Try the following:
Step 1: Connect the Phone/Dongle to the COM Port via USB.
Step 2: Call the code for fetching sms via smslib.jar
Sample Code to fetch sms:
public void sendSMS() throws Exception{
    OutboundNotification outboundNotification = new OutboundNotification();
    SerialModemGateway gateway = new SerialModemGateway("modem.com5", "COM5", 9600, "ZTE", "COM5");
    gateway.setInbound(true);
    gateway.setOutbound(true);
    gateway.setSmscNumber("+91XXXXXXXXXX"); // 10-digit Mobile Number
    Service.getInstance().setOutboundMessageNotification(outboundNotification);
    Service.getInstance().addGateway(gateway);
    Service.getInstance().startService();
    OutboundMessage msg = new OutboundMessage(ExcelConnect.strSMSTo, ExcelConnect.strSMSText);
    Service.getInstance().sendMessage(msg);
    System.out.println(msg);
    System.out.println(ExcelConnect.strSMSTo + "-" + ExcelConnect.strSMSText);
    Service.getInstance().stopService();
    Service.getInstance().removeGateway(gateway);
}
Step 3: Parse sms to get the OTP from the fetched list by latest received sms.