Community acquired febrile illness with thrombocytopenia in India can be caused by Dengue , Malaria , Leptospirosis , Scrub Typhus & Sepsis . It is essential to investigate for these diseases also , as co- infections are also common ( Malaria + Leptospirosis ) . Dengue & Malaria can be diagnosed on day 2 with available investigations , while leptospirosis & scrub typhus would take a week to be diagnosed , as PCR is not easily available . We need more data on other viral diseases causing thrombocytopenia in our country & should be considered after excluding other infections .
Besides Chikungunya virus and other pathogens mentioned above, you might also look into the possibility of Zika virus. The clinical picture of Zika differs from that of Dengue, and typically is much more mild and self limiting. Nevertheless, there are some similarities, and the epidemiology, vector, and other characteristics are similar. I am not sure that Zika has been definitively isolated yet from south India, but there has been seropositivity in humans there, and the mosquitoes are present. Also, Zika is now spreading quite rapidly in the Americas (especially Brazil) and the Asia-Pacific region. A useful reference is: Emerg Infect Dis. 2009 Sep; 15(9): 1347–1350.
A similar disease that have almost same clinical picture as the dengue like clinical picture in south India, is the Measles virus commonly found in west Africa, one of the six-killer diseases in children. The signs and symptoms are almost the same except that that of measles tend to have conjunctivitis in addition to the signs. A useful reference is a book written by Olukoye Ransomkuti (1989) Understanding Tropical Diseases 2nd Ed. Longman Publications
Besides what has been mentioned I think you should consider Hantavirus (Indian J Med Res. 2005 Sep;122(3):211-5.), Yellow Fever (http://promedmail.org/direct.php?id=20150708.3491031), and Kyasanur Forest Disease (http://wwwnc.cdc.gov/eid/article/21/1/14-1227_article).
Out of curiosity, why are you focusing on viral etiologies only?
Because we have ruled out bacterial infections with appropriate tests and left with a huge chunk of patients with clinical picture similar to Dengue fever
additionally to JM Easow remark, beyond viral pathogens well-known to circulate in your geographical area, you should look very carefully about other flaviviruses, especially West Nile Virus and Zika virus.
The recent detection of three cases of WNV encephalitis in Sri Lanka (Lohitharajah J et al, BMC infect Dis 2015; 15: 305. August 3 [Epub head of print]) indicates the possibility of an underdiagnosed outbreak, as WNV neuroinvasive is the tip of the iceberg of the burden of WNV disease
Burden of WNV infection, in the USA:
60%-80% asymptomatic infections
1 WNV neuroinvasive per 140 infections infections (0.73%)
thrombocytopenia classical but unknown rate ?
Zika virus has recently emerged in West Pacific, Brazil but was also detected in Thailand in 2012-2014 (Buathong R et al, Am Trop Med Hyg 2015).
One of them is chikungunya. Transmitted by aedes sp esp aegypti. Similar symptoms , more prominent are the rashes and joints pain. Clinically not as severe as dengue, seldom causing death. Platelet count though is not as low as in dengue.. seldom less than 100,000.
I would like to highlight Zika virus as well. It is extremely underdiagnosed because of lacking diagnostic capacities. From a clinical point of view not easy to distinguish from dengue.