South Asia for the latter half of the Holocene. Since it was first proposed as a factor in the demise of the Indus Civilization, debates about the role of climate and environmental changes have raged on but it has become increasingly clear that by 2800 B.C., aridity levels in the Indus Valley were broadly similar to contemporary levels until a period of destabilized environment—fluctuating rainfall, increased seasonality, and accelerate channel migration—began in the Indus Valley after 2000 B.C. From 2200-1700 B.C., a significant rapid climate change event in South Asia saw disruptions in monsoon rainfall and significant changes in fluvial dynamics along the Indus Rivers, including the Beas River.
Increasing aridity initially occurred in the context of a flourishing interaction sphere that spanned West and South Asia in the third millennium B.C. Historical records from Mesopotamia describe regular trade with ‘Meluhha’ (the Indus Valley) from 2400-2000 B.C. Harappans manufactured etched, biconical carnelian beads, shell, faience and steatite ornaments, ivory, copper, and ceramic items, cotton, silk, jute, cloth, barley, oil and other perishables. Exports focused on raw materials for these products, items which have been recovered from sites around the Persian Gulf region; Harappan seals have also been recovered; and cylindrical seals resembling those from Mesopotamia have been recovered at Indus urban centers as well.
Participation in the interaction sphere facilitated a period of rapid urbanization at the city of Harappa, creating a dense and heterogeneous population in the ancient city. Cities are political, economic, and ceremonial centers that can offer opportunities unavailable in the hinterlands. Technology, production, and consumption transformed Indus society, particularly in period IIIC, when population growth was at its fastest rate: high levels of immigration disrupted the formerly organized settlement pattern; houses in the core areas of the city spilled over onto the streets and ‘suburban’ areas sprang up on low mounds to the west and northwest of the city center.
After 1900 B.C., in the Late Harappan phase, population density was diminished and settlement focused largely in the core areas of the city. Declining sanitation conditions and an increasingly disorganized settlement plan indicate disruptions to authority were systemic. Disruptions in the exchange network also occurred after 2000 B.C. at a time when West Asian trading partners were responding to their own rapid climate change event. At this point, Magan and Dilmun are mentioned more frequently in Mesopotamian writings while references to Meluhha largely disappear and material evidence of trade interactions declines. Large-scale depopulation of Indus cities in the Late Harappan phase weakened Indus society. Late Harappan settlements flourished in Gujarat and Rajasthan while only a handful of settlements remained occupied in the Beas River Valley.
These finds include those from Cemetery H, which corroborates and dates a transition in funerary practices closely associated with the appearance of Indo-Europeans in the region that is mentioned in early Rig Vedic materials, which are some of the earliest written materials from the region.
Ultimate source: Gwen Robbins Schug, K. Elaine Blevins, Brett Cox, Kelsey Gray, V. Mushrif-Tripathy. Infection, Disease, and Biosocial Processes at the End of the Indus CivilizationPLoS ONE, 2013; 8 (12): e84814 DOI:10.1371/journal.pone.0084814