Citing Paul in Romans XI on the olive tree, and Zechariah, Newton also reads that the two witnesses of Revelation 11 and 13 are churches, and not new churches. I read these not in connection with the seven churches of Rev. 2-3, but rather the two legs of the dream image in Daniel 2. We read the churches not as all good, as the Christians will, nor the Roman church as all evil, as the Protestants and Newton do, but as both, as human things are in this world.
These are usually read as individuals, repeating the prophesy that Elijah would precede the Messiah, as John the Baptist did. This is the first reader I have found to see the olive trees of Revelation 11:3:
While the Gentiles tread the holy city under foot, God gives power to his two Witnesses, and they prophesy a thousand two hundred and threescore days clothed in sackcloth. They are called the two Olive-trees, with relation to the two Olive-trees, which in Zechary‘s vision, chap. iv. stand on either side of the golden candlestick to supply the lamps with oil: and Olive-trees, according to the Apostle Paul, represent Churches, Rom. xi. They supply the lamps with oil, by maintaining teachers. They are also called the two candlesticks; which in this Prophecy signify Churches, the seven Churches of Asia being represented by seven candlesticks. Five of these Churches were found faulty, and threatned if they did not repent; the other two were without fault, and so their candlesticks were fit to be placed in the second Temple. These were the Churches in Smyrna and Philadelphia. They were in a state of tribulation and persecution, and the only two of the seven in such a state: and so their candlesticks were fit to represent the Churches in affliction in the times of the second Temple, and the only two of the seven that were fit. The two Witnesses are not new Churches: they are the posterity of the primitive Church, the posterity of the two wings of the woman, and so are fitly represented by two of the primitive candlesticks. We may conceive therefore, that when the first Temple was destroyed, and a new one built for them who worship in the inward court, two of the seven candlesticks were placed in this new Temple.Isaac Newton Observations upon the Prophecies of Daniel and the Apocalypse of St. John, II,iii